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1. Storm impacts on phytoplankton community dynamics in lakes

Author

Vijay P. Patil, Wim Thiery, Emily R. Nodine, Stephen J. Thackeray, Aleksandra M. Lewandowska, Alfred Theodore Nutefe Kwasi Kpodonu, Francesco Pomati, Maria Eugenia del Rosario Llames, Ruchi Bhattacharya, Tanner J. Williamson, Orlane Anneville, Patrick Venail, Cayelan C. Carey, Nico Salmaso, Marc J. Lajeunesse, Harriet L. Wilson, Josef Hejzlar, Lisette N. de Senerpont Domis, Jason D. Stockwell, B.W. Ibelings, Rita Adrian, Gaël Dur, R. Iestyn Woolway, James A. Rusak, Lars G. Rudstam, Peeter Nõges, Christian Torsten Seltmann, Pablo Urrutia-Cordero, Piet Verburg, Laurence Carvalho, Karsten Rinke, Dietmar Straile, Shin-ichiro S. Matsuzaki, Hans-Peter Grossart, Tamar Zohary, Marieke A. Frassl, Jonathan P. Doubek, Nasime Janatian, Mikkel René Andersen, University of Vermont [Burlington], Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Institute of Biology at the Department of Biology, Chemistry and Pharmacy, Free University of Berlin (FU), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virginia Tech [Blacksburg], Netherlands Institute of Ecology (NIOO-KNAW), Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Shizuoka University of Art and Culture (SUAC), Griffith University [Brisbane], State University of New York at Potsdam (SUNY Potsdam), State University of New York (SUNY), Tata Memorial Centre, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Fdn Edmund Mach, IASMA Research and Innovation Centre, Limnological Institute, University of Konstanz, Konstanz, Germany, G17AC00044U.S. Geological SurveyNE/J024279/1Natural Environment Research CouncilFondation pour la Recherche sur la BiodiversiteG16AP00087Vermont Water Resources and Lake Studies CenterOIA-1556770U.S. National Science FoundationEF-1702506U.S. National Science FoundationCNS-1737424U.S. National Science FoundationICER-1517823U.S. National Science FoundationDEB-1753639U.S. National Science FoundationH2020-MSCA-ITN-2016MANTELPBA/FS/16/02Irish Government791812European UnionU.S. Department of StateCentre Alpin de Recherche sur les Reseaux Trophiques des Ecosystemes Limniques2017-06421Swedish Research Council, AKWA, Aquatic Ecology (AqE), Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Hydrology and Hydraulic Engineering, Biological stations, Marine Ecosystems Research Group, and Tvärminne Zoological Station

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, Biodiversity & Conservation, Oceanografi, hydrologi och vattenresurser, 01 natural sciences, Oceanography, Hydrology and Water Resources, Water column, ddc:550, functional traits, watershed, General Environmental Science, ddc:333.7-333.9, DIFFERENT CLIMATIC CONDITIONS, changement climatique, Global and Planetary Change, Plan_S-Compliant-TA, Ecology, SPECIES-DIVERSITY, Research Review, lacs, tempête, climate change, Oceanography, WATER-QUALITY, WIND-EXPOSED LAKE, International, 1181 Ecology, evolutionary biology, articles, Biodiversity Conservation, climate change, environmental disturbance, extreme events, functional traits, mixing, nutrients, stability, watershed, Life Sciences & Biomedicine, extreme events, Biogeochemical cycle, environmental disturbance, mixing, nutrients, stability, Storms, Climate Change, Climate change, Environmental Sciences & Ecology, 010603 evolutionary biology, Ecology and Environment, Extreme weather, Rivers, Settore BIO/07 - ECOLOGIA, ddc:570, Phytoplankton, Environmental Chemistry, DISSOLVED ORGANIC-CARBON, CYANOBACTERIAL BLOOM FORMATION, Ecosystem, 0105 earth and related environmental sciences, Functional ecology, Science & Technology, LARGE SHALLOW LAKE, phytoplancton, nutriment, Storm, 15. Life on land, Lakes, Invited Research Review, FUNCTIONAL TRAITS, 13. Climate action, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, THERMAL STRATIFICATION, Surface runoff, Environmental Sciences
Abstract

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short‐term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well‐developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short‐ and long‐term. We summarize the current understanding of storm‐induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions., Our understanding of ecosystem‐scale responses to storm events is fragmented, and terminological variability in defining a “storm” hinders resolution of generalizable impacts. We provide a comprehensive synthesis of the interactions between physical properties and biological responses in lakes that demonstrates the context‐dependency of storm impacts; lake/watershed attributes and their antecedent conditions mediate the extent to which storms impact lake ecosystems. We develop a framework which conceptualizes how abrupt, storm‐induced changes in the lake environment influence phytoplankton community dynamics through functional traits, identifies current limitations, and highlights several avenues of research to narrow knowledge gaps in synthetic and interdisciplinary ways.

