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

Author

Li, Mei, Hu, Jie, Wei, Zhong, Jousset, Alexandre, Pommier, Thomas, Yu, Xiangyang, Xu, Yangchun, Shen, Qirong, Li, Mei, Hu, Jie, Wei, Zhong, Jousset, Alexandre, Pommier, Thomas, Yu, Xiangyang, Xu, Yangchun, and Shen, Qirong

Abstract

In nature, diverse microorganisms do not act as individuals but rather interact and communicate with one another in a dynamically changing microbial community, they are essential for maintaining the Earth's biosphere and for the survival of plants and animals as they contribute to nearly all biogeochemical cycles on earth. However, studying microbial populations directly in their natural environment poses significant challenges due to their vast population size and complex interaction network. This difficulty hampers our ability to predict the behavior of microbial communities in nature, thereby limiting our understanding of the functionality of microorganisms in the natural environmental systems and developing and utilizing microbial resources. Further, the inherent complexity of the natural microbiota makes it immensely challenging to establish causality and, subsequently, dissect mechanisms. One emerging strategy to tackle the aforementioned challenge is to use simplified, synthetic microbial communities (SynComs).

Published
2024

3. Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

Author

Le Roux, Xavier, Bouskill, Nicholas J, Niboyet, Audrey, Barthes, Laure, Dijkstra, Paul, Field, Chris B, Hungate, Bruce A, Lerondelle, Catherine, Pommier, Thomas, Tang, Jinyun, Terada, Akihiko, Tourna, Maria, and Poly, Franck

Subjects
Biological Sciences, Ecology, Life Below Water, bacterial functional traits, elevated CO2, nitrifiers, nitrogen fertilisation, trait-based modeling, Environmental Science and Management, Soil Sciences, Microbiology, Medical microbiology
Abstract

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 CO2 concentration, 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

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

Author

Li, Mei, Hu, Jie, Wei, Zhong, Jousset, Alexandre, Pommier, Thomas, Yu, Xiangyang, Xu, Yangchun, and Shen, Qirong

Subjects
MICROBIAL communities, BIOTIC communities, SOILS, PLANT competition, TOLERATION, ENTEROTYPES, SOIL biodiversity, MICROBIAL physiology
Abstract

This document explores the use of synthetic microbial communities (SynComs) to improve soil health and resilience. SynComs are artificial combinations of microorganisms that can enhance soil fertility, pollutant removal, and soil-borne disease suppression. The document emphasizes the importance of microbial interactions and biodiversity in designing efficient SynComs. It also calls for further research to develop more complex SynComs and establish predictive models for soil community structure and ecological function. The authors declare no conflict of interest. [Extracted from the article]

Published
2024
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5. Larval density in the invasive Drosophila suzukii: Immediate and delayed effects on life‐history traits.

Author

Reyes‐Ramírez, Alicia, Belgaidi, Zaïnab, Gibert, Patricia, Pommier, Thomas, Siberchicot, Aurélie, Mouton, Laurence, and Desouhant, Emmanuel

Subjects
LIFE history theory, DROSOPHILA suzukii, POPULATION dynamics, DENSITY, PRODUCTION losses, AGRICULTURAL productivity
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. [ABSTRACT FROM AUTHOR]

Published
2023
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9. Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions

Author

Li, Mei, Pommier, Thomas, Yin, Yue, Cao, Wenhui, Zhang, Xiaohui, Hu, Jie, Hautier, Yann, Yang, Tianjie, Xu, Yangchun, Shen, Qirong, Kowalchuk, George A, Jousset, Alexandre, Wei, Zhong, Ecology and Biodiversity, Sub Ecology and Biodiversity, Nanjing Agricultural University (NAU), Utrecht University [Utrecht], 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), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Ecology and Biodiversity, and Sub Ecology and Biodiversity

Subjects
Taverne, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microbiology, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here we use Resource Availability (RA) as model parameter altering resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.

