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5 results on '"Erwan Delage"'

1. Disentangling temporal associations in marine microbial networks

Author

Ina Maria Deutschmann, Anders K. Krabberød, Francisco Latorre, Erwan Delage, Cèlia Marrasé, Vanessa Balagué, Josep M. Gasol, Ramon Massana, Damien Eveillard, Samuel Chaffron, Ramiro Logares, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Oslo (UiO), Laboratoire des Sciences du Numérique de Nantes (LS2N), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Instituto de Ciencias del Mar de Barcelona (ICM), European Commission, Ministerio de Economía y Competitividad (España), Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), and Centre National de la Recherche Scientifique (France)

Subjects
Ocean, Microbiology (medical), Time series, Temporal network, Association network, Microorganisms, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Plankton, Microbiology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Microbial interactions, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Conserve and sustainably use the oceans, seas and marine resources for sustainable development, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

16 pages, 4 figures, 2 tables, supplementary information https://doi.org/10.1186/s40168-023-01523-z.-- Availability of data and materials: The BBMO microbial sequence abundances (ASV tables), taxonomic classifications, environmental data including nutrients, networks, and R-Markdowns for the data analysis including commands to run eLSA and EnDED (environmentally driven-edge-detection and computing Jaccard index) are publicly available: https://github.com/InaMariaDeutschmann/TemporalNetworkBBMO. DNA sequences are publicly available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena; accession numbers PRJEB23788 for 18S rRNA genes & PRJEB38773 for 16S rRNA genes), Background: Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network. Results: A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions. Conclusions: Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems, Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This project and IMD received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 675752 (ESR2, https://www.singek.eu) to RL. RL was supported by a Ramón y Cajal fellowship (RYC-2013–12554, MINECO, Spain). This work was also supported by the projects INTERACTOMICS (CTM2015-69936-P, MINECO, Spain), MicroEcoSystems (240904, RCN, Norway), and MINIME (PID2019-105775RB-I00, AEI, Spain) to RL. FL was supported by the Spanish National Program FPI 2016 (BES-2016–076317, MICINN, Spain). SC was supported by the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant). DE and SC were supported by the H2020 project AtlantECO (award number 862923). A range of projects from the EU and the Spanish Ministry of Science funded the data collection and ancillary analyses at the BBMO. We acknowledge funding of the Spanish government through the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000,928-S)

Published
2023

2. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Author

Ahmed A, Zayed, James M, Wainaina, Guillermo, Dominguez-Huerta, Eric, Pelletier, Jiarong, Guo, Mohamed, Mohssen, Funing, Tian, Akbar Adjie, Pratama, Benjamin, Bolduc, Olivier, Zablocki, Dylan, Cronin, Lindsey, Solden, Erwan, Delage, Adriana, Alberti, Jean-Marc, Aury, Quentin, Carradec, Corinne, da Silva, Karine, Labadie, Julie, Poulain, Hans-Joachim, Ruscheweyh, Guillem, Salazar, Elan, Shatoff, Ralf, Bundschuh, Kurt, Fredrick, Laura S, Kubatko, Samuel, Chaffron, Alexander I, Culley, Shinichi, Sunagawa, Jens H, Kuhn, Patrick, Wincker, Matthew B, Sullivan, Silvia G, Acinas, Marcel, Babin, Peer, Bork, Emmanuel, Boss, Chris, Bowler, Guy, Cochrane, Colomban, de Vargas, Gabriel, Gorsky, Lionel, Guidi, Nigel, Grimsley, Pascal, Hingamp, Daniele, Iudicone, Olivier, Jaillon, Stefanie, Kandels, Lee, Karp-Boss, Eric, Karsenti, Fabrice, Not, Hiroyuki, Ogata, Nicole, Poulton, Stéphane, Pesant, Christian, Sardet, Sabrinia, Speich, Lars, Stemmann, Shinichi, Sungawa, Department of Microbiology [Columbus], Ohio State University [Columbus] (OSU), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Physics, The Ohio State University, Department of Statistics, the Ohio State University Columbus, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Université Laval [Québec] (ULaval), Institute of Microbiology, Department of Biology, ETH Zurich, Institute of Microbiology, Department of Microbiology, The Ohio state university, Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, and Nantes Université (Nantes Univ)

Subjects
Multidisciplinary, Virome, Oceans and Seas, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Genome, Viral, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biological Evolution, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDE]Environmental Sciences, Viruses, RNA, RNA Viruses, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem, Phylogeny, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth’s RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. “Species”-rank abundance determination revealed that viruses of the new phyla “ Taraviricota ,” a missing link in early RNA virus evolution, and “ Arctiviricota ” are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.

