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1. Synthetic microbial communities: Sandbox and blueprint for soil health enhancement

Author: Mei Li, Jie Hu, Zhong Wei, Alexandre Jousset, Thomas Pommier, Xiangyang Yu, Yangchun Xu, and Qirong Shen
Subjects: Computer applications to medicine. Medical informatics, R858-859.7
Published: 2024
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2. Larval density in the invasive Drosophila suzukii: Immediate and delayed effects on life‐history traits

Author: Alicia Reyes‐Ramírez, Zaïnab Belgaidi, Patricia Gibert, Thomas Pommier, Aurélie Siberchicot, Laurence Mouton, and Emmanuel Desouhant
Subjects: crowding, Drosophila, life‐history traits, trade‐off, Ecology, QH540-549.5
Abstract: Abstract The effects of density are key in determining population dynamics, since they can positively or negatively affect the fitness of individuals. These effects have great relevance for polyphagous insects for which immature stages develop within a single site of finite feeding resources. Drosophila suzukii is a crop pest that induces severe economic losses for agricultural production; however, little is known about the effects of density on its life‐history traits. In the present study, we (i) investigated the egg distribution resulting from females' egg‐laying strategy and (ii) tested the immediate (on immatures) and delayed (on adults) effects of larval density on emergence rate, development time, potential fecundity, and adult size. The density used varied in a range between 1 and 50 larvae. We showed that 44.27% of the blueberries used for the oviposition assay contained between 1 and 11 eggs in aggregates. The high experimental density (50 larvae) has no immediate effect in the emergence rate but has effect on larval developmental time. This trait was involved in a trade‐off with adult life‐history traits: The time of larval development was reduced as larval density increased, but smaller and less fertile females were produced. Our results clearly highlight the consequences of larval crowding on the juveniles and adults of this fly.
Published: 2023
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3. Biochar stimulates tomato roots to recruit a bacterial assemblage contributing to disease resistance against Fusarium wilt

Author: Xue Jin, Yang Bai, Muhammad Khashi u Rahman, Xiaojun Kang, Kai Pan, Fengzhi Wu, Thomas Pommier, Xingang Zhou, and Zhong Wei
Subjects: bacterial diversity, disease suppression, Fusarium wilt, microbiome recruitment, Computer applications to medicine. Medical informatics, R858-859.7
Abstract: Abstract Biochar amendment is acknowledged to favor plant resistance against soil‐borne diseases. Although plant‐beneficial bacteria enrichment in the rhizosphere is often proposed to be associated with this protection, the mechanism behind this stimulating effect remains unelucidated. Here, we tested whether biochar promotes plants to recruit beneficial bacteria to the rhizosphere, and thus develop a disease‐suppressive rhizosphere microbiome. In a pot experiment, biochar amendment decreased tomato Fusarium wilt disease severity. Using a transplanting rhizosphere microbiome experiment, we showed that biochar enhanced the suppressiveness of tomato rhizosphere microbiome against Fusarium wilt disease. High‐throughput sequencing of 16S ribosomal RNA gene and in vitro cultures further indicated that the recruited suppressive rhizosphere microbiome was associated with the increase of plant‐beneficial bacteria, such as Pseudomonas sp. This amendment also enhanced the in vitro chemoattraction and biofilm promotion activity of tomato root exudates. Collectively, our results demonstrate that biochar amendment induces tomato seedlings to efficiently recruit a disease‐suppressive rhizosphere microbiome against Fusarium wilt.
Published: 2022
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4. Microbiome Analysis of New, Insidious Cave Wall Alterations in the Apse of Lascaux Cave

Author: Lise Alonso, Thomas Pommier, Danis Abrouk, Mylène Hugoni, Van Tran Van, Guillaume Minard, Claire Valiente Moro, and Yvan Moënne-Loccoz
Subjects: Paleolithic caves, anthropization, cave alterations, microbial diversity, pigmented fungi, collembola, Biology (General), QH301-705.5
Abstract: Lascaux Cave is a UNESCO site that was closed to the public following wall surface alterations. Most black stains that had formed on wall surface are stable or receding, but a new type of alteration visually quite different (termed dark zones) developed in Lascaux’s Apse room in the last 15 years. Here, we tested the hypothesis that dark zones displayed a different microbial community than black stains previously documented in the same room, using metabarcoding (MiSeq sequencing). Indeed, dark zones, black stains and neighboring unstained parts displayed distinct microbial communities. However, similarly to what was observed in black stains, pigmented fungi such as Ochroconis (now Scolecobasidium) were more abundant and the bacteria Pseudomonas less abundant in dark zones than in unstained parts. The collembola Folsomia candida, which can disseminate microorganisms involved in black stain development, was also present on dark zones. Illumina sequencing evidenced Ochroconis (Scolecobasidium) in all collembola samples from dark zones, as in collembola from black stains. This study shows that the microbial properties of dark zones are peculiar, yet dark zones display a number of microbial resemblances with black stains, which suggests a possible role of collembola in promoting these two types of microbial alterations on wall surfaces.
Published: 2022
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5. Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Author: Lise Alonso, Charline Creuzé-des-Châtelliers, Théo Trabac, Audrey Dubost, Yvan Moënne-Loccoz, and Thomas Pommier
Subjects: Lascaux Cave, Microbial degradation, Bacterial-fungal co-occurrence, Microbial community, Microbial ecology, QR100-130
Abstract: Abstract Background The World-famous UNESCO heritage from the Paleolithic human society, Lascaux Cave (France), has endeavored intense microclimatic perturbations, in part due to high touristic pressure. These perturbations have resulted in numerous disturbances of the cave ecosystem, including on its microbial compartment, which resulted in the formation of black stains especially on the rock faces of the passage. We investigated the cave microbiome in this part of Lascaux by sampling three mineral substrates (soil, banks, and inclined planes) on and outside stains to assess current cave microbial assemblage and explore the possibility that pigmented microorganisms involved in stain development occur as microbial consortia. Methods Microbial abundance and diversity were assessed by means of quantitative PCR and high-throughput sequencing (Illumina MiSeq) of several DNA and cDNA taxonomic markers. Five sampling campaigns were carried out during winter and summer to embrace potential seasonal effect in this somewhat stable environment (based on measurements of temperature and CO2 concentration). Results While the season or type of mineral substrate did not affect the abundances of bacteria and micro-eukaryotes on or outside stains, mineral substrate rather than stain presence appears to be the most significant factor determining microbial diversity and structuring microbial community, regardless of whether DNA or cDNA markers were considered. A phylogenetic signal was also detected in relation to substrate types, presence of stains but not with season among the OTUs common to the three substrates. Co-occurrence network analyses showed that most bacterial and fungal interactions were positive regardless of the factor tested (season, substrate, or stain), but these networks varied according to ecological conditions and time. Microorganisms known to harbor pigmentation ability were well established inside but also outside black stains, which may be prerequisite for subsequent stain formation. Conclusions This first high throughput sequencing performed in Lascaux Cave showed that black stains were secondary to mineral substrate in determining microbiome community structure, regardless of whether total or transcriptionally active bacterial and micro-eukaryotic communities were considered. These results revealed the potential for new stain formation and highlight the need for careful microbiome management to avoid further cave wall degradation.
Published: 2018
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6. Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia

Author: Shaohua Gu, Tianjie Yang, Zhengying Shao, Tao Wang, Kehao Cao, Alexandre Jousset, Ville-Petri Friman, Cyrus Mallon, Xinlan Mei, Zhong Wei, Yangchun Xu, Qirong Shen, and Thomas Pommier
Subjects: Siderophore, microbial interactions, plant health, plant pathogens, soil microbiology, Microbiology, QR1-502
Abstract: ABSTRACT Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secreted siderophore molecules might influence microbial interaction outcomes. Here, we tested if bacterial interactions mediated by iron-scavenging siderophores can be used to predict the disease suppressiveness of microbial consortia against soilborne Ralstonia solanacearum, a bacterial pathogen in the tomato rhizosphere. Iron availability significantly affected the interactions within inoculated consortia and between the consortia and the pathogen. We observed contrasting effects of siderophores and other nonsiderophore metabolites on the pathogen growth, while the siderophore effects were relatively much stronger. Specifically, disease incidence was reduced in vivo when the inoculated consortia produced siderophores that the pathogen could not use for its own growth. Employing siderophore-mediated interactions to engineer functionally robust microbial inoculants shows promise in protecting plants from soilborne pathogens. IMPORTANCE Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens.
Published: 2020
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7. Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities

Author: Alessandro Florio, Thomas Pommier, Jonathan Gervaix, Annette Bérard, and Xavier Le Roux
Subjects: Medicine, Science
Abstract: Abstract Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N2O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (
Published: 2017
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8. Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance

Author: Cécile Capdeville, Thomas Pommier, Jonathan Gervaix, François Fromard, Jean-Luc Rols, and Joséphine Leflaive
Subjects: mangrove ecosystem, anthropic disturbance, wastewater discharge, in situ long term monitoring, microbial community, N-cycle, Microbiology, QR1-502
Abstract: Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagal. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.
Published: 2019
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9. Influence of plant traits, soil microbial properties, and abiotic parameters on nitrogen turnover of grassland ecosystems

Author: Nicolas Legay, Sandra Lavorel, Catherine Baxendale, Ute Krainer, Michael Bahn, Marie‐Noëlle Binet, Amélie A. M. Cantarel, Marie‐Pascale Colace, Arnaud Foulquier, Eva‐Maria Kastl, Karl Grigulis, Bello Mouhamadou, Franck Poly, Thomas Pommier, Michael Schloter, Jean‐Christophe Clément, and Richard D. Bardgett
Subjects: ammonia‐oxidizing archaea and bacteria, arbuscular mycorrhizal colonization, ecosystem properties, grasslands, leaf traits, nitrite oxidizers, Ecology, QH540-549.5
Abstract: Abstract Although it is known that multiple interactions among plant functional traits, microbial properties, and abiotic soil parameters influence the nutrient turnover, the relative contribution of each of these groups of variables is poorly understood. We manipulated grassland plant functional composition and soil nitrogen (N) availability in a multisite mesocosm experiment to quantify their relative effects on soil N turnover. Overall, root traits, arbuscular mycorrhizal colonization, denitrification potential, as well as N availability and water availability, best explained the variation in measured ecosystem properties, especially the trade‐off between nutrient sequestration and plant biomass production. Their relative contributions varied with soil N availability. In relatively N‐poor soils (10–20 μg·N·g−1 soil), N turnover was mainly controlled by microbial properties and abiotic soil parameters, whereas in the relatively N‐rich soils (110–120 μg·N·g−1 soil), N turnover was mainly controlled by plant traits and microbial properties. This experiment is a strong demonstration of the importance of functional characteristics of both plants and soil microbes, and their interplay with soil N availability, for N turnover in grassland soils.
Published: 2016
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10. Contrasted effects of diversity and immigration on ecological insurance in marine bacterioplankton communities.

Author: Thierry Bouvier, Patrick Venail, Thomas Pommier, Corinne Bouvier, Claire Barbera, and Nicolas Mouquet
Subjects: Medicine, Science
Abstract: The ecological insurance hypothesis predicts a positive effect of species richness on ecosystem functioning in a variable environment. This effect stems from temporal and spatial complementarity among species within metacommunities coupled with optimal levels of dispersal. Despite its importance in the context of global change by human activities, empirical evidence for ecological insurance remains scarce and controversial. Here we use natural aquatic bacterial communities to explore some of the predictions of the spatial and temporal aspects of the ecological insurance hypothesis. Addressing ecological insurance with bacterioplankton is of strong relevance given their central role in fundamental ecosystem processes. Our experimental set up consisted of water and bacterioplankton communities from two contrasting coastal lagoons. In order to mimic environmental fluctuations, the bacterioplankton community from one lagoon was successively transferred between tanks containing water from each of the two lagoons. We manipulated initial bacterial diversity for experimental communities and immigration during the experiment. We found that the abundance and production of bacterioplankton communities was higher and more stable (lower temporal variance) for treatments with high initial bacterial diversity. Immigration was only marginally beneficial to bacterial communities, probably because microbial communities operate at different time scales compared to the frequency of perturbation selected in this study, and of their intrinsic high physiologic plasticity. Such local "physiological insurance" may have a strong significance for the maintenance of bacterial abundance and production in the face of environmental perturbations.
Published: 2012
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11. Escherichia coli concentration, multiscale monitoring over the decade 2011–2021 in the Mekong River basin, Lao PDR