Published
2022

10. <i>Escherichia coli</i> concentration, multiscale monitoring over the decade 2011–2021 in the Mekong River basin, Lao PDR

Author

Boithias, Laurie, primary, Ribolzi, Olivier, additional, Rochelle-Newall, Emma, additional, Thammahacksa, Chanthanousone, additional, Nakhle, Paty, additional, Soulileuth, Bounsamay, additional, Pando-Bahuon, Anne, additional, Latsachack, Keooudone, additional, Silvera, Norbert, additional, Sounyafong, Phabvilay, additional, Xayyathip, Khampaseuth, additional, Zimmermann, Rosalie, additional, Rattanavong, Sayaphet, additional, Oliva, Priscia, additional, Pommier, Thomas, additional, Evrard, Olivier, additional, Huon, Sylvain, additional, Causse, Jean, additional, Henry-des-Tureaux, Thierry, additional, Sengtaheuanghoung, Oloth, additional, Sipaseuth, Nivong, additional, and Pierret, Alain, additional

Published
2022
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13. Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition

Author

Ecology and Biodiversity, Sub Ecology and Biodiversity, Li, Mei, Pommier, Thomas, Yin, Yue, Wang, Jianing, Gu, Shaohua, Jousset, Alexandre, Keuskamp, Joost, Wang, Honggui, Wei, Zhong, Xu, Yangchun, Shen, Qirong, Kowalchuk, George A., Ecology and Biodiversity, Sub Ecology and Biodiversity, Li, Mei, Pommier, Thomas, Yin, Yue, Wang, Jianing, Gu, Shaohua, Jousset, Alexandre, Keuskamp, Joost, Wang, Honggui, Wei, Zhong, Xu, Yangchun, Shen, Qirong, and Kowalchuk, George A.

Published
2022

14. Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions

Author

Ecology and Biodiversity, Sub Ecology and Biodiversity, Li, Mei, Pommier, Thomas, Yin, Yue, Cao, Wenhui, Zhang, Xiaohui, Hu, Jie, Hautier, Yann, Yang, Tianjie, Xu, Yangchun, Shen, Qirong, Kowalchuk, George A, Jousset, Alexandre, Wei, Zhong, Ecology and Biodiversity, Sub Ecology and Biodiversity, Li, Mei, Pommier, Thomas, Yin, Yue, Cao, Wenhui, Zhang, Xiaohui, Hu, Jie, Hautier, Yann, Yang, Tianjie, Xu, Yangchun, Shen, Qirong, Kowalchuk, George A, Jousset, Alexandre, and Wei, Zhong

Published
2022

15. Microbiome analysis in Lascaux Cave in relation to black stain alterations of rock surfaces and collembola.

Author

Alonso, Lise, Pommier, Thomas, Simon, Laurent, Maucourt, Flavien, Doré, Jeanne, Dubost, Audrey, Trân Van, Van, Minard, Guillaume, Valiente Moro, Claire, Douady, Christophe J., and Moënne‐Loccoz, Yvan

Subjects
*COLLEMBOLA, *CAVES, *ISOTOPIC analysis, *BLACK children, *FUNGAL growth, *CANDIDA albicans, *CANDIDA
Abstract

Anthropization of Palaeolithic caves open for tourism may favour collembola invasion and result in the formation of black stains attributed to pigmented fungi. However, ecological processes underpinning black stain formation are not fully understood. Here, we tested the hypotheses that black stains from the Apse room of Lascaux Cave display a specific microbiota enriched in pigmented fungi, and that collembola thriving on the stains have the potential to consume and disseminate these black fungi. Metabarcoding showed that the microbiota of black stains and neighbouring unstained parts strongly differed, with in black stains a higher prevalence of Ochroconis and other pigmented fungi and the strong regression of Pseudomonas bacteria (whose isolates inhibited in vitro the growth of pigmented fungi). Isotopic analyses indicated that Folsomia candida collembola thriving on stains could feed on black stain in situ and assimilate the pigmented fungi they were fed with in vitro. They could carry these fungi and disseminate them when tested with complex black stains from Lascaux. This shows that black stain formation is linked to the development of pigmented fungi, which coincides with the elimination of antagonistic pseudomonads, and points towards a key role of F. candida collembola in the dynamics of pigmented fungi. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Escherichia coli concentration, multiscale monitoring over the decade 2011-2021 in the Mekong River basin, Lao PDR