Published
2020
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2. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls

Author

Helene Muranty, Michela Troggio, Caroline Denancé, Nicholas P. Howard, Charles-Eric Durel, Luca Bianco, John Tillman, Eric van de Weg, Univ Minnesota, Grad Program Plant Biol, St Paul, MN 55108 USA, Partenaires INRAE, Institute of Biology and Environmental Science, Carl von Ossietzky University Oldenburg, Fdn Edmund Mach, IASMA Research and Innovation Centre, Institut de Recherche en Horticulture et Semences (IRHS), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen Univ, Lab Plant Breeding, Wageningen University and Research [Wageningen] (WUR), European Project: 265582,EC:FP7:KBBE,FP7-KBBE-2010-4,FRUIT BREEDOMICS(2011), Fakultät V, Institut für Biologie und Umweltwissenschaften, Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Fondazione Edmund Mach [San Michele all'Adige], Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO 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), University of Minnesota, St Paul, MN United States, Wageningen UR Plant Breeding, Niedersächsisches Ministerium für Wissenschaft und Kultur through the EGON project: 'Research for a sustainable agricultural production : Development of organically bred fruit cultivars in creative commons initiatives.', European Project: 265582,FruitBreedomics, and Carl Von Ossietzky Universität Oldenburg

Subjects
0106 biological sciences, Genotyping, Genotype, lcsh:QH426-470, Computer science, lcsh:Biotechnology, Concordance, [SDV]Life Sciences [q-bio], Outcrossing, Single-nucleotide polymorphism, Computational biology, Biology, computer.software_genre, Polymorphism, Single Nucleotide, 01 natural sciences, Set (abstract data type), [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, SNP Array, lcsh:TP248.13-248.65, Genetics, Humans, SNP, Axiom, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Genome, Malus, High-Throughput Nucleotide Sequencing, PE&RC, Single nucleotide polymorphism, Settore AGR/07 - GENETICA AGRARIA, Plant Breeding, lcsh:Genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, EPS, computer, Research Article, 010606 plant biology & botany, Biotechnology, SNP array, Data integration
Abstract

Background Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new technology and of improved probe design using new genome sequence and panel data, a need to integrate data from different arrays and array platforms has arisen. This study was undertaken in view of our need for an integrated high-quality dataset of Illumina Infinium® 20 K and Affymetrix Axiom® 480 K SNP array data in apple (Malus × domestica). In this study, we qualify and quantify the compatibility of SNP calling, defined as SNP calls that are both accurate and concordant, across both arrays by two approaches. First, the concordance of SNP calls was evaluated using a set of 417 duplicate individuals genotyped on both arrays starting from a set of 10,295 robust SNPs on the Infinium array. Next, the accuracy of the SNP calls was evaluated on additional germplasm (n = 3141) from both arrays using Mendelian inconsistent and consistent errors across thousands of pedigree links. While performing this work, we took the opportunity to evaluate reasons for probe failure and observed discordant SNP calls. Results Concordance among the duplicate individuals was on average of 97.1% across 10,295 SNPs. Of these SNPs, 35% had discordant call(s) that were further curated, leading to a final set of 8412 (81.7%) SNPs that were deemed compatible. Compatibility was highly influenced by the presence of alternate probe binding locations and secondary polymorphisms. The impact of the latter was highly influenced by their number and proximity to the 3′ end of the probe. Conclusions The Infinium and Axiom SNP array data were mostly compatible. However, data integration required intense data filtering and curation. This work resulted in a workflow and information that may be of use in other data integration efforts. Such an in-depth analysis of array concordance and accuracy as ours has not been previously described in the literature and will be useful in future work on SNP array data integration and interpretation, and in probe/platform development.

