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1. Genome-scale community modelling reveals conserved metabolic cross-feedings in epipelagic bacterioplankton communities

Author

Nils Giordano, Marinna Gaudin, Camille Trottier, Erwan Delage, Charlotte Nef, Chris Bowler, and Samuel Chaffron

Subjects
Science
Abstract

Abstract Marine microorganisms form complex communities of interacting organisms that influence central ecosystem functions in the ocean such as primary production and nutrient cycling. Identifying the mechanisms controlling their assembly and activities is a major challenge in microbial ecology. Here, we integrated Tara Oceans meta-omics data to predict genome-scale community interactions within prokaryotic assemblages in the euphotic ocean. A global genome-resolved co-activity network revealed a significant number of inter-lineage associations across diverse phylogenetic distances. Identified co-active communities include species displaying smaller genomes but encoding a higher potential for quorum sensing, biofilm formation, and secondary metabolism. Community metabolic modelling reveals a higher potential for interaction within co-active communities and points towards conserved metabolic cross-feedings, in particular of specific amino acids and group B vitamins. Our integrated ecological and metabolic modelling approach suggests that genome streamlining and metabolic auxotrophies may act as joint mechanisms shaping bacterioplankton community assembly in the global ocean surface.

Published
2024
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2. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean

Author

Ina M. Deutschmann, Erwan Delage, Caterina R. Giner, Marta Sebastián, Julie Poulain, Javier Arístegui, Carlos M. Duarte, Silvia G. Acinas, Ramon Massana, Josep M. Gasol, Damien Eveillard, Samuel Chaffron, and Ramiro Logares

Subjects
Science
Abstract

Abstract Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.

Published
2024
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3. 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, and Ramiro Logares

Subjects
Association network, Temporal network, Time series, Microbial interactions, Microorganisms, Ocean, Microbial ecology, QR100-130
Abstract

Abstract 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. Video Abstract

Published
2023
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4. Faeces‐derived extracellular vesicles participate in the onset of barrier dysfunction leading to liver diseases

Author

Lionel Fizanne, Alexandre Villard, Nadia Benabbou, Sylvain Recoquillon, Raffaella Soleti, Erwan Delage, Mireille Wertheimer, Xavier Vidal‐Gómez, Thibauld Oullier, Samuel Chaffron, M. Carmen Martínez, Michel Neunlist, Jérôme Boursier, and Ramaroson Andriantsitohaina

Subjects
extracellular vesicles, gut microbiota, intestinal permeability, non‐alcoholic fatty liver disease, Cytology, QH573-671
Abstract

Abstract The role of extracellular vesicles (EVs) from faeces (fEVs) and small circulating EVs (cEVs) in liver diseases such as non‐alcoholic fatty diseases (NAFLD) and non‐alcoholic steatohepatitis (NASH) has not been demonstrated. fEVs and cEVs of healthy donors, NAFLD and NASH patients were isolated and characterized. The effects of EVs were evaluated in intestinal, endothelial, Kupffer and stellate cells. Non‐muscular myosin light chain kinase (nmMLCK) deficient mice were used in vivo. Bacterial origins of fEVs were analysed by 16s rDNA gene sequencing. fEVs and small cEVs were composed of prokaryotic and eukaryotic origins. Only NASH‐fEVs exerted deleterious effects. NASH‐fEVs increased intestinal permeability and reduced expression of tight junction proteins that were prevented by nmMLCK inhibition, increased endothelial cell permeability and inflammatory cytokines and chemokines requiring TLR4/lipopolysaccharide pathway. NASH‐fEVs and NASH‐cEVs activated profibrotic and proinflammatory proteins of hepatic stellate cells. Treatment with NASH‐fEVs evoked an increase in intestinal permeability in wild type but not in nmMLCK deficient mice. Bacterial origins of fEVs were different between NAFLD and NASH patients and 16 amplicon sequence variants were differentially abundant. We demonstrate that fEVs actively participate in barrier dysfunctions leading to liver injuries underscoring the role of nmMLCK and lipopolysaccharide carried by fEVs.