Author

Boithias, Laurie, Ribolzi, Olivier, Rochelle-Newall, Emma, Thammahacksa, Chanthanousone, Nakhle, Paty, Soulileuth, Bounsamay, Pando-Bahuon, Anne, Latsachack, Keooudone, Silvera, Norbert, Sounyafong, Phabvilay, Xayyathip, Khampaseuth, Zimmermann, Rosalie, Rattanavong, Sayaphet, Oliva, Priscia, Pommier, Thomas, Evrard, Olivier, Huon, Sylvain, Causse, Jean, Henry-Des-Tureaux, Thierry, Sengtaheuanghoung, Oloth, Sipaseuth, Nivong, Pierret, Alain, 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), 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), Université de Lyon, 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), École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Agricultural Land Management [Vientiane] (DALaM), Ministry of Agriculture and Forestry of Laos, This research has been supported by the Consultative Group on International Agricultural Research (CGIAR, Humidtropics program, ECOFILTER program, 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), 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), and Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
[SDU]Sciences of the Universe [physics], [SDV]Life Sciences [q-bio], [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Panoply
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

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

Author

Cantarel, Amélie, Allard, Vincent, Andrieu, Bruno, Barot, Sébastien, Enjalbert, Jérôme, Gervaix, Jonathan, Goldringer, Isabelle, Pommier, Thomas, Saint-Jean, Sébastien, Le Roux, Xavier, Cantarel, Amélie, Allard, Vincent, Andrieu, Bruno, Barot, Sébastien, Enjalbert, Jérôme, Gervaix, Jonathan, Goldringer, Isabelle, Pommier, Thomas, Saint-Jean, Sébastien, and Le Roux, Xavier

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

21. Experimental niche evolution alters the strength of the diversity-productivity relationship

Author

Gravel, Dominique, Bell, Thomas, Barbera, Claire, Bouvier, Thierry, Pommier, Thomas, Venail, Patrick, and Mouquet, Nicolas

Subjects
Marine bacteria -- Research, Evolution -- Research, Ecosystems -- Research, Biological diversity -- Research, Niche (Ecology) -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The relationship between biodiversity and ecosystem functioning (BEF) has become a cornerstone of community and ecosystem ecology (1-3) and an essential criterion for making decisions in conservation biology and policy planning (4,5). It has recently been proposed that evolutionary history should influence the BEF relationship because it determines species traits and, thus, species' ability to exploit resources (6,7). Here we test this hypothesis by combining experimental evolution with a BEF experiment. We isolated 20 bacterial strains from a marine environment and evolved each to be generalists or specialists (8). We then tested the effect of evolutionary history on the strength of the BEF relationship with assemblages of 1 to 20 species constructed from the specialists, generalists and ancestors (9). Assemblages of generalists were more productive on average because of their superior ability to exploit the environmental heterogeneity (10). The slope of the BEF relationship was, however, stronger for the specialist assemblages because of enhanced niche complementarity. These results show how the BEF relationship depends critically on the legacy of past evolutionary events., Two fundamental ecological mechanisms can generate positive BEF relationships (11,12). First, species may occupy complementary ecological niches, for example by feeding on different resources. In communities of complementary species, more [...]

Published
2011
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22. Siderophore interactions drive the ability of Pseudomonasspp.consortia to protect tomato against Ralstonia solanacearum

Author

Shao, Zhengying, Gu, Shaohua, Zhang, Xiaoni, Xue, Jiao, Yan, Tao, Guo, Saisai, Pommier, Thomas, Jousset, Alexandre, Yang, Tianjie, Xu, Yangchun, Shen, Qirong, and Wei, Zhong

Abstract

The soil-borne bacterial pathogen Ralstonia solanacearumcauses significant losses in Solanaceae crop production worldwide, including tomato, potato, and eggplant. To efficiently prevent outbreaks, it is essential to understand the complex interactions between pathogens and the microbiome. One promising mechanism for enhancing microbiome functionality is siderophore-mediated competition, which is shaped by the low iron availability in the rhizosphere. This study explores the critical role of iron competition in determining microbiome functionality and its potential for designing high-performance microbiome engineering strategies. We investigated the impact of siderophore-mediated interactions on the efficacy of Pseudomonas spp.consortia in suppressing R. solanacearum, both in vitroand in vivo. Our findings show that siderophore production significantly enhances the inhibitory effects of Pseudomonasstrains on pathogen growth, while other metabolites are less effective under iron-limited conditions. Moreover, siderophores play a crucial role in shaping interactions within the consortia, ultimately determining the level of protection against bacterial wilt disease. This study highlights the key role of siderophores in mediating consortium interactions and their impact on tomato health. Our results also emphasize the limited efficacy of other secondary metabolites in iron-limited environments, underscoring the importance of siderophore-mediated competition in maintaining tomato health and suppressing disease.