Author: Laurie Boithias, Olivier Ribolzi, Emma Rochelle-Newall, Chanthanousone Thammahacksa, Paty Nakhle, Bounsamay Soulileuth, Anne Pando-Bahuon, Keooudone Latsachack, Norbert Silvera, Phabvilay Sounyafong, Khampaseuth Xayyathip, Rosalie Zimmermann, Sayaphet Rattanavong, Priscia Oliva, Thomas Pommier, Olivier Evrard, Sylvain Huon, Jean Causse, Thierry Henry-des-Tureaux, Oloth Sengtaheuanghoung, Nivong Sipaseuth, and Alain Pierret
Subjects: General Earth and Planetary Sciences
Abstract: Bacterial pathogens in surface waters may threaten human health, especially in developing countries, where untreated surface water is often used for domestic needs. The objective of the long-term multiscale monitoring of Escherichia coli ([E. coli]) concentration in stream water, and that of associated variables (temperature (T), electrical conductance (EC), dissolved oxygen concentration ([DO]) and saturation (DO%), pH (pH), oxidation-reduction potential (ORP), turbidity (Turb), and total suspended sediment concentration ([TSS])), was to identify the drivers of bacterial dissemination across tropical catchments. This data description paper presents three datasets (see “Data availability” section) collected at 31 sampling stations located within the Mekong River and its tributaries in Lao PDR (0.6–25 946 km2) from 2011 to 2021. The 1602 records have been used to describe the hydrological processes driving in-stream E. coli concentration during flood events, to understand the land-use impact on bacterial dissemination on small and large catchment scales, to relate stream water quality and diarrhea outbreaks, and to build numerical models. The database may be further used, e.g., to interpret new variables measured in the monitored catchments, or to map the health risk posed by fecal pathogens.
Published: 2022

12. Early spring snowmelt and summer droughts strongly impair the resilience of bacterial community and N cycling functions in a subalpine grassland ecosystem

Author: Farhan Hafeez, Jean‐Christophe Clément, Lionel Bernard, Franck Poly, and Thomas Pommier
Subjects: Ecology, Evolution, Behavior and Systematics
Published: 2023

13. Escherichia coli concentration, multiscale monitoring over the decade 2011–2021 in the Mekong basin, Lao PDR

Author: Laurie Boithias, Olivier Ribolzi, Emma Rochelle-Newall, Chanthanousone Thammahacksa, Paty Nakhle, Bounsamay Soulileuth, Anne Pando-Bahuon, Keooudone Latsachack, Norbert Silvera, Phabvilay Sounyafong, Khampaseuth Xayyathip, Rosalie Zimmermann, Sayaphet Rattanavong, Priscia Oliva, Thomas Pommier, Olivier Evrard, Sylvain Huon, Jean Causse, Thierry Henry-Des-Tureaux, Oloth Sengtaheuanghoung, Nivong Sipaseuth, and Alain Pierret
Abstract: Bacterial pathogens in surface waters may threaten human health, especially in developing countries, where untreated surface water is often used for domestic needs. The objective of the long-term multiscale monitoring of Escherichia coli concentration in stream water, and that of associated variables (temperature, electrical conductance, dissolved oxygen concentration and saturation, pH, oxidation-reduction potential, turbidity, and total suspended sediment concentration), was to identify the drivers of bacterial dissemination across tropical catchments. This data description paper presents three datasets (see section Data availability) collected at 31 sampling stations located within the Mekong river and its tributaries in Lao PDR (0.6–25,946 km2) from 2011 to 2021. The 1,602 records have been used to describe the hydrological processes driving in-stream Escherichia coli concentration during flood events, to understand land-use impact on bacterial dissemination on small and large catchment scales, to relate stream water quality and diarrhea outbreaks, and to build numerical models. The database may be further used e.g. to interpret new variables measured in the monitored catchments, or to map the health risk posed by fecal pathogens.
Published: 2022

14. Water Depth and Seasonal Effects on Potential Nitrification and Denitrification in Phragmites Australis Reed Beds of Two Water-Level Regulated Lakes

Author: Baptiste Boggio, Jean-Christophe Clément, Jean-Noël Avrillier, Thomas Pommier, and Florent Arthaud
Subjects: History, Polymers and Plastics, Business and International Management, Industrial and Manufacturing Engineering
Published: 2022

15. Overland flow during a storm event strongly affects stream water chemistry and bacterial community structure

Author: Huong T. Le, Thomas Pommier, Olivier Ribolzi, Bounsamay Soulileuth, Sylvain Huon, Norbert Silvera, Emma Rochelle-Newall, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Vietnam Academy of Science and Technology (VAST), 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)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Geosciences Environment Toulouse, Centre National de la Recherche Scientifique (CNRS), Representation du Laos (IRD), Institute of Research for sustainable Development (IRD), ANR-13-AGRO-0007,TecItEasy,Effets conjugués de l'expansion des plantations d'arbres et du changement climatique sur le fonctionnement hydro-sédimentaire des bassins versants tropicaux de montagne: la diversité microbienne aquatique comme un proxy de la conversion d'usage des terres(2013), and 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)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 2. Zero hunger, 0303 health sciences, 010504 meteorology & atmospheric sciences, Ecology, Lao PDR (Laos), DOC, 15. Life on land, Aquatic Science, Southeast Asia, 01 natural sciences, 6. Clean water, 03 medical and health sciences, Sustainability, 13. Climate action, [SDE]Environmental Sciences, CDOM, Land degradation, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0105 earth and related environmental sciences, Water Science and Technology
Abstract: International audience; As flood events are expected to become more frequent due to climate change, investigating how overland flow exports terrestrial nutrients, carbon and living organisms into aquatic systems is essential for understanding both soil and stream ecosystem status. Here we assessed how dissolved organic carbon (DOC), total suspended sediments (TSS), and stream bacterial diversity responded to stream discharge and overland flow during stormflow in a tropical catchment. A higher humification index and a decreasing ratio of allochthonous to autochthonous DOC indicated that DOC from soils was exported to stream during the flood. The delta C-13 and delta N-15 of particulate matter was indicative of a source in the cultivated areas of the upper catchment and of subsurface soils (stream banks and gullies) in the downstream section. Bacterial richness of particle-attached (PA) and the free-living (FL) fractions increased with the flood progression in the upstream section. Moreover, the community structure of the PA fraction in the stream was more similar to that of overland flow than was the FL fraction. This suggests that the soil PA bacterial community was washed-out with overland flow during the flood recession. The relative contribution of sources and the composition of TSS, rather than hydrological regime, significantly drove the composition of bacterial community. In conclusion, our results emphasize that overland flow during a flood event strongly influences the structure of stream bacterial communities further underlining the biological connectivity between terrestrial runoff and stream flow.
Published: 2021

16. Microbial ecology of tourist Paleolithic caves

Author: Zelia Bontemps, Lise Alonso, Mylène Hugoni, Yvan Moënne-Loccoz, Thomas Pommier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Environmental Engineering, [SDV]Life Sciences [q-bio], 03 medical and health sciences, Cave, Microbial ecology, Three-domain system, Environmental Chemistry, Animals, Taxonomic rank, Microbiome, Waste Management and Disposal, 030304 developmental biology, 0303 health sciences, geography.geographical_feature_category, Bacteria, 030306 microbiology, Ecology, Phylum, Microbiota, Fungi, Anthropization, social sciences, 15. Life on land, musculoskeletal system, Pollution, Archaea, humanities, Caves, Geography, 13. Climate action, Tourism
Abstract: International audience; Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.
Published: 2021

17. Different groups of nitrite-reducers and N2O-reducers have distinct ecological niches and functional roles in West African cultivated soils

Author: Féline L. Assémien, Jean T. Gonnety, Amélie A. M. Cantarel, Alessandro Florio, Xavier Le Roux, Thomas Pommier, Catherine Lerondelle, UMR 1418 LEM Ecologie Microbienne. Centre de recherche Auvergne-Rhône-Alpes, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Laboratoire Biocatalyse and Bioprocess, Unité Formation et Recherche Scientifique et Technologie des Aliments, Université Nangui Abrogoua, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), PAES UEMOA program P-Z1 - IAD - 002, Institut National de la Recherche Agronomique (INRA, EFPA Department), CAMPUS France program (AMRUGE-CI/SCAC), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: dénitrification, sol, [SDV]Life Sciences [q-bio], Microorganism, Soil Science, Biology, Microbiology, soil, Crop, chemistry.chemical_compound, Nitrate, nosZ, nitrate, carbone organique du sol, nirK, nirS, 2. Zero hunger, Ecological niche, Soil organic carbon, Niche differentiation, 04 agricultural and veterinary sciences, Soil carbon, Soil nitrate, 15. Life on land, Agronomy, chemistry, 13. Climate action, Soil water, Denitrification, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Mulch
Abstract: Increasing attention has been paid to microorganisms able to produce nitrous oxide (N2O), a potent greenhouse gas, or reduce it to harmless N2. Based on previous studies, niche differentiation could exist between nirK- and nirS-nitrite reducers and nosZI- and nosZII-N2O reducers, and nosZII-bacteria would have a key role for N2O reduction in soils. Most previous studies have been performed for agricultural systems but never in the moist savanna zone which covers half a million km2 in West Africa and whose soils are among the poorest in nitrogen (N) on earth. Here, we quantified potential gross and net N2O production rates along with the abundances of nirK-, nirS-, nosZI- and nosZII-harbouring bacteria for soils under six agricultural practices with maize rotations (slash-and-burn, chemical fertilization, mulching with or without inclusion of crop legumes, and without any input) after 4 and 5 crop cycles at nine sites in Ivory Coast. Sites and practices influenced denitrifier abundances and activities, the ratio of total abundances of nitrite-to-N2O reducers being highest and lowest for the mulching + green soya and slash-and-burn practices, respectively. Using structural equation modelling, we showed that nirS- and nosZI-bacteria both strongly depended on nitrate availability whereas nirK- and nosZII-bacteria were related to soil organic carbon and pH. Furthermore, potential gross and net N2O production rates depended strongly and only on the abundances of nirS- and nosZI-bacteria. Our results support the view of a clear niche differentiation between these four microbial groups but invalidate the assumption of a prominent functional role of soil nosZII-N2O reducers.
Published: 2019

18. Early Spring Snowmelt and Summer Droughts Strongly Impair the Resilience of Key Microbial Communities in Subalpine Grassland Ecosystems

Author: Lionel Bernard, Thomas Pommier, Jean-Christophe Clément, F. Poly, and Hafeez F
Subjects: 0106 biological sciences, 2. Zero hunger, Biomass (ecology), Resistance (ecology), Ecology, Biodiversity, Growing season, 04 agricultural and veterinary sciences, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Denitrifying bacteria, 13. Climate action, Abundance (ecology), Snowmelt, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Ecosystem
Abstract: Subalpine grassland ecosystems are important from biodiversity, agriculture, and touristic perspectives but their resilience to seasonally occurring climatic extremes is increasingly challenged with climate change, accelerating their vulnerability to tipping points. Microbial communities, which are central in ecosystem functioning, are usually considered as more resistant and highly resilient to such extreme events due to their functional redundancy and strong selection in residing habitats. To investigate this, we explored soil microbial responses upon recurrent summer droughts associated with early snowmelt in subalpine grasslands mesocosms set-up at the Lautaret Pass (French Alps). Potential respiration, nitrification and denitrification were monitored over a period of two growing seasons along with quantification of community gene abundances of total bacteria as well as (de)nitrifiers. Results revealed that droughts had a low and short-term adverse impact on bacterial total respiration supporting their hypothesized high resilience, i.e., resistance and ability to recover. Nitrification and abundances of the corresponding functional guilds showed relatively strong resistance to summer droughts but declined in response to early snowmelt. This triggered a cascading effect on denitrification but also on abundances of denitrifying communities which recovered from all climatic extremes except from the summer droughts where nitrifiers were collapsed. Denitrification and respective functional groups faced high impact of applied stresses with strong reduction in abundance and activity of this specialized community. Although, consequently lower microbial competition for nitrate may be positive for plant biomass production, warnings exist when considering the potential nitrogen leaching from these ecosystems as well as risks of greenhouses gases emission such as N2O.
Published: 2021

19. Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection

Author: Isabelle Goldringer, Xavier Le Roux, Sébastien Saint-Jean, Bruno Andrieu, Jonathan Gervaix, Jérôme Enjalbert, Amélie A. M. Cantarel, Vincent Allard, Sébastien Barot, Thomas Pommier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAE meta-programme EcoServ INRAE meta-programme EcoServ DIVERSITAS/Future Earth German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, DIVERSITAS/Future Earth, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, ANR-13-AGRO-0008,WHEATAMIX,Augmenter la diversité génétique au sein des parcelles de blé pour renforcer la multifonctionnalité et la durabilité de la production dans le Bassin Parisien(2013), 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), and INRAE meta-programme EcoServANR Wheatamix INRAE meta-programme EcoServ DIVERSITAS/Future Earth German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
Subjects: 0106 biological sciences, wheat variety selection, Physiology, Plant Science, Crop species, root nutrient absorption capacity, 010603 evolutionary biology, 01 natural sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, MAGIC lines, Common wheat, Triticum, Selection (genetic algorithm), 2. Zero hunger, Ecology, biology, landraces, organic farming varieties, Syndrome, 15. Life on land, biology.organism_classification, Pooideae, conventional varieties, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Phenotype, Evolutionary biology, Above- and below-ground functional traits, intraspecific trait variation, Plant species, Absorption capacity, Trait, 010606 plant biology & botany
Abstract: Although widely used in ecology, trait-based approaches are seldom used to study agroecosystems. In particular, there is a need to evaluate how functional trait variability among varieties of a crop species compares to the variability among wild plant species and how variety selection can modify trait syndromes. Here, we quantified 18 above- and below-ground functional traits for 57 varieties of common wheat representative of different modern selection histories. We compared trait variability among varieties and among Pooideae species, and analyzed the effect of selection histories on trait values and trait syndromes. For traits under strong selection, trait variability among varieties was less than 10% of the variability observed among Pooideae species. However, for traits not directly selected, such as root N uptake capacity, the variability was up to 75% of the variability among Pooideae species. Ammonium absorption capacity by roots was counter-selected for conventional varieties compared with organic varieties and landraces. Artificial selection also altered some trait syndromes classically reported for Pooideae. Identifying traits that have high or low variability among varieties and characterizing the hidden effects of selection on trait values and syndromes will benefit the selection of varieties to be used especially for lower N input agroecosystems.
Published: 2021