Published
2023
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5. Maternal prebiotic supplementation impacts colitis development in offspring mice

Author

Amélie Lê, Amandine Selle, Philippe Aubert, Tony Durand, Carole Brosseau, Philippe Bordron, Erwan Delage, Samuel Chaffron, Camille Petitfils, Nicolas Cenac, Michel Neunlist, Marie Bodinier, and Malvyne Rolli-Derkinderen

Subjects
prebiotics, IBD, microbiota, colitis, DOHaD, offspring, Nutrition. Foods and food supply, TX341-641
Abstract

Background and aimsMaternal diet plays a key role in preventing or contributing to the development of chronic diseases, such as obesity, allergy, and brain disorders. Supplementation of maternal diet with prebiotics has been shown to reduce the risk of food allergies and affect the intestinal permeability in offspring later in life. However, its role in modulating the development of other intestinal disorders, such as colitis, remains unknown. Therefore, we investigated the effects of prebiotic supplementation in pregnant mice on the occurrence of colitis in their offspring.Materials and methodsOffspring from mothers, who were administered prebiotic galacto-oligosaccharides and inulin during gestation or fed a control diet, were subjected to three cycles of dextran sulphate sodium (DSS) treatment to induce chronic colitis, and their intestinal function and disease activity were evaluated. Colonic remodelling, gut microbiota composition, and lipidomic and transcriptomic profiles were also assessed.ResultsDSS-treated offspring from prebiotic-fed mothers presented a higher disease score, increased weight loss, and increased faecal humidity than those from standard diet-fed mothers. DSS-treated offspring from prebiotic-fed mothers also showed increased number of colonic mucosal lymphocytes and macrophages than the control group, associated with the increased colonic concentrations of resolvin D5, protectin DX, and 14-hydroxydocosahexaenoic acid, and modulation of colonic gene expression. In addition, maternal prebiotic supplementation induced an overabundance of eight bacterial families and a decrease in the butyrate caecal concentration in DSS-treated offspring.ConclusionMaternal prebiotic exposure modified the microbiota composition and function, lipid content, and transcriptome of the colon of the offspring. These modifications did not protect against colitis, but rather sensitised the mice to colitis development.

Published
2023
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6. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

Author

Yajuan Lin, Carly Moreno, Adrian Marchetti, Hugh Ducklow, Oscar Schofield, Erwan Delage, Michael Meredith, Zuchuan Li, Damien Eveillard, Samuel Chaffron, and Nicolas Cassar

Subjects
Science
Abstract

Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in this region.

Published
2021
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7. Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic

Author

Seaver Wang, Weiyi Tang, Erwan Delage, Scott Gifford, Hannah Whitby, Aridane G. González, Damien Eveillard, Hélène Planquette, and Nicolas Cassar

Subjects
Medicine, Science
Abstract

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
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8. Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota

Author

Sarah Huet, Jean-Bernard Pouvreau, Erwan Delage, Sabine Delgrange, Coralie Marais, Muriel Bahut, Philippe Delavault, Philippe Simier, and Lucie Poulin

Subjects
parasitic weeds, seed germination, host adaptation, seed microbiota, core microbiota, Plant culture, SB1-1110
Abstract

Seeds of the parasitic weed Phelipanche ramosa are well adapted to their hosts because they germinate and form haustorial structures to connect to roots in response to diverse host-derived molecular signals. P. ramosa presents different genetic groups that are preferentially adapted to certain hosts. Since there are indications that microbes play a role in the interaction especially in the early stages of the interaction, we studied the microbial diversity harbored by the parasitic seeds with respect to their host and genetic group. Twenty-six seed lots from seven cropping plots of three different hosts—oilseed rape, tobacco, and hemp—in the west of France were characterized for their bacterial and fungal communities using 16S rRNA gene and ITS (Internal transcribed spacer) sequences, respectively. First seeds were characterized genetically using twenty microsatellite markers and phenotyped for their sensibility to various germination stimulants including strigolactones and isothiocyanates. This led to the distinction of three P. ramosa groups that corresponded to their host of origin. The observed seed diversity was correlated to the host specialization and germination stimulant sensitivity within P. ramosa species. Microbial communities were both clustered by host and plot of origin. The seed core microbiota was composed of seventeen species that were also retrieved from soil and was in lower abundances for bacteria and similar abundances for fungi compared to seeds. The host-related core microbiota of parasitic seeds was limited and presumably well adapted to the interaction with its hosts. Two microbial candidates of Sphingobacterium species and Leptosphaeria maculans were especially identified in seeds from oilseed rape plots, suggesting their involvement in host recognition and specialization as well as seed fitness for P. ramosa by improving the production of isothiocyanates from glucosinolates in the rhizosphere of oilseed rape.