Published
2024
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24. Rhizosphere immunity: targeting the underground for sustainable plant health management

Author

Wei, Zhong, Friman, Ville-petri, Pommier, Thomas, Geisen, Stefan, Jousset, Alexandre, Shen, Qirong, Ecology and Biodiversity, Sub Ecology and Biodiversity, 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), Ecology and Biodiversity, and Sub Ecology and Biodiversity

Subjects
0106 biological sciences, rhizosphere|soil microbiome|plant immunity|microbial ecology|plant health|soilborne pathogens, [SDV]Life Sciences [q-bio], Plant health, microbial ecology, 01 natural sciences, Microbial ecology, Soilmicrobiome, 03 medical and health sciences, Plant immunity, Immunity, soil microbiome, Microbiome, lcsh:Agriculture (General), soilborne pathogens, Environmental planning, Laboratorium voor Nematologie, Ecosystem level, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Rhizosphere, General Veterinary, Health management system, business.industry, fungi, Common ground, food and beverages, 15. Life on land, PE&RC, Soilborne pathogens, lcsh:S1-972, Disease control, 13. Climate action, Agriculture, [SDE]Environmental Sciences, plant immunity, Laboratory of Nematology, rhizosphere, plant health, General Agricultural and Biological Sciences, business, 010606 plant biology & botany, Biotechnology
Abstract

International audience; Managing plant health is a great challenge for modern food production and is further complicated by the lack of common ground between the many disciplines involved in disease control. Here we present the concept of rhizosphere immunity, in which plant health is considered as an ecosystem level property emerging from networks of interactions between plants, microbiota and the surrounding soil matrix. These interactions can potentially extend the innate plant immune system to a point where the rhizosphere immunity can fulfil all four core functions of a full immune system: pathogen prevention, recognition, response and homeostasis. We suggest that considering plant health from a meta-organism perspective will help in developing multidisciplinary pathogen management strategies that focus on steering the whole plant-microbe-soil networks instead of individual components. This might be achieved by bringing together the latest discoveries in phytopathology, microbiome research, soil science and agronomy to pave the way toward more sustainable and productive agriculture.

Published
2020

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

Author

Boithias, Laurie, Ribolzi, Olivier, Rochelle-Newall, Emma, Thammahacksa, Chanthanousone, Nakhle, Paty, Soulileuth, Bounsamay, Pando-Bahuon, Anne, Latsachack, Keooudone, Silvera, Norbert, Sounyafong, Phabvilay, Xayyathip, Khampaseuth, Zimmermann, Rosalie, Rattanavong, Sayaphet, Oliva, Priscia, Pommier, Thomas, Evrard, Olivier, Huon, Sylvain, Causse, Jean, Henry-Des-Tureaux, Thierry, and Sengtaheuanghoung, Oloth

Subjects
ESCHERICHIA coli, OXIDATION-reduction potential, BACTERIAL cell surfaces, SUSPENDED sediments, COMPOSITION of sediments, OXYGEN saturation
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. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Facilitation promotes invasions in plant-associated microbial communities

Author

Sub Ecology and Biodiversity, Ecology and Biodiversity, Li, Mei, Wei, Zhong, Wang, Jianing, Jousset, Alexandre, Friman, Ville-Petri, Xu, Yangchun, Shen, Qirong, Pommier, Thomas, Sub Ecology and Biodiversity, Ecology and Biodiversity, Li, Mei, Wei, Zhong, Wang, Jianing, Jousset, Alexandre, Friman, Ville-Petri, Xu, Yangchun, Shen, Qirong, and Pommier, Thomas

Published
2019

31. Indirect reduction of Ralstonia solanacearumvia pathogen helper inhibition

Author

Li, Mei, Pommier, Thomas, Yin, Yue, Wang, Jianing, Gu, Shaohua, Jousset, Alexandre, Keuskamp, Joost, Wang, Honggui, Wei, Zhong, Xu, Yangchun, Shen, Qirong, and Kowalchuk, George A.