20. Siderophore-Mediated Interactions Determine the Disease Suppressiveness of Microbial Consortia

Author: Cyrus A. Mallon, Xinlan Mei, Yangchun Xu, Qirong Shen, Tao Wang, Zhong Wei, Alexandre Jousset, Thomas Pommier, Tianjie Yang, Shaohua Gu, Kehao Cao, Zhengying Shao, Ville-Petri Friman, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Key Research and Development Program of China 2018YFD1000800National Natural Science Foundation of China (NSFC)418070453197250441922053Natural Science Foundation of Jiangsu ProvinceBK20170085BK20180527Fundamental Research Funds for the Central UniversitiesKY2201719KJYQ202002KJQN201745KJQN201922KYXK202010Royal Society Research Grants at the University of York RSG\R1\180213CHL\R1\180031Netherlands Organization for Scientific Research (NWO)ALW.870.15.050Koninklijke Nederlandse Akademie van Wetenschappen 530-5CDP18, and Falcao Salles lab
Subjects: 0106 biological sciences, 0301 basic medicine, Siderophore, Physiology, media_common.quotation_subject, [SDV]Life Sciences [q-bio], lcsh:QR1-502, Ecological and Evolutionary Science, Biology, microbial interactions, plant pathogens, 010603 evolutionary biology, 01 natural sciences, Biochemistry, Microbiology, lcsh:Microbiology, Competition (biology), 03 medical and health sciences, Genetics, Colonization, Molecular Biology, Pathogen, Microbial inoculant, Ecology, Evolution, Behavior and Systematics, media_common, 2. Zero hunger, Ralstonia solanacearum, Rhizosphere, food and beverages, 15. Life on land, biology.organism_classification, soil microbiology, QR1-502, Computer Science Applications, 030104 developmental biology, 13. Climate action, Modeling and Simulation, [SDE]Environmental Sciences, plant health, Soil microbiology, Research Article
Abstract: Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens., Interactions between plant pathogens and root-associated microbes play an important role in determining disease outcomes. While several studies have suggested that steering these interactions may improve plant health, such approaches have remained challenging in practice. Because of low iron availability in most soils, competition for iron via secreted siderophore molecules might influence microbial interaction outcomes. Here, we tested if bacterial interactions mediated by iron-scavenging siderophores can be used to predict the disease suppressiveness of microbial consortia against soilborne Ralstonia solanacearum, a bacterial pathogen in the tomato rhizosphere. Iron availability significantly affected the interactions within inoculated consortia and between the consortia and the pathogen. We observed contrasting effects of siderophores and other nonsiderophore metabolites on the pathogen growth, while the siderophore effects were relatively much stronger. Specifically, disease incidence was reduced in vivo when the inoculated consortia produced siderophores that the pathogen could not use for its own growth. Employing siderophore-mediated interactions to engineer functionally robust microbial inoculants shows promise in protecting plants from soilborne pathogens. IMPORTANCE Soil-borne pathogens cause high losses in crop yields globally. The development of environmentally friendly approaches is urgently needed, but is often constrained by complex interactions between root-associated microbes and pathogens. Here, we demonstrate that the interactions within microbial consortia mediated by iron-scavenging siderophores play an important role in reducing pathogen infection and enhancing plant health. This study provides a promising and novel research direction for dealing with a wide range of microbial infections through iron exploitation, which is important for the colonization and infection of both plant and human hosts by pathogens.
Published: 2020

21. Land use strongly influences soil organic carbon and bacterial community export in runoff in tropical uplands

Author: Sylvain Huon, Olivier Ribolzi, Thomas Pommier, Huong T. Le, Keooudone Latsachack, Jean-Louis Janeau, Emma Rochelle-Newall, Vietnam Academy of Science and Technology (VAST), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris), Institut National de la Recherche Agronomique (INRA)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées, Soils and Fertilizers Research Institute (SFRI), Vietnam Academy of Agricultural Sciences (VAAS), UMR 242, Institut de Recherche pour le Développement (IRD [France-Ouest]), Institut de Recherche pour le Développement, Partenaires INRAE, French National Research Agency (ANR) ANR-13-AGRO-0007, ANR-13-AGRO-0007,TecItEasy,Effets conjugués de l'expansion des plantations d'arbres et du changement climatique sur le fonctionnement hydro-sédimentaire des bassins versants tropicaux de montagne: la diversité microbienne aquatique comme un proxy de la conversion d'usage des terres(2013), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), and 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)
Subjects: [SDV]Life Sciences [q-bio], Soil Science, 010501 environmental sciences, Development, unsustainable land use, 01 natural sciences, complex mixtures, Soil functions, Dissolved organic carbon, Environmental Chemistry, Nitrogen cycle, 0105 earth and related environmental sciences, General Environmental Science, 2. Zero hunger, Total organic carbon, soil erosion, land degradation, 04 agricultural and veterinary sciences, Soil carbon, 15. Life on land, Soil quality, Agronomy, rain simulation, 13. Climate action, bacterial function, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Surface runoff, Surface water
Abstract: Early Access: NOV 2019; International audience; Rapid development and associated land-use change have resulted in increased soil erosion and widespread land degradation in tropical ecosystems. Precipitation-induced soil erosion causes the export of soil organic carbon (SOC) and the associated bacterial community affecting soil quality and functioning. We assessed the transfer of SOC and soil bacterial diversity and functions in surface water runoff from different land uses: Teak with and without understory (TW and TWO, respectively) and upland rice (UR) in a tropical, upland catchment during a simulated rain event. Total suspended sediment (TSS) concentration was higher in TWO (1.23 +/- 0.21 g L-1) than in TW (0.37 +/- 0.16 g L-1) and UR (0.44 +/- 0.2 g L-1), whereas dissolved organic carbon (DOC) concentration was lower under TWO (3.8 +/- 0.7 mg L-1) than under TW or UR (13.4 +/- 7.5 and 9.57 +/- 4.8 mg L-1, respectively). Runoff from TWO harboured the highest proportion of bacterial taxa common to soil (27% and 29.5%) as compared with TW (22.8% and 13%) and UR (17.3% and 7%) for both particle attached and free-living fractions, respectively. Bacterial community export in surface runoff was driven by changes in DOC and TSS, suggesting that eroded soil particles simultaneously carry organic carbon and attached bacterial taxa in surface runoff. Consequently, the export of soil functional groups relating to organic carbon degradation and nitrogen cycle was higher under TWO than in TW or UR. Our results underline that teak plantations with unsustainable practices such as the removal of understory degrades soil functions and accelerates land degradation through soil erosion and surface runoff on the long term.
Published: 2020

22. Plant growth drives soil nitrogen cycling and N-related microbial activity through changing root traits

Author: M-N Binet, F. Poly, Bello Mouhamadou, Eleanor Personeni, Fabrice Grassein, Sandra Lavorel, Thomas Matthew Robson, Nicolas Legay, Thomas Pommier, Jean-Christophe Clément, Servane Lemauviel-Lavenant, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Cités, Territoires, Environnement et Sociétés (CITERES), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), 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), Ecophysiologie Végétale, Agronomie et Nutritions NCS (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Helsinki, ECOSERVE project during the writing up ANR, NWO, FCT, MINECO Swedish Research Council Formas Swiss National Science Foundation (SNSF), ANR-08-BDVA-0008,VITAL,Services écologiques issus du couplage entre la diversité fonctionnelle des plantes et des microorganismes du sol dans les prairies(2008), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Institute of Plant Sciences [Berne], Université de Berne, Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Service de Cardiologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Centre National de la Recherche Scientifique (CNRS)-Université de Tours, Canopy Spectral Ecology and Ecophysiology, Viikki Plant Science Centre (ViPS), Biosciences, Organismal and Evolutionary Biology Research Programme, and Plant Biology
Subjects: DYNAMICS, 0106 biological sciences, Denitrification, DIVERSITY, BACTERIAL COMMUNITY, Arbuscular mycorrhizal fungi, Plant Science, 010603 evolutionary biology, 01 natural sciences, Nitrification enzymatic activity, BIOMASS, Nutrient, ORGANIC-CARBON, Plant functional traits, Colonization, 1172 Environmental sciences, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Ecology, biology, Ecological Modeling, fungi, food and beverages, Mineralization (soil science), 15. Life on land, 11831 Plant biology, biology.organism_classification, EXTRACTION METHOD, Dactylis glomerata, FUNCTIONAL TRAITS, GRASSLAND SOIL, Agronomy, [SDE]Environmental Sciences, Denitrification enzymatic activity, Nitrification, RAPID ASSESSMENT, Soil fertility, Cycling, Plant-microbe interactions, 010606 plant biology & botany, Potential N mineralization
Abstract: Relationships between plants and nitrogen-related microbes may vary with plant growth. We investigated these dynamic relationships over three months by analyzing plant functional traits (PFT), arbuscular mycorrhizal fungal (AMF) colonization, potential N mineralization (PNM), potential nitrification (PNA) and denitrification activities (PDA) in Dactylis glomerata cultures. D. glomerata recruited AMF during early growth, and thereafter maintained a constant root colonization intensity. This may have permitted high enough plant nutrient acquisition over the three months as to offset reduced soil inorganic N. PFT changed with plant age and declining soil fertility, resulting in higher allocation to root biomass and higher root C:N ratio. Additional to root AMF presence, PR' changes may have favored denitrification over mineralization through changes in soil properties, particularly increasing the quality of the labile carbon soil fraction. Other PFT changes, such as N uptake, modified the plants' ability to compete with bacterial groups involved in N cycling. (C) 2020 Elsevier Ltd and British Mycological Society. All rights reserved.
Published: 2020

23. Anthropization level of Lascaux Cave microbiome shown by regional‐scale comparisons of pristine and anthropized caves

Author: Yvan Moënne-Loccoz, Lise Alonso, Jeanne Doré, David Chapulliot, Christophe J. Douady, Audrey Dubost, Bernard Kaufmann, Thomas Pommier, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), 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), and DRAC Nouvelle Aquitaine (Bordeaux, France)
Subjects: 0106 biological sciences, 0301 basic medicine, Range (biology), anthropization, Biodiversity, microbiome, Biology, 010603 evolutionary biology, 01 natural sciences, Natural (archaeology), 03 medical and health sciences, Cave, Genetics, Humans, karstic caves, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, geography, geography.geographical_feature_category, Geography, Ecology, Microbiota, paleolithic art, Community structure, Biota, Anthropization, 15. Life on land, Karst, Caves, 030104 developmental biology, Eukaryotic Cells, Prokaryotic Cells, metabarcoding, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Limestone areas across the world develop karstic caves, which are populated by a wide range of macro‐ and microorganisms. Many of these caves display Paleolithic art or outstanding speleothems, and in the last century they have been subjected to anthropization due to touristic management and intense human frequentation. Despite their cultural importance and associated conservation issues, the impact of anthropization on cave biodiversity is not known. Here, we show that anthropization is associated with specific cave biota modifications. We compared diversity in four pristine caves, four anthropized show caves, and the iconic Lascaux Cave with even stronger anthropization. The predominant microbial higher taxa were the same in all caves, but the most anthropized cave (Lascaux) was unique as it differed from the eight others by a higher proportion of Bacteroidetes bacteria and the absence of Euryarchaeota and Woesearchaeota archaea. Anthropization resulted in lower diver‐sity and altered community structure for bacteria and archaea on cave walls, espe‐cially in Lascaux, but with a more limited effect on microeukaryotes and arthropods. Our findings fill a key gap in our understanding of the response of karstic communi‐ties to anthropization, by revealing that tourism‐related anthropization impacts on the prokaryotic microbiome rather than on eukaryotic residents, and that it shapes cave biota irrespective of cave natural features.
Published: 2019