Published
2021
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3. Data sharing in PredRet for accurate prediction of retention time: Application to plant food bioactive compounds

Author

Mark Philo, Kateřina Valentová, Ana Rodriguez-Mateos, Pierre Micheau, F. A. T. Barberán, Ville M. Koistinen, Pedro Mena, Gözde Gürdeniz, Marynka Ulaszewska, Sonia de Pascual-Teresa, Christof Van Poucke, László Abrankó, Stéphanie Durand, Conceição Almeida, Dorrain Yanwen Low, Dilip K. Rai, Wiesław Wiczkowski, Letizia Bresciani, Jan Stanstrup, Cristina Andres-Lacueva, Gesine Schmidt, Andreia Bento da Silva, Lars O. Dragsted, Senem Kamiloglu, Claudine Manach, Raúl González-Domínguez, Lucie Petrásková, Kati Hanhineva, Maria Rosário Bronze, Fulvio Mattivi, Esra Capanoglu, Rocío García-Villalba, European Cooperation in Science and Technology, European Commission, European Research Council, Nanyang Technological University, Prime Minister's Office Singapore, Agence Nationale de la Recherche (France), Czech Science Foundation, Universidade Nova de Lisboa, Fundação para a Ciência e a Tecnologia (Portugal), Lantmännen Research Foundation, Academy of Finland, University of Eastern Finland, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad (España), Generalitat de Catalunya, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Institución Catalana de Investigación y Estudios Avanzados, Consejo Superior de Investigaciones Científicas (España), Fundación Séneca, Gobierno de la Región de Murcia, Norwegian Institute of Food, Fisheries and Aquaculture Research, Carlsberg Foundation, Hungarian Academy of Sciences, Unité de Nutrition Humaine (UNH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institute of Public Health and Clinical Nutrition, University of Turku, Szent István University, King‘s College London, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), University Institute of Lisbon (ISCTE), Research Institute for Agricultural, Fisheries and Food (ILVO), University of Barcelona, CIBER de Fragilidad y Envejecimiento Saludable, Teagasc Ashtown Food Research Centre (Teagasc), Istanbul Technical University (ITÜ), Centro de Edafologia y Biologia aplicada del Segura (CEBAS - CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Taif University (TU), Partenaires INRAE, Fdn Edmund Mach, IASMA Research and Innovation Centre, University of Trento [Trento], Norwegian Institute of Food,Fisheries and Aquaculture Research (NOFIMA), IT University of Copenhagen (ITU), Institute of Microbiology of the Czech Academy of Sciences [Prague, Czech Republic] (MBU / CAS), Czech Academy of Sciences [Prague] (CAS), Università degli studi di Parma = University of Parma (UNIPR), Department of Nutrition, Exercise and Sports [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Quadram Institute Bioscience [Norwich, U.K.] (QIB), Biotechnology and Biological Sciences Research Council (BBSRC), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Department of Food & Drugs, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, MetaboHUB-MetaboHUB, and Institute of Animal Reproduction and Food Research of Polish Academy of Sciences

Subjects
Mean squared prediction error, Computational biology, Plant foods, 01 natural sciences, Plant food bioactive compounds, Analytical Chemistry, 0404 agricultural biotechnology, Metabolomics, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, UHPLC, Faculty of Science, Metabolites, liquid chromatography, Settore CHIM/10 - CHIMICA DEGLI ALIMENTI, 2. Zero hunger, Predicted retention time, 010401 analytical chemistry, External validation, Metabolomikk, 04 agricultural and veterinary sciences, General Medicine, NUTRITION&DIETETICS, 040401 food science, 0104 chemical sciences, Data sharing, Untargeted metabolomics, Predicted retention time, metabolomics, plant food bioactive compounds, metabolites, data sharing, PredRet, liquid chromatography, HPLC, UHPLC, HPLC, PredRet, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Retention time, Food Science
Abstract