Abstract

The rhizosphere microbiome forms a first line of defense against soilborne pathogens. To date, most microbiome enhancement strategies have relied on bioaugmentation with antagonistic microorganisms that directly inhibit pathogens. Previous studies have shown that some root-associated bacteria are able to facilitate pathogen growth. We therefore hypothesized that inhibiting such pathogen helpers may help reduce pathogen densities. We examined tripartite interactions between a model pathogen, Ralstonia solanacearum, two model helper strains and a collection of 46 bacterial isolates recovered from the tomato rhizosphere. This system allowed us to examine the importance of direct (effects of rhizobacteria on pathogen growth) and indirect (effects of rhizobacteria on helper growth) pathways affecting pathogen growth. We found that the interaction between rhizosphere isolates and the helper strains was the major determinant of pathogen suppression both in vitro and in vivo. We therefore propose that controlling microbiome composition to prevent the growth of pathogen helpers may become part of sustainable strategies for pathogen control.

Published
2022
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32. Additional file 6: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Author

Alonso, Lise, Creuzé-Des-Châtelliers, Charline, Trabac, Théo, Dubost, Audrey, Moënne-Loccoz, Yvan, and Pommier, Thomas

Abstract

Figure S3. The co-occurrence networks of bacteria and fungi based on 16S rRNA and ITS MiSeq Illumina sequences. Connections materialize strong (Spearman’s ǀρǀ > 0.6 for banks and Spearman’s ǀρǀ > 0.75 for inclined planes) and significant (P

Published
2018
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33. Additional file 2: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Author

Alonso, Lise, Creuzé-Des-Châtelliers, Charline, Trabac, Théo, Dubost, Audrey, Moënne-Loccoz, Yvan, and Pommier, Thomas

Abstract

Figure S1. Biodiversity of microbial communities in the passage according to sampling time. Biodiversity was considered using Chao1 richness index, Shannon H′ index and Simpson evenness index. Variations were not significant for Chao1 (P = 0.15) and Shannon H′ (P = 0.29) (ANOVA), and for Simpson 1-D (P > 0.05) (Wilcoxon test). (PDF 437 kb)

Published
2018
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34. Additional file 1: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Author

Alonso, Lise, Creuzé-Des-Châtelliers, Charline, Trabac, Théo, Dubost, Audrey, Moënne-Loccoz, Yvan, and Pommier, Thomas

Abstract

Figure S2. Bacterial and micro-eukaryotic abundances according to time (along with mean temperature and CO2 concentration) (A) or mineral substrate (B). Abundance data are shown as mean log number of 16S rRNA and 18S rRNA genes copies ± standard errors. Quantitative PCR analysis was performed in duplicate. The letters represented the statistical differences between histograms. (PDF 153 kb)

Published
2018
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35. Additional file 5: of Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

Author

Alonso, Lise, Creuzé-Des-Châtelliers, Charline, Trabac, Théo, Dubost, Audrey, Moënne-Loccoz, Yvan, and Pommier, Thomas

Abstract

Figure S5. ITS read counts affiliated to Ochroconis lascauxensis according to relative abundance of rpoB gene count assessed by quantitative PCR. Samples taken inside (crosses) or outside (circles) stains originated from banks (blue), inclined planes (red) and soil (green). Linear correlations for stained and unstained samples are indicated in dashed or plain lines, respectively. (PDF 150 kb)

Published
2018
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38. Plant functional trait variability and trait syndromes among wheat varieties: the footprint of artificial selection.