24. Mangrove Facies Drives Resistance and Resilience of Sediment Microbes Exposed to Anthropic Disturbance

Author: Joséphine Leflaive, Jonathan Gervaix, Jean-Luc Rols, Thomas Pommier, Cécile Capdeville, François Fromard, Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), 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)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Centre National de la Recherche Scientifique (CNRS), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Toulouse III - Paul Sabatier (UT3), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Office National de l'Eau et des Milieux Aquatiques (ONEMA) 2014/03, SIEAM (CNRS) 111098, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), UMR 1418 LEM Ecologie Microbienne. Centre de recherche Auvergne-Rhône-Alpes, Institut National de la Recherche Agronomique (INRA), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: surveillance systems, Microbiology (medical), lcsh:QR1-502, in situ long term monitoring, écosystème, Microbiology, lcsh:Microbiology, cycle de l'azote, 03 medical and health sciences, N-cycle, Ceriops tagal, anthropic disturbance, nitrogen cycle, Ecosystem, facteur anthropique, 14. Life underwater, Original Research, anthropogenic factor, 030304 developmental biology, ecosystem, 0303 health sciences, communauté microbienne, Rhizophora mucronata, biology, Resistance (ecology), 030306 microbiology, Ecology, Microbiology and Parasitology, Sediment, Vegetation, 15. Life on land, biology.organism_classification, faune de mangrove, Microbiologie et Parasitologie, mangrove ecosystem, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Microbial population biology, 13. Climate action, surveillance, wastewater discharge, Environmental science, microbial community, Mangrove
Abstract: Mangrove forests are coastal ecosystems continuously affected by various environmental stresses and organized along constraint gradients perpendicular to the coastline. The aim of this study was to evaluate the resistance and resilience of sediment microbial communities in contrasted vegetation facies, during and after exposure to an anthropic disturbance. Our hypothesis was that microbial communities should be the most stable in the facies where the consequences of the anthropic disturbance are the most similar to those of natural disturbances. To test this, we focused on communities involved in N-cycle. We used an in situ experimental system set up in Mayotte Island where 2 zones dominated by different mangrove trees are daily exposed since 2008 to pretreated domestic wastewater (PW) discharges. These freshwater and nutrients inputs should increase microbial activities and hence the anoxia of sediments. We monitored during 1 year the long-term impact of this disturbance, its short-term impact and the resilience of microbial communities on plots where PW discharges were interrupted. Microorganism densities were estimated by qPCR, the nitrification (NEA) and denitrification (DEA) enzyme activities were evaluated by potential activity measurements and pigment analyses were performed to assess the composition of microbial photosynthetic communities. At long-term PW discharges significantly modified the structure of phototrophic communities and increased the total density of bacteria, the density of denitrifying bacteria and DEA. Similar effects were observed at short-term, notably in the facies dominated by Ceriops tagal. The results showed a partial resilience of microbial communities. This resilience was faster in the facies dominated by Rhizophora mucronata, which is more subjected to tides and sediment anoxia. The higher stability of microbial communities in this facies confirms our hypothesis. Such information should be taken into account in mangrove utilization and conservation policies.
Published: 2019

25. Facilitation promotes invasions in plant-associated microbial communities

Author: Alexandre Jousset, Qirong Shen, Zhong Wei, Ville-Petri Friman, Jianing Wang, Thomas Pommier, Mei Li, Yangchun Xu, Nanjing Agricultural University, Utrecht University [Utrecht], Department of Biology, University of York [York, UK], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), National Key Basic Research Program of China 2015CB150503, National Natural Science Foundation of China41471213 41671248, Natural Science Foundation of Jiangsu Province BK20170085, 111 project B12009, Young Elite Scientist Sponsorship Program by CAST 2015QNRC001, Qing Lan Project, Wellcome Trust through the Centre for Chronic Diseases and Disorders (C2D2) 105624,Royal Society Research Grant at the University of York RSG\R1\180213, Nederlandse Organisatie voor Wetenschappelijk Onderzoek ALW.870.15.050,Koninklijke Nederlandse Akademie van Wetenschappen 530-5CDP18, Sub Ecology and Biodiversity, and Ecology and Biodiversity
Subjects: 0106 biological sciences, media_common.quotation_subject, Population Dynamics, microbe-microbe-plant interactions, Positive correlation, 010603 evolutionary biology, 01 natural sciences, Competition (biology), facilitation, invasion resistance, Ecology, Evolution, Behavior and Systematics, media_common, Antagonism, Ralstonia solanacearum, Rhizosphere, Community, biology, Resistance (ecology), Bacteria, Ecology, 010604 marine biology & hydrobiology, Microbiota, Antibiosis, food and beverages, Plants, biology.organism_classification, Facilitation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, rhizosphere, community ecology
Abstract: International audience; While several studies have established a positive correlation between community diversity and invasion resistance, it is less clear how species interactions within resident communities shape this process. Here, we experimentally tested how antagonistic and facilitative pairwise interactions within resident model microbial communities predict invasion by the plant-pathogenic bacterium Ralstonia solanacearum. We found that facilitative resident community interactions promoted and antagonistic interactions suppressed invasions both in the lab and in the tomato plant rhizosphere. Crucially, pairwise interactions reliably explained observed invasion outcomes also in multispecies communities, and mechanistically, this was linked to direct inhibition of the invader by antagonistic communities (antibiosis), and to a lesser degree by resource competition between members of the resident community and the invader. Together, our findings suggest that the type and strength of pairwise interactions can reliably predict the outcome of invasions in more complex multispecies communities.
Published: 2019

26. Quantifying the effect of overland flow on Escherichia coli pulses during floods: Use of a tracer-based approach in an erosion-prone tropical catchment

Author: Olivier Ribolzi, Cyril Zouiten, Laurie Boithias, Bounsamay Soulileuth, Guillaume Lacombe, Emma Rochelle-Newall, Olivier Evrard, Elodie Robert, Thomas Pommier, Chanthamousone Thammahacksa, Norbert Silvera, Keooudone Latsachack, Yves Auda, Marion Viguier, Sylvain Huon, Oloth Sengtaheuanghoung, Géosciences Environnement Toulouse (GET), 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)-Observatoire Midi-Pyrénées (OMP), 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), Gestion de l'Eau, Acteurs, Usages (UMR G-EAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - 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), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Recherche pour le Développement (IRD), 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), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochimie Des Impacts (GEDI), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Agricultural Land Management [Vientiane] (DALaM), Ministry of Agriculture and Forestry of Laos, ANR-13-AGRO-0007,TecItEasy,Effets conjugués de l'expansion des plantations d'arbres et du changement climatique sur le fonctionnement hydro-sédimentaire des bassins versants tropicaux de montagne: la diversité microbienne aquatique comme un proxy de la conversion d'usage des terres(2013), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-AgroParisTech-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), 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)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), and 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)
Subjects: Turbidité, 010504 meteorology & atmospheric sciences, Drainage basin, 02 engineering and technology, 01 natural sciences, Panoply, Turbidity, 020701 environmental engineering, Hydrologie, Water Science and Technology, geography.geographical_feature_category, Northern uplands of Lao PDR, Inondation, Contamination biologique, Surface runoff, Ruissellement, 6. Clean water, Circulation de l'eau, S50 - Santé humaine, [SDE]Environmental Sciences, Erosion, Surface-sub surface flow separation, Storm flow, Land-use change, 0207 environmental engineering, faecal pollution [EN], Indicator bacteria, Context (language use), parasitic diseases, Escherichia coli, P10 - Ressources en eau et leur gestion, [SDU.STU.HY]Sciences of the Universe [physics]/Earth Sciences/Hydrology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, Hydrology, geography, Flood myth, fungi, Fecal coliform, Fecal indicator bacteria, 13. Climate action, Environmental science
Abstract: International audience; Bacterial pathogens in surface waters threaten human health. The health risk is especially high in developing countries where sanitation systems are often lacking or deficient. Considering twelve flash-flood events sampled from 2011 to 2015 at the outlet of a 60-ha tropical montane headwater catchment in Northern Lao PDR, and using Escherichia coli as a fecal indicator bacteria, our objective was to quantify the contributions of both surface runoff and sub-surface flow to the in-stream concentration of E. coli during flood events, by (1) investigating E. coli dynamics during flood events and among flood events and (2) designing and comparing simple statistical and mixing models to predict E. coli concentration in stream flow during flood events. We found that in-stream E. coli concentration is high regardless of the contributions of both surface runoff and sub-surface flow to the flood event. However, we measured the highest concentration of E. coli during the flood events that are predominantly driven by surface runoff. This indicates that surface runoff, and causatively soil surface erosion, are the primary drivers of in-stream E. coli contamination. This was further confirmed by the step-wise regression applied to instantaneous E. coli concentration measured in individual water samples collected during the flood events, and by the three models applied to each flood event (linear model, partial least square model, and mixing model). The three models showed that the percentage of surface runoff in stream flow was the best predictor of the flood event mean E. coli concentration. The mixing model yielded a Nash-Sutcliffe efficiency of 0.65 and showed that on average, 89% of the in-stream concentration of E. coli resulted from surface runoff, while the overall contribution of surface runoff to the stream flow was 41%. We also showed that stream flow turbidity and E. coli concentration were positively correlated, but that turbidity was not a strong predictor of E. coli concentration during flood events. These findings will help building adequate catchment-scale models to predict E. coli fate and transport, and mapping the related risk of fecal contamination in a global changing context.
Published: 2021

27. Plant species identities and fertilization influence on arbuscular mycorrhizal fungal colonisation and soil bacterial activities

Author: Thomas Pommier, Emmanuelle Personeni, Jean-Christophe Clément, F. Poly, Nicolas Legay, Sophie Périgon, Fabrice Grassein, Sandra Lavorel, Jeremy Puissant, Bello Mouhamadou, Cindy Arnoldi, Marie-Noëlle Binet, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Institut National de la Recherche Agronomique (INRA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), 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, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Ecophysiologie Végétale, Agronomie et Nutritions ( EVA ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Recherche Agronomique ( INRA ), 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 ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), 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), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0106 biological sciences, Nutrient cycle, [SDE.MCG]Environmental Sciences/Global Changes, media_common.quotation_subject, Soil Science, 010603 evolutionary biology, 01 natural sciences, Competition (biology), [ SDE ] Environmental Sciences, Nutrient, Botany, Colonization, Nitrification enzyme activity, Bromus erectus, media_common, 2. Zero hunger, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Mycorrhizal colonization, Ecology, biology, fungi, food and beverages, Root traits, 15. Life on land, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Colonisation, [ SDE.MCG ] Environmental Sciences/Global Changes, Dactylis glomerata, Agronomy, Leaf traits, [SDE]Environmental Sciences, Shoot, Nutrient availability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Denitrification enzyme activity, 010606 plant biology & botany
Abstract: International audience; Plant species influence soil microbial communities, mainly through their functional traits. However, mechanisms underlying these effects are not well understood, and in particular how plant/ microorganism interactions are affected by plant identities and/or environmental conditions. Here, we performed a greenhouse experiment to assess the effects of three plant species on arbuscular mycorrhizal fungal (AMF) colonization, bacterial potential nitrification (PNA) and denitrification activities (PDA) through their functional traits related to nitrogen acquisition and turnover. Three species with contrasting functional traits and strategies (from exploitative to conservative), Dactylis glomerata (L.), Bromus erectus (Hudson) and Festuca paniculata (Schinz and Tellung), were cultivated in monocultures on soil grassland with or without N fertilization. Fertilization impacted some plant traits related to nutrient cycling (leaf and root N concentration, root C:N) but did not affect directly microbial parameters. The highest PDA and PNA were observed in D. glomerata and F. paniculata monocultures, respectively. The highest AMF colonization was obtained for F. paniculata, while B. erectus exhibited both the lowest AMF colonization and bacterial activities. Bacterial activities were influenced by specific above-ground plant traits across fertilization treatments: above-ground biomass for PDA, shoot:root ratio and leaf C:N ratio for PNA. Mycorrhizal colonization was influenced by below-ground traits either root dry matter content or root C:N. Hence, AMF colonization and bacterial activities were impacted differently by species-specific plant biomass allocation, root traits and nutrient requirement. We suggest that such effects may be linked to distinct root exudation patterns and plant abilities for nutrient acquisition and/or nutrient competition.
Published: 2016

28. The added value of including key microbial traits to determine nitrogen-related ecosystem services in managed grasslands

Author: Karl Grigulis, Amélie A. M. Cantarel, Thomas Pommier, Michael Bahn, Richard D. Bardgett, Jean-Christophe Clément, Nicolas Legay, Franck Poly, Sandra Lavorel, Catherine Baxendale, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Cités, Territoires, Environnement et Sociétés (CITERES), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA), Lancaster Environment Centre, Soil and Ecosystem Ecology Laboratory, Faculty of Life Sciences University of Manchester, University of Manchester [Manchester], Institute of Ecology, Technische Universität Berlin (TUB), 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 la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de la Recherche Scientifique (CNRS)-Université de Tours, Lancaster University, Technische Universität Berlin (TU), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), ANR, MESR, FW F, NERC, BMBF, Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Cités, Territoires, Environnement et Sociétés ( CITERES ), Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Ecole de la nature et du paysage – INSA Centre Val de Loire, CNRS UMR 7324 CITERES, Blois, Technical University of Berlin, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), and Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] )
Subjects: 0106 biological sciences, agroecology, Nutrient cycle, above- and below-ground interactions, 010603 evolutionary biology, 01 natural sciences, complex mixtures, Ecosystem services, [ SDE ] Environmental Sciences, nitrogen retention, Microbial ecology, N-cycle, functional traits, Leaching (agriculture), Agroecology, 2. Zero hunger, Functional ecology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Ecology, Agroforestry, Soil organic matter, soil fertility, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, grass-based agroecosystems, 13. Climate action, subalpine grassland, [SDE]Environmental Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Soil fertility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecosystem services
Abstract: International audience; 1. Despite playing central roles in nutrient cycles and plant growth, soil microbes are generally neglected in the study of ecosystem services (ES), due to difficulties to assess their diversity and functioning. However, to overcome these hurdles, new conceptual approaches and modern tools now provide a means to assess the role of microorganisms in the evaluation of ES. 2. In managed grasslands, soil microbes are central in providing nitrogen (N)-related ES such as maintenance of soil fertility and retention of mineral forms of N. Here, we applied state-of-the-art techniques in microbial ecology and plant functional ecology to uncover the intrinsic link between N-related bacterial functional groups, important plant functional traits, environmental factors and three proxies of maintenance of soil fertility and potential for N-leaching across managed grasslands in three regions of Europe. 3. By constructing well-defined structural equation modelling, we showed that including key microbial traits improve on average more than >50% of the total variances of ES proxies, that is, ammonium (NH + 4) or nitrate (NO − 3) leaching, and soil organic matter content. Geographic differences arose when considering the direct relationships of these ES proxies with specific microbial traits: nitrate leaching was positively correlated to the maximum rate of nitrification, except in the Austrian site and potentially leached NH + 4 –N was negatively correlated to the fungi/bacteria ratio, with the exception of the French site. 4. Synthesis and applications. The integration of soil microbial functional traits in the assessment of nitrogen-related grassland ecosystem services has direct contributions for understanding sustainable management of grassland ecosystems. The fundamental aspects of this study suggest that integrating a soil microbial component in grassland management may enhance sustainability of such grass-based agroecosystems.
Published: 2018