Prediction of retention times (RTs) is increasingly considered in untargeted metabolomics to complement MS/MS matching for annotation of unidentified peaks. We tested the performance of PredRet (http://predret.org/) to predict RTs for plant food bioactive metabolites in a data sharing initiative containing entry sets of 29–103 compounds (totalling 467 compounds, >30 families) across 24 chromatographic systems (CSs). Between 27 and 667 predictions were obtained with a median prediction error of 0.03–0.76 min and interval width of 0.33–8.78 min. An external validation test of eight CSs showed high prediction accuracy. RT prediction was dependent on shape and type of LC gradient, and number of commonly measured compounds. Our study highlights PredRet’s accuracy and ability to transpose RT data acquired from one CS to another CS. We recommend extensive RT data sharing in PredRet by the community interested in plant food bioactive metabolites to achieve a powerful community-driven open-access tool for metabolomics annotation., The authors acknowledge networking support by the European Cooperation in Science and Technology (COST) Action FA 1403 POSITIVe (Interindividual Variation in Response to Consumption of Plant Food Bioactives and Determinants Involved). Dorrain Low has received the support of EU H2020 in the framework of the FP7-Marie Curie-COFUND People Programme, through award of the AgreenSkills+ Fellowship (grant number 609398) and Nanyang Technological University, Singapore, through award of the Presidential Postdoctoral Fellowship (grant number 001991-00001). The MetaboHUB French infrastructure has supported the INRAE platform (PFEM, MetaboHUB-Clermont) involved in this work (grant number ANR-INBS-0010). Kateřina Valentová and Lucie Petrásková acknowledge financial support from the Czech Science Foundation (grant number 19-00043S). The Faculty of Pharmacy of Lisbon University acknowledges FUNDAÇÃO PARA A CIÊNCIA E TECNOLOGIA and PORTUGAL 2020 for financial support of the Portuguese Mass Spectrometry Network (grant number LISBOA-01-0145-FEDER-402-022125). Kati Hanhineva and Ville Koistinen have received funding from the Academy of Finland (grant numbers 277986 and 312550), Lantmännen Foundation and EU H2020 FP7-Marie Curie-COFUND MoRE Programme (grant number 754412). Biocenter Finland has financially supported the LC-MS metabolomics unit of University of Eastern Finland. Cristina Andres-Lacueva and Raúl González-Domínguez thank CIBERFES and ISCIII projects AC19/00111 and AC19/00096 (co-funded by FEDER Program from EU, “A way to make Europe”), Generalitat de Catalunya’s Agency AGAUR (grant number 2017SGR1546), “Juan de la Cierva” program from MINECO (grant number IJC2019-041867-I) and ICREA Academia award 2018. Francisco A. Tomás-Barberán has received financial support from the Spanish National Research program (grant numbers AGL-2015-73107-EXP/AEI, CSIC 201870E014) and Fundación Seneca Región de Murcia (grant number 19900/GERM/15). Gesine Schmidt acknowledges support through the Norwegian Agriculture and Food Industry Research Funds (grant number 262300). Lars Dragsted and Jan Stanstrup thank the Carlsberg Foundation for a Semper Ardens grant to support this work. László Abrankó acknowledges the Hungarian Academy of Sciences for the János Bolyai Scholarship, and support of the EU and ESF co-financed project of SZIU (grant number EFOP-3.6.3-VEKOP-16-2017-00005). Sonia de Pascual-Teresa thanks the Spanish MINECO for financial support (grant number AGL2016-76832-R). Dilip K. Rai acknowledges Teagasc for the financial support through the Walsh Fellowship (grant number 2016038).

Published
2021
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4. 'Large lakes – Small world': common issues and challenges presented during the joint ELLS-IAGLR 2018 Conference

Author

Tomas O. Höök, Peeter Nõges, Jordi Prats, Yerubandi R. Rao, Orlane Anneville, Nico Salmaso, Brigitte Vinçon-Leite, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Purdue University [West Lafayette], Estonian University of Life Sciences (EMU), Segula Technologies, Fdn Edmund Mach, IASMA Research and Innovation Centre, École des Ponts ParisTech (ENPC), and Environment and Climate Change Canada

Subjects
0106 biological sciences, Ecology, freshwater ecosystems, 010604 marine biology & hydrobiology, Ell, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Data science, grand lac, Settore BIO/07 - ECOLOGIA, lakes, articles, Environmental science, Joint (building), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract

As freshwater ecosystems, lakes are essential resources on Earth and offer a wide variety of services to nature and society. Large lakes are iconic waterbodies due to their size and the wealth of ecosystem services they provide at local and regional scales. Ecosystem services provided by large lakes usually encompass all four major categories: provisioning, regulating, supporting, and cultural. Accordingly, it is common that large lakes supply fish and water to surrounding populations that can reach millions of people. At the same time, large lakes provide water storage and facilitate varied recreational activities, making them attractive for tourism activities. Tourism, fisheries, power generation, and transportation are important categories of ecosystem services that deliver easily quantifiable economic benefits (Sterner et al., 2020), making large lakes of remarkable value. Conversely, degradation of lake ecosystems causes costly damages (Mueller et al., 2016; Sterner et al., 2020). As a consequence, managing the quality of large lakes has become a challenge for stakeholders and governmental entities.

Published
2020
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5. A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins

Author

Moritz Buck, David García, Nur Filiz, Luděk Bláha, Teresa Vegas-Vilarrúbia, Manel Leira, David Parreño Duque, Donald C. Pierson, Pablo Alcaraz-Párraga, Justyna Kobos, Bárbara Úbeda, Triantafyllos Kaloudis, Elif Neyran Soylu, Eloísa Ramos-Rodríguez, Kerstin Häggqvist, Aleksandra Pełechata, Elżbieta Szeląg-Wasielewska, Meral Apaydın Yağcı, Anna Kozak, Edward Walusiak, Meryem Beklioglu, Monserrat Real, Nusret Karakaya, Carlos Rochera, Iwona Jasser, Kristiina Mustonen, José María Blanco, Delphine Latour, Nilsun Demir, Evanthia Mantzouki, Jutta Fastner, Carmen Cillero-Castro, Danielle Machado-Vieira, Tunay Karan, Jeremy Fonvielle, Kemal Celik, Mehmet Ali Turan Koçer, Miquel Lürling, Rafael Marcé, Dietmar Straile, Valerie McCarthy, Petar Žutinić, Korhan Özkan, Özden Fakioglu, Fuat Bilgin, Maria G. Antoniou, Sarah O'Leary, Itana Bokan Vucelić, Kersti Kangro, Trine Perlt Warming, Hatice Tunca, Kirsten Christoffersen, Lidia Nawrocka, Estela Rodríguez-Pérez, Abdulkadir Yağcı, Justyna Sieńska, Jessica Richardson, Elísabeth Fernández-Morán, Beata Madrecka, Barbara Pawlik-Skowrońska, Hans-Peter Grossart, Petra M. Visser, Leonardo Cerasino, Joanna Rosińska, Ülkü Nihan Tavşanoğlu, Elvira Romans, Boris Aleksovski, Agnieszka Bańkowska-Sobczak, Pauliina Salmi, Latife Köker, Cayelan C. Carey, Magdalena Toporowska, Lauri Arvola, Antonio Picazo, Elisabeth J. Faassen, Cafer Bulut, Joana Mankiewicz-Boczek, William Colom-Montero, Gregory Giuliani, Markéta Fránková, Ulrike Obertegger, Spela Remec-Rekar, Rahmi Uysal, Tanja Žuna Pfeiffer, Sigrid Haande, Jose Luis Cereijo, Victoria Bergkemper, Eilish Beirne, Agnieszka Ochocka, Uğur Işkın, Meriç Albay, Karl-Otto Rothhaupt, Nico Salmaso, Lea Tuvikene, Roberto L. Palomino, Bastiaan Willem Ibelings, Gizem Bezirci, Carmen Pérez-Martínez, Tuğba Ongun Sevindik, Dubravka Špoljarić Maronić, Ana Maria Antão-Geraldes, Jūratė Kasperovičienė, Christos Avagianos, João Morais, Daniel Szymański, Vítor Gonçalves, Susana Romo, Jorge Juan Montes-Pérez, Kristel Panksep, J. A. Gálvez, James B. Campbell, Biel Obrador, Mehmet Cesur, Irma Vitonytė, Andrea Törökné, Hannah Cromie, Tõnu Feldmann, Eti E. Levi, Ryszard Gołdyn, Mikołaj Kokociński, Lisette N. de Senerpont