Author

Cantarel, Amélie A M, Allard, Vincent, Andrieu, Bruno, Barot, Sébastien, Enjalbert, Jérôme, Gervaix, Jonathan, Goldringer, Isabelle, Pommier, Thomas, Saint-Jean, Sébastien, and Roux, Xavier Le

Subjects
PLANT species, CULTIVARS, WILD plants, SYNDROMES, MODERN history
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. [ABSTRACT FROM AUTHOR]

Published
2021
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39. The added value of including key microbial traits to determine nitrogen-related ecosystem services in managed grasslands

Author

Pommier, Thomas, Amelie, Cantarel, Grigulis, K, Lavorel, Sandra, Legay, N, Baxendale, Catherine Louise, Bardgett, Richard David, Bahn, Michael, Poly, Franck, Clément, J-C, Pommier, Thomas, Amelie, Cantarel, Grigulis, K, Lavorel, Sandra, Legay, N, Baxendale, Catherine Louise, Bardgett, Richard David, Bahn, Michael, Poly, Franck, and Clément, J-C

Abstract

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 micro-organisms in the evaluation of ES. 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. 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 (math formula) or nitrate (math formula) 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 math formula–N was negatively correlated to the fungi/bacteria ratio, with the exception of the French site. 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

40. Carbon and nitrogen limitation explains the contrasting responses of rhizospheric N-cycling microbial communities to maize inoculation by Azospirillum lipoferum CRT1

Author

Florio, Alessandro, Pommier, Thomas, Gervaix, Jonathan, Bréfort, Caroline, Berard, Annette, Le Roux, Xavier, 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 National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), European Geosciences Union (EGU). Vienne, AUT., and ProdInra, Archive Ouverte

Subjects
[SDV] Life Sciences [q-bio], dénitrification, communauté microbienne, absorption racinaire, maïs, [SDV]Life Sciences [q-bio], inoculation, microbial community, root absorption, maize, stimulation, rhizosphère, nitrification
Abstract

Carbon and nitrogen limitation explains the contrasting responses of rhizospheric N-cycling microbial communities to maize inoculation by Azospirillum lipoferum CRT1. EGU 2017, European Geophysical Union General Assembly 2017

Published
2017

41. Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities

Author

FLORIO, Alessandro, Pommier, Thomas, Gervaix, Jonathan, Berard, Annette, Le Roux, Xavier, 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), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AZODURE project (ANR-12-AGRO-0008), 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 ), Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes ( EMMAH ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), 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
[ SDV ] Life Sciences [q-bio], Nitrogen, maïs, rhizobactérie promotrice de la croissance, azospirillum, Science, [SDV]Life Sciences [q-bio], technique d'inoculation, maize, Nitrification, Plant Roots, Zea mays, Carbon, Article, Soil, Denitrification, Microbial Interactions, Medicine, Nitrogen Oxides, bactérie nitrifiante, Soil Microbiology
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

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

Author

Legay, Nicolas, primary, Lavorel, Sandra, additional, Baxendale, Catherine, additional, Krainer, Ute, additional, Bahn, Michael, additional, Binet, Marie‐Noëlle, additional, Cantarel, Amélie A. M., additional, Colace, Marie‐Pascale, additional, Foulquier, Arnaud, additional, Kastl, Eva‐Maria, additional, Grigulis, Karl, additional, Mouhamadou, Bello, additional, Poly, Franck, additional, Pommier, Thomas, additional, Schloter, Michael, additional, Clément, Jean‐Christophe, additional, and Bardgett, Richard D., additional

Published
2016
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46. Validation of CFD simulation with PIV measurements for Open Rotor Noise Predictions

Author

POMMIER, THOMAS JEAN BERNARD

Subjects
Teknik och teknologier, Engineering and Technology
Abstract

CROR means Contra--‐Rotating Open Rotor. Its efficiency is better than usual in aeronautics thanks to its geometry (open rotor and thus high bypass ratio) but also by adding a second rotor. Indeed it enables to recover the swirl loss of the first rotor. However, this engine is rarely used today in civil aviation for acoustic reasons. Studies are carried out in order to reduce its noise emissions. One of its biggest sources is the interaction between both rotors with the impact of first rotor wake on second rotor blades. This report focuses on the aerodynamics of this wake. The goal is to quantify CFD uncertainties comparing them to wind tunnel testing results. PIV (Particle Image Velocimetry) and hot--‐wire measurements were carried out by a team located in Bremen, Germany. They obtained flow mean and turbulent velocities. I was in charge of CFD simulations, processed with RANS equations and two turbulence models. But most of my work was to post--‐process both CFD and wind tunnel testing results with Python Programming and then compare them. In addition, other effects on these mean and turbulent velocities are studied in this report: test variability, blade--‐to--‐blade variability, transition effect and rpm effect.