29. Vicinal land use change strongly drives stream bacterial community in a tropical montane catchment

Author: Olivier Ribolzi, Emma Rochelle-Newall, Bounsamay Soulileuth, Yves Auda, Thomas Pommier, Huong T. Le, Elisa Thébault, Oloth Sengtaheuanghoung, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), French National Research Agency ANR-13-AGRO-0007, USTH, Vietnam, and IRD (ARTS)
Subjects: 0301 basic medicine, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Land management, Drainage basin, Biology, DOC, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, LU legacy, 03 medical and health sciences, hyporheic zone, Rivers, Dissolved organic carbon, Hyporheic zone, Land use, land-use change and forestry, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Tropical Climate, geography, geography.geographical_feature_category, Bacteria, Ecology, Land use, bacterial diversity, land management, 15. Life on land, Carbon, 6. Clean water, Colored dissolved organic matter, 030104 developmental biology, 13. Climate action, CDOM, Seasons, Species richness
Abstract: International audience; Impact of land use (LU) change on stream environmental conditions and the inhabiting bacterial community remains rarely investigated, especially in tropical montane catchments. We examined the effects of LU change and its legacy along a tropical stream by comparing seasonal patterns of dissolved organic carbon (DOC) / colored dissolved organic matter (CDOM) in relation to variations in structure, diversity and metabolic capacities of particle-attached (PA) and free-living (FL) bacterial communities. We hypothesized that despite seasonal differences, hydrological flows that accumulate allochthonous carbon along the catchment are a major controlling factor of the bacterial community. Surprisingly, local environmental conditions that were largely related to nearby LU and the legacy of LU change were more important for stream bacterial diversity than hydrological connectivity. DOC was strongly correlated with PA richness and diversity. The legacy of LU change between teak plantation and annual crops induced high DOC and high diversity and richness of PA in the adjacent waters, while banana plantations were associated with high diversity of FL. The community structures of both PA and FL differed significantly between seasons. Our results highlight the importance of vicinal LU change and its legacy on aquatic bacterial communities in mixed used tropical watersheds.
Published: 2018

30. Soil legacy effects of climatic stress, management and plant functional composition on microbial communities influence the response of Lolium perenne to a new drought event

Author: Jean-Christophe Clément, Bello Mouhamadou, Arnaud Foulquier, Gabin Piton, Marie-Noëlle Binet, Thomas Pommier, Nicolas Legay, Sandra Lavorel, Cindy Arnoldi, Lionel Bernard, Cités, Territoires, Environnement et Sociétés (CITERES), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), 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 la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), ANR, NWO, FCT BiodivERsA/001/2014, MINECO, FORMAS, SNSF, French Agence Nationale pour la Recherche (ANR), Centre National de la Recherche Scientifique (CNRS)-Université de Tours, Cités, Territoires, Environnement et Sociétés ( CITERES ), Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), and Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] )
Subjects: 0106 biological sciences, plant functional trait, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, Soil Science, Plant Science, soil legacy, 010603 evolutionary biology, 01 natural sciences, Lolium perenne, extracellular enzymatic activitie, complex mixtures, Grassland, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Ecosystem, mycorrhizae, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, geography, Biomass (ecology), geography.geographical_feature_category, biology, Resistance (ecology), food and beverages, Plant community, 04 agricultural and veterinary sciences, 15. Life on land, lolium perenne, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, Agronomy, 13. Climate action, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, climatic stress
Abstract: International audience; Background and aims: drought events, agricultural practices and plant communities influence microbial and soil abiotic parameters which can feedback to fodder production. This study aimed to determine which soil legacies influence plant biomass production and nutritional quality, and its resistance and recovery to extreme weather events.Methods: In a greenhouse experiment, soil legacy effects on Lolium perenne were examined, first under optimal conditions, and subsequently during and after drought. We used subalpine grassland soils previously cultivated for two years with grass communities of distinct functional composition, and subjected to combinations of climatic stress and simulated management.Results: The soil legacy of climatic stress increased biomass production of Lolium perenne and its resistance and recovery to a new drought. This beneficial effect resulted from higher nutrient availability in soils previously exposed to climatic stresses due to lower competitive abilities and resistance of microbial communities to a new drought. This negative effect on microbial communities was strongest in soils from previously cut and fertilized grasslands or dominated by conservative grasses.Conclusion: In subalpine grasslands more frequent climatic stresses could benefit fodder production in the short term, but threaten ecosystem functioning and the maintenance of traditional agricultural practices in the long term.
Published: 2018

31. Microbial metacommunity: a METABAR coding approach

Author: Marc Buee, Matthieu Barret, Maria Bernard, Didier Debroas, Isabelle Domaizon, Laure Fauchery, Claude Husson, Valerie Laval, Géraldine Pascal, Charlie Pauvert, Christophe Mougel, Thomas Pommier, Dirk Redecker, Aymé Spor, Sébastien Terrat, Veronique Edel-Hermann, Corinne Vacher, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), BIOlogie et GEstion des Risques en agriculture (BIOGER), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), 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-Université Bourgogne Franche-Comté [COMUE] (UBFC), 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 National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes ( IAM ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Génétique Animale et Biologie Intégrative ( GABI ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne ( LMGE ), Université Clermont Auvergne ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques ( CARRTEL ), Institut National de la Recherche Agronomique ( INRA ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ), BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, Institut National de la Recherche Agronomique ( INRA ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), 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 ), ProdInra, Archive Ouverte, AGROCAMPUS OUEST, 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 National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: [SDV] Life Sciences [q-bio], communauté microbienne, [ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], microbial community
Abstract: Microbial metacommunity: a METABAR coding approach. 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens)
Published: 2017

32. Adaptation of soil nitrifiers to very low nitrogen level jeopardizes the efficiency of chemical fertilization in west african moist savannas

Author: Jonathan Gervaix, Thomas Pommier, Féline L. Assémien, Jean T. Gonnety, Xavier Le Roux, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), PAES UEMOA program P-Z1 - IAD - 002, INRA-EFPA, CAMPUS France program (AMRUGE-CI/SCAC), and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)
Subjects: 0301 basic medicine, sol, [SDV]Life Sciences [q-bio], lcsh:Medicine, Article, fertilisation, 03 medical and health sciences, chemistry.chemical_compound, Human fertilization, Ammonium, Ecosystem, lcsh:Science, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Multidisciplinary, biology, afrique de l'ouest, lcsh:R, Nitrobacter, 04 agricultural and veterinary sciences, 15. Life on land, biology.organism_classification, nitrification, 030104 developmental biology, efficacité, Agronomy, chemistry, Soil water, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, Nitrification, Terrestrial ecosystem, lcsh:Q, savane humide, Nitrospira
Abstract: The moist savanna zone covers 0.5 × 106 km2 in West Africa and is characterized by very low soil N levels limiting primary production, but the ecology of nitrifiers in these (agro)ecosystems is largely unknown. We compared the effects of six agricultural practices on nitrifier activity, abundance and diversity at nine sites in central Ivory Coast. Treatments, including repeated fertilization with ammonium and urea, had no effect on nitrification and crop N status after 3 to 5 crop cycles. Nitrification was actually higher at low than medium ammonium level. The nitrifying community was always dominated by ammonia oxidizing archaea and Nitrospira. However, the abundances of ammonia oxidizing bacteria, AOB, and Nitrobacter increased with fertilization after 5 crop cycles. Several AOB populations, some affiliated to Nitrosospira strains with urease activity or adapted to fluctuating ammonium levels, emerged in fertilized plots, which was correlated to nitrifying community ability to benefit from fertilization. In these soils, dominant nitrifiers adapted to very low ammonium levels have to be replaced by high-N nitrifiers before fertilization can stimulate nitrification. Our results show that the delay required for this replacement is much longer than ever observed for other terrestrial ecosystems, i.e. > 5 crop cycles, and demonstrate for the first time that nitrifier characteristics jeopardize the efficiency of fertilization in moist savanna soils.
Published: 2017

33. Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA

Author: Beatriz Fernández-Gómez, Thomas Pommier, B. G. Crespo, Carlos Pedrós-Alió, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), Spanish MICINN CTM2005-04795/MAR CTM2010-20361, International Census of Marine Microbes (ICoMM) via a grant from the Keck Foundation, CSIC, and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL)
Subjects: DNA, Bacterial, Firmicutes, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Zoology, microbial communities, Marine bacteria, microbial ecology, particle attached, pyrosequencing, PHYLOGENETIC DIVERSITY, ORGANIC-MATTER, RARE BIOSPHERE, COMMUNITIES, BACTERIOPLANKTON, BAY, DEGRADATION, POPULATIONS, ADAPTATIONS, PATTERNS, Microbial communities, Biology, Bacterial Physiological Phenomena, Microbiology, DNA, Ribosomal, Bacterial Adhesion, Actinobacteria, Microbial ecology, 03 medical and health sciences, Mediterranean sea, Abundance (ecology), RNA, Ribosomal, 16S, Mediterranean Sea, Cluster Analysis, Seawater, 14. Life underwater, Phylogeny, 030304 developmental biology, Original Research, 0303 health sciences, Bacteria, 030306 microbiology, Ecology, Verrucomicrobia, Bacteroidetes, Pyrosequencing, Sequence Analysis, DNA, biology.organism_classification, Biota, Species richness, Particle attached
Abstract: 12 pages, 8 figures, 2 tables, Free-living (FL) and particle-attached (PA) bacterial assemblages in the Northwest Mediterranean Sea were studied using pyrosequencing data of the 16S rRNA. We have described and compared the richness, the distribution of Operational Taxonomic Units (OTUs) within the two fractions, the spatial distribution, and the taxonomic composition of FL and PA bacterial assemblages. The number of OTUs in the present work was two orders of magnitude higher than in previous studies. Only 25% of the total OTUs were common to both fractions, whereas 49% OTUs were exclusive to the PA fraction and 26% to the FL fraction. The OTUs exclusively present in PA or FL assemblages were very low in abundance (6% of total abundance). Detection of the rare OTUs revealed the larger richness of PA bacteria that was hidden in previous studies. Alpha-Proteobacteria dominated the FL bacterial assemblage and gamma-Proteobacteria dominated the PA fraction. Bacteroidetes were important in the PA fraction mainly at the coast. The high number of sequences in this study detected additional phyla from the PA fraction, such as Actinobacteria, Firmicutes, and Verrucomicrobia, The Modivus cruise was supported by the Spanish MICINN project MODIVUS (CTM2005-04795/MAR). We thank the captain and the crew of the RV García del Cid. We thank V. Balagué for help with sampling and P. J. Wallhead for statistical advice. We thank two anonymous reviewers for their valuable comments. Pyrosequencing was carried out at the Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, U.S.A., under the auspices of the International Census of Marine Microbes (ICoMM) via a grant from the Keck Foundation. Initial analysis of the data was carried out at the VAMPS portal, supported by the Josephine Bay Paul -Center and the Alfred P. Sloan Foundation. Additional work was supported by Spanish MICINN grant MarineGems (CTM2010-20361). B. G. C. was supported by Juan de la Cierva contract from the Spanish “Ministerio de Ciencia e Innovación”. B. F.-G. was supported by a predoctoral I3P Grant from CSIC. This is a contribution to the International Census of Marine Microbes (ICoMM)
Published: 2013

