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5,477 results on '"Kunming Institute of Botany"'

1. Replication data for: Seasonal Response of Grasslands to Climate Change on

Author: Haiying, Yu (Key Laboratory Of Biodiversity And Biogeography, Kunming Institute Of Botany, Chinese Academy Of Sciences, Kunming, China), Jianchu Xu (World Agroforestry Centre (ICRAF)), Erick Okuto (World Agroforestry Centre (ICRAF)), and Eike Luedeling (World Agroforestry Centre (ICRAF))
Published: 2014
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2. The genus Phylloporus (Boletaceae, Boletales), from Mekong river basin (Yunnan Province, China)

Author: Ye, Lei (Mae Fah Luang University, Chiang Rai 57100, Thailand, World Agroforestry Centre, East And Central Asia, Kunming 650201, Yunnan, China), Mortimer, Peter Edward (World Agroforestry Centre, East And Central Asia, Kunming 650201, Yunnan, China, Key Laboratory Of Economic Plants And Biotechnology, Kunming Institute Of Botany, Chinese Academy Of Sciences, 132 Lanhei Road, Kunming 650201, China), Xu, Jianchu (World Agroforestry Centre, East And Central Asia, Kunming 650201, Yunnan, China, Karunarathna, Samantha (Mae Fah Luang University, Chiang Rai 57100, Thailand), and Hyde, Kevin (Mae Fah Luang University, Chiang Rai 57100, Thailand)
Published: 2014
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3. Replication data for: Flowering phenology of tree rhododendron along an elevation gradient in two sites in the Eastern Himalayas

Author: Ranjitkar, Sailesh (Center For Mountian Ecosystem Studies, China), Luedeling, Eike (World Agroforestry Center, Kenya), Shrestha, Krishna Kumar (Central Department Of Botany, Tribhuvan University, Nepal), Guan, Kaiyun (Kunming Institute Of Botany, China), and Xu, Jianchu (World Agroforestry Center East Asia Node, China)
Published: 2014
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4. Sporopollenin chemistry and its durability in the geological record: an integration of extant and fossil chemical data across the seed plants

Author: Phillip E. Jardine, Huajie He, Guillaume Dupont-Nivet, Amber Woutersen, William D. Gosling, Matteo Sciumbata, Wesley T. Fraser, Natasha Barbolini, Huasheng Huang, Barry H. Lomax, Giovanni Bogota-Angel, Carina Hoorn, Maxine A.M. Beer, Kustatscher, Evelyn, Jardine, Phillip E., 1Institute of Geology & Palaeontology University of Münster 48149 Münster Germany, Hoorn, Carina, 2Department of Ecosystem & Landscape Dynamics Institute for Biodiversity & Ecosystem Dynamics (IBED) University of Amsterdam 1090 GE Amsterdam The Netherlands, Beer, Maxine A.M., Barbolini, Natasha, Woutersen, Amber, Bogota‐Angel, Giovanni, Gosling, William D., Fraser, Wesley T., 5Geography, Department of Social Sciences Oxford Brookes University Oxford OX3 0BP UK, Lomax, Barry H., 6Agriculture & Environmental Science University of Nottingham Sutton Bonington Campus Leicestershire LE12 5RD UK, Huang, Huasheng, Sciumbata, Matteo, He, Huajie, 7Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan China, Dupont‐Nivet, Guillaume, 8Institute of Geosciences University of Potsdam 14476 Potsdam Germany, Westfälische Wilhelms-Universität Münster = University of Münster (WWU), University of Amsterdam [Amsterdam] (UvA), Stockholm University, Universidad Distrital Francisco Jose de Caldas [Bogota], Oxford Brookes University, University of Nottingham, UK (UON), Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), University of Potsdam = Universität Potsdam, Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), UK Research & Innovation (UKRI), NERC Natural Environment Research Council, German Research Foundation (DFG), European Project: 649081,H2020,ERC-2014-CoG,MAGIC(2015), Systems Ecology, University of Münster, University of Potsdam, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Ecosystem and Landscape Dynamics (IBED, FNWI)
Subjects: 0106 biological sciences, 010506 paleontology, Range (biology), Geologic record, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, Nitraria, Paleontology, Fourier transform infrared (FTIR) microspectroscopy Palaeontology Palaeontology, Sporopollenin, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Pollen, medicine, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Palynology, biology, seed plants, 15. Life on land, biology.organism_classification, Diagenesis, chemotaxonomy, Taxon, sporopollenin, Fourier transform infrared (FTIR) microspectroscopy, pollen, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, 560.47, diagenesis
Abstract: Sporopollenin is a highly resistant biopolymer that forms the outer wall of pollen and spores (sporomorphs). Recent research into sporopollenin chemistry has opened up a range of new avenues for palynological research, including chemotaxonomic classification of morphologically cryptic taxa. However, there have been limited attempts to directly integrate extant and fossil sporopollenin chemical data. Of particular importance is the impact of sample processing to isolate sporopollenin from fresh sporomorphs, and the extent of chemical changes that occur once sporomorphs enter the geological record. Here, we explore these issues using Fourier transform infrared (FTIR) microspectroscopy data from extant and fossil grass, Nitraria (a steppe plant), and conifer pollen. We show a 98% classification success rate at subfamily level with extant grass pollen, demonstrating a strong taxonomic signature in isolated sporopollenin. However, we also reveal substantial chemical differences between extant and fossil sporopollenin, which can be tied to both early diagenetic changes acting on the sporomorphs and chemical derivates of sample processing. Our results demonstrate that directly integrating extant and late Quaternary chemical data should be tractable as long as comparable sample processing routines are maintained. Consistent differences between extant and deeper time sporomorphs, however, suggests that classifying fossil specimens using extant training sets will be challenging. Further work is therefore required to understand and simulate the effects of diagenetic processes on sporopollenin chemistry., Natural Environment Research Council http://dx.doi.org/10.13039/501100000270, H2020 European Research Council http://dx.doi.org/10.13039/100010663
Published: 2021

5. Young shade trees improve soil quality in intensively managed coffee systems recently converted to agroforestry in Yunnan Province, China

Author: Clément Rigal, Jianchu Xu, Philippe Vaast, Kunming Institute of Botany, World Agroforestry Center (ICRAF), World Agroforestry Centre, Chinese Academy of Sciences [Beijing] (CAS), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Kunming Institute of Botany [CAS] (KIB), World Agroforestry Center [CGIAR, Philippines] (ICRAF), University of the Philippines Los Baños (UP Los Baños), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)
Subjects: P33 - Chimie et physique du sol, 0106 biological sciences, Cinnamomum camphora, F08 - Systèmes et modes de culture, Arbre d'ombrage, Soil Science, Coffea, Conservation des sols, Plant Science, 01 natural sciences, Jacaranda, Soil retrogression and degradation, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, P36 - Érosion, conservation et récupération des sols, 2. Zero hunger, biology, Soil organic matter, Shade tree, P34 - Biologie du sol, Intercropping, 04 agricultural and veterinary sciences, 15. Life on land, Plant litter, biology.organism_classification, Soil quality, K10 - Production forestière, Agronomy, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: International audience; Background and aims The trend of soil degradation in intensive open coffee systems is well-documented. This study highlights the impact of young shade trees on soil quality only 4 years after their intercropping with coffee. Methods 18 young shade trees belonging to three tree species (Cinnamomum camphora, Bishofia javanica and Jacaranda mimosifolia) were selected in an intensive coffee system in Southern Yunnan. Soil samples (0-20 cm) were tested for chemical composition, soil communities and soil enzyme activities under their canopies and in open areas, both in coffee rows and inter-rows, once during the rainy and once during the dry season. Additionally, root systems were characterized using trenches. Soil water profiles and litterfall were monitored along the production cycle. Coffee yield was recorded for two consecutive years. Results We detected a positive impact of all shade tree species on soil chemical, biological and biochemical components, especially during the dry season. This positive impact included higher soil organic matter (+10%) and more abundant soil microbial communities (+64%) under shaded coffee than under open coffee. Furthermore , shaded coffee trees yielded as much as open coffee trees, except under C. camphora, probably due to high below-ground competition. Conclusions These results demonstrate that carefully selected shade trees can rapidly contribute to preserving and/or restoring soil quality in intensive coffee systems, while maintaining high coffee yield.
Published: 2019

6. The amazing potential of fungi: 50 ways we can exploit fungi industrially

Author: Nimali I. de Silva, Rajesh Jeewon, Jake Winiski, Pattana Kakumyan, Marc Stadler, Jaturong Kumla, Jiye Yan, Ruvishika S. Jayawardena, Chayanard Phukhamsakda, Kanaporn Sujarit, Siraprapa Brooks, Achala R. Rathnayaka, Meghan O’Brien, Naritsada Thongklang, Eleni Gentekaki, Pranami D. Abeywickrama, Peter E. Mortimer, Dulanjalee Harishchandra, Peter Mueller, Nakarin Suwannarach, Thatsanee Luangharn, Kevin D. Hyde, Sylvie Rapior, Benjarong Thongbai, Thitipone Suwunwong, Karaba N. Nataraja, Jianchu Xu, Rashika S. Brahamanage, Craig B. Faulds, Hridya Hemachandran, Sehroon Khan, Samantha C. Karunarathna, Trichur S. Suryanarayanan, Sinang Hongsanan, Boontiya Chuankid, Birthe Sandargo, Ning-Guo Liu, Sadia Nadir, Janith V. S. Aluthmuhandiram, Mingkwan Doilom, Diana S. Marasinghe, Watsana Penkhrue, K. W. Thilini Chethana, Anuruddha Karunarathna, Venkat Gopalan, Allen Grace Niego, Resurreccion B. Sadaba, Clara Chepkirui, Putarak Chomnunti, Erandi Yasanthika, Uma Shaanker Ramanan, Danushka S. Tennakoon, Saisamorn Lumyong, Binu C. Samarakoon, Amornrat Chaiyasen, Sureeporn Nontachaiyapoom, Wasan Sriprom, Jian-Kui Liu, S. Nuwanthika Wijesinghe, Ramamoorthy Siva, Allan Patrick G. Macabeo, Dan Meeks, De-Ping Wei, Mae Fah Luang University [Thaïlande] (MFU), Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Biodiversité et Biotechnologie Fongiques (BBF), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), Faculty of Computer Science, Dalhousie University [Halifax], Institute of Excellence in Fungal Research and School of Science, German Centre for Infection Research (DZIF), XDB31000000, DBG6180015, 621C1535, DBG6180033, 2018PC0006, 256108A3070006, 41761144055 41771063 Y4ZK111B01, PHD57I0015, DBT-NER/Agri/24/2013, NAHEP/CAAST/2018-19, HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Kunming Institute of Botany, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Fungal biodiversity, Resource (biology), Biocontrôle, Exploit, Mushrooms, [SDV]Life Sciences [q-bio], champignon, Biotechnologies, Biology, biodiversité, 03 medical and health sciences, application industrielle, Mycology, [CHIM]Chemical Sciences, Ecology, Evolution, Behavior and Systematics, Economic potential, 030304 developmental biology, 2. Zero hunger, Biocontrol, Biodiversity, Biotechnology, Food, Fungi, 0303 health sciences, Ecology, 030306 microbiology, Agroforestry, fungi, biotechnologie alimentaire, Flow chart, [SDE]Environmental Sciences
Abstract: Fungi are an understudied, biotechnologically valuable group of organisms. Due to the immense range of habitats that fungi inhabit, and the consequent need to compete against a diverse array of other fungi, bacteria, and animals, fungi have developed numerous survival mechanisms. The unique attributes of fungi thus herald great promise for their application in biotechnology and industry. Moreover, fungi can be grown with relative ease, making production at scale viable. The search for fungal biodiversity, and the construction of a living fungi collection, both have incredible economic potential in locating organisms with novel industrial uses that will lead to novel products. This manuscript reviews fifty ways in which fungi can potentially be utilized as biotechnology. We provide notes and examples for each potential exploitation and give examples from our own work and the work of other notable researchers. We also provide a flow chart that can be used to convince funding bodies of the importance of fungi for biotechnological research and as potential products. Fungi have provided the world with penicillin, lovastatin, and other globally significant medicines, and they remain an untapped resource with enormous industrial potential. © 2019, The Author(s).
Published: 2019

7. Fossil endocarps of Aralia (Araliaceae) from the upper Pliocene of Yunnan in southwest China, and their biogeographical implications

Author: Zhou, Zhe [Kunming Institute of Botany, Chinese Academy of Sciences, Kunming (China); Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla (China)]
Published: 2015
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8. Coffee production during the transition period from monoculture to agroforestry systems in near optimal growing conditions, in Yunnan Province

Author: Clément Rigal, Philippe Vaast, Minghua Qiu, Jianchu Xu, Guilin Hu, Kunming Institute of Botany, Chinese Academy of Sciences [Beijing] (CAS), World Agroforestry Center (ICRAF), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kunming Institute of Botany [CAS] (KIB), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Fonctionnement et conduite des systèmes de culture tropicaux et méditerranéens (UMR SYSTEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 010504 meteorology & atmospheric sciences, F08 - Systèmes et modes de culture, Arbre d'ombrage, Microclimate, Cinnamomum camphora, F62 - Physiologie végétale - Croissance et développement, rendement, Agroforesterie, Biology, 01 natural sciences, K01 - Foresterie - Considérations générales, Dry season, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, 2. Zero hunger, Jacaranda mimosifolia, Agroforestry, Coffea arabica, Shade tree, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, services écosystémiques, 040103 agronomy & agriculture, Microclimat, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Monoculture, Agronomy and Crop Science, Pruning
Abstract: Large-scale conversions from monoculture arabica coffee systems to agroforestry systems started in 2012 in southern Yunnan Province. This study analyses the impact of young shade trees (Cinnamomum camphora, Bishofia javanica and Jacaranda mimosifolia) on microclimate, coffee fruit development cycle, coffee yield, and coffee quality only 4 years after their introduction. The results show that young shade trees reduced diurnal fluctuations in temperatures, buffered high temperatures in the rainy season (−3 to −6 °C), and protected coffee trees from cold temperatures in the dry season (+0.5 to +1 °C). Coffee flower set decreased with shade intensity, as did fruit losses during the bean filling and maturation stages. Consequently, coffee trees under B. javanica and J. mimosifolia, which both provide light shade intensity, produced yields similar to those of coffee trees in open conditions. Only coffee trees under the dense shade of C. camphora had lower yields. Shade trees did not affect the physical and organoleptic attributes of coffee beans. This study hence demonstrates that carefully selected shade trees can rapidly provide positive ecosystem services related to microclimate and coffee physiology, while maintaining a coffee yield and quality similar to those found in monoculture coffee systems. With their diffused shade, B. javanica and J. mimosifolia are suitable options for the agro-ecological intensification of coffee systems, while the use of C. camphora requires active management and pruning practices in order to sustain high coffee yield.
Published: 2020

9. Using farmers' local knowledge of tree provision of ecosystem services to strengthen the emergence of coffee-agroforestry landscapes in southwest China

Author: Philippe Vaast, Clément Rigal, Jianchu Xu, Kunming Institute of Botany, Chinese Academy of Sciences [Beijing] (CAS), World Agroforestry Center (ICRAF), World Agroforestry Centre, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut National de la Recherche Agronomique (INRA)-Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Kunming Institute of Botany [CAS] (KIB), World Agroforestry Center [CGIAR, Philippines] (ICRAF), University of the Philippines Los Baños (UP Los Baños), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)
Subjects: F08 - Systèmes et modes de culture, lcsh:Medicine, 010501 environmental sciences, Agroforesterie, Connaissance indigène, 01 natural sciences, Coffee, Ecosystem services, Trees, K01 - Foresterie - Considérations générales, Ethnicities, lcsh:Science, 2. Zero hunger, Agroforests, Multidisciplinary, Farmers, Ecology, Agroforestry, Eukaryota, Agriculture, Forestry, 04 agricultural and veterinary sciences, Biodiversity, Coffea arabica, Plants, Livelihood, Professions, Pratique culturale, Geography, Knowledge, Agroécosystème, Agricultural Workers, P01 - Conservation de la nature et ressources foncières, Research Article, China, Conservation of Natural Resources, Farms, Écologie, Ecological Metrics, Context (language use), Ecosystems, Fruits, Traditional knowledge, Ecosystem, 0105 earth and related environmental sciences, business.industry, Shade tree, Ecology and Environmental Sciences, lcsh:R, Organisms, Biology and Life Sciences, Species Diversity, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, services écosystémiques, Sustainability, People and Places, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Population Groupings, lcsh:Q, Système de culture, Pest Control, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Agroecology
Abstract: International audience; Intensive monoculture coffee farms quickly expanded in Yunnan Province in the 1990's and 2000's. In 2012, local authorities in Pu'er and Xishuangbanna Prefectures, the main coffee producing centre in the province, initiated a large-scale conversion program of these farms towards coffee-agroforestry systems to promote "ecologically-friendly coffee". Shade tree inventories and household interviews were conducted in these two prefectures to characterize coffee farms and the Local Ecological Knowledge (LEK) of farmers on the provision of ecosystem services by associated tree species. This study on newly emerging coffee farming systems revealed a high level of tree species diversity at both farm and landscape levels despite the previous dominance of intensive coffee monoculture and the large-scale distribution of a limited number of shade tree species by the government. 162 tree species were encountered during farm inventories, out of which the community of coffee farmers was able to rank 30 against 9 ecosystem services and disservices. This study reveals that this LEK is a type of hybrid knowledge that still relies mostly on traditional knowledge of tree species combined with experience acquired from newly-implemented coffee-agroforestry practices. This study also pointed out knowledge gaps regarding the impact of mature trees on coffee yield, coffee quality and pest control. The participatory approach resulted in the identification of non-promoted species with a high potential to provide locally relevant ecosystem services in coffee-agroforestry systems. These results lead to the upgrade of an online tool (www. shadetreeadvice.org) which allows extension services generating lists of recommended shade tree species tailored to the local ecological context and individual farmers' needs. This tool will benefit farmers' livelihood, support landscape health and contribute to the sustainability of the emerging Yunnan coffee agriculture sector.
Published: 2018

10. Report of the Special Committee on Registration of Algal and Plant Names (including fossils)

Author: Willem F. Prud'homme van Reine, Xian-Chun Zhang, Hidetoshi Nagamasu, Jiřina Dašková, Jiří Kvaček, Peter F. Stevens, Richard C. K. Chung, Hugh F. Glen, Michelle J. Price, Ali A. Dönmez, Gideon F. Smith, Niels Klazenga, Valéry Malécot, Kanchi N. Gandhi, Liliana Katinas, Wolf-Henning Kusber, Craig W. Schneider, Dmitry V. Geltman, Paul M. Kirk, Alan Paton, Mark F. Watson, Stefan Dressler, Alexander N. Sennikov, Alexander B. Doweld, Zhu-Liang Yang, Irina V. Belyaeva, Fred R. Barrie, David J. Patterson, Nicky Nicolson, Mary E. Barkworth, Werner Greuter, Karol Marhold, Regine Jahn, Martin J. Head, Gerrit Davidse, Malapati K. Janarthanam, David G. Mann, Christina Flann, Giuseppe C. Zuccarello, Intermountain Herbarium, Utah State University (USU), Herbarium, Royal Botanic Garden Edinburgh, Missouri Botanical Garden, Herbarium, Botany Department, Department of Science and Education, Field Museum of Natural History [Chicago, USA], Science Directorate, Herbarium, Royal Botanic Gardens, The Herbarium, Forest Biodiversity Division, Forest Research Institute Malaysia (FRIM), Department of Palaeontology, National Institutes of Health [Bethesda] (NIH)-The Natural History Museum (NHM), Faculty of Science, Department of Botany, University of South Bohemia, Gaertnerian Institution, National Institute of Carpology, Senckenberg Forschungsinstitut und Naturmuseum, Herbarium Senckenbergianum, Naturmuseum, Species 2000, Naturalis Biodiversity Center, Herbaria, Harvard University [Cambridge], Komarov Botanical Institute, Russian Academy of Sciences [Moscow] (RAS), Box 1781, Orto botanico di Palermo, Botanischer Garten und Botanisches Museum Berlin, Free University of Berlin (FU), Department of Earth Sciences [St. Catharines], Brock University [Canada], Department of Botany, Goa University, División Plantas Vasculares [La Plata], Facultad de Ciencias Naturales y Museo [La Plata] (FCNyM), Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Jodrell Laboratory, Royal Botanic Garden , Kew, Royal Botanic Gardens Victoria, Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Aquatic Ecosystems, Institut de Recerca i Tecnologia Agroalimentaries, Department of Botany, Faculty of Science, Kasetsart University, Institute of Botany, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), The Kyoto University Museum, Kyoto University, Biodiversity Informatics, School of Biological Sciences [Sydney], The University of Sydney, Conservatoire et Jardin Botaniques de Genève, Department of Biology, Trinity College (TCD), Herbarium, Komarov Botanical Institute, the Russian Academy of Sciences [Moscow, Russia] (RAS), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, National University of Ireland [Galway] (NUI Galway), Centre for Functional Ecology, Departamento de Ciências da Vida, University of Coimbra, Northern Arizona University [Flagstaff], Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), The National Herbarium, Institute of Botany, Chinese Academy of Sciences [Changchun Branch] (CAS), Missouri Botanical Garden (USA), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Russian Academy of Sciences, Kunming Institute of Botany, Naturalis Biodiversity Center [Leiden], and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: 0106 biological sciences, 010506 paleontology, Registration, [SDV]Life Sciences [q-bio], Zoology, Library science, Plant Science, Biology, 010603 evolutionary biology, 01 natural sciences, Botanical nomenclature, purl.org/becyt/ford/1 [https], registration, purl.org/becyt/ford/1.6 [https], Nomenclature, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Code, 15. Life on land, International Botanical Congress, International code, ddc:580, Nomenclature Section, Mandate, Plant names registration
Abstract: The Special Committee on Registration of Algal and Plant Names (including fossils) was established at the XVIII International Botanical Congress (IBC) in Melbourne in 2011, its mandate being to consider what would be involved in registering algal and plant names (including fossils), using a procedure analogous to that for fungal names agreed upon in Melbourne and included as Art. 42 in the International Code of Nomenclature for algae, fungi, and plants. Because experience with voluntary registration was key to persuading mycologists of the advantages of mandatory registration, we began by asking institutions with a history of nomenclatural indexing to develop mechanisms that would permit registration. The task proved more difficult than anticipated, but considerable progress has been made, as is described in this report. It also became evident that the Nomenclature Section needs a structure that will allow ongoing discussion of registration and associated issues. Simultaneously with this report we are submitting four proposals that would provide such a structure. Fil: Barkworth, Mary E.. State University of Utah; Estados Unidos Fil: Watson, Mark. Royal Botanic Gardens; Reino Unido Fil: Barrie, Fred R.. Field Museum of National History; Estados Unidos Fil: Belyaeva, Irina V.. Royal Botanic Gardens; Reino Unido Fil: Chung, Richard C. K.. Forest Research Institute Malaysia; Malasia Fil: Dašková, Jiřina. National Museum; República Checa Fil: Davidse, Gerrit. Missouri Botanical Garden; Estados Unidos Fil: Dönmez, Ali A.. Hacettepe Üniversitesi; Turquía Fil: Alexander B. Doweld. National Institute of Carpology; Rusia Fil: Dressler, Stefan. Senckenberg Forschungsinstitut und Naturmuseum; Alemania Fil: Flann, Christina. Naturalis Biodiversity Center; Países Bajos Fil: Gandhi, Kanchi. Harvard University; Estados Unidos Fil: Geltman, Dmitry. Institute of the Russian Academy of Sciences; Rusia Fil: Glen, Hugh F.. Forest Hills; Sudáfrica Fil: Greuter, Werner. Freie Universität Berlin; Alemania Fil: Head, Martin J.. Brock University; Canadá Fil: Jahn, Regine. Freie Universität Berlin; Alemania Fil: Janarthanam, Malapati K.. Goa University; India Fil: Katinas, Liliana. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División de Plantas Vasculares; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Kirk, Paul M.. Royal Botanic Gardens; Reino Unido Fil: Klazenga, Niels. Royal Botanic Gardens; Australia Fil: Kusber, Wolf Henning. Freie Universität Berlin; Alemania Fil: Kvaček, Jiří. National Museum; República Checa Fil: Malécot, Valéry. Université d’Angers; Francia Fil: Mann, David G.. Royal Botanic Gardens; Reino Unido. Institute for Food and Agricultural Research and Technology; España Fil: Marhold, Karol. Charles University; República Checa Fil: Nagamasu, Hidetoshi. Kyoto University; Japón Fil: Nicolson, Nicky. Royal Botanic Gardens; Reino Unido Fil: Paton, Alan. Royal Botanic Gardens; Reino Unido Fil: Patterson, David J.. University of Sydney; Australia Fil: Price, Michelle J.. Conservatoire et Jardin botaniques de la Ville de Genève; Italia Fil: Prud'homme van Reine, Willem F.. Naturalis Biodiversity Center; Países Bajos Fil: Schneider, Craig W.. Trinity College; Estados Unidos Fil: Sennikov, Alexander. University of Helsinski; Finlandia Fil: Smith, Gideon F.. Nelson Mandela Metropolitan University; Sudáfrica Fil: Stevens, Peter F.. Missouri Botanical Garden; Estados Unidos. University of Missouri-St; Estados Unidos Fil: Yang, Zhu-Liang. Chinese Academy of Sciences; República de China Fil: Zhang, Xian-Chun. Chinese Academy of Sciences; República de China Fil: Zuccarello, Giuseppe C.. Victoria University of Wellington; Nueva Zelanda
Published: 2016

11. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

Author: Azani, Nasim, Babineau, Marielle, Bailey, C. Donovan, Banks, Hannah, Barbosa, Ariane R., Pinto, Rafael Barbosa, Boatwright, James S., Borges, Leonardo M., Brown, Gillian K., Bruneau, Anne, Candido, Elisa, Cardoso, Domingos, Chung, Kuo-Fang, Clark, Ruth P., Conceicao, Adilva S., Crisp, Michael, Cubas, Paloma, Delgado-Salinas, Alfonso, Dexter, Kyle G., Doyle, Jeff J., Duminil, Jerome, Egan, Ashley N., La Estrella, Manuel, Falcao, Marcus J., Filatov, Dmitry A., Fortuna-Perez, Ana Paula, Fortunato, Renee H., Gagnon, Edeline, Gasson, Peter, Rando, Juliana Gastaldello, Goulart Azevedo Tozzi, Ana Maria, Gunn, Bee, Harris, David, Haston, Elspeth, Hawkins, Julie A., Herendeen, Patrick S., Hughes, Colin E., Iganci, Joao R. V., Javadi, Firouzeh, Kanu, Sheku Alfred, Kazempour-Osaloo, Shahrokh, Kite, Geoffrey C., Klitgaard, Bente B., Kochanovski, Fabio J., Koenen, Erik J. M., Kovar, Lynsey, Lavin, Matt, Le Roux, Marianne, Lewis, Gwilym P., Lima, Haroldo C., Lopez-Roberts, Maria Cristina, Mackinder, Barbara, Maia, Vitor Hugo, Malecot, Valery, Mansano, Vidal F., Marazzi, Brigitte, Mattapha, Sawai, Miller, Joseph T., Mitsuyuki, Chika, Moura, Tania, Murphy, Daniel J., Nageswara-Rao, Madhugiri, Nevado, Bruno, Neves, Danilo, Ojeda, Dario I., Pennington, R. Toby, Prado, Darirn E., Prenner, Gerhard, Queiroz, Luciano Paganucci, Ramos, Gustavo, Ranzato Filardi, Fabiana L., Ribeiro, Petala G., Rico-Arce, Maria Lourdes, Sanderson, Michael J., Santos-Silva, Juliana, Sao-Mateus, Wallace M. B., Silva, Marcos J. S., Simon, Marcelo F., Sinou, Carole, Snak, Cristiane, Souza, Elvia R., Sprent, Janet, Steele, Kelly P., Steier, Julia E., Steeves, Royce, Charles Stirton, Tagane, Shuichiro, Torke, Benjamin M., Toyama, Hironori, Cruz, Daiane Trabuco Da, Vatanparast, Mohammad, Wieringa, Jan J., Wink, Michael, Wojciechowski, Martin F., Yahara, Tetsukazu, Yi, Tingshuang, Zimmerman, Erin, Department of Plant Science, University of Oxford [Oxford], Institut de Recherche en Biologie Végétale, Université de Montréal (UdeM), Département de Sciences Biologiques, University of Montreal, Department of Biology, Northern Arizona University [Flagstaff], Royal Botanic Gardens, Kew, Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Departamento de Biologia Vegetal, Universidad de Barcelona, Department of Biodiversity and Conservation Biology, University of Western Cape, Departamento de Botânica, Universidade Federal da Bahia (UFBA), School of BioSciences, Australia and Queensland Herbarium, University of Melbourne, Instituto de Biologia, Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), School of Forestry and Resource Conservation, National Taiwan University, Departamento de Educação, Campus VIII, Universidade do Estado da Bahia, Research School of Biology, Australian National University (ANU), Departamento de Biología Vegetal II, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Instituto de Biología – Botánica, Universidad Nacional Autónoma de México (UNAM), School of GeoSciences, University of Edinburgh, Plant Biology Department, Cornell University [New York], Service Évolution Biologique et Écologie, Université libre de Bruxelles (ULB), Department of Botany, Smithsonian Institution, National Museum of Natural History, Jardim Botânico do Rio de Janeiro, Instituto de Pesquisas, Department of Plant Sciences, University of California, Instituto de Recursos Biologicos, Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Instituto Nacional de Tecnología Agropecuaria (INTA), University of Morón, Ciências Ambientais, Universidade Federal do Oeste da Bahia (UFOB), Royal Botanic Gardens, School of Biological Sciences [Reading], University of Reading (UOR), Chicago Botanic Garden, Department of Systematic and Evolutionary Botany, University of Vienna [Vienna], Institute of Decision Science for a Sustainable Society, Kyushu University, Department of Agriculture and Animal Health, University of South Africa (UNISA), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Department Plant Sciences and Plant Pathology [Bozeman], Montana State University (MSU), South African National Biodiversity Institute, Department of Botany and Plant Biotechnology (DBPB), Department of Botany and Plant Biotechnology-Universite of Johannesburg, Departamento de Biologia, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Museo Cantonale di Storia Naturale, Office of International Science and Engineering, National Science Foundation, Missouri Botanical Garden, Plant Sciences and Biodiversity, Royal Botanic Gardens Victoria, Instituto de Investigaciones en Ciencias Agrarias de Rosario [Zavalla] (IICAR), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Agrarias [Zavalla] (FCAGR), Universidad Nacional de Rosario [Santa Fe]-Universidad Nacional de Rosario [Santa Fe], Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Sistemática e Evolução, Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Departamento de Botânica, Instituto de Ciências Biológicas, Federal University of Goiás (UFG), Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Institute of Systematic Botany, New York Botanical Garden (NYBG), Naturalis Biodiversity Center, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Natural Sciences and Engineering Research Council of Canada, U.K. Natural Environment Research Council [NE/I028122/1], Swiss National Science Foundation [31003A_13552], Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES/Program POS CSF) [1951/13-0], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Sisbiota) [563084/2010-3], Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (Project Casadinho/Procad) [5525892011-0], Fundacao de Amparo a Pesquisa do Estado da Bahia (FAPESB PES) [0053/2011], Fundacao de Amparo a Pesquisa do Estado de Sao Paulo FAPESP, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico CNPq of Brazil, Smithsonian Institution, U.S. National Science Foundation [DEB-1352217], Environment Research and Technology Development Fund (S9) of the Ministry of the Environment of Japan, Arizona State University, Université de Montréal [Montréal], Royal Botanic Gardens Kew, Universidad Complutense de Madrid [Madrid] (UCM), Cornell University, Université Libre de Bruxelles [Bruxelles] (ULB), Universidade Federal do Oeste da Bahia, The Royal Veterinary and Agricultural University, Pontificia Universidade Católica do Rio de Janeiro, Missouri Botanical Garden (USA), Kunming Institute of Botany, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), and Naturalis Biodiversity Center [Leiden]
Subjects: plastid matK phylogeny, Caesalpinioideae, [SDV]Life Sciences [q-bio], Cercidoideae, mimosoid clade, Papilionoideae, Detarioideae, Duparquetioideae, Dialioideae
Abstract: The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.
Published: 2017

12. Polyporus umbellatus, an edible-medicinal cultivated mushroom with multiple developed health-care products as food, medicine and cosmetics: a review

Author: Sunita Chamyuang, Darbhe J. Bhat, Pattana Kakumyan, Kevin D. Hyde, Sylvie Rapior, Jianchu Xu, Asanka R. Bandara, Mae Fah Luang University [Thaïlande] (MFU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Department of Botany, Goa University, World Agroforestry Center (ICRAF), Kunming Institute of Botany, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Kunming Institute of Botany [CAS] (KIB), and Chinese Academy of Sciences [Beijing] (CAS)
Subjects: Medicinal mushroom, Bioactive molecules, media_common.quotation_subject, [SDV]Life Sciences [q-bio], Family Polyporaceae, Biology, Cosmetics, 030308 mycology & parasitology, 03 medical and health sciences, Ingredient, Polysaccharides, [CHIM]Chemical Sciences, Steroid, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common, 0303 health sciences, Mushroom, Polyporus umbellatus, business.industry, Immunity, Antitumor, biology.organism_classification, 3. Good health, Biotechnology, Anticancer, [SDE]Environmental Sciences, Antimicrobial, Antioxidant, business
Abstract: International audience; Polyporus umbellatus is a medicinal mushroom belonging to the family Polyporaceae which forms characteristic underground sclerotia. These sclerotia have been used in Traditional Chinese Medicine for centuries and are used to treat edema and promote diuretic processes. Over the past few decades, researchers have found this taxon to contain many bioactive compounds shown to be responsible for antitumor, anticancer,antioxidant, free radical scavenging, immune system enhancement and antimicrobial activities. Due to its promising medicinal value, P. umbellatus is used as an ingredient in many medicinal products and food supplements. Thus demand for P. umbellatus has increased. To supply the high global demand, P. umbellatus is cultivated under natural or industrial conditions. In this review we discuss optimal conditions for the cultivation and culture of P. umbellatus. We also focus on the medicinal uses of P. umbellatus, the diversity of bioactive metabolites with various pharmacological properties and the medicinal products of great interest for health care or as alternative drugs.
Published: 2015