Published
2015

47. Facilitation promotes invasions in plant‐associated microbial communities.

Author

Li, Mei, Wei, Zhong, Wang, Jianing, Jousset, Alexandre, Friman, Ville‐Petri, Xu, Yangchun, Shen, Qirong, Pommier, Thomas, and Kloronomos, John

Subjects
INVASIVE plants, MICROBIAL communities, PLANT communities, BIODIVERSITY, ECOLOGY
Abstract

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. [ABSTRACT FROM AUTHOR]

Published
2019
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48. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species

Author

Hagstrom, Ake, Pommier, Thomas, Rohwer, Forest, Simu, Karin, Stolte, Willem, Svensson, Dominika, and Zweifel, Ulla Li

Subjects
Marine bacteria -- Identification and classification, DNA -- Analysis, Nucleotide sequence -- Analysis, Plankton research -- Analysis, Biological sciences
Abstract

Analysis of the 16S ribosomal DNA sequences from the marine bacterioplankton reveals 1,117 ribotypes of which 609 are from uncultured environmental clones and 508 from cultured bacteria.

Published
2002

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

Author

Trinh, Duc Anh, Luu, Thi Nguyet Minh, Trinh, Quan Hong, Tran, Hai Sy, Tran, Tien Minh, Le, Thi Phuong Quynh, Duong, Thuy Thi, Orange, Didier, Janeau, Jean Louis, Pommier, Thomas, Rochelle-Newall, Emma, Trinh, Duc Anh, Luu, Thi Nguyet Minh, Trinh, Quan Hong, Tran, Hai Sy, Tran, Tien Minh, Le, Thi Phuong Quynh, Duong, Thuy Thi, Orange, Didier, Janeau, Jean Louis, Pommier, Thomas, and Rochelle-Newall, Emma

Abstract

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
2016
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50. Four years of experimental climate change modifies the community structure of denitrifiers and the related microbial drivers of N2O fluxes in an upland grassland ecosystem

Author

Pommier, Thomas, Cantarel, Amélie, Bloor, Juliette, Poly, Franck, Ecologie Mircobienne, Institut National de la Recherche Agronomique (INRA), 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), UR 0874 Unité de recherche sur l'Ecosystème Prairial, and Institut National de la Recherche Agronomique (INRA)-Unité de recherche sur l'Ecosystème Prairial (UREP)-Ecologie des Forêts, Prairies et milieux Aquatiques (EFPA)

Subjects
changement climatique, [SDE.MCG]Environmental Sciences/Global Changes, n2o, prairie, gaz à effet de serre, Milieux et Changements globaux, écosystème prairial
Abstract

Emissions of the trace gas nitrous oxide (N 2 O) play an important role for the greenhouse effect and stratospheric ozone depletion, but the impacts of climate change on community structure of denitrifiers and the underlying microbial drivers of N 2 O fluxes remain unclear. The aim of this study was to determine the effects of sustained climate change on field community structure of denitrifiers and associated N 2 O fluxes, microbial enzymatic activities, and microbial population abundance in an extensively managed, upland grassland. We simulated global warming effect by exposing a grassland for 4 years to elevated atmospheric CO 2 (+200 ppm), elevated temperature (+3.5 °C) and reduction of summer precipitations (-20%) as part of a long-term, multifactor climate change experiment. While recording N 2 O fluxes, potential nitrification and denitrification, microbial population size involved in these processes, we assessed the community structure of nitrite reducers ( nir K) that perform the first step of denitrification. Our results showed that specific lineages of nir K denitrifier communities responded significantly to temperature. In addition, nir K community composition showed significant changes in response to drought. Both warming and simultaneous application of warming, summer drought and elevated CO 2 had a positive effect on N 2 O fluxes, nitrification, N 2 O release by denitrification and the population size of N 2 O reducers and NH 4 oxidizers. In situ N 2 O fluxes showed a stronger correlation with microbial population size under warmed conditions compared with the control site. Path analysis explained more than 85% of in situ N 2 O fluxes variance by specific denitrifying lineages, soil temperature and denitrification activity. Overall, our study underlines that climate-induced changes in grassland N 2 O emissions reflect climate-induced changes in microbial community structure, with a potential selection of more adapted types. These in turn may modify microbial processes.

Published
2013

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