34. Responses of Aquatic Bacteria to Terrestrial Runoff: Effects on Community Structure and Key Taxonomic Groups

Author: Jean L. Janeau, Emma Rochelle-Newall, Quan H. Trinh, Minh T. N. Luu, Hai S. Tran, Duc Anh Trinh, Didier Orange, Cuong Tu Ho, Huong T. Le, Thomas Pommier, Asmaa Merroune, Vietnam Academy of Science and Technology (VAST), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), Soils and Fertilizers Research Institute (SFRI), Vietnam Academy of Agricultural Sciences (VAAS), 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)-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), LOTUS 44/2012/HD-NDT, MOST, PHC Hoa Sen Lotus 23970QM, JEAI BioGEAQ, Institut de Recherche pour le Developpement (IRD), UMR laboratories iEES-Paris, LEM, USTH, Vietnam, IRD (ARTS), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institute of Ecology and Environmental Sciences, University Pierre et Marie Curie, 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), Vietnam Academy of Science and Technology ( VAST ), Institut d'écologie et des sciences de l'environnement de Paris ( IEES ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Soils and Fertilizers Research Institute ( SFRI ), VAAS, Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes ( Eco&Sols ), 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 ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), 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: 0301 basic medicine, Microbiology (medical), compost, engrais organique, engineering.material, DOC, Microbiology, complex mixtures, 03 medical and health sciences, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Dissolved organic carbon, Biochar, biochar, Original Research, 2. Zero hunger, Total organic carbon, communauté microbienne, Ecology, Compost, Aquatic ecosystem, Microbiology and Parasitology, fungi, 04 agricultural and veterinary sciences, 15. Life on land, ruissellement, Microbiologie et Parasitologie, carbone organique, écosystème aquatique, fertilité du sol, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, Environmental chemistry, 040103 agronomy & agriculture, engineering, 0401 agriculture, forestry, and fisheries, Environmental science, aquatic microbial community, mesocosms, Surface runoff, Organic fertilizer, Vermicompost
Abstract: International audience; Organic fertilizer application is often touted as an economical and effective method to increase soil fertility. However, this amendment may increase dissolved organic carbon (DOC) runoff into downstream aquatic ecosystems and may consequently alter aquatic microbial community. We focused on understanding the effects of DOC runoff from soils amended with compost, vermicompost, or biochar on the aquatic microbial community of a tropical reservoir. Runoff collected from a series of rainfall simulations on soils amended with different organic fertilizers was incubated for 16 days in a series of 200 L mesocosms filled with water from a downstream reservoir. We applied 454 high throughput pyrosequencing for bacterial 16S rRNA genes to analyze microbial communities. After 16 days of incubation, the richness and evenness of the microbial communities present decreased in the mesocosms amended with any organic fertilizers, except for the evenness in the mesocosms amended with compost runoff. In contrast, they increased in the reservoir water control and soil-only amended mesocosms. Community structure was mainly affected by pH and DOC concentration. Compared to the autochthonous organic carbon produced during primary production, the addition of allochthonous DOC from these organic amendments seemed to exert a stronger effect on the communities over the period of incubation. While the Proteobacteria and Actinobacteria classes were positively associated with higher DOC concentration, the number of sequences representing key bacterial groups differed between mesocosms particularly between the biochar runoff addition and the compost or vermi-compost runoff additions. The genera of Propionibacterium spp. and Methylobacterium spp. were highly abundant in the compost runoff additions suggesting that they may represent sentinel species of complex organic carbon inputs. Overall, this work further underlines the importance of studying the off-site impacts of organic fertilizers as their impact on downstream aquatic systems is not negligible.
Published: 2016

35. Predicting the responses of soil nitrite-oxidizers to multi-factorial global change: a trait-based approach

Author: Jinyun Tang, Nicholas J. Bouskill, Bruce A. Hungate, Christopher B. Field, Xavier Le Roux, Maria Tourna, Audrey Niboyet, Paul Dijkstra, Franck Poly, Laure Barthes, Akihiko Terada, Thomas Pommier, Catherine Lerondelle, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Lawrence Berkeley National Laboratory [Berkeley] ( LBNL ), Ecologie Systématique et Evolution ( ESE ), Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Northern Arizona University [Flagstaff], Stanford University [Stanford], Technical University of Denmark [Lyngby] ( DTU ), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Technical University of Denmark [Lyngby] (DTU), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Stanford University, and INRA, CNRS, EC2CO program, US Department of Energy, US NSF DEB-0092642/0145324, Packard Foundation, Morgan Family Foundation
Subjects: concentration elevee en co2, 0301 basic medicine, WATER TREATMENT PLANTS, Environmental change, Biodiversity, lcsh:QR1-502, bacterial functional trait, elevated CO2, nitrifier, nitrogen fertilisation, trait-based modeling, NITROSPIRA, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Microbiology, bacterial functional traits, Soil functions, nitrifiers, SDG 15 - Life on Land, Original Research, 2. Zero hunger, Abiotic component, Ecology, Microbiology and Parasitology, 04 agricultural and veterinary sciences, Microbiologie et Parasitologie, Trait-based modelling, fertilisation azotée, GRASSLAND RESPONSES, bactérie nitrifiante, global change and microbial response, COMMUNITY STRUCTURE, AMMONIA-OXIDIZERS, Microbiology (medical), MICROBIOLOGY, Biogeochemical cycle, Environmental Science and Management, [ SDV.SA.SDS ] Life Sciences [q-bio]/Agricultural sciences/Soil study, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, Biology, Microbiology, 03 medical and health sciences, bacterial community composition, Ecosystem, NITRIFYING BACTERIA, modélisation, NITROBACTER, [ SDV.BID ] Life Sciences [q-bio]/Biodiversity, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Biogeochemistry, Global change, 15. Life on land, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, 13. Climate action, Soil Sciences, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MICROBIAL DIVERSITY, BIOGEOGRAPHY
Abstract: © 2016 Le Roux, Bouskill, Niboyet, Barthes, Dijkstra, Field, Hungate, Lerondelle, Pommier, Tang, Terada, Tourna and Poly. Soil microbial diversity is huge and a few grams of soil contain more bacterial taxa than there are bird species on Earth. This high diversity often makes predicting the responses of soil bacteria to environmental change intractable and restricts our capacity to predict the responses of soil functions to global change. Here, using a long-term field experiment in a California grassland, we studied the main and interactive effects of three global change factors (increased atmospheric CO2concentration, precipitation and nitrogen addition, and all their factorial combinations, based on global change scenarios for central California) on the potential activity, abundance and dominant taxa of soil nitrite-oxidizing bacteria (NOB). Using a trait-based model, we then tested whether categorizing NOB into a few functional groups unified by physiological traits enables understanding and predicting how soil NOB respond to global environmental change. Contrasted responses to global change treatments were observed between three main NOB functional types. In particular, putatively mixotrophic Nitrobacter, rare under most treatments, became dominant under the 'High CO2+Nitrogen+Precipitation' treatment. The mechanistic trait-based model, which simulated ecological niches of NOB types consistent with previous ecophysiological reports, helped predicting the observed effects of global change on NOB and elucidating the underlying biotic and abiotic controls. Our results are a starting point for representing the overwhelming diversity of soil bacteria by a few functional types that can be incorporated into models of terrestrial ecosystems and biogeochemical processes.
Published: 2016

36. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

Author: Thomas Pommier, Agnès Richaume, Marie Simonin, Julien P. Guyonnet, Audrey Dubost, Jean M.F. Martins, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon, Centre National de la Recherche Scientifique ( CNRS ), Center for the Environmental Implications of Nanotechnology, Duke University, Department of Biology, Northern Arizona University [Flagstaff], UMR 5564 Laboratoire d'étude des Transferts en Hydrologie et Environnement (LTHE), Université Grenoble Alpes ( UGA ), Rhone-Alpes Region - ARC Environnement, French National Program EC2CO-CNRS AT-Microbien, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes (UGA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Richaume-Jolion, Agnès
Subjects: 2. Zero hunger, 0301 basic medicine, Soil health, Multidisciplinary, Denitrification, [ SDV ] Life Sciences [q-bio], Ecology, [SDV]Life Sciences [q-bio], Microorganism, technology, industry, and agriculture, 15. Life on land, 010501 environmental sciences, 01 natural sciences, Article, 03 medical and health sciences, 030104 developmental biology, Microbial population biology, 13. Climate action, Soil water, Environmental science, Nitrification, Ecosystem, Nitrogen cycle, 0105 earth and related environmental sciences
Abstract: Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg−1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.
Published: 2016

37. Influence of plant traits, soil microbial properties, and abiotic parameters on nitrogen turnover of grassland ecosystems

Author: Richard D. Bardgett, Thomas Pommier, Arnaud Foulquier, Sandra Lavorel, Catherine Baxendale, Bello Mouhamadou, Michael Schloter, Marie-Noëlle Binet, Franck Poly, Jean-Christophe Clément, Marie-Pascale Colace, Ute Krainer, Eva-Maria Kastl, Michael Bahn, Amélie A. M. Cantarel, Nicolas Legay, Karl Grigulis, Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université Grenoble Alpes (UGA), Lancaster Environment Centre, Soil and Ecosystem Ecology Laboratory, Institute of Ecology, Technische Universität Berlin (TUB), 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-Université Bourgogne Franche-Comté [COMUE] (UBFC), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Research Unit for Environmental Genomics, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz-Zentrum München (HZM), Station alpine Joseph Fourier - UMS 3370 (SAJF), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF), Faculty of Life Sciences, Michael Smith Building, University of Manchester, ERA-Net BiodivERsA project VITAL [ANR-08-BDVA-008], ANR, FWF, NERC [NE/G002258/2], BMBF, Austrian Science Fund (FWF) [I 242-B17], ECO-SERVE project, NWO, FCT, MINECO, FORMAS, SNSF, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Technische Universität Berlin (TU), Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Station alpine Joseph Fourier - UMS 3370 (SAJF ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Universität Innsbruck [Innsbruck], Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), Institut National de la Recherche Agronomique (INRA)-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)-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Faculty of Life Sciences University of Manchester, University of Manchester [Manchester], UMR 5553 Laboratoire d’Ecologie Alpine, Centre National de la Recherche Scientifique ( CNRS ), Université Grenoble Alpes ( UGA ), Technical University of Berlin, 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 ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Helmholtz-Zentrum München ( HZM ), UMS 3370 Station Alpine Joseph Fourier, Université Joseph Fourier (Grenoble 1) ( UJF ), Lancaster University, 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 de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche sur l'Ecosystème Prairial, Institut National de la Recherche Agronomique ( INRA ), Station alpine Joseph Fourier - UMS 3370 ( SAJF ), and Centre National de la Recherche Scientifique ( CNRS ) -Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Grenoble Alpes ( UGA )
Subjects: 0106 biological sciences, leaf traits, Soil biology, [SDV]Life Sciences [q-bio], ammonia‐oxidizing archaea and bacteria, water availability, 010603 evolutionary biology, 01 natural sciences, complex mixtures, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, Mesocosm, nitrite reducers, Nutrient, lcsh:QH540-549.5, Ammonia-oxidizing Archaea And Bacteria, Arbuscular Mycorrhizal Colonization, Ecosystem Properties, Grasslands, Leaf Traits, Nitrite Oxidizers, Nitrite Reducers, Nutrient Availability, Root Traits, Water Availability, Ecosystem, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, [ SDV ] Life Sciences [q-bio], Ecology, Soil organic matter, grasslands, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, nitrite oxidizers, ammonia-oxidizing archaea and bacteria, root traits, Agronomy, Soil water, 040103 agronomy & agriculture, arbuscular mycorrhizal colonization, 0401 agriculture, forestry, and fisheries, Environmental science, ecosystem properties, lcsh:Ecology, nutrient availability, Soil fertility, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Although it is known that multiple interactions among plant functional traits, microbial properties , and abiotic soil parameters influence the nutrient turnover, the relative contribution of each of these groups of variables is poorly understood. We manipulated grassland plant functional composition and soil nitrogen (N) availability in a multisite mesocosm experiment to quantify their relative effects on soil N turnover. Overall, root traits, arbuscular mycorrhizal colonization, denitrification potential, as well as N availability and water availability, best explained the variation in measured ecosystem properties, especially the trade-off between nutrient sequestration and plant biomass production. Their relative contributions varied with soil N availability. In relatively N-poor soils (10–20 μg·N·g −1 soil), N turnover was mainly controlled by microbial properties and abiotic soil parameters, whereas in the relatively N-rich soils (110–120 μg·N·g −1 soil), N turnover was mainly controlled by plant traits and microbial properties. This experiment is a strong demonstration of the importance of functional characteristics of both plants and soil microbes, and their interplay with soil N availability, for N turnover in grassland soils.
Published: 2016

38. Management of Microbial Communities through Transient Disturbances Enhances the Functional Resilience of Nitrifying Gas-Biofilters to Future Disturbances