Published
2022

3. Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic

Author

Seaver Wang, Erwan Delage, Nicolas Cassar, Aridane G. González, Weiyi Tang, Hannah Whitby, Scott M. Gifford, Hélène Planquette, Damien Eveillard, Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Interdisciplinary Graduate School for the Blue planet, ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (COMBI), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Tara Oceans-GOSEE (FR2022)

Subjects
0301 basic medicine, Science, 030106 microbiology, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Biology, Article, Haptophyte, 03 medical and health sciences, Microbial ecology, Element cycles, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Marine biology, Multidisciplinary, Ecology, 15. Life on land, Plankton, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030104 developmental biology, Taxon, Microbial population biology, 13. Climate action, Nitrogen fixation, Medicine, Diazotroph, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.

Published
2021

4. Environmental vulnerability of the global ocean plankton community interactome

Author

Ahmed A. Zayed, Silvia G. Acinas, Pedro C. Junger, Patrick Wincker, Damien Vintache, Charlotte Nef, Daniele Iudicone, Chris Bowler, Lee Karp-Boss, Connie Lovejoy, Samuel Chaffron, Olivier Jaillon, Eric Karsenti, Marcel Babin, Marko Budinich, Mathieu Ardyna, Alison E. Murray, Hugo Sarmento, Pierre E. Galand, Erwan Delage, Matthew B. Sullivan, C. de Vargas, Nelly Henry, Damien Eveillard, Combinatoire et Bioinformatique (COMBI), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Tara Oceans-GOSEE (FR2022)

Subjects
0303 health sciences, Environmental change, 030306 microbiology, Ecology, Biome, fungi, Community structure, Climate change, Westerlies, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], 15. Life on land, Plankton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Food web, Environmental niche modelling, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, 13. Climate action, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Environmental science, 14. Life underwater, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030304 developmental biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles, and help regulate climate. Though global surveys are starting to reveal ecological drivers underlying planktonic community structure, and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network – the community interactome – and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar), and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change, and forecasted most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios, while identifying plausible plankton bioindicators for ocean monitoring of climate change.

Published
2021

5. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

Author

Alejandro Maass, Beatriz Fernández-Gómez, Pablo Cabrera, Mauricio González, Jonathan Maldonado, Verónica Cambiazo, Alexis Gaete, Sergio A. Navarrete, Claudio Latorre, Dante Travisany, Damien Eveillard, Erwan Delage, Audrey Bihouée, Francisca P. Díaz, Rodrigo A. Gutiérrez, Mauricio Latorre, Dinka Mandakovic, Géraldine Jean, Claudia Rojas, Millennium Nucleus in Plant Cell Biology and Plant Biotechnology Center, Universidad Andrés Bello [Santiago] (UNAB), Universidad de Santiago de Chile [Santiago] (USACH), Center for Mathematical Modelling - Centro de Modelamiento Matematico [Santiago] (CMM), Universidad de Chile = University of Chile [Santiago] (UCHILE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (COMBI), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Neurology, University of Miami Leonard M. Miller School of Medicine (UMMSM), Laboratorio de Bioinformática y Expresión Génica, Pontifical Catholic University of Chile, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, FONDAP Center for Genome Regulation (CGR), Centre de Modélisation Mathématique / Centro de Modelamiento Matemático (CMM), Centre National de la Recherche Scientifique (CNRS), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)

Subjects
0301 basic medicine, media_common.quotation_subject, Ecology (disciplines), [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], 030106 microbiology, lcsh:Medicine, Biology, Bacterial Physiological Phenomena, complex mixtures, Environmental stress, Article, 03 medical and health sciences, Taxonomic composition, Soil functions, Stress, Physiological, RNA, Ribosomal, 16S, lcsh:Science, Soil Microbiology, media_common, Multidisciplinary, Ecology, Microbiota, lcsh:R, Co-occurrence, 15. Life on land, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Archaea, 030104 developmental biology, Microbial population biology, Soil water, lcsh:Q, Psychological resilience, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.

Published
2017

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