13. Global urban environmental change drives adaptation in white clover

Author: James S. Santangelo, Rob W. Ness, Beata Cohan, Connor R. Fitzpatrick, Simon G. Innes, Sophie Koch, Lindsay S. Miles, Samreen Munim, Pedro R. Peres-Neto, Cindy Prashad, Alex T. Tong, Windsor E. Aguirre, Philips O. Akinwole, Marina Alberti, Jackie Álvarez, Jill T. Anderson, Joseph J. Anderson, Yoshino Ando, Nigel R. Andrew, Fabio Angeoletto, Daniel N. Anstett, Julia Anstett, Felipe Aoki-Gonçalves, A. Z. Andis Arietta, Mary T. K. Arroyo, Emily J. Austen, Fernanda Baena-Díaz, Cory A. Barker, Howard A. Baylis, Julia M. Beliz, Alfonso Benitez-Mora, David Bickford, Gabriela Biedebach, Gwylim S. Blackburn, Mannfred M. A. Boehm, Stephen P. Bonser, Dries Bonte, Jesse R. Bragger, Cristina Branquinho, Kristien I. Brans, Jorge C. Bresciano, Peta D. Brom, Anna Bucharova, Briana Burt, James F. Cahill, Katelyn D. Campbell, Elizabeth J. Carlen, Diego Carmona, Maria Clara Castellanos, Giada Centenaro, Izan Chalen, Jaime A. Chaves, Mariana Chávez-Pesqueira, Xiao-Yong Chen, Angela M. Chilton, Kristina M. Chomiak, Diego F. Cisneros-Heredia, Ibrahim K. Cisse, Aimée T. Classen, Mattheau S. Comerford, Camila Cordoba Fradinger, Hannah Corney, Andrew J. Crawford, Kerri M. Crawford, Maxime Dahirel, Santiago David, Robert De Haan, Nicholas J. Deacon, Clare Dean, Ek del-Val, Eleftherios K. Deligiannis, Derek Denney, Margarete A. Dettlaff, Michelle F. DiLeo, Yuan-Yuan Ding, Moisés E. Domínguez-López, Davide M. Dominoni, Savannah L. Draud, Karen Dyson, Jacintha Ellers, Carlos I. Espinosa, Liliana Essi, Mohsen Falahati-Anbaran, Jéssica C. F. Falcão, Hayden T. Fargo, Mark D. E. Fellowes, Raina M. Fitzpatrick, Leah E. Flaherty, Pádraic J. Flood, María F. Flores, Juan Fornoni, Amy G. Foster, Christopher J. Frost, Tracy L. Fuentes, Justin R. Fulkerson, Edeline Gagnon, Frauke Garbsch, Colin J. Garroway, Aleeza C. Gerstein, Mischa M. Giasson, E. Binney Girdler, Spyros Gkelis, William Godsoe, Anneke M. Golemiec, Mireille Golemiec, César González-Lagos, Amanda J. Gorton, Kiyoko M. Gotanda, Gustaf Granath, Stephan Greiner, Joanna S. Griffiths, Filipa Grilo, Pedro E. Gundel, Benjamin Hamilton, Joyce M. Hardin, Tianhua He, Stephen B. Heard, André F. Henriques, Melissa Hernández-Poveda, Molly C. Hetherington-Rauth, Sarah J. Hill, Dieter F. Hochuli, Kathryn A. Hodgins, Glen R. Hood, Gareth R. Hopkins, Katherine A. Hovanes, Ava R. Howard, Sierra C. Hubbard, Carlos N. Ibarra-Cerdeña, Carlos Iñiguez-Armijos, Paola Jara-Arancio, Benjamin J. M. Jarrett, Manon Jeannot, Vania Jiménez-Lobato, Mae Johnson, Oscar Johnson, Philip P. Johnson, Reagan Johnson, Matthew P. Josephson, Meen Chel Jung, Michael G. Just, Aapo Kahilainen, Otto S. Kailing, Eunice Kariñho-Betancourt, Regina Karousou, Lauren A. Kirn, Anna Kirschbaum, Anna-Liisa Laine, Jalene M. LaMontagne, Christian Lampei, Carlos Lara, Erica L. Larson, Adrián Lázaro-Lobo, Jennifer H. Le, Deleon S. Leandro, Christopher Lee, Yunting Lei, Carolina A. León, Manuel E. Lequerica Tamara, Danica C. Levesque, Wan-Jin Liao, Megan Ljubotina, Hannah Locke, Martin T. Lockett, Tiffany C. Longo, Jeremy T. Lundholm, Thomas MacGillavry, Christopher R. Mackin, Alex R. Mahmoud, Isaac A. Manju, Janine Mariën, D. Nayeli Martínez, Marina Martínez-Bartolomé, Emily K. Meineke, Wendy Mendoza-Arroyo, Thomas J. S. Merritt, Lila Elizabeth L. Merritt, Giuditta Migiani, Emily S. Minor, Nora Mitchell, Mitra Mohammadi Bazargani, Angela T. Moles, Julia D. Monk, Christopher M. Moore, Paula A. Morales-Morales, Brook T. Moyers, Miriam Muñoz-Rojas, Jason Munshi-South, Shannon M. Murphy, Maureen M. Murúa, Melisa Neila, Ourania Nikolaidis, Iva Njunjić, Peter Nosko, Juan Núñez-Farfán, Takayuki Ohgushi, Kenneth M. Olsen, Øystein H. Opedal, Cristina Ornelas, Amy L. Parachnowitsch, Aaron S. Paratore, Angela M. Parody-Merino, Juraj Paule, Octávio S. Paulo, João Carlos Pena, Vera W. Pfeiffer, Pedro Pinho, Anthony Piot, Ilga M. Porth, Nicholas Poulos, Adriana Puentes, Jiao Qu, Estela Quintero-Vallejo, Steve M. Raciti, Joost A. M. Raeymaekers, Krista M. Raveala, Diana J. Rennison, Milton C. Ribeiro, Jonathan L. Richardson, Gonzalo Rivas-Torres, Benjamin J. Rivera, Adam B. Roddy, Erika Rodriguez-Muñoz, José Raúl Román, Laura S. Rossi, Jennifer K. Rowntree, Travis J. Ryan, Santiago Salinas, Nathan J. Sanders, Luis Y. Santiago-Rosario, Amy M. Savage, J.F. Scheepens, Menno Schilthuizen, Adam C. Schneider, Tiffany Scholier, Jared L. Scott, Summer A. Shaheed, Richard P. Shefferson, Caralee A. Shepard, Jacqui A. Shykoff, Georgianna Silveira, Alexis D. Smith, Lizet Solis-Gabriel, Antonella Soro, Katie V. Spellman, Kaitlin Stack Whitney, Indra Starke-Ottich, Jörg G. Stephan, Jessica D. Stephens, Justyna Szulc, Marta Szulkin, Ayco J. M. Tack, Ítalo Tamburrino, Tayler D. Tate, Emmanuel Tergemina, Panagiotis Theodorou, Ken A. Thompson, Caragh G. Threlfall, Robin M. Tinghitella, Lilibeth Toledo-Chelala, Xin Tong, Léa Uroy, Shunsuke Utsumi, Martijn L. Vandegehuchte, Acer VanWallendael, Paula M. Vidal, Susana M. Wadgymar, Ai-Ying Wang, Nian Wang, Montana L. Warbrick, Kenneth D. Whitney, Miriam Wiesmeier, J. Tristian Wiles, Jianqiang Wu, Zoe A. Xirocostas, Zhaogui Yan, Jiahe Yao, Jeremy B. Yoder, Owen Yoshida, Jingxiong Zhang, Zhigang Zhao, Carly D. Ziter, Matthew P. Zuellig, Rebecca A. Zufall, Juan E. Zurita, Sharon E. Zytynska, Marc T. J. Johnson, Ecological Science, Animal Ecology, Biology, Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Medicine and Pharmacy, ON, University of North Carolina, LA, QC, DePaul University, IN, Universidad San Francisco de Quito USFQ, University of Georgia, Uppsala University, Hokkaido University, NSW, Programa de Pós-Graduação em Geografia da UFMT, University of British Columbia, A. C., CT, Universidad de Chile, Mount Allison University, Instituto de Ecología A. C., University of Cambridge, FL, Universidad Bernardo O'Higgins, Ghent University, West Long Branch, Lisboa, KU Leuven, Massey University, University of Cape Town, University of Münster, AB, University of Sussex, Stockholm University, Universidad San Francisco de Quito, East China Normal University, Shanghai Engineering Research Center of Sustainable Plant Innovation, MI, TX, Facultad de Agronomía, NS, Université de Rennes, IA, MN, Manchester Metropolitan University, UNAM, Aristotle University of Thessaloniki, University of Helsinki, University of Glasgow, Hendrix College, Vrije Universiteit Amsterdam, Universidad Técnica Particular de Loja, Universidade Federal de Sergipe (UFS), University of Tehran, Norwegian University of Science and Technology, AZ, Max Planck Institute for Plant Breeding Research, Universidad Nacional Autónoma de México, Potsdam-Golm, University of Alaska Anchorage, Tropical Diversity, Université de Moncton, MB, University of New Brunswick, Lincoln University, Universidad Adolfo Ibáñez, Brock University, ICB - University of Talca, Curtin University, Murdoch University, Western Oregon University, Facultad de Ciencias de la Vida, Institute of Ecology and Biodiversity (IEB), Lund University, Universidad Autónoma de Guerrero -CONACYT, University of Illinois at Chicago, Dufferin-Peel Catholic District School Board, U.S. Army ERDC-CERL, Tübingen, University of Zurich, Urban Wildlife Institute, Universidad Católica de la Santísima Concepción, CO, MS, Rutgers University-Camden, Chinese Academy of Sciences, Beijing Normal University, NM, University of Wisconsin - Eau Claire, Iranian Research Organization for Science and Technology (IROST), ME, Universidad de Antioquia, MA, Universidad de Sevilla, Universidad Mayor, Naturalis Biodiversity Center, Kyoto University, University of Alaska Fairbanks, Senckenberg Research Institute and Natural History Museum Frankfurt, Universidade Estadual Paulista (UNESP), WI, Swedish University of Agricultural Sciences, Universidad CES, Hofstra University, Nord University, VA, University of Almería, Faculty of Biological Sciences, Leiden University, Jyväskylä, KY, University of Tokyo, Ecologie Systématique et Evolution, Martin Luther University Halle-Wittenberg, University of Warsaw, Davidson College, Huazhong Agricultural University, Technical University of Munich, Lanzhou University, University of Bern, University of Liverpool, Repositório da Universidade de Lisboa, University of Toronto at Mississauga, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), University of Louisiana, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Biodiversité agroécologie et aménagement du paysage (UMR BAGAP), Ecole supérieure d'Agricultures d'Angers (ESA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Huazhong Agricultural University [Wuhan] (HZAU), California State University [Northridge] (CSUN), Saint Mary's University [Halifax], Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Concordia University [Montreal], University of Houston, Universidad San Francisco de Quito (USFQ), Technische Universität München = Technical University of Munich (TUM), and The Global Urban Evolution project was primarily funded by an NSERC DiscoveryGrant, Canada Research Chair and NSERC Steacie Fellowship to M.T.J.J.. J.S.S. receivedfunding from an NSERC CGS and C.R.F. is funded by an NSERC PDF. P.R.P.-N., R.W.N. andJ.C.C. were supported by NSERC Discovery grants. M.A. was funded by NSF RCN DEB-1840663. F.A. received funding from CAPES. MTKA was funded by CONICYT PIA APOYOCCTE AFB170008. J.R.B, T.C.L., and S.A.S were supported by Monmouth University Sch. ofSci. SRP. E.G. was funded by D. Biologie, Université de Moncton. C.G.-L. received fundingfrom the Center of Applied Ecology and Sustainability (CAPES), and ANID PIA/BASALFB0002. S.G. was funded by the Max Planck Society. P.J.-A. was funded by ANID PIA/BASALFB210006. I.N. and M.S. were supported by Leiden Municipality. K.M.O. was funded by USNSF awards IOS-1557770 and DEB-1601641. J.C.P. thanks FAPESP process 2018/00107-3, andM.C.R. thanks CNPq and FAPESP.
Subjects: sopeutuminen, Rural Population, valkoapila, Multidisciplinary, Urbanization, evoluutio, kasvillisuus, Genes, Plant, Adaptation, Physiological, Biological Evolution, SDG 11 - Sustainable Cities and Communities, evoluutioekologia, Hydrogen Cyanide, 570 Life sciences, biology, Trifolium, kaupungistuminen, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Cities, ympäristönmuutokset, Ecosystem, Genome, Plant
Abstract: Made available in DSpace on 2022-04-28T19:52:06Z (GMT). No. of bitstreams: 0 Previous issue date: 2022-03-18 Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale. Department of Biology University of Toronto Mississauga ON Centre for Urban Environments University of Toronto Mississauga ON Department of Biology University of North Carolina, Chapel Hill Department of Biology University of Louisiana LA Department of Biology Queen's University ON Department of Biology Concordia University QC Department of Biological Sciences DePaul University Department of Biology DePauw University IN Department of Urban Design and Planning, University of Washington, Seattle, WA, USA Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito USFQ Department of Genetics University of Georgia Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Field Science Center for Northern Biosphere Hokkaido University Natural History Museum Zoology University of New England NSW Programa de Pós-Graduação em Geografia da UFMT campus de Rondonópolis Department of Botany and Biodiversity Research Centre University of British Columbia Graduate Program in Genome Sciences and Technology Genome Sciences Centre University of British Columbia Department of Microbiology and Immunology University of British Columbia Red de Biología Evolutiva Instituto de Ecología A. C. School of the Environment Yale University CT Departamento de Ciencias Ecológicas Universidad de Chile, Facultad de Ciencias Instituto de Ecología y Biodiversidad Universidad de Chile Department of Biology Mount Allison University Red de Ecoetología Instituto de Ecología A. C. Department of Biology University of Ottawa ON Department of Zoology University of Cambridge Department of Biology, Washington University in St. Louis, St. Louis, MO, USA Department of Biology University of Miami FL Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS) Universidad Bernardo O'Higgins Department of Biology, University of La Verne, La Verne, CA, USA Département des sciences du bois et de la forêt Université Laval QC Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences UNSW Sydney NSW Department of Biology Ghent University Department of Biology Monmouth University West Long Branch Centre for Ecology Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa Lisboa Department of Biology KU Leuven School of Agriculture and Environment Wildlife and Ecology group Massey University, Palmerston North Department of Biological Sciences University of Cape Town Institute of Landscape Ecology University of Münster Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA Department of Biological Sciences University of Alberta AB Louis Calder Center and Department of Biological Sciences, Fordham University, Armonk, NY, USA Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, México School of Life Sciences University of Sussex Department of Ecology Environment and Plant Sciences Stockholm University iBIOTROP Instituto de Biodiversidad Tropical Universidad San Francisco de Quito Department of Biology, San Francisco State University, San Francisco, CA, USA Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán AC, Mérida, Yucatán, México School of Ecological and Environmental Sciences East China Normal University Shanghai Engineering Research Center of Sustainable Plant Innovation Centre for Ecosystem Science School of Biological Earth and Environmental Sciences UNSW Sydney NSW Department of Ecology and Evolutionary Biology University of Michigan MI Department of Biosciences Rice University TX IFEVA Universidad de Buenos Aires Facultad de Agronomía, CONICET Biology Department Saint Mary's University NS Department of Biological Sciences, Universidad de los Andes Department of Biology and Biochemistry University of Houston TX Université de Rennes Department of Zoology and Biodiversity Research Centre University of British Columbia Department of Environmental Studies Dordt University Sioux Center IA Department of Biology Minneapolis Community and Technical College MN Department of Natural Sciences Ecology and Environment Research Centre Manchester Metropolitan University Instituto de Investigaciones en Ecosistemas y Sustentabilidad UNAM Department of Botany School of Biology Aristotle University of Thessaloniki Faculty of Biological and Environmental Science Organismal & Evolutionary Biology Research Programme University of Helsinki Institute of Biodiversity Animal Health and Comparative Medicine University of Glasgow Department of Biology Hendrix College Department of Ecological Science Vrije Universiteit Amsterdam Departamento de Ciencias Biológicas y Agropecuarias Universidad Técnica Particular de Loja Departamento de Biologia Universidade Federal de Santa Maria (UFSM) Department of Plant Sciences School of Biology College of Science University of Tehran NTNU University Museum Norwegian University of Science and Technology Red de Estudios Moleculares Avanzados Instituto de Ecología A. C. School of Biological Sciences, University of Reading, Whiteknights Park, Reading, Berkshire, UK Department of Biology Northern Arizona University AZ Department of Biological Sciences MacEwan University AB Max Planck Institute for Plant Breeding Research Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Max Planck Institute of Molecular Plant Physiology Potsdam-Golm BIO5 Institute University of Arizona AZ Alaska Center for Conservation Science University of Alaska Anchorage Tropical Diversity, Royal Botanical Garden of Edinburgh Département de biologie Université de Moncton Department of Biological Sciences University of Manitoba MB Departments of Microbiology & Statistics University of Manitoba MB Department of Biology University of New Brunswick Department of Biology Kalamazoo College MI BioProtection Research Centre Lincoln University Departamento de Ciencias Facultad de Artes Liberales Universidad Adolfo Ibáñez Department of Ecology Evolution Behaviour University of Minnesota MN Department of Biological Sciences Brock University Department of Environmental Toxicology, University of California, Davis, CA, USA ICB - University of Talca School of Molecular and Life Science Curtin University College of Science Health Engineering and Education Murdoch University, Murdoch School of Life and Environmental Sciences University of Sydney NSW School of Biological Sciences, Monash University, Melbourne, VIC, Australia Department of Biological Sciences Wayne State University MI Department of Biology Western Oregon University, OR School of Natural Resources and the Environment University of Arizona AZ Departamento de Ecología Humana, Cinvestav Mérida Departamento de Ciencias Biológicas y Departamento de Ecología y Biodiversidad Facultad de Ciencias de la Vida, Universidad Andrés Bello Institute of Ecology and Biodiversity (IEB) Department of Biology Lund University Department of Biology Norwegian University of Science and Technology Escuela Superiro de Desarrollo Sustentable Universidad Autónoma de Guerrero -CONACYT Clarkson Secondary School Peel District School Board ON Homelands Sr. Public School Peel District School Board ON Department of Biological Sciences University of Illinois at Chicago Dufferin-Peel Catholic District School Board, St. James Catholic Global Learning Centre Department of Biosciences University of Calgary AB Ecological Processes Branch U.S. Army ERDC-CERL Department of Biology, Oberlin College, Oberlin, OH, USA Escuela Nacional de Estudios Superiores Unidad Morelia UNAM Institute of Evolution and Ecology University of Tübingen Tübingen Department of Evolutionary Biology and Environmental Studies University of Zurich, Winterthurerstrasse Urban Wildlife Institute Department of Conservation and Science, Lincoln Park Zoo Departamento de Ecología Universidad Católica de la Santísima Concepción Department of Biological Sciences University of Denver CO Department of Biological Sciences Mississippi State University MS Department of Biology Center for Computational & Integrative Biology Rutgers University-Camden Kunming Institute of Botany Chinese Academy of Sciences Department of Chemistry & Biochemistry Laurentian University ON Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University School of BioSciences, University of Melbourne, Melbourne, VIC, Australia Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México Department of Biological Sciences, Auburn University, Auburn, AL, USA Department of Entomology and Nematology, University of California, Davis, CA, USA Department of Biology University of New Mexico NM Department of Biology University of Wisconsin - Eau Claire Agriculture Institute Iranian Research Organization for Science and Technology (IROST) Department of Biology Colby College ME Instituto de Biología Universidad de Antioquia Department of Biology University of Massachusetts Boston MA Agricultural Biology Colorado State University CO Departamento de Biología Vegetal y Ecología Facultad de Biología Universidad de Sevilla, Av. Reina Mercedes s/n Facultad de Estudios Interdisciplinarios Centro GEMA- Genómica Universidad Mayor Evolutionary Ecology Group Naturalis Biodiversity Center Department of Biology and Chemistry Nipissing University ON, North Bay Center for Ecological Research Kyoto University Bonanza Creek Long Term Ecological Research Program University of Alaska Fairbanks Department of Botany and Molecular Evolution Senckenberg Research Institute and Natural History Museum Frankfurt Departamento de Biodiversidade Instituto de Biociências Univ Estadual Paulista - UNESP Nelson Institute for Environmental Studies University of Wisconsin-Madison WI Department of Biology, California State University, Northridge, Los Angeles, CA, USA Department of Ecology Swedish University of Agricultural Sciences Facultad de Ciencias y Biotecnologia Universidad CES Department of Biology Hofstra University Faculty of Biosciences and Aquaculture Nord University, Bodø Division of Biological Sciences, University of California San Diego, San Diego, CA, USA Department of Biology University of Richmond VA Estación de Biodiversidad Tiputini Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito USFQ Department of Biological Sciences Institute of Environment Florida International University FL Agronomy Department University of Almería Department of Biological Sciences and Center for Urban Ecology and Sustainability Butler University IN Department of Biological Sciences Louisiana State University LA Faculty of Biological Sciences, Goethe University Frankfurt Institute of Biology Leiden Leiden University Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Department of Biology University of Louisville KY Organization for Programs on Environmental Science University of Tokyo CNRS AgroParisTech Ecologie Systématique et Evolution, Université Paris-Saclay Department of Biology, Providence College, Providence, RI, USA General Zoology Institute for Biology Martin Luther University Halle-Wittenberg International Arctic Research Center University of Alaska Fairbanks Science, Technology and Society Department, Rochester Institute of Technology, Rochester, NY, USA SLU Swedish Species Information Centre Swedish University of Agricultural Sciences Department of Biology Westfield State University MA Centre of New Technologies University of Warsaw Department of Biology, Stanford University, Stanford, CA, USA Plant Biology Department Michigan State University MI Biology Department Davidson College College of Horticulture and Forestry Sciences/ Hubei Engineering Technology Research Center for Forestry Information Huazhong Agricultural University School of Life Sciences Technical University of Munich School of Life Sciences Lanzhou University Institute of Ecology and Evolution University of Bern Department of Evolution Ecology and Behaviour University of Liverpool Departamento de Biodiversidade Instituto de Biociências Univ Estadual Paulista - UNESP
Published: 2022

14. Ranges of critical temperature and water potential values for the germination of species worldwide

Author: Durr, Carolyne, Dickie, J.B., Yang , X.Y., Pritchard, H.W., Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Royal Botanic Gardens, Kew, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Seventh Framework Programme (FP7) collaborative research project - Impacts of Environmental Conditions on Seed Quality (EcoSeed) - KBBE2012.1.1-01, INRA meta-program ACCAF 'Adaptation of Agriculture and Forest to Climate Change', Royal Botanic Gardens Kew, and Kunming Institute of Botany
Subjects: germination, wild species, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, trees, crops, database
Abstract: Germination is the first essential stage in crop and food production, as well as for the establishment of trees and regeneration of wild species. Temperature and water potential are the primary environmental factors that control germination in all species, and affect both the rate and final percentage germination. A comprehensive description of intra- and inter-variations between groups of species (perennials and annuals, trees, grasses, crops and wild species) helps understand where these species are currently able to grow on earth and will be in the future. By collecting germination trait data on 243 species from the literature and unpublished data, we provide a wide spectrum of species’ seed germination traits, in the form of a set of parameter values describing germination responses to variations in temperature and water potential. Major differences in germination traits were seen to depend on the climatic conditions where the species grow or originated, with species able to germinate on ice and others unable to germinate below 18 ◦C. By contrast, within the different plant groups, similar ranges of threshold values were found, linked to the species geo-climatic origin. Crops however germinate faster, their range of threshold temperatures and water potential values is wider, and some crops have higher optimum and maximum temperatures as well as lower water potential threshold values. This is likely the result of human selection for rapid germination and for species able to grow in the wide range of environmental conditionswhere agriculture was developed. Our analyses revealed correlation between traits: negative correlations appeared between germination speed and temperature thresholds, and between temperature andwater potential thresholds. The collected data also form a valuable database, enabling plant establishmentto be better taken into account in modeling and simulation studies of vegetation boundaries (wild or cultivated) under changing land-use and climate.
Published: 2014

15. A framework for identifying plant species to be used as 'ecological engineers' for fixing soil on unstable slopes

Author: Murielle Ghestem, Alexia Stokes, Nick P. Rowe, Kun-Fang Cao, Wenzhang Ma, Clément Gadenne, Raphaêlle Leclerc, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences [Beijing] (CAS), Kunming Institute of Botany, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), AgroParisTech, Ghestem, Murielle, Kunming Institute of Botany [CAS] (KIB), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: Topography, Bending, lcsh:Medicine, Introduced species, Plant Science, Root system, Forests, physiologie de la plante, Plant Roots, Invasive species, Soil, Spatial and Landscape Ecology, Biomechanics, lcsh:Science, Plant stem, 2. Zero hunger, Multidisciplinary, Ecology, Geography, biology, Reforestation, Plants, Deformation, Erosion, Engineers, Species delimitation, déformation, Research Article, China, Shepherdia, Plant physiology, Biophysics, érosion, Ecosystems, Species Specificity, Plant-Environment Interactions, Soil ecology, espèce invasive, Cellulose, Ecosystem, Plant Physiological Phenomena, chine, Landforms, Elaeagnus, Plant Ecology, Ecology and Environmental Sciences, lcsh:R, Organisms, Biology and Life Sciences, Computational Biology, Geomorphology, 15. Life on land, biology.organism_classification, Landform Dynamics, Ecosystem Engineering, Earth Sciences, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem Modeling
Abstract: International audience; Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume) both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits
Published: 2014

16. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Author: Dirk Redecker, Johannes Z. Groenewald, B. Stielow, Ibai Olariaga, Wendy A. Untereiner, Steven D. Leavitt, Scott Federhen, Samantha C. Karunarathna, Pedro W. Crous, Katerina Fliegerova, Jianping Xu, Ana Crespo, M. Teresa Telleria, Soili Stenroos, Martha J. Powell, Sajeewa S. N. Maharachchikumbura, Gianluigi Cardinali, Laszlo Irinyi, Hiran A. Ariyawansa, Javier Diéguez Uribeondo, Andrew M. Minnis, Paul M. Kirk, Zai-Wei Ge, Duong Vu, Richard C. Hamelin, Conrad L. Schoch, Jian-Kui Liu, Wieland Meyer, Kevin D. Hyde, Csaba Vágvölgyi, Bryn T. M. Dentinger, Ning Zhang, Dhanushka Udayanga, Tamás Petkovits, Qing Cai, Cletus P. Kurtzman, Raquel Pino-Bodas, Jie Chen, Michael Weiß, Karl-Henrik Larsson, Leho Tedersoo, María P. Martín, Peter M. Letcher, Gábor M. Kovács, Liang-Dong Guo, Kazuaki Tanaka, Bhushan Shrestha, Andrew N. Miller, Krishna V. Subbarao, Nicolas Feau, Urmas Kõljalg, Huzefa A. Raja, D. Jean Lodge, Karen K. Nakasone, Jean-Marc Moncalvo, Nalin N. Wijayawardene, Sung-Oui Suh, Cécile Gueidan, Teun Boekhout, Wen Ying Zhuang, Marieka Gryzenhout, Jullie M. Sarmiento-Ramírez, Bart Buyck, H. Thorsten Lumbsch, Marizeth Groenewald, Seung-Beom Hong, Keith A. Seifert, Peter R. Johnston, Janet Jennifer Luangsa-ard, Barbara Robbertse, Kessy Abarenkov, Dimuthu S. Manamgoda, Z. Wilhelm de Beer, Pradeep K. Divakar, Tuula Niskanen, Patrik Inderbitzin, M. Catherine Aime, Bevan S. Weir, Sarah Hambleton, Zhu L. Yang, R. Henrik Nilsson, Kare Liimatainen, Cobus M. Visagie, Krisztina Krizsán, Michael J. Wingfield, Ulrike Damm, Gareth W. Griffith, Donald M. Walker, Tamás Papp, Vincent Robert, Miguel A. García, Valérie Hofstetter, Martin I. Bidartondo, Karen Hansen, Margarita Dueñas, Jos Houbraken, Karen W. Hughes, Kerstin Voigt, Giuseppina Mulè, Martin Grube, Ekaphan Kraichak, National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH), NLM, National Institutes of Health, CBS-KNAW Fungal Biodiversity Centre, Department of Pharmaceutical Sciences – Microbiology, Università degli Studi di Perugia (UNIPG), Molecular Mycology Research Laboratory, University of Sydney, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The Westmead Institute for Medical Research, Faculty of Biological and Environmental Sciences [Helsinki], University of Helsinki, Ecology and Evolutionary Biology, University of Tennessee System, Illinois Natural History Survey, University of Illinois System-University of Illinois System, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, University of Tartu, Department of Botany and Plant Pathology, Oregon State University (OSU), Institute of Excellence in Fungal Research and School of Science, Mae Fah Luang University [Thaïlande] (MFU), Imperial College London, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Chinese Academy of Sciences [Beijing] (CAS), School of Science, Departamento de Biologia Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Museum of Natural History Görlitz, Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UPSpace), Real Jardin Botanico (RJB), Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia (UBC), Czech Academy of Sciences [Prague] (CAS), Department of Biology, Northern Arizona University [Flagstaff], Aberystwyth University, Institute of Plant Sciences, Karl Franzens University, Department of Plant Sciences, University of California, Plant Industry, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food [Ottawa] (AAFC), Department of Botany, National University of Ireland [Galway] (NUI Galway), Département de recherche en Protection des végétaux grandes cultures et vigne/Viticulture et oenologie, Agroscope, Korean Agricultural Culture Collection, National Academy of Agricultural Science, Davis Department of Plant Pathology, Manaaki Whenua – Landcare Research [Lincoln], Institute of Biology, Department of Plant Anatomy, Eötvös Loránd University (ELTE), Plant Protection Institute [Budapest] (ATK NOVI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Science and Education, Field Museum, Department of Microbiology [Szeged], University of Szeged [Szeged], Bacterial Foodborne Pathogens and Mycology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research (NCAUR), United States Department of Agriculture (USDA)-United States Department of Agriculture (USDA), The Natural History Museum [London] (NHM), Department of Biological Sciences, The Open University [Milton Keynes] (OU), Plant Biology, Department of Biosciences, Forest Service, United States Department of Agriculture, Biotec - National Center for Genetic Engineering and Biotechnology, Department of Medical Microbiology and Immunology [Göteborg], University of Gothenburg (GU), Department of Natural History, Royal Ontario Museum, Department of Ecology Evolutionary Biology, University of Toronto, Institute of Sciences of Food Production (ISPA), Consiglio Nazionale delle Ricerche (CNR), Northern Research Station, U.S. Forest Service, Center for Forest Mycology Research (CFMR), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, Department of Chemistry and Biochemistry, University of California [Los Angeles] (UCLA), University of California-University of California, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institute of Life Science and Biotechnology, Sungkyunkwan University [Suwon] (SKKU), Mycology and Botany Program, American Type Culture Collection (ATCC), Faculty of Agriculture and Life Science, University of Maribor, Natural History Museum, University of Kansas [Lawrence] (KU), University of California [Davis] (UC Davis), Jena Microbial Resource Collection, Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Department of Natural Sciences, University of Findlay, Institute of Evolution and Ecology, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, McMaster University, Kunming Institute of Botany [CAS] (KIB), Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), National Center for Biotechnology Information, National Library of Medicine, Schoch, Conrad L., Département Systématique et Evolution, Muséum national d'Histoire naturelle (MNHN), Chinese Academy of Sciences, Kunming Institute of Botany, Universidad Complutense de Madrid [Madrid] (UCM), Czech Academy of Sciences [Prague] (ASCR), Landcare Research, United States Department of Agriculture - USDA (USA)-United States Department of Agriculture - USDA (USA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Friedrich-Schiller-Universität Jena, Eberhard Karls Universität Tübingen, National Center for Biotechnology Information ( NCBI ), National Institutes of Health ( NIH ), Università degli Studi di Perugia, Westmead Institute for Medical Research, Department of Biological and Environmental Sciences, University of Tennessee, Oregon State University ( OSU ), Mae Fah Luang University [Thaïlande] ( MFU ), Muséum National d’Histoire Naturelle ( MNHN ), Universidad Complutense de Madrid [Madrid] ( UCM ), Forestry and Agricultural Biotechnology Institute ( FABI ), University of Pretoria ( UPSpace ), Real Jardin Botanico ( RJB ), University of British Columbia ( UBC ), Czech Academy of Sciences [Prague] ( ASCR ), Commonwealth Scientific and Industrial Research Organisation [Canberra] ( CSIRO ), Chinese Academy of Sciences [Changchun Branch] ( CAS ), Agriculture and Agri-Food Canada ( AAFC ), National University of Ireland [Galway] ( NUI Galway ), Eotvos Lorand University, Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences [Budapest], National Center for Agricultural Utilization Research, The Open University [Milton Keynes] ( OU ), University of Gothenburg ( GU ), Institute of Sciences of Food Production, Center for Forest Mycology Research ( CFMR ), Botanical Museum, Finnish Museum of Natural History, University of California at Los Angeles [Los Angeles] ( UCLA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Sungkyunkwan University, American Type Culture Collection ( ATCC ), University of Kansas [Lawrence] ( KU ), University of California Davis, Leibniz Institute for Natural Product Research and Infection Biology, Rutgers University (State University of New Jersey), Università degli Studi di Perugia = University of Perugia (UNIPG), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Pretoria [South Africa], University of California (UC), Agriculture and Agri-Food (AAFC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and University of California (UC)-University of California (UC)
Subjects: [SDV]Life Sciences [q-bio], sequence analyses, ribosomal dna, Intergenic region, 0807 Library And Information Studies, Databases, Genetic, RefSeq, Cluster Analysis, donnée de séquence moléculaire, DNA, Fungal, Genetics, DNA, Intergenic, Genes, Fungal, Molecular Sequence Annotation, Fungi, Sequence Analysis, DNA, Medicine (all), Phylogenetic tree, EPS-4, 3. Good health, internal transcribed spacer, Fungal, Identification (biology), Original Article, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, Sequence Analysis, Information Systems, specimen, life, Sequence analysis, arbuscular mycorrhizal fungi, interspecific hybridization, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Genetic, evolution, Internal transcribed spacer, species complex, Science & Technology, Intergenic, [ SDV ] Life Sciences [q-bio], barcode, 0804 Data Format, DNA, Laboratorium voor Phytopathologie, MATHEMATICAL & COMPUTATIONAL BIOLOGY, référence, Genes, Laboratory of Phytopathology, identification
Abstract: DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi., B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine
Published: 2014