Author: Léa Cabrol, Jean-Louis Fanlo, Anne-Sophie Lepeuple, Franck Poly, Luc Malhautier, Catherine Lerondelle, Thomas Pommier, Xavier Le Roux, Willy Verstraete, Pontificia Universidad Católica de Valparaíso, Laboratoire de Génie de l'Environnement Industriel ( LGEI ), IMT - Mines Alès Ecole Mines - Télécom ( IMT - MINES ALES ), Veolia Environnement, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Lab Microbial Ecol & Technol LabMET, Ghent University [Belgium] ( UGENT ), Pontificia Universidad Católica de Valparaíso (PUCV), Laboratoire de Génie de l'Environnement Industriel (LGEI), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ghent University [Belgium] (UGENT), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Universiteit Gent = Ghent University [Belgium] (UGENT), Veolia Environnement Recherche et Innovation (VERI), Maisons Laffitte, France through ANRT agreement CIFRE [2006/497], and Veolia Environnement Recherche et Innovation (VERI), Maisons Laffitte, France through a 'Contrat de Cooperation dans le Cadre d'Etudes et de Recherches' established in 2006 between Veolia, LEM-CNRS and ARMINES-EMA
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDE.MCG]Environmental Sciences/Global Changes, Microbial Consortia, Nitrobacter, Nitrosomonas eutropha, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [ SDE.IE ] Environmental Sciences/Environmental Engineering, 03 medical and health sciences, Ammonia, Environmental Chemistry, Ecosystem, Bioprocess, Nitrosomonas, Nitrites, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, biology, [SDE.IE]Environmental Sciences/Environmental Engineering, Environmental engineering, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, General Chemistry, biology.organism_classification, Nitrification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Nitrobacter hamburgensis, [ SDE.MCG ] Environmental Sciences/Global Changes, 030104 developmental biology, Environmental biotechnology, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Microbial communities have a key role for the performance of engineered ecosystems such as waste gas biofilters. Maintaining constant performance despite fluctuating environmental conditions is of prime interest, but it is highly challenging because the mechanisms that drive the response of microbial communities to disturbances still have to be disentangled. Here we demonstrate that the bioprocess performance and stability can be improved and reinforced in the face of disturbances, through a rationally predefined strategy of microbial resource management (MRM). This strategy was experimentally validated in replicated pilot-scale nitrifying gas-biofilters, for the two steps of nitrification. The associated biological mechanisms were unraveled through analysis of functions, abundances and community compositions for the major actors of nitrification in these biofilters, that is, ammonia-oxidizing bacteria (AOB) and Nitrobacter-like nitrite-oxidizers (NOB). Our MRM strategy, based on the application of successive, transient perturbations of increasing intensity, enabled to steer the nitrifier community in a favorable way through the selection of more resistant AOB and NOB sharing functional gene sequences close to those of, respectively, Nitrosomonas eutropha and Nitrobacter hamburgensis that are well adapted to high N load. The induced community shifts resulted in significant enhancement of nitrification resilience capacity following the intense perturbation.
Published: 2016

39. Pole-to-pole biogeography of surface and deep marine bacterial communities

Author: Patricia L. Yager, Carlos Pedrós-Alió, Alison E. Murray, Connie Lovejoy, Thomas Pommier, Stefan Bertilson, Jean-François Ghiglione, Pierre E. Galand, David L. Kirchman, Kevin M. Bakker, Elizabeth W. Maas, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Sloan Foundation, W.M. Keck Foundation award, Institut Francais pour la Recherche et la Technologie Polaires, Spanish Ministry of Education and Science, New Zealand International Polar Year-Census of Antarctic Marine Life Project [So001IPY, IPY2007-01], Natural Sciences and Engineering Council (NSERC) of Canada, National Science Foundation [OPP-0124733, ANT-0632389, ANT-0741409], and Swedish Polar Research Secretariat
Subjects: [SDV]Life Sciences [q-bio], Biogeography, Antarctic Regions, Marine Biology, Biology, Deep sea, Latitude, Microbial ecology, 03 medical and health sciences, 14. Life underwater, Phylogeny, 030304 developmental biology, Marine biology, 0303 health sciences, Multidisciplinary, Bacteria, Geography, Arctic Regions, 030306 microbiology, Ecology, fungi, Ocean current, Community structure, Biodiversity, Bacterioplankton, Biological Sciences, Oceanography, Arctic, RNA, Ribosomal, 13. Climate action, Bipolar, Next-generation sequencing, Water Microbiology, geographic locations
Abstract: 6 pages, 4 figures, The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation, We thank the members of field teams, shipboard crews, and logistics support personnel from all national polar programs involved in sample collection, without whom this study would not have been possible. The Census of Antarctic Marine Life, funded by the Sloan Foundation, facilitated this collaboration. Pyrosequencing was provided by the International Census of Marine Microbes (ICoMM) with financial support from a W. M. Keck Foundation award to the Marine Biological Laboratory in Woods Hole. Funding to support sample collection was provided by the Institut Français pour la Recherche et la Technologie Polaires (J.-F.G.); the Spanish Ministry of Education and Science (C.P.-A.); the New Zealand International Polar Year-Census of Antarctic Marine Life Project [Phases 1 (So001IPY) and 2 (IPY2007-01); to E.W.M.); the Natural Sciences and Engineering Council (NSERC) of Canada (C.L.); National Science Foundation Grants OPP-0124733 (to D.L.K.), ANT-0632389 (to A.E.M.), and ANT-0741409 (to P.L.Y.); and the Swedish Polar Research Secretariat (S.B.)
Published: 2012

40. Two decades of describing the unseen majority of aquatic microbial diversity

Author: Lucie Zinger, Thomas Pommier, and Angélique Gobet
Subjects: 0303 health sciences, 030306 microbiology, business.industry, Ecology, Microbial diversity, Aquatic ecosystem, Environmental resource management, Biodiversity, Context (language use), 15. Life on land, Biology, 6. Clean water, 03 medical and health sciences, 13. Climate action, Sustainability, Genetics, Degree of precision, 14. Life underwater, business, Ecology, Evolution, Behavior and Systematics, Water sampling, 030304 developmental biology
Abstract: Aquatic environments harbour large and diverse microbial populations that ensure their functioning and sustainability. In the current context of global change, characterizing microbial diversity has become crucial, and new tools have been developed to overcome the methodological challenges posed by working with microbes in nature. The advent of Sanger sequencing and now next-generation sequencing technologies has enabled the resolution of microbial communities to an unprecedented degree of precision. However, to correctly interpret microbial diversity and its patterns this revolution must also consider conceptual and methodological matters. This review presents advances, gaps and caveats of these recent approaches when considering microorganisms in aquatic ecosystems. We also discuss potentials and limitations of the available methodologies, from water sampling to sequence analysis, and suggest alternative ways to incorporate results in a conceptual and methodological framework. Together, these methods will allow us to gain an unprecedented understanding of microbial diversity in aquatic ecosystems.
Published: 2011

41. Diversification in temporally heterogeneous environments: effect of the grain in experimental bacterial populations

Author: Oliver Kaltz, Thomas Pommier, Patrick Venail, Nicolas Mouquet, and Isabelle Olivieri
Subjects: 0106 biological sciences, Experimental evolution, Disruptive selection, Ecology, Range (biology), Biology, Diversification (marketing strategy), 010603 evolutionary biology, 01 natural sciences, Spatial heterogeneity, 010601 ecology, Temporal heterogeneity, Specialization (logic), Ecology, Evolution, Behavior and Systematics
Abstract: Although theory established the necessary conditions for diversification in temporally heterogeneous environments, empirical evidence remains controversial. One possible explanation is the difficulty of designing experiments including the relevant range of temporal grains and the appropriate environmental trade-offs. Here, we experimentally explore the impact of the grain on the diversification of the bacterium Pseudomonas fluorescens SBW25 in a temporally fluctuating environment by including 20 different pairs of environments and four temporal grains. In general, higher levels of diversity were observed at intermediate temporal grains. This resulted in part from the enhanced capacity of disruptive selection to generate negative genotypic correlations in performance at intermediate grains. However, the evolution of reciprocal specialization was an uncommon outcome. Although the temporal heterogeneity is in theory less powerful than the spatial heterogeneity to generate and maintain the diversity, our results show that diversification under temporal heterogeneity is possible provided appropriate environmental grains.
Published: 2011

42. RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

Author: Thomas Pommier, Björn Canbäck, Anders Tunlid, Per Lundberg, and Åke Hagström
Subjects: Statistics and Probability, DNA, Bacterial, Population, Biology, Biochemistry, DNA, Ribosomal, DNA sequencing, Similarity (network science), Phylogenetics, education, Molecular Biology, Phylogeny, education.field_of_study, Internet, Phylogenetic tree, Bacteria, Ecology, Ribosomal RNA, Original Papers, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Genetic distance, Evolutionary biology, Identification (biology), Software
Abstract: Motivation: The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Commonly, the sequences are grouped into operational taxonomic units based on genetic distance (sequence similarity) instead of genetic change (patristic distance). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. An ease-of-use web application for this purpose has been missing. Results: We have developed RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly. Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html. Contact: tpommier@univ-montp2.fr; bcanback@acgt.se Supplementary information: http://www.acgt.se/RAMI/SuppInfo
Published: 2009

43. Using plant traits to explain plant–microbe relationships involved in nitrogen acquisition

Author: Marie Desclos-Theveniau, Thomas Pommier, Michael Schloter, Maxime Dumont, Servane Lemauviel-Lavenant, Philippe Laîné, Eva-Maria Kastl, Sylvain Diquélou, Amélie A. M. Cantarel, Franck Poly, Karl Grigulis, Emmanuelle Personeni, Fabrice Grassein, Sandra Lavorel, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Helmholtz-Zentrum München (HZM), 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), Chair for Soil Ecology, Technical University of Munich (TUM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Institut National de la Recherche Agronomique (INRA)-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), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), 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]), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), ANR [ANR-08-BDVA-008], MESR, FWF, NERC, BMBF, and ANR-08-BDVA-0008,VITAL,Services écologiques issus du couplage entre la diversité fonctionnelle des plantes et des microorganismes du sol dans les prairies(2008)
Subjects: 0106 biological sciences, Denitrification, Nitrogen, Microorganism, chemistry.chemical_element, Biology, Poaceae, 010603 evolutionary biology, 01 natural sciences, Grassland, Soil, plant strategy for N resource acquisition, Botany, Resource Acquisition Is Initialization, Soil Microbiology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Rhizosphere, geography, geography.geographical_feature_category, denitrification, Ecology, leaf economics spectrum, fungi, food and beverages, 04 agricultural and veterinary sciences, 15. Life on land, nitrification, Achillea, England, chemistry, Microbial population biology, plant traits, Austria, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Nitrification, France, rhizosphere
Abstract: Projet : ERA-Net BiodivERsA project VITAL; International audience; It has long been recognized that plant species and soil microorganisms are tightly linked, but understanding how different species vary in their effects on soil is currently limited. In this study, we identified those plant characteristics (identity, specific functional traits, or resource acquisition strategy) that were the best predictors of nitrification and denitrification processes. Ten plant populations representing eight species collected from three European grassland sites were chosen for their contrasting plant trait values and resource acquisition strategies. For each individual plant, leaf and root traits and the associated potential microbial activities (i.e., potential denitrification rate [DEA], maximal nitrification rate [NEA], and NH4+ affinity of the microbial community [NHScom]) were measured at two fertilization levels under controlled growth conditions. Plant traits were powerful predictors of plant-microbe interactions, but relevant plant traits differed in relation to the microbial function studied. Whereas denitrification was linked to the relative growth rate of plants, nitrification was strongly correlated to root trait characteristics (specific root length, root nitrogen concentration, and plant affinity for NH4+) linked to plant N cycling. The leaf economics spectrum (LES) that commonly serves as an indicator of resource acquisition strategies was not correlated to microbial activity. These results suggest that the LES alone is not a good predictor of microbial activity, whereas root traits appeared critical in understanding plant-microbe interactions.
Published: 2015

44. Impact of terrestrial runoff on organic matter, trophic state, and phytoplankton in a tropical, upland reservoir

Author: Thi Nguyet Minh Luu, Didier Orange, Quan Hong Trinh, Emma Rochelle-Newall, Duc Anh Trinh, Thomas Pommier, Thuy Thi Duong, Thi Phuong Quynh Le, Tien Minh Tran, Jean-Louis Janeau, Hai Sy Tran, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), LOTUS [44/2012/HD-NDT], NAFOSTED, Ministry of Science and Technology, Vietnam [104.99-2014.41], PHC Hoa Sen Lotus [23970QM], JEAI BioGEAQ, Institute of Chemistry, Vietnam Academy of Science and Technology, Vietnam, French Institut de Recherche pour le Developpement (IRD), UMR iEES-Paris, and Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)
Subjects: Freshwater & Marine Ecology, 010504 meteorology & atmospheric sciences, Floodplain, [SDV]Life Sciences [q-bio], 010501 environmental sciences, Aquatic Science, Aquatic mesocosm, Oceanography, 01 natural sciences, Mesocosm, Acacia mangium, Phytoplankton, Organic matter, Marine & Freshwater Sciences, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Water Science and Technology, 2. Zero hunger, Hydrology, chemistry.chemical_classification, geography, geography.geographical_feature_category, biology, Ecology, Aquatic ecosystem, Tropics, Life Sciences, 15. Life on land, biology.organism_classification, 6. Clean water, Limiting factor, chemistry, Vietnam, 13. Climate action, general, Environmental science, Incubation, ecology, Surface runoff
Abstract: International audience; The impact of organic matter inputs from agricultural, forest and domestic sources on aquatic processes has been considerably less studied in tropical reservoirs relative to temperate systems despite the high number of these small aquatic systems in the tropics. Here we present the results of an in situ mesocosm study that examined the impact of allochthonous organic matter on a headwater reservoir in Northern Vietnam. We examined the impact of wastewater and soils from floodplain paddies, Acacia mangium plantations and from upland slopes on the metabolic status of the reservoir. The addition of floodplain paddy soils to the reservoir water led to a rapid switch in metabolic status from net autotrophic to net heterotrophic. In contrast, the addition of wastewater in low concentrations had less impact on the metabolic status of the reservoir, reflecting the low population density in the area. The addition of floodplain paddy soils also increased phytoplankton diversity and evenness relative to the control. In summary, soils from floodplain paddies and from A. mangium plantations had the highest impact on the reservoir, with upland soils and wastewater having less of an impact. We also found that primary production in this reservoir was nitrogen limited. In order to avoid accelerating the impact of runoff on the reservoir, future management options should perhaps focus on minimizing water and sediment runoff from upstream paddy fields and from A. mangium plantations. These results also underline the importance of studying these upland tropical water bodies that can contribute an important but, on the whole, ignored part of the global carbon balance.
Published: 2015