Published
2020
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9. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author

Alison E. Murray, Nicole E. Avalon, Lucas Bishop, Karen W. Davenport, Erwan Delage, Armand E.K. Dichosa, Damien Eveillard, Mary L. Higham, Sofia Kokkaliari, Chien-Chi Lo, Christian S. Riesenfeld, Ryan M. Young, Patrick S.G. Chain, and Bill J. Baker

Subjects
Antarctica, ascidian, microbiome, microbial diversity, palmerolide A, co-occurrence, Biology (General), QH301-705.5
Abstract

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

Published
2020
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10. Allergic Sensitization Driving Immune Phenotyping and Disease Severity in a Mouse Model of Asthma

Author

Eléonore Dijoux, Martin Klein, Barbara Misme-Aucouturier, Marie-Aude Cheminant, Marion de Carvalho, Louise Collin, Dorian Hassoun, Erwan Delage, Mathilde Gourdel, Gervaise Loirand, Vincent Sauzeau, Antoine Magnan, Grégory Bouchaud, unité de recherche de l'institut du thorax UMR1087 UMR6291 (ITX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Centre hospitalier universitaire de Nantes (CHU Nantes), Hôpital Foch [Suresnes], Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Mibiogate consortium and the Fondation du souffle, INRAe Transfert and the 'Institut de Recherche en Santé Respiratoire des Pays de La Loire' IRSRPL. The Genavie Foundation., and ANR-16-IDEX-0007,NExT (I-SITE),NExT (I-SITE)(2016)

Subjects
Pulmonary and Respiratory Medicine, endotypes, barrier integrity, Immunology, Immunology and Allergy, [SDV.IMM.ALL]Life Sciences [q-bio]/Immunology/Allergology, Respiratory function, lung microbiota
Abstract

International audience; Purpose. Asthma is a frequent chronic inflammatory bronchial disease affecting more than 300 million patients worldwide, 70% of whom are secondary to allergy. The diversity of asthmatic endotypes contributes to their complexity. The inter-relationship between allergen and other exposure and the airway microbiome adds to the phenotypic diversity and defines the natural course of asthma. Here, we compared the mouse models of house dust mite (HDM)-induced allergic asthma. Allergic sensitization was performed via various routes and associated with outcomes.Methods: Mice were sensitized with HDM via the oral, nasal or percutaneous routes. Lung function, barrier integrity, immune response and microbiota composition were analyzed.Results: Severe impairment of respiratory function was observed in the mice sensitized by the nasal and cutaneous paths. It was associated with epithelial dysfunction characterized by an increased permeability secondary to junction protein disruption. Such sensitization paths induced a mixed eosinophilic and neutrophilic inflammatory response with high interleukin (IL)-17 airway secretion. In contrast, orally sensitized mice showed a mild impairment of respiratory function. Epithelial dysfunction was mild with increased mucus production, but preserved epithelial junctions. Regarding lung microbiota, sensitization provoked a significant loss of diversity. At the genus level, Cutibacterium, Acinetobacter, Streptococcus and Lactobacillus were found to be modulated according to the sensitization pathway. An increase in theanti-inflammatory microbiota metabolites was observed in the oral-sensitization group.Conclusions: Our study highlights the strong impact of the sensitization route on the pathophysiology and the critical phenotypic diversity of allergic asthma in a mouse model.

Published
2023

11. 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

12. Environmental vulnerability of the global ocean epipelagic plankton community interactome

Author

Samuel Chaffron, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Erwan Delage, Patrick Wincker, Lee Karp-Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-École Centrale de Nantes (ECN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Department of Microbiology [Columbus], Ohio State University [Columbus] (OSU), Federal University of São Carlos (UFSCar), Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Division of Earth and Ecosystem Sciences (DEES), Desert Research Institute (DRI), Department of Marine Biology and Oceanography, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 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 Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), University of Maine, Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), 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), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Helmut Horten Foundation, Ministerio de Ciencia, Innovación y Universidades (España), European Research Council, European Commission, Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Natural Sciences and Engineering Research Council of Canada, European Project: 862923,AtlantECO, and European Project: 835067,DIATOMIC