17. Bioactive metabolites from macrofungi: ethnopharmacology, biological activities and chemistry

Author: Marc Stadler, Kevin D. Hyde, Sylvie Rapior, Jianchu Xu, Dilani D. De Silva, Enge Sudarman, S. Aisyah Alias, Mae Fah Luang University [Thaïlande] (MFU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), German Centre for Infection Research (DZIF), Kunming Institute of Botany, Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Kunming Institute of Botany [CAS] (KIB), and Chinese Academy of Sciences [Beijing] (CAS)
Subjects: 0106 biological sciences, Anti malarial, [SDV]Life Sciences [q-bio], Anti-microbial, Pharmacology, Biology, 01 natural sciences, Anti-oxidant, Anti-tumor, 03 medical and health sciences, Human health, 010608 biotechnology, Food supplements, [CHIM]Chemical Sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Hypocholesterolemic, Antitumor activity, 0303 health sciences, Anti alzheimer, Ecology, Drug discovery, Anti hiv, business.industry, Anti-HIV, Anti oxidant, 3. Good health, Biotechnology, Anti-diabetic, Anti-Alzheimer, Anti-viral, Chemical diversity, [SDE]Environmental Sciences, Medicinal mushrooms, Anti-malarial, business
Abstract: International audience; Exploration of natural sources for novel bioactive compounds has been an emerging field of medicine over the past decades, providing drugs or lead compounds of considerable therapeutic potential. This research has provided exciting evidence on the isolation of microbe-derived metabolites having prospective biological activities. Mushrooms have been valued as traditional sources of natural bioactive compounds for many centuries and have been targeted as promising therapeutic agents. Many novel biologically active compounds have been reported as a result of research on medicinal mushrooms. In this review, we compile the information on bioactive structure-elucidated metabolites from macrofungi discovered over the last decade and highlight their unique chemical diversity and potential benefits to novel drug discovery. The main emphasis is on their anti-Alzheimer, antidiabetic, anti-malarial, anti-microbial, anti-oxidant, antitumor, anti-viral and hypocholesterolemic activities which are important medicinal targets in terms of drug discovery today. Moreover, the reader’s attention is brought to focus on mushroom products and food supplements available in the market with claimed biological activities and potential human health benefits.
Published: 2013

18. Diverse aging rates in ectothermic tetrapods provide insights for the evolution of aging and longevity

Author: Beth A. Reinke, Hugo Cayuela, Fredric J. Janzen, Jean-François Lemaître, Jean-Michel Gaillard, A. Michelle Lawing, John B. Iverson, Ditte G. Christiansen, Iñigo Martínez-Solano, Gregorio Sánchez-Montes, Jorge Gutiérrez-Rodríguez, Francis L. Rose, Nicola Nelson, Susan Keall, Alain J. Crivelli, Theodoros Nazirides, Annegret Grimm-Seyfarth, Klaus Henle, Emiliano Mori, Gaëtan Guiller, Rebecca Homan, Anthony Olivier, Erin Muths, Blake R. Hossack, Xavier Bonnet, David S. Pilliod, Marieke Lettink, Tony Whitaker, Benedikt R. Schmidt, Michael G. Gardner, Marc Cheylan, Françoise Poitevin, Ana Golubović, Ljiljana Tomović, Dragan Arsovski, Richard A. Griffiths, Jan W. Arntzen, Jean-Pierre Baron, Jean-François Le Galliard, Thomas Tully, Luca Luiselli, Massimo Capula, Lorenzo Rugiero, Rebecca McCaffery, Lisa A. Eby, Venetia Briggs-Gonzalez, Frank Mazzotti, David Pearson, Brad A. Lambert, David M. Green, Nathalie Jreidini, Claudio Angelini, Graham Pyke, Jean-Marc Thirion, Pierre Joly, Jean-Paul Léna, Anton D. Tucker, Col Limpus, Pauline Priol, Aurélien Besnard, Pauline Bernard, Kristin Stanford, Richard King, Justin Garwood, Jaime Bosch, Franco L. Souza, Jaime Bertoluci, Shirley Famelli, Kurt Grossenbacher, Omar Lenzi, Kathleen Matthews, Sylvain Boitaud, Deanna H. Olson, Tim S. Jessop, Graeme R. Gillespie, Jean Clobert, Murielle Richard, Andrés Valenzuela-Sánchez, Gary M. Fellers, Patrick M. Kleeman, Brian J. Halstead, Evan H. Campbell Grant, Phillip G. Byrne, Thierry Frétey, Bernard Le Garff, Pauline Levionnois, John C. Maerz, Julian Pichenot, Kurtuluş Olgun, Nazan Üzüm, Aziz Avcı, Claude Miaud, Johan Elmberg, Gregory P. Brown, Richard Shine, Nathan F. Bendik, Lisa O’Donnell, Courtney L. Davis, Michael J. Lannoo, Rochelle M. Stiles, Robert M. Cox, Aaron M. Reedy, Daniel A. Warner, Eric Bonnaire, Kristine Grayson, Roberto Ramos-Targarona, Eyup Baskale, David Muñoz, John Measey, F. Andre de Villiers, Will Selman, Victor Ronget, Anne M. Bronikowski, David A. W. Miller, Northeastern Illinois University, Pennsylvania State University (Penn State), Penn State System, Department of Ecology and Evolution [Lausanne], Université de Lausanne = University of Lausanne (UNIL), Iowa State University (ISU), W. K. Kellogg Biological Station (KBS), Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Texas A&M University [College Station], Earlham College, Partenaires INRAE, Department of Evolutionary Biology and Environmental Studies, Universität Zürich [Zürich] = University of Zurich (UZH), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Centro de Investigaciones Biológicas (CSIC), Department of Biological Sciences [Lubbock], Texas Tech University [Lubbock] (TTU), School of Biological Sciences [Wellington, New Zealand], Victoria University of Wellington, Tour du Valat, Research Institute for the conservation of Mediterranean Wetlands, Auteur indépendant, Department of Conservation Biology [UFZ Leipzig], Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Research Institute on Terrestrial Ecosystems [CNR, Italy] (IRET), Consiglio Nazionale delle Ricerche (CNR), Le Grand Momesson, Bouvron, France, Denison University, Fort Collins Science Center (FORT), US Geological Survey [Fort Collins], United States Geological Survey [Reston] (USGS)-United States Geological Survey [Reston] (USGS), University of Montana, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forest and Rangeland Ecosystem Science Center (FRESC), Info Fauna Karch 2000, Flinders University [Adelaide, Australia], Evolutionary Biology Unit, South Australian Museum, Université Paul-Valéry - Montpellier 3 (UPVM), University of Belgrade [Belgrade], Macedonian Ecological Society, University of Kent [Canterbury], Naturalis Biodiversity Center [Leiden], CEREEP-Ecotron Ile de France (UMS 3194), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Development, Ecology, Conservation and Cooperation [Rome, Italy], Rivers State University of Science and Technology, Université de Lomé [Togo], Museo Civico di Zoologia, U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Wildlife Biology Program, Department of Wildlife Ecology and Conservation, University of Florida, Department of Biodiversity, Conservation and Attractions [Australia], Parks and Wildlife Service of Northern Territory, Colorado State University [Fort Collins] (CSU), Redpath Museum, McGill University = Université McGill [Montréal, Canada], Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Macquarie University, Association Objectifs Biodiversités (OBIOS), Équipe 4 - Écophysiologie, Comportement, Conservation (E2C), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), CSIRO, EcoSciences Precinct, StatiPOP, scientific consulting, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Conservatoire d'Espaces Naturels de Nouvelle-Aquitaine, Ohio State University [Columbus] (OSU), Northern Illinois University, California Department of Fish and Wildlife, Universidad de Oviedo [Oviedo], Department of Biology [Mato Grosso], Universidade do Estado de Mato Grosso (UNEMAT), Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo = University of São Paulo (USP), Royal Melbourne Institute of Technology University (RMIT University), University of the Highlands and Islands (UHI), Naturhistorisches Museum [Bern], USDA Forest Service Rocky Mountain Forest and Range Experiment Station, United States Department of Agriculture (USDA), Deakin University [Waurn Ponds], Palmerston North Research Centre, Plant & Food Research, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universidad Austral de Chile, ONG Ranita de Darwin, U.S Geological Survey, Patuxent Wildlife Research Center, SO Conte Anadromous Fish Laboratory, School of Earth and Environmental Sciences [Wollongong], Faculty of Science, Medicine and Health [Wollongong], University of Wollongong [Australia]-University of Wollongong [Australia], Université de Rennes (UNIV-RENNES), Office national des forêts (ONF), University of Georgia [USA], Centre de Recherche et de Formation en Eco-éthologie (2C2A-CERFE), Université de Reims Champagne-Ardenne (URCA), Adnan Menderes Üniversitesi, University College of Kristianstad, Watershed Protection Department, Cornell Lab of Ornithology [New York], Cornell University [New York], Indiana University School of Medicine, Indiana University System, University of Virginia, Auburn University (AU), University of Richmond, Ministerio de Ciencia, Tecnología y Medio Ambiente (CITMA), Pamukkale University, Stellenbosch University, Millsaps College, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), This study was supported by National Institutes of Health grant R01AG049416 (to A.M.B., F.J.J., and D.A.W.M.). H.C. was supported as a postdoctoral researcher by the Swiss National Science Foundation (grant no. 31003A_182265)., Office National des Forêts (ONF), University of Virginia [Charlottesville], Éco-Anthropologie (EAE), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR), and Cornell Laboratory of Ornithology
Subjects: life history, demography, Aging, phenotype, [SDV]Life Sciences [q-bio], Longevity, tetrapod, ectothermy, phylogeny, Amphibia, Amphibians, VERTEBRADOS, evolution, Animals, animal, Multidisciplinary, nonhuman, article, Reptiles, mortality, Biological Evolution, phylogenetics, reptile, GN, [SDE]Environmental Sciences, environmental temperature, body size
Abstract: Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.
Published: 2022

19. Discovery of the first succulent bamboo (Poaceae, Bambusoideae) in a new genus from Laos’ karst areas, with a unique adaptation to seasonal drought

Author: Thomas Haevermans, Agathe Haevermans, Dulce Mantuano, Meng-Yuan Zhou, Patrick Blanc, De-Zhu Li, Vichith Lamxay, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Universidade Federal do Rio de Janeiro (UFRJ), Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), National University of Laos, and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Bamboo, Asia, desiccation tolerance, Liliopsida, Synchronous flowering, Plant Science, Poaceae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Xerophyte, Genus, lcsh:Botany, Flagship species, Plantae, Ecology, Evolution, Behavior and Systematics, Taxonomy, 030304 developmental biology, 0303 health sciences, biology, Ecology, Poales, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, Bambusinae, biology.organism_classification, lcsh:QK1-989, Bambusoideae, Tracheophyta, Bambusinae desiccation tolerance genetic resources xerophyte, genetic resources, Taxon, Laos, xerophyte, Research Article
Abstract: Lush jungle flagship species, woody bamboos (Poaceae–Bambusoideae) are famed for their synchronous flowering as well as the extensive “bamboo forests” some species can form in tropical or temperate environments. In portions of their natural distribution, Bambusoideae members developed various adaptations to seasonality in environmental parameters, such as frost or seasonal drought. A new taxon, Laobambos calcareus, described here, is extremely novel in showing the first documented case of succulence in bamboos, with its ability to seasonally vary the volume of its stem depending on the quantity of water stored. Anatomical studies presented in this paper document this specificity at the cellular level. Though no flowers or fruits are known yet, unique morphological characteristics along with an investigation of its phylogenetic affinities using molecular data show that this new taxon should belong to a new genus herein described.
Published: 2020

20. Outline of Fungi and fungus-like taxa

Author: David L. Hawksworth, R. G. U. Jayalal, L. F. Zhang, G. A. da Silva, Samantha C. Karunarathna, Saowaluck Tibpromma, Kazuaki Tanaka, Saranyaphat Boonmee, I. V. Issi, Sajeewa S. N. Maharachchikumbura, Rajesh Jeewon, Oleg N. Shchepin, J. Ma, Fritz Oehl, P. B. Gannibal, Cristina Maria de Souza-Motta, Dhanushka N. Wanasinghe, Kunhiraman C. Rajeshkumar, A. A. Lateef, Ting-Chi Wen, L. K. T. Al-Ani, Kevin D. Hyde, Armin Mešić, Hans-Peter Grossart, Gabriela Heredia, Roshni Khare, Einar Timdal, Shubhi Avasthi, F. A. de Souza, Mounes Bakhshi, Richard A. Humber, Subhash Gaikwad, Dmitry V. Leontyev, Noha H. Youssef, Alexandre G. S. Silva-Filho, Sudhir Navathe, María Prieto, Marco Thines, Paul M. Kirk, Yuri Tokarev, Marc Stadler, P. O. Fiuza, André Aptroot, Damien Ertz, Monika C. Dayarathne, Julia Pawłowska, P. Liu, H. T. Lumbsch, Peter E. Mortimer, Elaine Malosso, Nalin N. Wijayawardene, Belle Damodara Shenoy, Huzefa A. Raja, Mikhail P. Zhurbenko, Somayeh Dolatabadi, Jos Houbraken, S. Mohammad, Zdenko Tkalčec, Andrei Tsurykau, Rampai Kodsueb, Mubashar Raza, Darbhe J. Bhat, Dsa Wijesundara, Jadson D. P. Bezerra, Javier Etayo, Walter P. Pfliegler, Leho Tedersoo, Jurga Motiejunaite, James D. Lawrey, Felipe Wartchow, Anusha H. Ekanayaka, Laura Selbmann, Sinang Hongsanan, Gothamie Weerakoon, Rafael F. Castañeda-Ruiz, Francis Q. Brearley, Enikő Horváth, R. L Zhao, B. O. Sharma, Y. Wang, Iván Sánchez-Castro, Martin Schnittler, Steven L. Stephenson, Y. Kang, Renate Radek, Eleni Gentekaki, Dagmar Triebel, F. R. Barbosa, Martina Réblová, Q. R. Li, Sayanh Somrithipol, Y. M. Li, D. K. A. Silva, L. Z. Tang, Hugo Madrid, Asha J. Dissanayake, Satinee Suetrong, Eric H. C. McKenzie, Mingkwan Doilom, E. S. Nassonova, J. C. Cavender, Neven Matočec, A. L. Firmino, R. K. Saxena, Olinto Liparini Pereira, J. Xu, V. Vázquez, M. Q. He, Xinlei Fan, Khadija Jobim, Martin Kukwa, Andrey Yurkov, R. F. Xu, K. Kolaríková, Lakmali S. Dissanayake, P. Alvarado, Rungtiwa Phookamsak, Dong-Qin Dai, Qing Tian, Ulrike Damm, D. W. Li, Pradeep K. Divakar, Jian-Kui Liu, Ajay Kumar Gautam, Viktor Papp, Peter M. Letcher, Pamela Rodriguez-Flakus, E. Kuhnert, F. Tian, I. Kusan, Makbule Erdoğdu, Alejandra Gabriela Becerra, B. T. Goto, Eric W.A. Boehm, K. Bensch, Sally C. Fryar, Yuri K. Novozhilov, Han Zhang, V. P. Hustad, André Luiz Cabral Monteiro de Azevedo Santiago, Danny Haelewaters, Gregorio Delgado, V. Dima, C. Y. Deng, Y. Z. Lu, Moslem Papizadeh, Ave Suija, Janusz Błaszkowski, Paul G. Mungai, Bryce Kendrick, Leonor Costa Maia, Gerhard Rambold, Adam Flakus, Alan J. L. Phillips, Josiane Santana Monteiro, Susumu Takamatsu, Ziraat Fakültesi, Makbule Erdoğdu / 0000-0001-8255-2041, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Netherlands Institute for Neuroscience (NIN), Qujing Normal University, Abhilashi University, Jiwaji University, National Science and Technology Development Agency -NSTDA, University of Oslo, Universidade Federal da Paraíba, FRANCISCO ADRIANO DE SOUZA, CNPMS, Agroscope, Competence Div Plants & Plant Prod., Universidade Federal de Pernambuco, West Pomeranian University of Technology, Universidade Federal do Rio Grande do Norte, Universidade Federal de Mato Grosso, University of Ilorin, Kunming Institute of Botany, Mae Fah Luang University, ALVALAB, Shenzhen University, Hirosaki University, University of Electronic Science and Technology of China, Museu Paraense Emílio Goeldi, Leibnitz Institute of Freshwater Ecology and Inland Fisheries - IGB, University of Tartu, Helmholtz-Zentrum für Infektionsforschung GmbH, Institute of Microbiology Chinese Academy of Sciences, University of Mauritius, Russian Academy of Sciences, Universidad Rey Juan Carlos, University of Sri Lanka, K?r?ehir Ahi Evran University, Leibniz Institute, Ernst Moritz Arndt University Greifswald, Goethe University., USDA-ARS Emerging Pests and Pathogens Research, University of South Bohemia, National Fungal Culture Collection of India -NFCCI, State Key Laboratory of Mycology, Universidade Federal de Mato Grosso do Sul, Skovoroda Kharkiv National Pedagogical University, University Road, All-Russian Institute of Plant Protection, Universidade de Lisboa, University of Tuscia, University of Debrecen, Royal Botanic Gardens, Czech Academy of Sciences, University of North Carolina at Greensboro, Freie Universität Berlin, Szent István University, Eötvös Loránd University, Jiangxi Agricultural University, Flinders University, EMLab P&K Houston, Academy of Sciences, Chiang Mai University, Sabzevar University of New Technology, University of Warsaw, Pibulsongkram Rajabhat University, Universidad de Granada, Universidad Complutense de Madrid, CSIR-National Institute of Oceanography Regional Centre, Instituto de Investigaciones Fundamentales en AgriculturaTropical, BIOTEC, National Science and Technology Development Agency - NSTDA, Guizhou University, Valley Laboratory, Ru?er Boškovi? Institute, Pasteur Institute of Iran, Instituto de Ecolog? 'a A. C., Iranian Research Institute of Plant Protection, Oklahoma State University, Northwest Missouri State University, George Mason University, Universidade Federal de Uberlândia, The Natural History Museum, IES Zizur, Skorina Gomel State University, University of Málaga, Kenya Wildlife Service, Senckenberg Museum of Natural History Görlitz, Guizhou Medical University, Kunming University of Science and Technology, Universidad Nacional de Córdoba, Manchester Metropolitan University, Nature Research Centre, Agharkar Research Institute, National Institute of Fundamental Studies, Szafer Institute of Botany, Manaaki Whenua-Landcare Research, Jilin Agricultural University, Ohio University, Iranian Research Organization for Science and Technology -IROST, Guizhou Academy of Science, Universidade Federal de Viçosa, Beijing Forestry University, Leibniz University, Leibnitz Institute of Freshwater Ecology and Inland Fisheries -IGB, University of Baghdad, The University of Alabama, University of Arkansas, Botanic Garden Meise, The Field Museum, University of Gda?sk, Universidad Mayor, Mie University, Universität of Bayreuth, and Staatliche Naturwissenschaftliche Sammlungen Bayerns
Subjects: Plant Science, Blastocladiomycota, 030308 mycology & parasitology, purl.org/becyt/ford/1 [https], Glomeromycota, Genus, Neopereziida, Amblyosporida ord. nov, 0303 health sciences, Ascomycota, biology, ord. nov, Basal clades, Classification, FOUR NEW TAXA, GEN. NOV, CELLULAR SLIME-MOLDS, POLAR TUBE, SP.-NOV, Leotiomycetes, four new taxa, ascomycota, basal clades, basidiomycota, classification, emendation, microsporidia, Neopereziida ord. nov, Ovavesiculida ord. nov, Protosporangiaceae fam. nov, Redonographaceae stat nov, MOLECULAR PHYLOGENY, Four new taxa, BASAL CLADES, GENERIC NAMES, CLASSIFICATION, 03 medical and health sciences, Botany, MICROSPORIDIAN, NATURAL CLASSIFICATION, purl.org/becyt/ford/1.6 [https], Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Fungo, Entomophthoromycota, Phylum, Basidiomycota, Biology and Life Sciences, Emendation, 15. Life on land, biology.organism_classification, SUB-ANTARCTIC ISLANDS, Microsporidia, Polar tube, SP-NOV, Amblyosporidae, LEVEL PHYLOGENETIC CLASSIFICATION
Abstract: This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi., Nalin N. Wijayawardene thanks Mushroom Research Foundation and National Science Foundation of China (No. NSFC 31950410558) for financially supporting this project. Kevin D. Hyde acknowledges the Foreign Experts Bureau of Yunnan Province, Foreign Talents Program (2018; grant no. YNZ2018002), Thailand Research grants entitled Biodiversity, phylogeny and role of fungal endophytes on above parts of Rhizophora apiculata and Nypa fruticans (grant no: RSA5980068), the future of specialist fungi in a changing climate: baseline data for generalist and specialist fungi associated with ants, Rhododendron species and Dracaena species (grant no: DBG6080013), Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion (grant no: RDG6130001). H.T. Lumbsch thanks support by the Grainger Bioinformatics Center. E. Malosso is grateful to CAPES for financial support (grant no. 88881.062172/2014-01). B.T. Goto, G.A. Silva and K. Jobim, L.C. Maia acknowledges CNPq (Brazilian Scientific Council, grants no. 465.420/2014-1, 307.129/2015-2 and 408011/2016-5) and CAPES for support. The study was partially supported by the National Science Centre, Poland, under Grants No. 2015/17/D/NZ8/00778 and 2017/25/B/NZ8/00473 to Julia Pawłowska. The research of Martin Kukwa received support from the National Science Centre (NCN) in Poland (project no 2015/17/B/NZ8/02441). Alan J.L. Phillips acknowledges the support from UID/MULTI/04046/2019 Research Unit grant from FCT, Portugal to BioISI. H. Zhang is financially supported by the National Natural Science Foundation of China (Project ID: NSF 31500017). S. Boonmee would like to thank the Thailand Research Fund (Project No. TRG6180001). Dong-Qin Dai and Li-Zhou Tang would like to thank the National Natural Science Foundation of China (No. NSFC 31760013, NSFC 31260087, NSFC 31460561), the Scientific Research Foundation of Yunnan Provincial Department of Education (2017ZZX186) and the Thousand Talents Plan, Youth Project of Yunnan Provinces for support. R. Phookamsak, M. Doilom, D. N. Wanasinghe, S.C. Karunarathna and J.C. Xu express sincere appreciations to Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (grant no. QYZDY-SSW-SMC014) for research financial support. R. Phookamsak thanks the Yunnan Provincial Department of Human Resources and Social Security (grant no. Y836181261), Chiang Mai University and National Science Foundation of China (NSFC) project code 31850410489 for research financial support. S.C. Kaunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (No. 2018PC0006) and the National Science Foundation of China (NSFC) for funding this work under the project code 31851110759. S. Tibpromma would like to thank the International Postdoctoral Exchange Fellowship Program (number Y9180822S1), CAS President’s International Fellowship Initiative (PIFI) (number 2020PC0009), China Postdoctoral Science Foundation and the Yunnan Human Resources, and Social Security Department Foundation for funding her postdoctoral research. Yuri S. Tokarev, Elena S. Nassonova and Irma V. Issi are indebtful to Yuliya Y. Sokolova (Institute of Cytology RAS, St. Petersbug, Russia) and Anastasia V. Simakova (Tomsk State University, Tomsk, Russia) for kind permission of reproduction of electron microscopy images of Metchnikovella incurvata and Crepidulospora beklemishevi, respectively. Yuri S. Tokarev and Irma V. Issi thank Russian Foundation of Basic Research, grant number 17-04-00871 (taxonomy of Rozellomycota). Elena S. Nassonova thank Russian Foundation of Basic Research, grant number 18-04-01359 (early evolution of Microsporidia, phylogeny of Metchnikovellida). Adam Flakus and Pamela Rodriguez-Flakus are greatly indebted to all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz and the SERNAP (http://sernap.gob.bo), for their generous cooperation providing permits, assistance and facilities support for scientific studies. The research of AF and PRF were financially supported by the National Science Centre (NCN) in Poland (DEC-2013/11/D/NZ8/03274). Adam Flakus and Pamela Rodriguez-Flakus received additional support under statutory funds from the W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland. The authors would like to thank Yunnan Innovation Platform for Development and Utilization of Symbiotic Fungi Resources for finance support. Li-Fang Zhang would like to thank grant-in-aid from Science and Technology Department of Yunnan Province (2018FD080) for finance support. Chun-Ying Deng thanks the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (2019HJ2096001006). Yingqian Kang would like to thank Guizhou Scientific Plan Project [(2019) 2873]; Excellent Youth Talent Training Project of Guizhou Province [(2017) 5639]; Guiyang Science and Technology Project [(2017) No. 5-19]; Talent Base Project of Guizhou Province, China [FCJD2018-22]; Research Fund of Education Bureau of Guizhou Province, China [(2018) 481]. D. N. Wanasinghe would like to thank the CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2019PC0008), the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following grants: 41761144055, 41771063 and Y4ZK111B01. Yuri K. Novozhilov and Oleg N. Shchepin acknowledge support from the Russian Foundation of Basic Research, project 18-04-01232 А. Ivana Kušan, Neven Matočec, Armin Mešić and Zdenko Tkalčec are grateful to Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). K. Tanaka would like to thank the Japan Society for the Promotion of Science (JSPS 19K06802)
Published: 2020