Domis, Kinga Kwasizur, Burçin Önem, Michał Wasilewicz, Magdalena Grabowska, Iwona Kostrzewska-Szlakowska, Mete Yilmaz, Reyhan Akçaalan, Koray Ozhan, Jordi Noguero-Ribes, Antonio Camacho, Giovanna Flaim, Nikoletta Tsiarta, Joan Gomà, Jūratė Karosienė, Elżbieta Wilk-Woźniak, Wojciech Pęczuła, Maciej Karpowicz, Michał Niedźwiecki, Vitor Vasconcelos, Spyros Gkelis, Agnieszka Napiórkowska-Krzebietke, Laura Seelen, Juan M. Soria, Iosif Konstantinou, Kadir Çapkın, Birger Skjelbred, Agnieszka Pasztaleniec, Núria Catalán, Şakir Çinar, Anđelka Plenković-Moraj, Lucia Chomova, Mehmet Tahir Alp, Magdalena Frąk, Theodoros M. Triantis, Adriano Boscaini, Carmen Ferriol, Judita Koreivienė, Julita Dunalska, Andrea G. Bravo, Hana Nemova, Ilona Gagala, Ana García-Murcia, Mariusz Pełechaty, Enrique Moreno-Ostos, Yvon Verstijnen, Lars-Anders Hansson, Ksenija Savadova, Jolanda M. H. Verspagen, Svetislav Krstić, Anastasia Hiskia, Valeriano Rodríguez, Wojciech Krztoń, Filip Stević, Hanna Mazur-Marzec, Agnieszka Budzyńska, Faruk Maraşlıoğlu, R. Carballeira, Alo Laas, Valentini Maliaka, Micaela Vale, Piotr Domek, Jordi Delgado-Martín, Marija Gligora Udovič, Manthos Panou, Iveta Drastichova, Tina Elersek, Sven Teurlincx, Damian Chmura, Beata Messyasz, Arda Özen, Pedro M. Raposeiro, E. Emiel van Loon, Natalia Jakubowska-Krepska, Armand Hernández, Anna C. Santamans, Christine Edwards, Yang Yang, Pablo Urrutia-Cordero, Rodan Geriš, Victor C. Perello, Sevasti-Kiriaki Zervou, Hans W. Paerl, Alinne Gurjão de Oliveira, Mari Carmen Trapote, Marek Kruk, Tokat Gaziosmanpaşa Üniversitesi, Theoretical and Computational Ecology (IBED, FNWI), Freshwater and Marine Ecology (IBED, FNWI), Havran Meslek Yüksekokulu, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Antoniou, Maria-Paraskevi, Giuliani, Gregory, Ibelings, Bastiaan Willem, European Cooperation in Science and Technology, Hernández, Armand, School of Biology, Aristotle University of Thessaloniki, Masaryk University [Brno] (MUNI), Lammi Biological Station (LBS), University of Helsinki, German Federal Environmental Agency / Umweltbundesamt (UBA), Limnological Institute, University of Konstanz, Fdn Edmund Mach, IASMA Research and Innovation Centre, Department of Biology, Faculty of Sciences, Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa (INESC-ID), Instituto Superior Técnico, Universidade Técnica de Lisboa (IST)-Instituto de Engenharia de Sistemas e Computadores (INESC), University of Strathclyde [Glasgow], Instituto Catalán de Investigación del Agua - ICRA (SPAIN) (ICRA), Mälardalen University (MDH), Freiburg Institute for Advanced Studies-LifeNet, Albert-Ludwigs-Universität Freiburg, Department of Computer Science and Engineering [San Diego] (CSE-UCSD), University of California [San Diego] (UC San Diego), University of California-University of California, Department of Environmental Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Environmental Sciences, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Universitat de Barcelona, Fen Edebiyat Fakültesi, BAİBÜ, Mühendislik Fakültesi, Çevre Mühendisliği Bölümü, Karakaya, Nusret, Hernández, Armand [0000-0001-7245-9863], Hitit Üniversitesi, Fen Edebiyat Fakültesi, Biyoloji Bölümü, AKWA, Aquatic Ecology (AqE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Department of Computer Science and Engineering [Univ California San Diego] (CSE - UC San Diego), and University of California (UC)-University of California (UC)