Subjects
Multidisciplinary, Environmental change, Ecology, fungi, Biome, Community structure, Climate change, Environmental science, Pelagic zone, sense organs, Plankton, Food web, Environmental niche modelling
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. Although 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 the 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, This article is contribution number 120 of Tara Oceans.-- 15 pages, 4 figures, supplementary materials https://www.science.org/doi/suppl/10.1126/sciadv.abg1921/suppl_file/sciadv.abg1921_SM.pdf.-- Data and materials availability: Data described here are available at the EBI under the project identifiers PRJEB402 and PRJEB7988 and at PANGAEA (96). All data (raw abundance matrices and interactome graphML files) needed to evaluate the conclusions of the paper are available in the Supplementary Materials. A web server for exploring and searching the global ocean interactome is available at https://saas.ls2n.fr/Tara-Oceans-interactome/, We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ETH and the Helmut Horten Foundation, MEXT/JSPS/KAKENHI (projects 16H06429, 16K21723, 16H06437, and 18H02279), the Spanish Ministry of Economy and Competitiveness (project MAGGY-CTM2017-87736-R), ERC Advanced Award Diatomic (grant agreement 835067 to CB), the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant to SC), and the H2020 European Commission project AtlantECO (award number 862923). […]. E.D. is supported by the RFI ATLANSTIC2020 grant (PROBIOSTIC grant to DE). M.Bu. received financial support from the French Facility for Global Environment (FFEM) as part of the “Ocean Plankton, Climate and Development” project. P.C.J. was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP (PhD grant 2017/26786-1). H.S. is supported by a Brazilian Research Council (CNPq) productivity grant (process 309514/2017-7) and FAPESP (grant 2014/14139-3). […] Additional funding from the Natural Sciences and Engineering Council (NSERC) Canada Discovery program is gratefully acknowledged., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Published
2021

13. Disentangling marine microbial networks across space

Author

Ina M. Deutschmann, Josep M. Gasol, Damien Eveillard, Samuel Chaffron, Ramiro Logares, Erwan Delage, Caterina R. Giner, Marta Sebastián, Julie Poulain, Javier Arístegui, Carlos M. Duarte, Silvia G. Acinas, and Ramon Massana

Subjects
Political science, Library science, media_common.cataloged_instance, Christian ministry, European union, media_common
Abstract

Microbial interactions underpin ocean ecosystem function, but they remain barely known. Multiple studies have analyzed microbial interactions using static association networks based on omics data, yet microbial interactions are dynamic and can change across spatiotemporal scales. Understanding the dynamics of microbial interactions is needed for a better comprehension of ocean ecosystems. Here, we explored associations between archaea, bacteria, and picoeukaryotes along the water column, from the surface to the deep ocean, across the northern subtropical to the southern temperate ocean and the Mediterranean Sea by defining sample-specific subnetworks, which allowed us to examine changes in microbial associations across space. We found that associations tend to change with depth as well as with geographical scale, with a few associations being global (i.e., present across regions within the same depth layer) and 11-36% being regional within specific water layers. The lowest fraction of global associations was found in the bathypelagic zone, while associations restricted to certain regions increased with depth. The majority of associations observed in surface waters disappeared with depth, suggesting that surface ocean associations are not transferred to the deep sea, despite microbial sinking. Altogether, our results suggest that microbial associations have highly heterogeneous distributions in the horizontal and vertical dimensions of the ocean and that such distributions do not mirror taxonomic distributions. Our work contributes to better understand the dynamics of microbial interactions in the global ocean, which is urgently needed in a context of global change.

Published
2021

14. Disentangling temporal associations in marine microbial networks

Author

Ramiro Logares, Damien Eveillard, Balague, Cèlia Marrasé, Ina M. Deutschmann, Fran Latorre, Benites Lf, Samuel Chaffron, Erwan Delage, Josep M. Gasol, Anders K. Krabberød, and Ramon Massana

Subjects
Biogeochemical cycle, Mediterranean sea, Ecology, Environmental science, Ecosystem, Microbiome, Annual cycle, Bay
Abstract

Microbial interactions are fundamental for Earth’s ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. The omics-based censuses are helpful to predict microbial interactions through the inference of static association networks. However, since microbial interactions are highly dynamic, we have developed an approach to generate a temporal network from a single static network. We applied it to understand the monthly microbial associations’ dynamics occurring over ten years in the Blanes Bay Microbial Observatory (Mediterranean Sea). For the decade, we identified persistent, seasonal, and temporary microbial associations. Moreover, 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 repeatability in colder than warmer months. Altogether, our results indicate that marine microbial networks follow recurrent temporal dynamics, which need to be accounted to better understand the dynamics of the ocean microbiome.