21. Outline of Fungi and fungus-like taxa – 2021

Author: Wijayawardene, NN, Hyde, KD, Dai, DQ, Sánchez-García, M, Goto, BT, Saxena, RK, Erdoğdu, M, Selçuk, F, Rajeshkumar, KC, Aptroot, A, Błaszkowski, J, Boonyuen, N, da Silva, GA, de Souza, FA, Dong, W, Ertz, D, Haelewaters, Danny, Jones, EBG, Karunarathna, SC, Kirk, PM, Kukwa, M, Kumla, J, Leontyev, DV, Lumbsch, HT, Maharachchikumbura, SSN, Marguno, F, Martínez-Rodríguez, P, Mešić, A, Monteiro, JS, Oehl, F, Pawłowska, J, Pem, D, Pfliegler, WP, Phillips, AJL, Pošta, A, He, MQ, Li, JX, Raza, M, Sruthi, OP, Suetrong, S, Suwannarach, N, Tedersoo, L, Thiyagaraja, V, Tibpromma, S, Tkalčec, Z, Tokarev, YS, Wanasinghe, DN, Wijesundara, DSA, Wimalaseana, SDMK, Madrid, H, Zhang, GQ, Gao, Y, Sánchez-Castro, I, Tang, LZ, Stadler, M, Yurkov, A, Thines, M, Qujing Normal University, University of Warsaw, Mae Fah Luang Universit, University of Debrecen, Universidade de Lisboa, Ruder Boskovic Institute, Institute of Microbiology, Chinese Academy of Sciences, National Fungal Culture Collection of India -NFCCI, National Science and Technology Development Agency -NSTDA, Chiang Mai University, University of Tartu, Mae Fah Luang University, Kunming Institute of Botany, All-Russian Institute of Plant Protection, National Institute of Fundamental Studies, University of Ruhuna, Estación Experimental del Zaidín, Jiangxi normal University, Technische Universitat Braunschweig, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Goethe University., Swedish University of Agricultural Sciences, Universidade Federal do Rio Grande do Norte, University Road, Kirsehir Ahi Evran University, Universidade Federal de Mato Grosso do Sul, West Pomeranian University of Technology, Universidade Federal de Pernambuco, FRANCISCO ADRIANO DE SOUZA, CNPMS, Zhongkai University of Agriculture and Engineering, Botanic Garden Meise, University of South Bohemia, King Saud University, Royal Botanic Gardens, University of Gdansk, Skovoroda Kharkiv National Pedagogical University, The Field Museum, University of Electronic Science and Technology of China, University of Silesia in Katowice, Universidad de Granada, Museu Paraense Emílio Goeldi, Agroscope, Plant Protection Products - Impact and Assessment, Team Applied Ecotoxicology, National Natural Science Foundation of China, Guizhou University, and Croatian Science Foundation
Subjects: Fossil fungi, Evolution, MOLECULAR PHYLOGENY, Plant Science, Behavior and Systematics, Ascomycota, Basal fungi, PHYLOGENETIC ANALYSIS, INCORPORATING ANAMORPHIC FUNGI, NATURAL CLASSIFICATION, Biology, Ecology, Evolution, Behavior and Systematics, Fungo, basal fungi, Ecology, LICHENIZED FUNGI, Basidiomycota, Classification, Rozellomycota, Biology and Life Sciences, Forestry, MULTIGENE PHYLOGENY, Interdisciplinary Natural Sciences, FRESH-WATER ASCOMYCETE, Microsporidia, GEN. NOV, Amblyosporidae, SP.-NOV, TAXONOMIC REVISION
Abstract: This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results., National Natural Science Foundation of China (NSFC) NSFC 31950410558 NSFC 31760013 32100011, Department of Science and Technology of Yunnan Province 2018FB050, State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University FAMP201906K, Science and Technology Department of Guizhou Province QKHRCPT[2017] 5101, High-Level Talent Recruitment Plan of Yunnan Province ("Young Talents" Program), Chiang Mai University, Croatian Science Foundation HRZZ-IP-2018-01-1736 HRZZ-2018-09-7081, LOEWE initiative of the government of Hessen, Distinguished Scientist Fellowship (DSFP), King Saud University, Kingdom of Saudi Arabia, CAS President's International Fellowship Initiative (PIFI) 2020PB0115 2020PC0009 2018PC0006, National Science Centre, Poland 2017/25/B/NZ8/00473, International Postdoctoral Exchange Fellowship Program Y9180822S1, China Postdoctoral Science Foundation, Yunnan Human Resources, and Social Security Department Foundation, National Natural Science Foundation of China (NSFC) 31750110478, China Postdoctoral Science Foundation 2021M693361, Portuguese Foundation for Science and Technology, European Commission UIDB/04046/2020 UIDP/04046/2020, High-Level Talent Recruitment Plan of Yunnan Province ("High-End Foreign Experts" Program)
Published: 2022

22. Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

Author: Christopher Daum, Kurt LaButti, Joseph W. Spatafora, Alan Kuo, Jon Magnuson, Byoungnam Min, Anna Lipzen, Annegret Kohler, Francis Martin, Yang Cao, Jianping Xu, Emmanuelle Morin, Jonathan M. Plett, László Nagy, Hongjae Park, Jasmyn Pangilinan, Torda Varga, Gang Wu, Igor V. Grigoriev, In Geol Choi, Steven Ahrendt, Elodie Drula, Jenifer Johnson, Kerrie Barry, Bernard Henrissat, Hope Hundley, Shingo Miyauchi, Vivian Ng, Zhu-Liang Yang, Bang Feng, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Joint Genome Institute (JGI), United States Department of Energy, Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biological Research Centre [Szeged] (BRC), Korea University [Seoul], Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS), Hawkesbury Institute for the Environment [Richmond] (HIE), Western Sydney University, Pacific Northwest National Laboratory (PNNL), Oregon State University (OSU), and Department of Biology - MacMaster University
Subjects: 0106 biological sciences, Comparative genomics, Bolete, 0303 health sciences, biology, Physiology, Boletales, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Basidiomycota, Plant Science, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, Biological Evolution, 03 medical and health sciences, Phylogenetics, Evolutionary biology, Mycorrhizae, Gene duplication, Gene family, Symbiosis, Gene, Phylogeny, 030304 developmental biology
Abstract: International audience; - We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives.- Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae.- Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay.- This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.
Published: 2021

23. The powdery mildew disease of rubber (Oidium heveae) is jointly controlled by the winter temperature and host phenology

Author: Philippe Thaler, Yiqi Luo, Jianchu Xu, De-Li Zhai, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Northern Arizona University [Flagstaff], World Agroforestry Center [CGIAR, Chine] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), National Natural Science Foundation of China (NSFC) and the Belmont Forum Collaborative Research Action 'Mountains as Sentinels of Change -2015' (No. 41661144001), and Key Research Program of Frontier Sciences, the Chinese Academy of Sciences (QYZDY-SSW-SMC014). This work is also supported by Key Research Project (No. 2017YFC0505101)
Subjects: Atmospheric Science, 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Winter warming, Facteur climatique, 01 natural sciences, 0302 clinical medicine, Maladie des plantes, Developing regions, Oidium heveae, Ecology, biology, Phenology, Plant physiology, food and beverages, Horticulture, Hevea brasiliensis, visual_art, visual_art.visual_art_medium, Phénologie, Powdery mildew, Oidium (manifestation maladies), Conditions météorologiques, 03 medical and health sciences, Natural rubber, Rubber plantation, Partial least square (PLS) regression, 0105 earth and related environmental sciences, H20 - Maladies des plantes, 030203 arthritis & rheumatology, Host (biology), biology.organism_classification, Température, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Hiver, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Rubber powdery mildew disease (Oidium heveae) is a serious threat to natural rubber production (Hevea brasiliensis) in some rubber developing regions of the world. Both phenological- and meteorological-related factors have been reported influencing the powdery mildew disease. However, few studies have investigated the effects of both phenological- and meteorological-related factors on the disease. The objective of this study is to quantify the contributions of phenological- and meteorological-related factors to affect the disease. We used the partial least squares (PLS) regression method to comprehensively quantify the effects of thirty-five phenological related factors and six meteorological factors on the infection level of powdery mildew of rubber trees over 9-year records (2003–2011). The relative contributions of significant factors were further investigated by the variation partition analysis. We found that the most influential variables were the mean temperature during winter and the duration of leaf development to maturation which explained 32 and 26% of the variations in the infection level. We found the controlling role of winter mean temperature, for the first time, on the infection level of powdery mildew. The controlling role of winter temperature may have directly increase the infection level when winter temperature is high and indirectly increase the infection level through prolonging the duration of leaf development to maturation, although the duration itself had smaller influences. We detected a warming trend of the winter temperatures from 2003 to 2011, which indicates that the infection level of powdery mildew will be increased if the winter warming continues.
Published: 2021

24. Contrasted effects of temperature during defoliation vs. refoliation periods on the infection of rubber powdery mildew (Oidium heveae) in Xishuangbanna, China

Author: Jianchu Xu, De-Li Zhai, Jing Wang, Philippe Thaler, Yiqi Luo, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), East China Normal University [Shangaï] (ECNU), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Northern Arizona University [Flagstaff], World Agroforestry Center [CGIAR, Chine] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and National Natural Science Foundation of China (NSFC), by the Belmont Forum Collaborative Research Action 'Mountains as Sentinels of Change2015' (No. 41661144001), and by the Key Research Program of Frontier Sciences, Chinese Academy of Sciences (QYZDY-SSWSMC014)
Subjects: Atmospheric Science, 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Biology, 01 natural sciences, Défoliation, Partial least squares (PLS) regression, 03 medical and health sciences, 0302 clinical medicine, Leaf phenology, Natural rubber, [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, Analyse de régression, Rubber plantation, Xishuangbanna, Sw china, 0105 earth and related environmental sciences, H20 - Maladies des plantes, 030203 arthritis & rheumatology, Oidium heveae, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Phenology, Oidium (genre), food and beverages, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Fungicide, Horticulture, Hevea brasiliensis, visual_art, Température ambiante, visual_art.visual_art_medium, Phénologie, Powdery mildew
Abstract: International audience; Rubber powdery mildew caused by the foliar fungiOidium heveaeis one of the main diseases affecting rubber plantations (Hevea brasiliensis) worldwide. It is particularly serious in sub-optimal growing areas, such as Xishuangbanna in SW China. To prevent and control this disease, fungicides causing serious environmental problems are widely used. Strong correlations between the infection level and the temperature variables were reported previously, but they were related to monthly data that did not allow unraveling the patterns during the entire sensitive period. We correlated the infection level of powdery mildew of rubber trees recorded over 2003-2011 with antecedent 365 days daily temperature variables using partial least squares (PLS) regression. Our PLS regression results showed that the infection level of powdery mildew responded differently to the temperature variables of the defoliation and refoliation periods. Further analysis with Kriging interpolation showed that the infection level increased by 20% and 11%, respectively, per 1 degrees C rise of the daily maximum and mean temperature in the defoliation season, while it decreased by 8% and 10%, respectively, per 1 degrees C rise of the daily maximum and temperature difference in the refoliation season. This pattern was likely linked to the effects of temperature on leaf phenology. It seems highly possible that the infection level of powdery mildew increases, as increasing trends of maximum temperature and mean temperature during the defoliation continue.
Published: 2020

25. Metagenomics approaches for Understanding Fungal Ecology in Forest Ecosystems

Author: Buée, Marc, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kunming Institute of Botany, Yunnan, China, and Buée, Marc
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

26. Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition

Author: David G. Würth, Nikki Heherson A. Dagamac, R. Henrik Nilsson, Kevin D. Hyde, Sébastien J. Puechmaille, Mathilde Borg Dahl, Christian Wurzbacher, Serena E. Dool, Michael G. Schöner, Michelle Galla, Abu Bakar Siddique, Kristina Wicke, Martin Unterseher, Caroline R. Schöner, García Roberto Cruz, Annette Teltewskoi, Samantha C. Karunarathna, Lina Herbst, Ernst-Moritz-Arndt-Universität Greifswald, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), University of Gothenburg (GU), and Mae Fah Luang University [Thaïlande] (MFU)
Subjects: 0106 biological sciences, 0301 basic medicine, Biogeography, Biodiversity, 01 natural sciences, 03 medical and health sciences, Amorphophallus, Botany, Camellia sinensis, Mycobiome diversity, Internal transcribed spacer, Ecology, Evolution, Behavior and Systematics, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, High-throughput metabarcoding, Abiotic component, biology, Host (biology), fungi, food and beverages, Host specialization, Camellia, 030108 mycology & parasitology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Sympatric speciation, Tissue preferences of endophytes, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Multiple biotic and abiotic parameters influence the dynamics of individual fungal species and entire communities. Major drivers for tropical plant endophytes are undoubtedly seasonality, local habitat conditions and biogeography. However, host specialization and tissue preferences also contribute to the structuring of endophytic mycobiomes. To elucidate such specializations and preferences, we sampled two commercially important, unrelated plant species, Amorphophallus albispathus and Camellia sinensis (tea plant) simultaneously at close proximity. The mycobiomes of different tissue types were assessed with high-throughput amplicon sequencing of the internal transcribed spacer DNA region. Both plants hosted different fungal communities and varied in α-and β-diversity, despite their neighboring occurrence. However, the fungal assemblages of Amorphophallus leaflets shared taxa with the mycobiomes of tea leaves, thereby suggesting common driving forces for leaf-inhabiting fungi irrespective of host plant identity. The mycobiome composition and diversity of tea leaves was clearly driven by leaf age. We suggest that the very youngest tea leaves are colonized by stochastic processes, while mycobiomes of old leaves are rather similar as the result of progressive succession. The biodiversity of fungi associated with A. albispathus was characterized by a large number of unclassified OTUs (at genus and species level) and by tissue-specific composition.This study is the first cultivation-independent high-throughput assessment of fungal biodiversity of an Amorphophallus species, and additionally expands the knowledge base on fungi associated with tea plants.
Published: 2018