Subjects
Ecologia dels llacs, Data Descriptor, Water resources, Aquatic Ecology and Water Quality Management, thermocline, 010504 meteorology & atmospheric sciences, vesien tila, phytoplankton pigments, 010501 environmental sciences, 01 natural sciences, Ecosystem services, ympäristön tila, BU Contaminants & Toxins, Environmental monitoring, Limnology, lakes, ddc:550, Canvi climàtic, Geosciences, Multidisciplinary, Survey, ComputingMilieux_MISCELLANEOUS, ddc:333.7-333.9, Climate-Change, Europe Lakes, Environmental resource management, [Belirlenecek], Climate-change ecology, plankton, Eutrophication, 6. Clean water, Computer Science Applications, Europe, Disparate system, data, international, Bloom, Statistics, Probability and Uncertainty, Europa, Environmental Monitoring, Information Systems, environmental variables, Statistics and Probability, Biological pigments, Fitoplàncton, Climate Change, Cyanotoxins, ta1172, BU Contaminanten & Toxines, Climate change, observation design, Library and Information Sciences, Cyanobacteria, järvet, Education, European Multi Lake, cyanotoxins, ddc:570, Life Science, Ecosystem, 14. Life underwater, database creation objective, syanobakteerit, 0105 earth and related environmental sciences, WIMEK, business.industry, data analysis objective, nutrient, muuttujat, Pigments, Biological, 15. Life on land, Climatic changes, dataset, phytoplankton, pigments, mikrolevät, Aquatische Ecologie en Waterkwaliteitsbeheer, Environmental variables, Phytoplankton pigments, Multidisciplinär geovetenskap, Climatic change, Lakes, 13. Climate action, Nutrient pollution, Phytoplankton, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Lake ecology, Canvis climàtics, Waters
Abstract

Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment., The authors acknowledge COST Action ES 1105 “CYANOCOST – Cyanobacterial blooms and toxins in water resources: Occurrence impacts and management” and COST Action ES 1201 “NETLAKE – Networking Lake Observatories in Europe” for contributing to this study through networking and knowledge sharing with European experts in the field. Evanthia Mantzouki was supported by a grant from the Swiss State Secretariat for Education, Research and Innovation (SERI) to Bas Ibelings and by supplementary funding from University of Geneva. We thank Wendy Beekman for the nutrient analysis and the University of Wageningen for covering the costs of this analysis from the personal funding of dr. Miquel Lürling. We thank Pieter Slot for assisting with the pigment analysis and the University of Amsterdam for covering the costs of the analysis through funding from the group of Prof. Jef Huisman and dr. Petra Visser (IBED). We would like to thank the Environmental Data Initiative for covering the cost of archiving the EMLS dataset. We would like to thank the Leibniz Institute of Freshwater Ecology and Inland Fisheries, Dept. of Experimental Limnology and the Aquatic Microbial Ecology Group for logistic and technical support of J. Fonvielle and H.-P. Grossart; and the Leibniz Association for financial support. The collection of data for Lough Erne and Lough Neagh were funded by the Department of Agriculture, Environment and Rural Affairs, Northern Ireland.

Published
2018
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6. Toxic cyanobacteria and cyanotoxins in European waters – recent progress achieved through the CYANOCOST Action and challenges for further research

Author

Geoffrey A. Codd, Anastasia Hiskia, Jutta Fastner, Mikołaj Kokociński, Jussi Meriluoto, Triantafyllos Kaloudis, Damjana Drobac, Zorica Svirčev, Gorenka Bojadzija, Petra M. Visser, Rainer Kurmayer, Myriam Bormans, Nada Tokodi, Ludek Blaha, Nico Salmaso, Bastiaan Willem Ibelings, Luc Brient, Elisabeth J. Faassen, Antonio Quesada, Theodoros M. Triantis, Dijana Pantelić, University of Novi Sad, Research Centre for Toxic Compounds in the Environment [Brno] (RECETOX / MUNI), Faculty of Science [Brno] (SCI / MUNI), Masaryk University [Brno] (MUNI)-Masaryk University [Brno] (MUNI), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Environmental Sciences, Wageningen University and Research [Wageningen] (WUR), Institute for Limnology, Austrian Academy of sciences, Austrian Academy of Sciences (OeAW), Department of Biology, Universidad Autonoma de Madrid (UAM), Fdn Edmund Mach, IASMA Research and Innovation Centre, 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), Universidad Autónoma de Madrid (UAM), and Freshwater and Marine Ecology (IBED, FNWI)