45. Global patterns of diversity and community structure in marine bacterioplankton

Author: Björn Canbäck, Per Lundberg, Thomas Pommier, Åke Hagström, Lasse Riemann, Kjärstin H Boström, Anders Tunlid, and Karin Simu
Subjects: education.field_of_study, Ecology, Population, Community structure, Bacterioplankton, Biology, Abundance (ecology), Genetics, Biological dispersal, Species richness, Taxonomic rank, education, Endemism, Ecology, Evolution, Behavior and Systematics
Abstract: Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.
Published: 2006

46. Biogeographic analysis of ribosomal RNA clusters from marine bacterioplankton

Author: Thomas Pommier, Åke Hagström, and Jarone Pinhassi
Subjects: Ecology, GenBank, fungi, Nucleic acid sequence, Biological dispersal, Bacterioplankton, Aquatic Science, Biology, Ribosomal RNA, Endemism, Gene, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics
Abstract: Bacterial cosmopolitanism, which has for a long time been accepted by most micro- biologists, confronts recent reports of endemic species and restricted distributions. From a marine perspective, our current knowledge is lacking global pictures of bacterioplankton distribution. Public databases storing nucleotide sequences grow daily from recurrent environmental analyses of the microbial community using the small subunit ribosomal RNA gene (SSU rDNA) sequence as a marker of bacterial occurrence. These studies significantly contribute to our understanding of the global microbial processes. To address the question of whether marine bacterioplankton are cosmopolitan, 7070 SSU rDNA sequences submitted to GenBank were analyzed for sampling information and clustered into distinct ribotypes, based on sequence similarity levels. The resulting distribution maps displayed remarkable patterns of distributions of some members of the bacterioplankton community. Despite a strong bias toward sampling sites in the northern temperate regions of the globe, specific ribotypes showed ubiquitous dispersal whereas other ribotypes showed a distribution restricted to polar regions. These results suggest that marine bacterioplankton components present unexpected global patterns of distributions, where cosmopolitanism appears as an occasional trait.
Published: 2005

47. WHEATAMIX Project : Increasing within-field wheat diversity to foster ecosystem services in the Parisian basin

Author: Vincent Allard, Bruno Andrieu, Sébastien Barot, Julie Borg, Amélie Cantarel, Céline Cervek, François Coléno, Claude Pope de Vallavieille, Dominique Descoureaux, Florence Dubs, Jerome Enjalbert, Feret, M., Nathalie Galic, Arnaud Gauffreteau, Gilet, J. D., Isabelle Goldringer, Mourad Hannachi, Houivet, G., Sophie Pin, Marie-Helene Jeuffroy, Christian Kerbiriou, Pierre Labarthe, Jean Christophe Lata, Christophe Lecarpentier, Lejars, L., Lemain, B., Stephane Lemarié, Leny, F., Xavier Le Roux, Le Viol, M., Christophe Montagnier, Audrey Niboyet, Omond, B., Piaud, S., Franck Poly, Thomas Pommier, Emmanuelle Porcher, Sébastien Saint-Jean, Sandrine Salmon, Didier Tropee, Tiphaine Vidal, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Environnement et Grandes Cultures (EGC), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD [France-Ouest]), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Chambre Régionale d'Agriculture du Centre, Sciences pour l'Action et le Développement : Activités, Produits, Territoires (SADAPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, BIOlogie et GEstion des Risques en agriculture (BIOGER), CA 41, Chambre d'Agriculture du Loir et Cher, France., Chambre d'Agriculture du Loir et Cher (CA 41), Chambre d'Agriculture de l'Indre (CA 36), Agronomie, FDGEDA Cher, Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut d'écologie et des sciences de l'environnement de Paris (IEES), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Chambre d'Agriculture du Loiret, Laboratoire d'Economie Appliquée de Grenoble (GAEL), Institut National de la Recherche Agronomique (INRA)-Université Pierre Mendès France - Grenoble 2 (UPMF), Chambre d'Agriculture de l'Eure (CA 27), Domaine expérimental de Versailles-Grignon (UEVG), Institut National de la Recherche Agronomique (INRA), Chambre d'Agriculture de la Seine et Marne, Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Laboratoire d'Economie Appliquée = Grenoble Applied Economics Laboratory (GAEL), Université Pierre Mendès France - Grenoble 2 (UPMF)-Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Environnement et Grandes Cultures ( EGC ), AgroParisTech-Institut National de la Recherche Agronomique ( INRA ), Institut de Recherche pour le Développement ( IRD [France-Ouest] ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Sciences pour l'Action et le Développement : Activités, Produits, Territoires ( SADAPT ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), Chambre d'Agriculture du Loir et Cher ( CA 41 ), Chambre d'Agriculture de l'Indre ( CA 36 ), Centre d'Ecologie et des Sciences de la COnservation ( CESCO ), Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Muséum National d'Histoire Naturelle ( MNHN ), Institut d'écologie et des sciences de l'environnement de Paris ( IEES ), Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Economie Appliquée de Grenoble ( GAEL ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Institut National de la Recherche Agronomique ( INRA ), Chambre d'Agriculture de l'Eure ( CA 27 ), Domaine expérimental de Versailles-Grignon ( UEVG ), Institut National de la Recherche Agronomique ( INRA ), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Pierre Mendès France - Grenoble 2 (UPMF)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ProdInra, Archive Ouverte, and Muséum National d'Histoire Naturelle ( MNHN ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS )
Subjects: [SDE.MCG] Environmental Sciences/Global Changes, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, [ SDE.MCG ] Environmental Sciences/Global Changes, triticum, [SDE.MCG]Environmental Sciences/Global Changes, région parisienne, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, service écosystémique, winter wheat
Abstract: WHEATAMIX Project : Increasing within-field wheat diversity to foster ecosystem services in the Parisian basin. 3. International Conference on Biodiversity and the UN Millennium Development Goals,Biodiversity and Food Security – From Trade-offs to Synergies
Published: 2014

48. Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential

Author: Patrice Got, Thomas Pommier, Tran Duc Toan, Jean-Louis Janeau, Asmaa Merroune, Pascal Jouquet, Thuy Doan Thu, Yvan Bettarel, Emma Rochelle-Newall, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), French EC2CO programme 'COMPAQUA', Institut de Recherche pour le Developpement, UMR laboratory iEES, UMR laboratory EM, PHC Hoa Sen Lotus [23970QM], and LOTUS, MOST [44/2012/HD-NDT]
Subjects: Aquatic Organisms, SOL CULTIVE, [SDV]Life Sciences [q-bio], BACTERIE, DIVERSITE SPECIFIQUE, STRUCTURE DE POPULATION, Applied Microbiology and Biotechnology, Soil leachates, Soil, Off-site effects, Dissolved organic carbon, Biochar, LESSIVAGE, MATIERE ORGANIQUE DISSOUTE, Organic Chemicals, COMPOST, Soil Microbiology, chemistry.chemical_classification, VERMICOMPOST, Ecology, Compost, Aquatic ecosystem, Community structure, Agriculture, METABOLISME, Charcoal, Viruses, VIRUS, CONSEQUENCE ECOLOGIQUE, Microbial Consortia, engineering.material, Biology, Microbiology, Civil Engineering, complex mixtures, ABONDANCE, Organic matter, 14. Life underwater, Fertilizers, LAC, BIOCHAR, Bacteria, MICROORGANISME, 15. Life on land, CARBONE ORGANIQUE, Lakes, chemistry, Metabolic potential, 13. Climate action, engineering, EROSION HYDRIQUE, Species richness, Vermicompost
Abstract: International audience; While considered as sustainable and low-cost agricultural amendments, the impacts of organic fertilizers on downstream aquatic microbial communities remain poorly documented. We investigated the quantity and quality of the dissolved organic matter leaching from agricultural soil amended with compost, vermicompost or biochar and assessed their effects on lake microbial communities, in terms of viral and bacterial abundances, community structure and metabolic potential. The addition of compost and vermicompost significantly increased the amount of dissolved organic carbon in the leachate compared to soil alone. Leachates from these additions, either with or without biochar were highly bioavailable to aquatic microbial communities, though reducing the metabolic potential of the community and harboring more specific communities. Although not affecting bacterial richness or taxonomic distributions, the specific addition of biochar affected the original lake bacterial communities resulting in a strongly different community. This could be partly explained by viral burst and converging bacterial abundances throughout the samples. These results underline the necessity to include off-site impacts of agricultural amendments when considering their cascading effect on downstream aquatic ecosystems. This article is protected by copyright. All rights reserved.
Published: 2014

49. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

Author: Catherine Baxendale, Nicolas Legay, Jean-Christophe Clément, Maxime Dumont, Cindy Arnoldi, Karl Grigulis, Thomas Pommier, Ute Krainer, Sandra Lavorel, F. Poly, Eva-Maria Kastl, Michael Schloter, Michael Bahn, Richard D. Bardgett, Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Lancaster Environment Centre, Lancaster University, Ecology, University of Innsbruck, University of Innsbruck, Helmholtz-Zentrum München ( HZM ), Faculty of Life Sciences [Manchester], University of Manchester [Manchester], Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Helmholtz-Zentrum München (HZM), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), ERA-Net BiodivERsA project VITAL (ANR-08-BDVA-008), ANR, FWF, NERC, BMBF, Austrian Science Fund (FWF) (I 242-B17), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0106 biological sciences, leaf traits, soil microbial community, Plant Science, Plant Roots, 01 natural sciences, Soil, Abundance (ecology), bacteria, Soil Microbiology, 2. Zero hunger, Abiotic component, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, Community structure, food and beverages, Biodiversity, 04 agricultural and veterinary sciences, Plants, nitrite oxidizers, Grassland, Nitrification, Phenotype, Denitrification, Oxidation-Reduction, Soil microbiology, Nitrogen, Biology, 010603 evolutionary biology, [ SDV.EE ] Life Sciences [q-bio]/Ecology, environment, nitrite reducers, Botany, Ecosystem, Relative species abundance, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, plant functional traits, denitrifiers, Plant community, Original Articles, Plant Components, Aerial, 15. Life on land, Archaea, Ammonia-oxidizing archaea, root traits, Microbial population biology, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, nutrient availability, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aims: Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.
Published: 2014

50. Evidence for biological denitrification inhibition (BDI) by plant secondary metabolites

Author: Florence Piola, Thomas Pommier, Clément Bardon, Sara Puijalon, Franck Poly, Floriant Bellvert, Noelline Tsafack, Guillaume Meiffren, Gilles Comte, Feth el Zahar Haichar, Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Écologie Végétale et Zones Humides, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés ( LEHNA ), Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), 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)-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), French national programme EC2CO-MicrobiEn, TeraNoTro, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-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)-Institut National de la Recherche Agronomique (INRA)-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)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)
Subjects: nitro- gen cycle, Denitrification, Physiology, Microorganism, Plant Weeds, Fallopia spp, Plant Science, Secondary metabolite, catechin derivates, Soil, Denitrifying bacteria, Oxygen Consumption, Pseudomonas, Botany, medicine, Anaerobiosis, Food science, Nitrogen cycle, 2. Zero hunger, Rhizosphere, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, denitrification, Molecular Structure, biology, Plant Extracts, biological inhibition, 15. Life on land, biology.organism_classification, Polygonaceae, Fallopia, Aerobiosis, Kinetics, weeds, Biological Assay, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Introduced Species, rhizosphere, secondary metabo- lites, Bacteria, medicine.drug
Abstract: International audience; Previous studies on the effect of secondary metabolites on the functioning of rhizosphere microbial communities have often focused on aspects of the nitrogen (N) cycle but have over- looked biological denitrification inhibition (BDI), which can affect plant N-nutrition. Here, we investigated the BDI by the compounds of Fallopia spp., an invasive weed shown to be associ- ated with a low potential denitrification of the soil.Fallopia spp. extracts were characterized by chromatographic analysis and were used to test the BDI effects on the metabolic and respiratory activities of denitrifying bacteria, under aerobic and anaerobic (denitrification) conditions. The BDI of Fallopia spp. extracts was tested on a complex soil community by measuring denitrification enzyme activity (DEA), substrate induced respiration (SIR), as well as abundances of denitrifiers and total bacteria.In 15 strains of denitrifying bacteria, extracts led to a greater BDI (92%) than respiration inhibition (50%). Anaerobic metabolic activity reduction was correlated with catechin concen- trations and the BDI was dose dependent. In soil, extracts reduced the DEA/SIR ratio without affecting the denitrifiers: total bacteria ratio.We show that secondary metabolite(s) from Fallopia spp. inhibit denitrification. This pro- vides new insight into plant–soil interactions and improves our understanding of a plant’s abil- ity to shape microbial soil functioning.
Published: 2014

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