27. 滇南地区咖啡 - 农林复合系统遮荫处理对土壤肥力和咖啡生产力的影响

Author: Rigal, Clément, Rigal, Clément, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), university of chinese academy of sciences, Jianchu Xu, and Philippe Vaast
Subjects: [SDE] Environmental Sciences, [SDV] Life Sciences [q-bio], coffea arabica, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, services ecosystémiques, Agroforestry, Agroforesterie, ecosystem services
Abstract: Highly productive monoculture coffee (Coffea Arabica L.) farms have rapidly expanded in Yunnan Province since the 1990s. As of 2016, coffee farms covered more than 115000 ha, producing over 95% of all coffee grown in China. However, intensive monoculture coffee systems are known to have negative impacts on soil fertility and to expose farmers to high risks, notably financial risks stemming from rapid and strong variations in coffee prices on the international market as well as vulnerability to extreme climatic events. In an effort to prepare the coffee sector to face these challenges, the local governments of Pu’er and Xishuangbanna Prefectures initiated a large-scale transition program from monoculture systems to coffee-agroforestry systems in 2012; distributing free shade tree seedlings to all coffee farmers in their jurisdictions. These shade trees have the potential to provide multiple ecosystem services and thus contribute to more sustainable coffee production, while maintaining high yield, since coffee is a shade adapted species. The impacts of shade trees have been long studied in traditional coffee-producing countries. However, most of these studies were carried out in mature coffee-agroforestry systems, while there is a paucity of information on the transition period from monoculture to mature agroforestry systems. Furthermore, this knowledge gap is coupled with a lack of documentation on the specific shade tree species used in Yunnan coffee farms and their impacts in local growing conditions. To contribute to the successful transition from monoculture to coffee-agroforestry systems in Pu’er and Xishuangbanna Prefectures, the present research focuses on assessing the impacts of young and commonly used shade trees on soil fertility and coffee production in intensively managed coffee farms of southern Yunnan. Chapter I introduces the research topic and Chapter II describes the study area. Then, in the first study (Chapter III), 29 shade tree inventories were carried out in coffee farms in Pu’er and Xishuangbanna Prefectures. These inventories revealed an unexpectedly high level of diversity at both farm (average of 15 species per farm) and landscape levels (estimated 162 tree species overall), and thus highlighted the potential for agroforestry systems to contribute to biodiversity conservation. Based on these tree inventories, the 30 shade tree species most commonly found on coffee farms were identified. Using a participatory approach based on a ranking system (the Bradley-Terry method), 143 coffee farmers were interviewed to document their ethnobotanical knowledge regarding the ecosystem services and disservices provided by these common shade tree species. The nine tree species promoted by local governments – Alstonia scholaris, Bischofia javanica, Cerasus cerasoides, Cinnamomum camphora, Delonix regia, Dimocarpus longan, Litchi chinensis, Macadamia integrifolia and Mangifera indica – were highly favored for their perceived economic potential and the protection that they provided to coffee trees against environmental hazards. Non-promoted species, such as Artocarpus heterophyllus and Diospyros kaki, were also identified as tree species with high potential to provide locally relevant ecosystem services in coffee farms. These results led to the upgrade of an online tool (www.shadetreeadvice.org) which allows extension services generating lists of recommended shade tree species tailored to the specific local ecological context of southern Yunnan and to individual farmers’ needs. Lastly, this study pointed out knowledge gaps from coffee farmers regarding the impacts of shade trees on soil fertility, coffee yield, coffee quality and pests and diseases control. In the second and third studies (Chapters IV and V), a field experiment was set up in Liushun Township, located in Pu’er Prefecture, to assess the impacts of three commonly found shade tree species – B. javanica, C. camphora and Jacaranda mimosifolia – on soil fertility, coffee yield, and coffee quality only four years after their introduction into intensively managed monoculture coffee farms under near-optimal growing conditions. For soil fertility (Chapter IV), soil chemical parameters (total N, available P, exchangeable K, Ca and Mg, organic matter, pH), soil biological communities (nematodes and microbial communities) and soil enzyme activities (β-glucosidase, N-acetyl-glucosaminidase and acid phosphatase) were measured in the top (0-20 cm) soil layer, as well as root systems of shade trees and coffee trees and soil water profiles to a depth of 1.2m. All three shade tree species contributed to improving soil fertility. In particular, this translated in higher soil chemical fertility (higher pH, OM, N, P and Ca concentrations); similar or higher soil enzyme activities throughout the year (all three measured enzymes); more abundant fungi communities throughout the year; and more abundant microbial communities during the dry season below shade trees than in open areas. Soil water profiles highlighted that annual rainfalls were sufficient to provide enough water resources for both coffee trees and shade trees. On the other hand, root profiles pointed out fierce root competition between B. javanica and coffee trees in the 0-20 cm soil layer and between C. camphora and coffee trees below 20 cm depth. Overall, Chapter IV evidenced that shade trees rapidly contributed to preserving and/or restoring soil fertility and buffering seasonal variability in soil biological activity in intensively managed coffee farms. Chapter V assessed the above-ground impacts of these same shade trees on coffee yield and coffee quality. To do so, the yield of 309 coffee trees was estimated from their fruit load in November 2016, one month before harvest. In 2017, micro-climate data (air temperature and humidity every 30 minutes) was recorded for one year below the canopies of the three selected shade tree species and in open conditions. The coffee development cycle of 90 coffee trees located either below shade tree canopies, at the edge of shade tree canopies or in open conditions, was simultaneously monitored. Specifically, the number of flower buds, flowers, coffee pinheads/cherries and aborted fruits was recorded on a sample of branches during one growing period, from first flowers to harvest. In the winter of 2017-2018, these 90 coffee trees were manually harvested and their yields measured. Physical and organoleptic quality assessments were carried out on coffee samples. This study showed that young shade trees created micro-climates favorable to coffee production below their canopies, with lower vapor pressure deficit (-0.5 to -0.9 kPa) and lower maximum temperatures (-3 to -6°C) than in open areas in the summer days, and higher minimum temperatures (+0.5 to +1°C) than in open areas in the winter days. This protection from extreme temperatures was particularly important when temperatures hit 0°C in open areas in December 2017. Fruit set decreased with shade intensity; however fruit drop also decreased during the bean filling and maturation stages. As a result, coffee yields were similar in open areas and in shaded conditions over two consecutive years (2.8kg.tree-1 in 2016 and 4.5kg.tree-1 in 2017). Only coffee trees below C. camphora had significantly lower yield than other coffee trees (2.4kg.tree-1 in 2016 and 2.8kg.tree-1 in 2017). Lastly, shade trees had no visible impact on coffee quality. Overall, Chapter V showed that shade trees with low canopies - B. javanica and J. mimosifolia - provided a favorable micro-climate under their canopies, with no negative impacts on coffee yield and quality. On the other hand, shade trees with dense canopies - C. camphora – did provide protection from climatic hazards but at the expense of coffee yield. This highlighted the needs for adapted management practices of shade trees, such as pruning practices timed with the coffee production cycle. This PhD thesis demonstrates that carefully selected and managed shade trees provided substantial ecosystem services only four years after their introduction into intensively managed coffee farms in southern Yunnan. In particular, they contributed to biodiversity conservation, preservation and/or restoration of soil fertility and protection of coffee trees from climatic hazards. Furthermore, with adequate tree canopy density and shade level, farmers can maintain high coffee yield under shade, combined with cup quality similar to the one in open areas. Therefore, the conversion from monoculture to coffee-agroforestry systems in Pu’er and Xishuangbanna Prefectures, initiated by local governments, should bring both short-term and long-term benefits to coffee farmers, support landscape health and contribute to the sustainability of the coffee agriculture sector in southern Yunnan., L’agriculture intensive de café (Coffea Arabica L.) en plein soleil s’est rapidement développée dans la province du Yunnan dans les années 1990. En 2016, les fermes de café couvraient plus de 115000 ha et produisaient plus de 95% du café chinois. Cependant, l’agriculture intensive de café en plein soleil est connue pour provoquer des impacts négatifs sur la qualité des sols et soumettre les producteurs de café à de grands risques financiers dus aux rapides fluctuations des prix sur les marchés internationaux et à leur vulnérabilité aux aléas climatiques. Afin de préparer le secteur du café à ces défis, les gouvernements locaux des préfectures de Pu’er et du Xishuangbanna ont initié en 2012 un programme à grande échelle de conversion des systèmes de café en plein soleil vers des systèmes de café-agroforestiers. Pour cela, ces gouvernements ont distribué des plantules d’arbres d’ombrage à tous les producteurs de café présents dans leur juridiction. Ces arbres d’ombrage peuvent fournir de multiples services écosystémiques et contribuer à la durabilité socio-environnementale de la production de café tout en maintenant des rendements importants. L’impact des arbres d’ombrage a été longuement étudié dans les pays traditionnellement producteurs de café. Cependant, la majorité de ces études porte sur des systèmes agroforestiers matures. Il existe donc un manque d’information des impacts durant la période de transition des systèmes de café en plein soleil vers des systèmes de café-agroforestiers matures. De plus, ce manque d’information sur les impacts s’ajoute à un manque d’information sur les espèces d’ombrage plus spécialement utilisées dans les systèmes caféiers du Yunnan et leurs impacts spécifiques dans les conditions environnementales locales. La présente recherche s’attache donc à l’étude des impacts des jeunes arbres d’ombrage couramment utilisés dans les fermes de café du sud Yunnan, et plus spécifiquement les impacts de ces jeunes arbres sur la qualité des sols et la production du café. Dans le premier chapitre, j’introduis en détails le sujet de recherche. Dans le deuxième chapitre, je décris la zone d’étude. Dans le troisième chapitre, je présente 29 inventaires des arbres d’ombrage présents dans les fermes de café des préfectures de Pu’er et du Xishuangbanna. Ces inventaires ont révélé une diversité élevée à l’échelle de la ferme (15 espèces d’ombrage par ferme en moyenne) comme du paysage (richesse spécifique estimée à 162 espèces d’ombrage). Ces résultats confirment le potentiel des systèmes café-agroforestiers à la conservation de la biodiversité. A partir de ces inventaires, j’ai identifié les 30 espèces d’ombrage les plus courantes dans les fermes de café. 143 entretiens avec des producteurs de café et l’utilisation d’une méthodologie participative basée sur des exercices de classements lors de ces entretiens (méthode basée sur l’analyse Bradley-Terry) m’ont permis de documenter le savoir ethnobotanique de ces producteurs de café, concernant les services écosystémiques fournis par ces 30 espèces d’ombrage. Il apparait que les 9 espèces promues par les gouvernements locaux, à savoir Alstonia scholaris, Bischofia javanica, Cerasus cerasoides, Cinnamomum camphora, Delonix regia, Dimocarpus longan, Litchi chinensis, Macadamia integrifolia et Mangifera indica, étaient appréciées des producteurs de café pour leur potentiel économique et les services de protection des caféiers contre les aléas climatiques. Cette étude m’a également permis d’identifier des espèces d’ombrage avec un fort potentiel de fourniture de services écosystémiques mais non promues par les gouvernements locaux, telles qu’Artocarpus heterophyllus et Diospyros kaki. Ces résultats ont contribué à l’amélioration d’un outil d’aide à la décision en ligne à destination des services d’extension (www.shadetreeadvice.org), qui génère des listes d’espèces d’ombrage personnalisées, en fonction du contexte environnemental local et des objectifs spécifique de chaque producteur de café. Enfin, cette étude a mis le doigt sur des lacunes dans les savoirs locaux des producteurs de café concernant l’impact des espèces d’ombrage sur la qualité des sols, le rendement et la qualité du café, ainsi que sur les ravageurs. Les chapitres quatre et cinq traitent d’expérience dont le dispositif expérimental était situé dans la commune de Liuxun, dans la préfecture de Pu’er, et dont l’objectif était de quantifier l’impact de trois espèces d’ombrage courantes - B. javanica, C. camphora and Jacaranda mimosifolia – sur la qualité des sols, le rendement et la qualité du café seulement quatre ans après l’introduction de ces arbres d’ombrage dans des parcelles de café intensives et bénéficiant de conditions environnementales proches de l’optimal théorique. Le chapitre quatre se concentre sur la qualité des sols à travers les propriétés chimiques (azote total, phosphore disponible, potassium calcium et magnésium échangeables, matière organique, pH), les communautés biologiques (nématodes et communautés microbiennes), et l’activité enzymatique (β-glucosidase, N-acetyl-glucosaminidase et acid phosphatase) dans les 20 premiers centimètres du sol. Ce chapitre décrit également les profils racinaires des caféiers et des arbres d’ombrage ainsi que les profils hydriques dans les premiers 120 cm du sol. J’y apporte la preuve que ces trois espèces d’ombrage contribue à l’amélioration de la qualité des sols. Cette amélioration se traduit par une qualité chimique accrue (accroissement de pH, MO, et concentrations de N, P et Ca), une activité enzymatique constante ou accrue durant le cycle de production du café pour les trois enzymes mesurées, des communautés fungiques plus abondantes durant tout le cycle de production du café et des communautés bactériennes plus abondantes durant la saison sèche sous ombrage qu’en plein soleil. Les profils hydriques ont révélé que les précipitations annuelles apportaient des ressources hydriques suffisantes à la fois aux caféiers et aux arbres d’ombrage. Cependant, les profils racinaires ont révélé une forte compétition racinaire entre B. javanica et les caféiers dans les 20 premiers cm, et entre C. camphora et les caféiers aux profondeurs supérieures à 20 cm. D’une manière globale, le chapitre quatre met en évidence la rapide contribution des arbres d’ombrage à la préservation/restauration de la qualité des sols et à leur effet tampon sur l’activité biologique des sols durant la saison sèche. Dans le chapitre cinq, j’étudie l’impact aérien des trois espèces d’ombrage sur le rendement et la qualité du café. Pour ce faire, j’ai estimé le rendement de 309 caféiers en novembre 2016, à partir de leur charge en fruit un mois avant le début de la récolte. En 2017, j’ai mesuré le micro-climat (température et humidité de l’air toutes les 30 minutes) sur l’ensemble du cycle de production du café, sous ombrage et en plein soleil. En parallèle, j’ai suivi le développement des fruits de 90 caféiers situés sous ombrage des arbres, à la lisière de l’ombrage des arbres et en plein soleil. J’ai plus spécifiquement compté tout au long du cycle de développement du café, depuis les boutons floraux jusqu’à la récolte, le nombre de boutons floraux, de fleurs, de fruits et de coulure sur un échantillon de branches de ces 90 caféiers. Pendant l’hiver 2017-2018, j’ai récolté les fruits de ces 90 caféiers, mesuré le rendement et la qualité sur des échantillons de grains à partir de critères physiques et organoleptiques. Cette étude a démontré que les jeunes arbres d’ombrage contribuent à la création d’un microclimat favorable à la production de café sous leur canopée, à travers un déficit de pression de vapeur diminué (-0.5 à -0.9 kPa), des températures maximales plus douces en été (-3 to -6°C), et des températures minimales plus élevées en hiver (+0.5 to +1°C) sous ombrage qu’en plein soleil. Cette protection contre les températures extrêmes s’est avérées particulièrement importante lors d’une vague de froid en décembre 2017, lorsque les températures ont atteint 0°C. La charge en fruit a diminué avec l’intensité de l’ombrage. Cependant, la coulure en fruit durant les périodes de remplissage et de maturation des cerises de café a également diminué avec l’intensité de l’ombrage. Avec pour conséquence des rendements de café similaires sous ombrage et en plein soleil pendant les deux années mesurées (2.8kg.arbre-1 en 2016 et 4.5kg.arbre-1 en 2017). Seuls les caféiers sous l’ombrage de C. camphora avaient des rendements significativement inférieurs aux autres caféiers (2.4kg.arbre-1 en 2016 and 2.8kg.arbre-1 en 2017). Enfin, les arbres d’ombrage n’ont pas eu d’impact notable sur la qualité du café. D’une manière générale, ce chapitre démontre le fait que les espèces d’ombrage offrant un ombrage faible ou mesuré, telles que B. javanica et J. mimosifolia, contribuent à la création d’un microclimat favorable aux caféiers sous leur ombrage sans impact négatif sur le rendement et la qualité. Au contraire, les espèces d’ombrage offrant un ombrage dense, telles que C. camphora, contribuent elles-aussi à la protection des caféiers contre les températures extrêmes et les aléas climatiques mais impactent négativement les rendements de café. Cela souligne la nécessité d’adopter des pratiques de gestion personnalisées par espèce d’ombrage, qui incluent l’élagage des espèces d’ombrage aux canopées les plus denses.Ce doctorat apporte la preuve que des espèces d’ombrage sélectionnées et gérées d’une manière appropriée fournissent rapidement des services écosystémiques substantiels, ici seulement quatre ans après leur introduction dans des fermes de café intensive du sud Yunnan. Plus particulièrement, de telles espèces d’ombrage contribuent à la préservation de la biodiversité, à la préservation et restauration des sols, et à la protection des caféiers contre les aléas climatiques. De plus, si l’ombrage est géré de manière maintenir une intensité d’ombrage adaptée, les producteurs de café peuvent maintenir de hauts rendements sous ombrage, et une qualité du café sous ombrage similaire à celle du café en plein soleil. En conséquences, la conversion des systèmes de café en plein soleil en des systèmes de café-agroforestiers dans les préfectures de Pu’er et du Xishuangbanna, telle qu’initiée par les gouvernements locaux, devrait directement bénéficier aux producteurs de café non seulement à moyen terme mais également à court terme, contribuer à l’aménagement durable du paysage et à la soutenabilité de la filière café du sud Yunnan., 自20世纪90年代以来，云南高产的单一栽培咖啡(Coffea Arabica L.)迅速扩张。截至2016年，咖啡农场面积超过115000公顷，占中国咖啡种植面积的95%以上。然而，众所周知，密集的单一栽培咖啡系统对土壤肥力有负面影响，并使农民面临高风险，特别是由于国际市场上咖啡价格剧烈迅速且剧烈的波动,以及极端气候事件影响而产生的金融风险。为了让咖啡行业应对这些挑战，普洱和西双版纳的地方政府于2012年启动了从单一栽培系统向咖啡农林复合系统的大规模转型计划，并向其管辖范围内的所有咖啡农免费发放遮荫树苗。这些遮荫树具有提供多种生态系统服务的潜力，且咖啡是适应遮荫的物种，从而有助于咖啡的可持续生产，同时保持高产量。长期以来，在传统的咖啡生产国，人们一直在研究遮荫树的影响。然而，这些研究大多是在成熟的咖啡-农林复合系统中进行的，但关于从单一栽培到成熟农林复合系统过渡时期的信息很少。此外，这种知识缺口还与缺乏云南咖啡农场使用的特定遮荫树种及其对当地种植条件的影响的文献有关。为了促进普洱、西双版纳两地从单一栽培模式向咖啡农林复合经营模式的成功转型，本研究以云南南部集约经营的咖啡农场为研究对象，重点研究了幼树和常用遮荫树种对土壤肥力和咖啡产量的影响。第一章主要介绍研究课题，第二章主要介绍研究领域。然后，在第一项研究(第三章)中，我在普洱和西双版纳两州的咖啡农场进行了29个遮荫树试验点。这些研究地点的树木清单显示出农场(平均每个农场有15个物种)和景观水平(估计总共有162个树种)的多样性水平都很高，从而突显了农林复合系统有助于生物多样性保护的潜力。根据这些树木目录，我确定了30种遮荫树种，它们是咖啡农场中最常见的树种。使用基于排名系统(Bradley-Terry方法)的参与式方法，我采访了143名咖啡农，并记录了他们关于这些常见遮荫树种所提供的生态系统服务和危害的民族植物学知识。我发现当地政府推广的九种树种 - Alstonia scholaris（灯台叶），Bischofia javanica（茄苳），Cerasus cerasoides(樱花)，Cinnamomum camphora（番樟），Delonix regia（凤凰木），Dimocarpus longan（龙眼），Litchi chinensis（荔枝），Macadamia integrifolia（澳洲坚果）和Mangifera indica （芒果）-因其被认同的经济潜力和防止咖啡树受到环境危害的保护能力而受到高度青睐。我还发现了一些没有被推广的物种，比如菠萝蜜和柿子树，它们在咖啡农场提供与当地有关的生态系统服务上很有潜力。这些结果促进了在线工具(www.shadetreeadvice.org)的升级，该工具通过扩展服务生成推荐遮荫树种的列表，这些遮荫树种是根据云南南部特定的当地生态环境和农民个人的需求定制的。最后，本研究指出了在遮荫树对土壤肥力、咖啡产量、咖啡质量以及病虫害控制的影响方面，咖啡农户的知识缺口。在第二项和第三项研究(第四章和第五章),我在普洱州六顺乡建立一个现场试验, ,评估三个常见遮荫树种的影响：B. javanica （茄苳）、C. camphora （番樟）和 Jacaranda mimosifolia（蓝花楹），主要针对树种对土壤肥力，咖啡产量，还有咖啡质量三个方面，时间是仅在引入集约管理的单一咖啡农场4年后。对于土壤肥力(第四章),主要检测了表层（0-20cm）土壤化学参数(总N,有效P,可交换钾,钙,镁,有机质、pH值),土壤生物群落(线虫和微生物群落)和土壤酶活性(β-葡萄糖苷酶, N-乙酰氨基葡糖苷酶和酸性磷酸酶),以及遮荫树和咖啡树的根系和土壤水分剖面，深度1.2米。我论证了所有三种遮荫树种都有助于提高土壤肥力。特别地，我测量了更高的土壤化学肥力(更高的pH、OM、N、P和Ca浓度);全年类似或更高的土壤酶活性(所有三种测得的酶);全年真菌群落更丰富;在旱季，遮荫树下的微生物群落比开阔地区丰富。土壤水分剖面显示，每年的降雨足以为咖啡树和遮荫树提供足够的水资源。另一方面，根侧轮廓显示，0- 20cm土层的蓝花楹与咖啡树之间的根系竞争非常激烈，20 cm以下的番樟和咖啡树之间的根系竞争非常激烈。总的来说，第四章证明了在集中管理的咖啡农场中，遮荫树迅速有助于保持和/或恢复土壤肥力和缓冲土壤生物活动的季节性变化。在第五章中，我评估了这些遮荫树对地上咖啡产量和咖啡质量的影响。为此，2016年11月我估算了309棵咖啡树的产量，正是在收获的前一个月。在2017年，我记录了三个选定遮荫树种的树冠下，以及开放条件下一年的微气候数据(气温和湿度，30分钟/次)。同时跟踪了90棵咖啡树的发展周期，这些咖啡树有的位于树荫下，有的位于树荫檐的边缘，有的则位于开放条件下。具体来说，我在一个生长期内，记录了第一朵花到收获的单一样本枝条上花蕾、花、咖啡针尖/果实和败育果数量。在2017-2018年冬季，我收获了这90棵咖啡树，测量了产量，并对咖啡样品进行了物理和有机质量评估。这项研究显示,年轻的遮荫树行成的微气候可增加咖啡在遮荫下的产量。夏季相比开放区域显示出气压不足(-0.5 - -0.9 kPa)和最高温度较低(3到6°C), 在冬季相比开放区则显示出更高的最低温度(+ 0.5 + 1°C)。这对2017年12月开放区温度降到0℃的极端温度形成了保护。座果率随遮荫强度降低;然而，在豆类灌浆和成熟阶段，果实产量有所下降。因此，在连续两年的光照条件下，在开阔区域和阴凉条件下，咖啡产量相似（2016年为2.8公斤/棵，2017年为4.5公斤/棵）。只有C.camphora (番樟)下方的咖啡树的产量明显低于其他咖啡树（2016年为2.8公斤/棵，2017年为4.5公斤/棵）。最后，树荫对咖啡品质没有明显影响。总体而言，第五章表明，树冠较低的遮荫树B. javanica（茄冬）和J. mimosifolia（兰花楹）在树冠下提供了良好的微气候，对咖啡产量和品质没有负面影响。另一方面，树冠浓密的遮荫树—C.camphora(番樟)—确实能够保护咖啡树免受气候灾害的影响，但代价是咖啡的产量降低。这突出了对遮荫树的适应性管理实践的需求，例如：与咖啡生产周期同步的修剪管理。此项研究表明，经过精心挑选和管理的遮荫树在进入云南南部集中管理的咖啡农场仅仅四年之后就提供了大量的生态系统服务。它们特别有助于生物多样性的保护、保护和/或恢复土壤肥力和保护咖啡树免受气候灾害。此外，充足的树冠密度和遮荫水平，农民可以在遮荫下保持较高的咖啡产量，再加上类似开放地区的咖啡质量。因此，由地方政府发起的普洱和西双版纳地区从单一栽培向咖啡农用复合林业系统的转变，将给咖啡农带来短期和长期的利益，促进景观健康，以及云南南部咖啡行业的可持续发展。
Published: 2018