Subjects
0106 biological sciences, Cyanotoxins, BU Contaminanten & Toxines, Water supply, Gaps of knowledge, 010501 environmental sciences, Aquatic Science, Oceanography, Cyanobacteria, 01 natural sciences, BU Contaminants & Toxins, Settore BIO/07 - ECOLOGIA, lcsh:QH540-549.5, ddc:550, Cost action, Social media, Environmental planning, 0105 earth and related environmental sciences, Ecology, business.industry, 010604 marine biology & hydrobiology, European research, Cyanotoxin, 6. Clean water, Outreach, Water resources, Europe, Action (philosophy), 13. Climate action, lcsh:Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Trends, business
Abstract

International audience; This review aims to summarise the outcomes of some recent European research concerning toxic cyanobacteria and cyanotoxins, with an emphasis on developments within the framework of the CYANOCOST Action (COST Action ES1105, Cyanobacterial Blooms and Toxins in Water Resources: Occurrence, Impacts and Management). State of the art research and management capabilities in Europe on cyanobacteria have benefitted from input from the pure and applied life sciences, the human and animal health sectors, water engineers, economists and planners. Many of these professional groups have been brought together and they interacted favourably within the framework of CYANOCOST. Highlights of the Action include phycological and ecological studies, development of advanced techniques for cyanotoxin analysis, elucidation of cyanotoxin modes of action, management techniques to reduce cyanobacterial mass development, and research on methods and practices for cyanotoxin removal during drinking water treatment. The CYANOCOST Action has had an active outreach policy throughout its lifetime, resulting in e.g. three handbooks, two special issues in scientific journals and activities in the social media. The many contact channels to end-users, including environmental and drinking water supply authorities, health professionals and the general public are described in this review. Furthermore, the authors have identified a number of gaps in knowledge. Proposed directions for future research in the field of toxic cyanobacteria and cyanotoxins are also discussed

Published
2017
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7. Fire Blight: Applied Genomic Insights of the Pathogen and Host

Author

Marie-Anne Barny, George W. Sundin, Theo H. M. Smits, Mickael Malnoy, Stefan Martens, John L. Norelli, Brion Duffy, Dept Biol & Genom Fruit Plants, Fdn Edmund Mach, IASMA Research and Innovation Centre, Interactions Plantes Pathogènes (IPP), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National Agronomique Paris-Grignon (INA P-G), Dept Plant Pathol, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Agroscope Changins Wadenswil ACW, Div Plant Protect, and Swiss Natl Competence Ctr Fire Blight

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Virulence, Genomics, Plant Science, Erwinia, Plant disease resistance, Genes, Plant, 01 natural sciences, Microbiology, Pyrus, 03 medical and health sciences, transcriptomics, Pseudomonas syringae, Erwinia amylovora, DISEASE RESISTANCE, MALUS X DOMESTICA, Pathogen, Rosaceae, Plant Diseases, Genetics, 0303 health sciences, QUANTITATIVE TRAIT LOCI, III EFFECTOR, biology, 030306 microbiology, Host (biology), Pantoea, BIOCONTROL STRAIN C9-1, PANTOEA-AGGLOMERANS, evolutionary genomics, food and beverages, biology.organism_classification, Genes, Bacterial, Malus, Fire blight, Host-Pathogen Interactions, DEFENSE RESPONSES, ERWINIA-AMYLOVORA FUNCTIONS, PSEUDOMONAS-SYRINGAE, Settore AGR/12 - PATOLOGIA VEGETALE, UBIQUITOUS PLASMID PEA29, 010606 plant biology & botany
Abstract

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; The enterobacterial phytopathogen Erwinia amylovora causes fire blight, an invasive disease that threatens a wide range of commercial and ornamental Rosaceae host plants. The response elicited by E. amylovora in its host during disease development is similar to the hypersensitive reaction that typically leads to resistance in an incompatible host-pathogen interaction, yet no gene-for-gene resistance has been described for this host-pathogen system. Comparative genomic analysis has found an unprecedented degree of genetic uniformity among strains of E. amylovora, suggesting that the pathogen has undergone a recent genetic bottleneck. The genome of apple, an important host of E. amylovora, has been sequenced, creating new opportunities for the study of interactions between host and pathogen during fire blight development and for the identification of resistance genes. This review includes recent advances in the genomics of both host and pathogen.

Published
2012
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