28. Phylogeny, biogeography and taxonomic re-assessment of Multifurca (Russulaceae, Russulales) using three-locus data

Author: Bart Buyck, Roy E. Halling, Teresa Lebel, Xiang-Hua Wang, Valérie Hofstetter, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Royal Botanic Gardens Victoria, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0301 basic medicine, lcsh:Medicine, Forests, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Trees, Geographical Locations, Database and Informatics Methods, lcsh:Science, Phylogeny, Data Management, Multidisciplinary, biology, Ecology, Geography, Paleogenetics, Eukaryota, Phylogenetic Analysis, 030108 mycology & parasitology, Plants, Island hopping, Terrestrial Environments, Phylogenetics, Phylogeography, Biogeography, Multifurca, Russulaceae, Sequence Analysis, Research Article, Computer and Information Sciences, Asia, Bioinformatics, Disjunct, Research and Analysis Methods, Ecosystems, Evolution, Molecular, 03 medical and health sciences, Vicariance, Evolutionary Systematics, Taxonomy, Evolutionary Biology, Basidiomycota, Ecology and Environmental Sciences, lcsh:R, Organisms, Computational Biology, Biology and Life Sciences, Paleontology, 15. Life on land, biology.organism_classification, Evolutionary biology, People and Places, Earth Sciences, lcsh:Q, Pines, Sequence Alignment, Russulales
Abstract: International audience; Multifurca is a small genus newly established to accommodate lactarioid and russuloid species with some characters reminiscent of corticoid members of Russulaceae. It shows an amphi-pacific distribution with strong preference for the tropical zone of the Northern Hemisphere and thus has particular significance for biogeographical study. Using worldwide samples and three loci (ITS, 28S rDNA and rpb2), we demonstrated that Multifurca is split into two highly supported major clades that are here recognized at the subgeneric level: subg. Furcata subg. nov. exclusively includes lactarioid species, while subg. Multifurca includes species with a russuloid habit. Using phylogenetic species recognition and comparison of genetic distances we recognize five new and six previously described species, almost double the known number of species before this study. Molecular dating using a Bayesian method suggested that Multifurca originated in early Paleocene and diversified in the Eocene. The most recent interspecific divergences occurred both in Asia and America, roughly at the same time around the Pliocene. Ancestral area reconstruction and comparisons of genetic distances and morphology suggested an early divergence within Australasia or tropical Asia. From the early Miocene to Pliocene, multiple dispersals/migrations to Australasia and North America by island hopping or land bridge likely happened. Vicariance at the late Tertiary might be the most likely mechanism accounting for the eastern Asia—southeastern North America and Australasia—tropical Asia disjunct distributions. The shared polymorphisms in the ITS alignment, numerous degenerated base pairs in the rpb2 sequences and weak conflict between the ITS and LSU genealogies of M. subg. Furcata suggest recent speciation. Host specificity of Multifurca species or species pairs is relatively low. Host shifts are believed to have aided establishment in new territories during the dispersals and migrations.
Published: 2018

29. Study in Agaricus subgenus Minores and allied clades reveals a new American subgenus and contrasting phylogenetic patterns in Europe and Greater Mekong Subregion

Author: Samantha C. Karunarathna, Komsit Wisitrassameewong, Jie Chen, Rui-Lin Zhao, Olivier Raspé, Kevin D. Hyde, Mao-Qiang He, Philippe Callac, Magalie Moinard, Luis A. Parra, A. De Kesel, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Center of Excellence in Fungal Research, Mae Fah Luang University [Thaïlande] (MFU), Avda, Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, World Agroforestry Center [CGIAR, Chine] (ICRAF), World Agroforestry Center [CGIAR, Kenya] (ICRAF), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Botanic Garden Meise, Department of Biology, Faculty of Science, University of Isfahan, Unité de recherche Mycologie et Sécurité des Aliments (MSA), World Agroforestry Centre, China & East-Asia Office, and Naturalis journals & series
Subjects: 0301 basic medicine, taxonomie, [SDV]Life Sciences [q-bio], Subtropics, Agaricus sect. Minores, analyse phylogénétique, 03 medical and health sciences, taxonomy, Botany, Agaricaceae, Clade, Ecology, Evolution, Behavior and Systematics, divergence times, multi-gene phylogeny, Phylogenetic tree, biology, Species diversity, 15. Life on land, 030108 mycology & parasitology, biology.organism_classification, Evolutionary biology, Phylogenetic Pattern, Taxonomy (biology), agaricus, Subgenus, Research Article
Abstract: Within Agaricus subg. Minores, A. sect. Minores remains a little-studied section due generally to its delicate sporocarps often lacking taxonomically relevant morphological characters. To reconstruct the section, using the recent taxonomic system based on divergence times, and to evaluate the species diversity of A. sect. Minores in the Greater Mekong Subregion, 165 specimens were incorporated in phylogenetic analyses. A dated tree based on nuclear ITS, LSU and tef1-α sequence data allowed us to better circumscribe A. subg. Minores and to propose a new subgenus, A. subg. Minoriopsis, which is only known from tropical and subtropical regions of the Americas. A larger tree based on ITS sequences indicated that, with 81 phylogenetic species, the reconstructed section Minores is now one of the largest sections in the genus. Within A. subg. Minores, a new section, A. sect. Leucocarpi, and eleven new species are described from the Greater Mekong Subregion. Thirty-eight species of A. sect. Minores from this region of Asia were distributed in multiple clades that successively diverged over the past 24 million years. In contrast, species reported from Europe mostly grouped in a single non-tropical clade, suggesting a major species diversification following the middle Miocene climatic optimum.
Published: 2017

30. Mycosphere Essay 8: A review of genus Agaricus in tropical and humid subtropical regions of Asia

Author: J. C. Xu, Rui-Lin Zhao, Kevin D. Hyde, Peter E. Mortimer, Chen Junzhu, Samantha C. Karunarathna, Philippe Callac, Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences [Changchun Branch] (CAS), China & East-Asia Office, Mae Fah Luang University [Thaïlande] (MFU), Mushroom Research Foundation, Partenaires INRAE, State Key Laboratory of Mycology, Institute of Microbiology, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), and Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, champignon médicinal, région tropicale, taxonomie, [SDV]Life Sciences [q-bio], Humid subtropical climate, Plant Science, Biology, 03 medical and health sciences, Agaricus, edible mushroom, Botany, champignon comestible, Ecology, Evolution, Behavior and Systematics, molecular phylogeny, Mushroom, check list, région subtropicale, food and beverages, medicinal mushroom, poisonous mushroom, 030108 mycology & parasitology, biology.organism_classification, 3. Good health, Edible mushroom, Molecular phylogenetics, [SDE]Environmental Sciences, Taxonomy (biology), agaricus, Agaricus subrufescens, Agaricus bisporus
Abstract: International audience; The genus Agaricus includes both edible and poisonous species, with more than 400 species worldwide. This genus includes many species, which are enormously important as sources of food and medicine, such as the button mushroom (Agaricus bisporus) and the almond mushroom (Agaricus subrufescens). This paper reviews the genus Agaricus in tropical and humid subtropical regions of Asia, including the history, characteristics, pertinent morphological and organoleptic taxonomic traits, molecular phylogeny and taxonomy advances, toxicity and edibility. This review includes Agaricus species that are known to be highly valued as edible and medicinal mushrooms, and provides a comprehensive checklist of species described from the tropical and humid subtropical regions of Asia until the end of 2015.
Published: 2016

31. Towards standardizing taxonomic ranks using divergence times – a case study for reconstruction of the Agaricus taxonomic system

Author: Santiago Sánchez-Ramírez, Guo-Jie Li, Simona Margaritescu, Kevin D. Hyde, Philippe Callac, Luis A. Parra, Rui-Lin Zhao, Jie Chen, Jun-Liang Zhou, Jean-Marc Moncalvo, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences [Changchun Branch] (CAS), Beijing Forestry University, Mae Fah Luang University [Thaïlande] (MFU), Department of Natural History, Royal Ontario Museum, Department of Ecology and Evolutionary Biology, University of Toronto, Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), and Avda
Subjects: 0301 basic medicine, Systematics, Ecology, [SDV]Life Sciences [q-bio], Linnaean taxonomy, Zoology, 030108 mycology & parasitology, 15. Life on land, Biology, multi-gene phylogenetics, agaricaceae, 03 medical and health sciences, symbols.namesake, Monophyly, taxonomy, Taxon, divergence times, [SDE]Environmental Sciences, symbols, Taxonomy (biology), Taxonomic rank, Subgenus, Clade, systematics, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The recognition of taxonomic ranks in the Linnean classification system is largely arbitrary. Some authors have proposed the use of divergence time as a universally standardized criterion. Agaricus (Agaricaceae, Agaricales) is a mushroom genus that contains many species of high commercial value. Recent studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus, however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional taxonomy. In this study, we analyzed ITS sequence data from 745 collections (nearly 600 being newly generated) including 86 from type specimens of previously recognized subgenera and sections. Many monophyletic groups were recognized, but most basal relationships were unresolved. One hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU, tef-1α, and rpb2 sequence data. Divergence times within the multi-gene phylogeny were estimated using BEAST v1.8. Based on phylogenetic relationships and with respect to morphology, we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic ranks. We propose to segregate Agaricus into five subgenera and 20 sections. Subgenus Pseudochitonia is substantially emended; circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses, respectively; and two new subgenera (Minores and Spissicaules) are introduced. Within Pseudochitonia, sections Bivelares, Brunneopicti, Chitonioides, Nigrobrunnescentes, Sanguinolenti and Xanthodermatei are maintained, but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses; and sections Rubricosi, Crassispori, Flocculenti, and Amoeni are introduced. Section Laeticolores is placed in the subgenus Minores and sections Rarolentes and Subrutilescentes are placed in the subgenus Spissicaules. Twenty-two new species belonging to various sections are described. This work exemplifies that ITS data, while useful at lower taxonomic levels (i.e., detection of species and species groups), are of limited value for inferring deeper phylogenetic relationships. Finally, we suggest that the establishment of a standardized taxonomic system based on divergence times could result in a more objective, and biologically more meaningful, taxonomic ranking of fungi.
Published: 2016

32. Proposals to provide for registration of new names and nomenclatural acts (276-279)

Author: Barkworth, Mary E., Watson, Mark, Barrie, Fred R., Belyaeva, Irina V., Chung, Richard C. K., Daskova, Jirina, Davidse, Gerrit, Donmez, Ali A., Doweld, Alexander B., Dressler, Stefan, Flann, Christina, Gandhi, Kanchi, Geltman, Dmitry, Glen, Hugh F., Greuter, Werner, Head, Martin J., Jahn, Regine, Janarthanam, Malapati K., Katinas, Liliana, Kirk, Paul M., Klazenga, Niels, Kusber, Wolf-Henning, Kvacek, Jiri, Malécot, Valéry, Mann, David G., Marhold, Karol, Nagamasu, Hidetoshi, Nicolson, Nicky, Paton, Alan, Patterson, David J., Price, Michelle J., van Reine, Willem F. Prud'homme, Schneider, Craig W., Sennikov, Alexander, Smith, Gideon F., Stevens, Peter F., Yang, Zhu-Liang, Zhang, Xian-Chun, Zuccarello, Giuseppe C., Intermountain Herbarium, Utah State University (USU), Herbarium, Royal Botanic Garden Edinburgh, Missouri Botanical Garden, Herbarium, Botany Department, Department of Science and Education, Field Museum of Natural History [Chicago, USA], Herbarium, Science Directorate, Royal Botanic Gardens, Forest Biodiversity Division, Herbarium, Forest Research Institute Malaysia (FRIM), Department of Palaeontology, National Institutes of Health [Bethesda] (NIH)-The Natural History Museum (NHM), Faculty of Science, Department of Botany, University of South Bohemia, Gaertnerian Institution, National Institute of Carpology, Senckenberg Forschungsinstitut und Naturmuseum, Herbarium Senckenbergianum, Species 2000, Naturalis Biodiversity Center, Herbaria, Harvard University [Cambridge], Komarov Botanical Institute, Russian Academy of Sciences [Moscow] (RAS), Box 1781, Botanischer Garten und Botanisches Museum Berlin, Free University of Berlin (FU), Orto botanico di Palermo, Department of Earth Sciences [St. Catharines], Brock University [Canada], Department of Botany, Goa University, División Plantas Vasculares [La Plata], Facultad de Ciencias Naturales y Museo [La Plata] (FCNyM), Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), Jodrell Laboratory, Royal Botanic Garden , Kew, Royal Botanic Gardens Victoria, Aquatic Ecosystems, Institut de Recerca i Tecnologia Agroalimentaries, Institute of Botany, Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU), Faculty of Science, Suez Canal University. Ismailia. Egypt, The Kyoto University Museum, Kyoto University, Biodiversity Informatics, School of Biological Sciences [Sydney], The University of Sydney, Conservatoire et Jardin Botaniques de Genève, Netherland Centre for Biodiversity Naturalis, Department of Biology, Trinity College (TCD), Herbarium, Komarov Botanical Institute, the Russian Academy of Sciences [Moscow, Russia] (RAS), Botany Unit, Finnish Museum of Natural History, Finnish Museum of Natural History (LUOMUS), University of Helsinki-University of Helsinki, National University of Ireland [Galway] (NUI Galway), Centre for Functional Ecology, Departamento de Ciências da Vida, University of Coimbra, Northern Arizona University [Flagstaff], Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), The National Herbarium, Institute of Botany, Chinese Academy of Sciences [Changchun Branch] (CAS), School of Biological Sciences [Clayton], Monash University [Clayton], and Naturalis Biodiversity Center [Leiden]
Subjects: [SDV]Life Sciences [q-bio]
Abstract: The Melbourne Congress of 2011 authorized a Special Committeeon Registration of Algal and Plant Names (including fossils), whichwas established the following year (Wilson in Taxon 61: 878–879.2012). Its explicit mandate was “to consider what would be involved inregistering algal and plant names (including fossils), using a procedureanalogous to that for fungal names agreed upon in Melbourne andincluded in the Code as Art. 42”, but expectations at the NomenclatureSection in Melbourne went farther than that. There was the hope thatregistration systems for at least some of the main groups would soonbe set up, to be used and tested on a voluntary basis and, if found tobe generally accepted, would persuade the subsequent Congress inShenzhen, in 2017, to declare registration of new names an additionalrequirement for valid publication.
Published: 2016

33. 4,5-Cis Unsaturated α-GalCer Analogues Distinctly Lead to CD1d-Mediated Th1-Biased NKT Cell Responses

Author: Zhiyuan Li, Chengfeng Xia, Zhaodong Cheng, Yongmin Zhang, Yanli Cui, Department of Chemistry, Zhejiang University, Kunming Institute of Botany [CAS] (KIB), Chinese Academy of Sciences [Beijing] (CAS), Glycochimie Organique Biologique et Supramoléculaire (GOBS), Institut Parisien de Chimie Moléculaire (IPCM), Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Stereochemistry, Enzyme-Linked Immunosorbent Assay, Galactosylceramides, Stereoisomerism, Toxicology, 01 natural sciences, Mice, 03 medical and health sciences, chemistry.chemical_compound, Glycolipid, In vivo, Tumor Cells, Cultured, Animals, [CHIM]Chemical Sciences, Glycosyl, Glycosyl donor, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Molecular Structure, Sphingosine, biology, 010405 organic chemistry, General Medicine, Th1 Cells, In vitro, 0104 chemical sciences, 3. Good health, Mice, Inbred C57BL, carbohydrates (lipids), chemistry, Biochemistry, CD1D, biology.protein, Cytokines, Natural Killer T-Cells, lipids (amino acids, peptides, and proteins), Antigens, CD1d
Abstract: The total synthesis of 4,5-cis unsaturated α-GalCer analogues was achieved, and their immune-response altering activity was assessed in vitro as well as in vivo in mice. Using glycosyl iodide as a glycosyl donor, construction of the sphingosine unit was shortened by four steps and single α-stereoselectivity was achieved in good yield (67%). With regard to the therapeutic use of α-GalCer, the novel analogues (1b and 1c) distinctly induced a Th1-biased cytokine response, avoiding induction of a contradictory response and overstimulation.
Published: 2015

34. Morphology and phylogeny of two appendaged genera of coelomycetes: Ciliochorella and Discosia

Author: silar, philippe, N, Tangthirasunun, Bhat, DJ, Maharachchikumbura, Sajeewa S.N., Wijayawardene, Nalin N., Bahkali, A.H., Hyde, K.D., Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Guizhou Key Laboratory of Agricultural Biotechnology, Partenaires INRAE, Guizhou University, King Saud University [Riyadh] (KSU), Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, and Chinese Academy of Sciences [Changchun Branch] (CAS)
Subjects: LSU, [SDV]Life Sciences [q-bio], Appendaged spores, Coelomycetes, Amphisphaeriaceae, TUB
Abstract: International audience; The taxonomy and phylogeny of the coelomycete genera Ciliochorella and Discosia which have appendaged conidia are examined in this paper. The phylogeny of taxa in Amphisphaeriaceae is reconstructed based on analysis of large subunit (28S) ribosomal DNA (LSU) sequence data. This analysis confirms that Ciliochorella and Discosia are members of Amphisphaeriaceae (Xylariales). A combination of morphological characters together with analysis of the ß-Tubulin (TUB) gene region can be used to distinguish species in Discosia. In addition Ciliochorella mangiferae and Discosia brasiliensis are characterized morphologically.
Published: 2015

35. Greeneria saprophytica sp. nov. on dead leaves of Syzygium cumini from Chiang Rai, Thailand

Author: Kevin D. Hyde, Narumon Tangthirasunun, Sajeewa S. N. Maharachchikumbura, Darbhe J. Bhat, Philippe Silar, Laboratoire Interdisciplinaire des Energies de Demain (LIED (UMR_8236)), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Guizhou Key Laboratory of Agricultural Biotechnology, Partenaires INRAE, Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, and Chinese Academy of Sciences [Changchun Branch] (CAS)
Subjects: Phylogenetic tree, biology, [SDV]Life Sciences [q-bio], Phialide, Plant Science, biology.organism_classification, Conidium, acervular, Type species, Conidiomata, Syzygium, Genus, Botany, asexual state, coelomycete, Diaporthales, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Greeneria saprophytica sp. nov. is described from fallen Syzygium cumini leaves collected in northern Thailand. The genus Greeneria is monotypic and represented by the type species G. uvicola. The novelty and placement of G. saprophytica is confirmed based on phylogenetic analyses of the 28S nuclear large subunit DNA (nuLSU). The new species differs from G. uvicola in the dimensions of acervular conidiomata, conidiogenous cells and conidia. The phialide collarette with a serrate margin, a rare feature in conidial fungi, is characteristic of the genus.
Published: 2014

36. Superparamagnetic photonic crystals with DNA probes for rapid visual detection of mercury.

Author: Pu Y, Gu Z, Bovee TFH, Yang Y, Ying Y, Li M, and Hong X
Subjects: Magnetite Nanoparticles chemistry, Photons, Colorimetry methods, Mercury analysis, Mercury chemistry, DNA Probes chemistry
Abstract: A novel superparamagnetic photonic crystal DNA probe (Fe 3 O 4 @SiO 2 @amino@DNA SPC) was developed to enable rapid visual detection of Hg 2+ . This unique photonic crystal (PC) was synthesized by combining superparamagnetic nanospheres with DNA probes. The DNA probe, rich in thymine (T), detects mercury ions through base mismatch, resulting in the formation of T-Hg 2+ -T loop hairpin structures. With the binding of Hg 2+ to the probe attached to superparamagnetic nanospheres, the PC structure assembled by these nanospheres, formed by the magnetic field, was changed. This change enhanced the reflection intensity; it could be quantified using a fiber optic spectrometer and was visible to the naked eye. The Fe 3 O 4 @SiO 2 @amino@DNA SPC, specific to Hg 2+ , exhibited a reflection peak at 679 nm, which intensified with increasing Hg 2+ concentration. The reflection intensity increased by 132.58 a.u., and the PC color shifted from red to yellow as the Hg 2+ concentration increased from 0.1 μg/L to 1 mg/L., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
Published: 2024
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37. Medicinal plants used by minority ethnic groups in China: Taxonomic diversity and conservation needs.

Author: Yao R, Gao J, Heinrich M, Yu S, Xue T, Zhang B, Wei X, Qi Y, and Gao W
Subjects: China ethnology, Humans, Medicine, Chinese Traditional, Ethnobotany, Phytotherapy, Plants, Medicinal classification, Conservation of Natural Resources, Ethnicity, Minority Groups statistics & numerical data
Abstract: Ethnopharmacological Relevance: Indigenous communities have long relied on medicinal plants (MPs) for primary healthcare. The ethnomedicinal knowledge are different among ethnic groups since the local flora and people's health beliefs generally vary among biocultural backgrounds. China with its diverse biocultural environment is rich in culturally important plant species including MPs. They are also essential in the context of conservation of plant resources and the related traditional medical knowledge, requiring an integrated perspective on these MPs., Aim of the Study: Focusing on the MPs used by the minority ethnic groups, this study assesses the diversity of MPs in China used in local indigenous traditions, as well as their conservation needs., Materials and Methods: The MPs used by the 18 selected minority ethnic groups were extracted from an ethnic MP dictionary. After standardizing, the names then were compiled as an inventory. Next, following statistics were computed: the number of species in each order and family, species used by each ethnic group, species documented in the national herbal resource dataset, species adopted in drug standards, and species at different levels of conservation lists. The overall similarity of the MPs used by the ethnic groups included was achieved using a cluster and principal component analysis., Results: In total 5886 vascular plant species are reported as medicines in the 18 ethnic groups, which belong to 1657 genera and 243 families. It is found that 3195 species are used exclusively by one ethnic group, indicating their cultural salience and potential restrictedness in ecological terms. Moreover, 1159 species are included in national/regional drug standards, indicating their importance in the national medical flora. However, only 3541 species of them are documented in the national herbal resource dataset, and 761 species are at different levels of threatened status, highlighting the conservation needs of Chinese MPs and the related traditional medical knowledge., Conclusions: Using a quantitative approach, for the first time the present study reveals the high level of taxonomic diversity of MPs used by minority ethnic groups of China. However, of these species, 40% are still not inventoried in the national herbal resource dataset, and more than half are used exclusively by one ethnic group, and around 13% are included in the conservation lists of different levels. These together urge the conservation of MP resources and related traditional medical knowledge. Additionally, we recommend fostering the cross-cultural communication the regional ethnomedicinal knowledge, for the purpose of maximizing the benefits of regional plants to human., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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38. Liver injury protection of Artemisia stechmanniana besser through PI3K/AKT pathway.

Author: Tian CB, Qin ML, Qian YL, Qin SS, Shi ZQ, Zhao YL, and Luo XD
Subjects: Animals, Mice, Male, Phosphatidylinositol 3-Kinases metabolism, Liver drug effects, Liver metabolism, Liver pathology, Oxidative Stress drug effects, Ethanol chemistry, Cell Line, Chemical and Drug Induced Liver Injury prevention & control, Chemical and Drug Induced Liver Injury drug therapy, Chemical and Drug Induced Liver Injury metabolism, Chemical and Drug Induced Liver Injury pathology, Protective Agents pharmacology, Liver Diseases, Alcoholic prevention & control, Liver Diseases, Alcoholic drug therapy, Humans, Artemisia chemistry, Proto-Oncogene Proteins c-akt metabolism, Molecular Docking Simulation, Signal Transduction drug effects, Plant Extracts pharmacology, Plant Extracts chemistry
Abstract: Ethnopharmacological Relevance: Artemisia stechmanniana Besser, one of the most prevalent botanical medicines in Chinese, has been traditionally used for hepatitis treatment. However, the bioactive components and pharmacological mechanism on alcohol-induced liver injury remains unclear., Aim of the Study: To investigate the effect of A. stechmanniana on alcohol-induced liver damage, and further explore its mechanism., Materials and Methods: Phytochemical isolation and structural identification were used to determine the chemical constituents of A. stechmanniana. Then, the alcohol-induced liver damage animal and cell model were established to evaluate its hepato-protective potential. Network pharmacology, molecular docking and bioinformatics were integrated to explore the mechanism and then the prediction was further supported by experiments. Moreover, both compounds were subjected to ADMET prediction through relevant databases., Results: 28 compounds were isolated from the most bioactive fraction, ethyl acetate extract A. stechmanniana, in which five compounds (abietic acid, oplopanone, oplodiol, hydroxydavanone, linoleic acid) could attenuate mice livers damage caused by alcohol intragastration, reduce the degree of oxidative stress, and serum AST and ALT, respectively. Furthermore, abietic acid and hydroxydavanone exhibited best protective effect against alcohol-stimulated L-O2 cells injury among five bioactive compounds. Network pharmacology and bioinformatics analysis suggested that abietic acid and hydroxydavanone exhibiting drug likeliness characteristics, were the principal active compounds acting on liver injury treatment, primarily impacting to cell proliferation, oxidative stress and inflammation-related PI3K-AKT signaling pathways. Both of them displayed strong binding energies with five target proteins (HRAS, HSP90AA1, AKT1, CDK2, NF-κB p65) via molecular docking. Western blotting results further supported the predication with up-regulation of protein expressions of CDK2, and down-regulation of HRAS, HSP90AA1, AKT1, NF-κB p65 by abietic acid and hydroxydavanone., Conclusion: Alcohol-induced liver injury protection by A. stechmanniana was verified in vivo and in vitro expanded its traditional use, and its two major bioactive compounds, abietic acid and hydroxydavanone exerted hepatoprotective effect through the regulation of PI3K-AKT signaling pathway., Competing Interests: Declaration of competing interest The authors declare that they have no conflict of interest., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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39. Traditional medicinal knowledge of Sherpa people: Assessment in Xizang, China.

Author: Ding X, Zhang L, Ali M, Shida, Bianba, Shi Y, He J, and Wang Y
Subjects: Humans, China, Female, Male, Adult, Middle Aged, Medicine, Chinese Traditional, Aged, Young Adult, Phytotherapy, Indigenous Peoples, Plants, Medicinal, Health Knowledge, Attitudes, Practice
Abstract: Ethnopharmacological Relevance: The people of the Pan-Himalayan region are among the most isolated and economically disadvantaged populations worldwide. The Sherpa people, located along the China and Nepal border, rely largely on the natural environment to access essential healthcare services. The region's ongoing economic and social developments threaten indigenous medicinal practices and biodiversity. However, there has been limited comprehensive investigation and documentation of traditional medicine and its associated knowledge in this region., Aim of the Study: The aims are to document the traditional medicinal knowledge of the Sherpa community, assess the conservation status of medicinal plants, and explore the historical factors that have influenced their traditional medicine practices., Material and Methods: Semi-structured interviews with 78 Sherpa people were conducted in Chenthang Town, Xizang, China. Use reports (URs) was used to determine the most frequently mentioned medicinal plants or a specific ailment or disease category. The International Classification of Primary Care-2nd edition (ICPC-2) was used to transform the original records into an internationally unified classification., Results: A total of 51 plant species, one fungus (Ophiocordyceps sinensis (Berk.) G.H.Sung, J.M.Sung, Hywel-Jones & Spatafora), two lichens (Flavopunctelia soredica (Nyl.) Hale and Parmotrema cetratum (Ach.) Hale), and four minerals were documented, resulting in 824 URs. Ranunculaceae had the most species (5 spp.). The most commonly used method for preparing medicinal substances was decoction (23 species, 40%). Oral application was the preferred route of administration for 81% (41 medicinal substances). Forty-four ailments across 14 ICPC-2 disease categories were documented. Respiratory (320 URs) and digestive (122 URs) categories are among the most common diseases. The top-five ailments were influenza (18 substances; URs = 227), injury blood/lymph/spleen other (11 substances; URs = 66), cough (10 substances; URs = 62), headache (7 substances; URs = 63), and abdominal pain/cramps general (6 substances; URs = 37). The most frequently reported medicinal substances were Panax pseudoginseng Wall. (URs = 128) and Neopicrorhiza scrophulariiflora (Pennell) D. Y. Hong (URs = 79). Two special therapies (hot spring therapy and dietary therapy) were described. In-depth ethnographic information on the livelihood and exchange history of Sherpa people were documented. A total of 25 species were sold, of which four species were listed as VU in the IUCN Red List (2023-1), six species were listed as VU, four species were NT, and one species was EN in the China Biodiversity Red list 2021., Conclusion: This study provides the first comprehensive documentation of the 58 traditional medicine substances and two special therapies (hot spring therapy and dietary therapy) used by the Sherpa people in Chenthang. Sherpa's medicinal knowledge has been shaped by historical interactions and contemporary trade practices. To better protect the biocultural diversity of the Himalayan region, priority should be given to the rapid assessment of medicinal plants, knowledge, and use status in this area., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)
Published: 2024
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40. Development of α-Helical Antimicrobial Peptides with Imperfect Amphipathicity for Superior Activity and Selectivity.

Author: Wu Z, Cai Y, Han Y, Su Y, Zhang T, Wang X, Yan A, Wang L, Wu S, Wang G, and Zhang Z
Subjects: Humans, Hemolysis drug effects, Biofilms drug effects, Structure-Activity Relationship, Antimicrobial Cationic Peptides pharmacology, Antimicrobial Cationic Peptides chemistry, Antimicrobial Cationic Peptides chemical synthesis, Animals, Microbial Sensitivity Tests, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Anti-Bacterial Agents chemical synthesis, Antimicrobial Peptides pharmacology, Antimicrobial Peptides chemistry, Antimicrobial Peptides chemical synthesis, Protein Conformation, alpha-Helical
Abstract: The advancement of antimicrobial peptides (AMPs) as therapeutic agents is hindered by their poor selectivity. Recent evidence indicates that controlled disruption of the amphipathicity of α-helical AMPs may increase the selectivity. This study investigated the role of imperfect amphipathicity in optimizing AMPs with varied sequences to enhance their activity and selectivity. Among these, the lead peptide RI-18, characterized by an imperfectly amphipathic α-helical structure, demonstrated potent and broad-spectrum antibacterial activity without inducing hemolytic or cytotoxic effects. RI-18 effectively eliminated planktonic and biofilm-associated bacteria as well as persister cells and exhibited high bacterial plasma membrane affinity, inducing rapid membrane permeabilization and rupture. Notably, RI-18 significantly reduced bacterial loads without promoting bacterial resistance, highlighting its therapeutic potential. Overall, this study identified RI-18 as a promising antimicrobial candidate. The rational strategy of tuning imperfect amphipathicity to enhance the AMP activity and selectivity may facilitate the design and development of AMPs.
Published: 2024
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41. Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae).

Author: Lindstrom A, Habib S, Dong S, Gong Y, Liu J, Calonje M, Stevenson D, and Zhang S
Subjects: Biological Evolution, Gene Flow, Phylogeny, Phylogeography, Zamiaceae genetics, Zamiaceae anatomy & histology, Transcriptome
Abstract: Background and Aims: Cycads are a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved., Methods: Here, using 2901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.e. Zamia, based on phylotranscriptomic analyses of 90 % extant Zamia species. Based on a well-resolved phylogenetic framework, we performed gene flow analyses, molecular dating and biogeographical reconstruction to examine the spatiotemporal evolution of Zamia. We also performed ancestral state reconstruction of a total of 62 traits of the genus to comprehensively investigate its morphological evolution., Key Results: Zamia comprises seven major clades corresponding to seven distinct distribution areas in the Americas, with at least three reticulation nodes revealed in this genus. Extant lineages of Zamia initially diversified around 18.4-32.6 (29.14) million years ago in Mega-Mexico, and then expanded eastward into the Caribbean and southward into Central and South America. Ancestral state reconstruction revealed homoplasy in most of the morphological characters., Conclusions: This study revealed congruent phylogenetic relationships from comparative methods/datasets, with some conflicts being the result of incomplete lineage sorting and ancient/recent hybridization events. The strong association between the clades and the biogeographic areas suggested that ancient dispersal events shaped the modern distribution pattern, and regional climatic factors may have resulted in the following in situ diversification. Climate cooling starting during the mid-Miocene is associated with the global expansion of Zamia to tropical South America that has dramatically driven lineage diversification in the New World flora, as well as the extinction of cycad species in the nowadays cooler regions of both hemispheres, as indicated by the fossil records., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
Published: 2024
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42. Structural analysis and adjuvant activity of a new polysaccharide from Urtica macrorrhiza.

Author: Wang Z, Yang Q, Wu G, Ma J, Luo L, Yin W, and Wu M
Abstract: Developing new vaccine adjuvants for clinical use remains a significant challenge. Herein, we reported a novel polysaccharide (UMRG) from Urtica macrorrhiza. It has a molecular weight of 743.35 kDa and is composed of rhamnose (Rha), glucuronic acid (GlcA), galacturonic acid (GalA), and galactose (Gal) in a molar ratio of 1.94: 1.00: 4.17: 1.79. Structural analysis revealed that UMRG contains a rhamnogalacturonan I backbone with short side chains of β-Galp-(1→4)-β-GlcAp-(1→4)-β-Glap-(1→ linked at the C-4 position of →2,4)-α-Rhap-(1→. In vivo, UMRG significantly increased the production of antigen-specific IgG, IgG1, and IgG2a by 1.91-, 2.09-, and 3.43-fold, respectively, on day 42 post-immunization. It also promoted the proliferation of splenic lymphocytes, increasing the proportion of CD3 + and CD3 + CD4 + T lymphocytes from 32.63 ± 1.13 % to 38.13 ± 2.03 % and from 21.05 ± 0.93 % to 24.34 ± 1.21 %, respectively. Further investigation demonstrated that UMRG promoted the phagocytosis of antigens by dendritic cells, improved their maturation, and stimulated the secretion of the cytokines TNF-α, IL-12, and IL-6. Additionally, both in vitro and in vivo experiments demonstrated that UMRG displayed good biosafety. Our results suggested the Urtica macrorrhiza polysaccharide may exhibit the potential to be developed as a highly efficient and low-toxicity immune adjuvant., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)
Published: 2024
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43. Evolution of sex-linked genes and the role of pericentromeric regions in sex chromosomes: insights from diploid willows.

Author: Wang Y, Zhang RG, Hörandl E, Zhang ZX, Charlesworth D, and He L
Abstract: The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex-linkage., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Published: 2024
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44. Phenolic Components And Biological Activity Of Pomegranate.

Author: Zhao QS, Zhou Z, Ma C, Peng L, Hao P, and Zhang SY
Abstract: Pomegranate (Punica granatum L.) have been subject of extensive studies for its abundance of phytochemicals and numerous biological and medicinal properties. It is a fruit-bearing tree, which is widely consumed as a nutraceutical source as well as functional food for putative health benefits. The phenolic components are the characteristic bioactive constitutes of pomegranate, including hydrolysable tannins, flavonoids, and phenolic acids. The whole plant of this tree has many medicinal folkloric uses and good therapeutic effect, such as anticancer, antioxidant, antibacterial, antiviral, hypoglycemic, lipid-lowering, cardioprotection and digestive system protection. Through comprehensive search of available literature, this narrative review can provide an up-to-date overview of the current knowledge of characteristic bioactive constituents's structure and potential health benefits of Pomegranate, which can be used as reference for the future clinical and basic research, and also helpful for the development of pomegranate into functional food and nutraceuticals., (© 2024 Wiley‐VCH GmbH.)
Published: 2024
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45. Phylogeography of Pleurospermum foetens (Apiaceae) From the Sky Islands of Southwest China.

Author: Yu S, Zhang J, Li Z, Li W, Ma X, and Sun W
Abstract: Sky islands provide insights on how glacial-interglacial cycles have shaped species distribution and help for predicting species' responses to climate warming. The alpine subnival belt of southwest China, especially in the Hengduan Mountains and adjacent areas, is sky island-like. Among them, the Yunnan-Kweichow Plateau harbors several isolated mountains with well-developed alpine subnival vegetation, sharing a similar species composition with the Hengduan Mountains. However, the relationship between the sky islands of the Hengduan Mountains and the Yunnan-Kweichow Plateau remains insufficiently explored. Pleurospermum foetens (Apiaceae) is a species endemic to the alpine screes of the Yunnan-Kweichow Plateau and the Hengduan Mountains. We used DNA sequence data from 59 individuals across 9 populations, combined with ecological niche modeling, to investigate the evolution history and future distribution of P. foetens within this sky island region. The results indicate the following: (1) P. foetens exhibits a significant phylogeographic structure and can be classified into three nrDNA clades and two cpDNA clades, respectively, (2) a nuclear-plastid discordance observed in P. foetens and its relatives based on phylogenetic analysis. P. foetens is monophyletic in the nrDNA phylogeny, while two major clades (HDM and YGP) are present in the cpDNA phylogeny, each forming a clade with other congeneric species. (3) Ecological niche modeling of P. foetens indicated that the species had the most extensive suitable habitat during the last glacial maximum (LGM). However, anticipated climate warming in the coming decades is expected to reduce the suitable range of P. foetens , posing a significant threat to isolated marginal populations (e.g., Shizi Mountain) with restricted alpine scree habitats. In conclusion, our study highlights the substantial effect of sky island and glacial-interglacial cycles on the population divergence of P. foetens . Conservation efforts for marginal populations of alpine plants in the Yunnan-Kweichow Plateau require increased attention and prioritization., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)
Published: 2024
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46. Anti-Inflammatory Secoiridoids from the Medicinal Herb Gentianopsis barbata.

Author: Liu H, Cheng HZ, Qi XY, Fan YZ, Yuan ZZ, Xu YL, Liu Y, Guo K, and Li SH
Abstract: Five new secoiridoids, gentianopsins A-E (1-5), along with two known analogues (6 and 7) were isolated from the whole plants of the medicinal herb Gentianopsis barbata. Their structures were elucidated by a comparison of extensive spectroscopic analysis (1D and 2D NMR, and HRMS) and quantum chemical calculations. Gentianopsins A (1) and B (2) represented two unusual skeletons of trihomo-secoiridoids. Anti-inflammatory activity of these isolates was evaluated via suppressing the secretion of cytokines TNF-α and IL-6 in LPS-induced macrophages RAW264.7. Significant inhibitory activity was observed for compounds 3 and 7 on IL-6 secretion with IC50 values of 10.22 and 13.30 μM, respectively., (© 2024 Wiley‐VCH GmbH.)
Published: 2024
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47. New resorcylic acid derivatives of Lysimachia tengyuehensis against MRSA and VRE by interfering with bacterial metabolic imbalance.

Author: Shi N, Wang ZJ, Shi YZ, Jiang L, Zhu YY, He XC, Zhou ZS, Wei MZ, Zhao YL, and Luo XD
Subjects: Animals, Humans, Mice, Biofilms drug effects, Dose-Response Relationship, Drug, Lysimachia, Molecular Structure, Structure-Activity Relationship, Anti-Bacterial Agents pharmacology, Anti-Bacterial Agents chemistry, Anti-Bacterial Agents chemical synthesis, Methicillin-Resistant Staphylococcus aureus drug effects, Microbial Sensitivity Tests, Primulaceae chemistry, Vancomycin-Resistant Enterococci drug effects
Abstract: The abuse of antibiotics leads to the rapid spread of bacterial resistance, which seriously threatens human life and health. Now, 8 resorcylic acid derivatives, including 4 new compounds (1-4) were isolated from Lysimachia tengyuehensis by bio-guided isolation, and they inhibited both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) (MIC = 4-8 μg/mL). Notably, 1 and 2 rapidly killed MRSA and VRE within 40 min without drug resistance in 20 days. Mechanically, they potently disrupted biofilm and cell membrane by interfering with bacterial metabolic imbalance. The structure-activity relationship (SAR) revealed that the lipophilic long carbon chains (C-5/C-6) and hydrophilic hydroxyl/carboxyl groups were essential for the anti-MRSA and VRE bioactivity. Additionally, they effectively recovered MRSA-infected skin wounds and VRE-infected peritoneal in vivo. Resorcylic acid derivatives showed significant anti-MRSA and VRE bioactivity in vitro and in vivo with potential application for the first time., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)
Published: 2024
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48. Mythimna separata herbivory primes Coix resistance in systemic leaves.

Author: Fan B, Liu Y, Wen R, Kong L, Wang X, Zhang J, Li J, and Qin Y
Subjects: Animals, Moths physiology, Transcriptome, Gene Expression Regulation, Plant, Gene Expression Profiling, Isoleucine analogs & derivatives, Plant Leaves metabolism, Oxylipins metabolism, Cyclopentanes metabolism, Herbivory
Abstract: Coix lacryma-jobi L. belongs to family Poaceae, is widely cultivated in tropical Asian countries for its nutritional and medicinal values. Coix is often threatened by lepidopteran such as Mythimna separata during its life cycle, resulting in severe yield reduction. Insect feeding can trigger defense signaling and increased defense responses in many other crops, yet little is known about whether simulated armyworm feeding on Coix leaves could induce anti-herbivory responses and whether armyworm feeding could activate priming in systemic leaves. In this study, Mythimna separata simulated herbivory elicited increased jasmonic acid (JA) level, JA-Ile (JA-isoleucine conjugate) and altered transcriptome in the Coix leaves. Meanwhile, M. separata simulated herbivory in local leaves primed the systemic leaves for increased accumulation of jasmonic acid and enhanced resistance to M. separata. Consistently, transcriptome analysis showed the systemic leaves were primed, which were up- or down-regulated comparing with the non-primed systemic leaves. In this study, we first reported Mythimna separata simulated herbivory induced increased defense response in leaves of Coix, also Mythimna separata herbivory primed Coix resistance in systemic leaves. This study provides new insight into the regulation of defense responses of Coix against M. separata and the ecological function of priming in Coix., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Fan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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49. Metabolome and transcriptome reveal the biosynthesis of flavonoids and amino acids in Isatis indigotica fruit during development.

Author: Huang H, Zhang L, Guan L, and Zhang L
Subjects: Anthocyanins metabolism, Anthocyanins biosynthesis, Gene Expression Profiling, Plant Proteins genetics, Plant Proteins metabolism, Flavonoids metabolism, Flavonoids biosynthesis, Fruit genetics, Fruit metabolism, Fruit growth & development, Transcriptome genetics, Gene Expression Regulation, Plant, Amino Acids metabolism, Metabolome, Isatis genetics, Isatis metabolism, Isatis growth & development
Abstract: Isatis indigotica Fort. is a famous medicinal plant that is also used as a natural dye and functional vegetable. The characteristics of the I. indigotica fruit during development are largely unknown, information that is essential for the exploitation and seedlings cultivation of I. indigotica. In this study, the biochemical, metabolite characteristics and gene expression profiling of I. indigotica at four developmental stages were investigated. A total of 428 metabolites were detected and categorized into 17 categories. High contents of anthocyanins, especially cyanidin 3-glucoside, might contribute to the purple colouration of I. indigotica fruits. Moreover, dozens of flavonoid components, including taxifolin, quercetin, astragalin and isovitexin 2″-O-beta-D-glucoside, and several other active components were also up-regulated in mature fruits. The abundance of antioxidants might endow a significantly stronger antioxidant activity of mature I. indigotica fruits compared to many other reported species. Enrichment analyses revealed that flavonoid and anthocyanin biosynthesis genes were mostly enriched in up-regulated gene sets during fruit development. The up-regulated structural genes, including IiCHS, IiCHI, IiF3H, IiDFR, IiANS, IiFLS, IiUGT, and transcription factors such as IiMYBs, IibHLHs and IiNACs were identified as candidate regulators of flavonoid and anthocyanin biosynthetic pathway. Furthermore, biosynthesis of amino acids was enriched in all pairwise comparisons of metabolites in fruits at four developmental stages. The differential accumulation of amino acids might result from the differentially expressed genes involved in amino acid biosynthesis. Taken together, these findings provide a comprehensive understanding of metabolite profiling and gene expression patterns in I. indigotica fruit during maturity, which is useful for pharmaceutical extractions and seedling cultivation of I. indigotica., (© 2024 Scandinavian Plant Physiology Society.)
Published: 2024
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50. Eudesmane-guaiane sesquiterpenoid dimers from Aucklandia costus trigger paraptosis-like cell death via ROS accumulation and MAPK hyperactivation.

Author: Xiao L, Zhao Y, Ding X, Liu H, Zhu G, Li Y, Yan H, Fang X, Zhao Y, and Liu H
Subjects: Humans, Molecular Structure, Sesquiterpenes, Guaiane chemistry, Sesquiterpenes, Guaiane pharmacology, Cell Line, Tumor, Mitogen-Activated Protein Kinases metabolism, Antineoplastic Agents, Phytogenic pharmacology, Antineoplastic Agents, Phytogenic chemistry, Plant Leaves chemistry, Dimerization, Paraptosis, Reactive Oxygen Species metabolism, Sesquiterpenes, Eudesmane pharmacology, Sesquiterpenes, Eudesmane chemistry, Cell Death drug effects
Abstract: Three novel sesquiterpenoid heterodimers, designated as auckcostusolides A-C (1-3), were isolated from Aucklandia costus leaves. The structures of compounds 1-3 were elucidated through comprehensive spectroscopic analysis, with their absolute configurations established using a combination of X-ray single-crystal diffraction and electronic circular dichroism (ECD) calculations. Notably, compounds 1 and 2, despite sharing identical planar structures derived from two identical sesquiterpenoids, exhibited opposite configurations at C-11 and C-8'. This configurational difference can be attributed to distinct Diels-Alder cycloaddition processes between the sesquiterpenoid monomers. Additionally, the cytotoxic effects of compounds 1-3 were evaluated against colorectal cancer HCT116 cells, fibrosarcoma HT1080 cells, and hepatocellular carcinoma HepG2 cells. Compounds 1-3 induced cell death was characterized by endoplasmic reticulum (ER) swelling and cytoplasmic vacuolization, typical morphological changes associated with paraptosis. Mechanistic studies revealed that compounds 1 and 3 triggered paraptosis-like cell death through the accumulation of reactive oxygen species (ROS), activation of ER stress, and stimulation of the MAPK signaling pathway., (Copyright © 2024 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.)
Published: 2024
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