Published
2021

15. 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

16. Oral exposure to bisphenol A exacerbates allergic inflammation in a mouse model of food allergy

Author

Barbara Misme-Aucouturier, Marion De Carvalho, Erwan Delage, Eleonore Dijoux, Martin Klein, Carole Brosseau, Marie Bodinier, Laurence Guzylack-Piriou, and Grégory Bouchaud

Subjects
Inflammation, Disease Models, Animal, Mice, Phenols, Animals, Benzhydryl Compounds, Toxicology, Food Hypersensitivity
Abstract

Allergic diseases are increasing worldwide, and their precise causes are not fully understood. However, this observation can be correlated with growing chemical pollution of the environment. Bisphenol A (BPA) alters the immune system, microbiota and barrier functions. Here, we studied the effect of oral BPA at levels equivalent to human exposure to understand the mechanisms of immunological, physiological and microbial action on food allergies. In a murine model of allergy, we evaluated the effect of direct oral exposure to BPA at 4 µg/kg bw/d corresponding to tolerable daily intake (TDI). We studied symptoms, intestinal physiology and humorall and cellular immune responses during food allergy. We explored the relationship between oral exposure to BPA and changes in the gut microenvironment. Markers of food allergy and intestinal permeability were increased following exposure to BPA. We also observed a modulated humorall and T-cell response with aggravation of food allergy inflammation. Moreover, BPA exposure induced gut dysbiosis and decreased microbial diversity induced by food allergy. Altogether, these results suggest that the 2015 European Food Safety Authority (EFSA) TDI should be reviewed to consider the immunotoxicity of BPA.

Published
2022

17. Decline in plankton diversity and carbon flux with reduced sea ice extent along the Western Antarctic Peninsula

Author

Yajuan Lin, Hugh W. Ducklow, Adrian Marchetti, Damien Eveillard, Zuchuan Li, Nicolas Cassar, Michael P. Meredith, Oscar Schofield, Erwan Delage, Carly M. Moreno, Samuel Chaffron, Nicholas School of the Environment, Duke University [Durham], 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), 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), 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), 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), and 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)

Subjects
Water microbiology, 010504 meteorology & atmospheric sciences, Science, Biodiversity, General Physics and Astronomy, Antarctic Regions, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Peninsula, Sea ice, Ecosystem, Ice Cover, 14. Life underwater, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Diatoms, Marine biology, 0303 health sciences, geography, Multidisciplinary, geography.geographical_feature_category, Microbiota, fungi, Temperature, Eukaryota, General Chemistry, Carbon cycle, 15. Life on land, Plankton, Carbon, Sea surface temperature, Oceanography, 13. Climate action, Species evenness, Environmental science, Species richness, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract

Since the middle of the past century, the Western Antarctic Peninsula has warmed rapidly with a significant loss of sea ice but the impacts on plankton biodiversity and carbon cycling remain an open question. Here, using a 5-year dataset of eukaryotic plankton DNA metabarcoding, we assess changes in biodiversity and net community production in this region. Our results show that sea-ice extent is a dominant factor influencing eukaryotic plankton community composition, biodiversity, and net community production. Species richness and evenness decline with an increase in sea surface temperature (SST). In regions with low SST and shallow mixed layers, the community was dominated by a diverse assemblage of diatoms and dinoflagellates. Conversely, less diverse plankton assemblages were observed in waters with higher SST and/or deep mixed layers when sea ice extent was lower. A genetic programming machine-learning model explained up to 80% of the net community production variability at the Western Antarctic Peninsula. Among the biological explanatory variables, the sea-ice environment associated plankton assemblage is the best predictor of net community production. We conclude that eukaryotic plankton diversity and carbon cycling at the Western Antarctic Peninsula are strongly linked to sea-ice conditions., Over the past century, the Western Antarctic Peninsula has experienced rapid warming and a substantial loss of sea ice with important implications for plankton biodiversity and carbon cycling. Using a 5-year DNA metabarcoding dataset, this study assesses how interannual variability in sea-ice conditions impacts biodiversity and biological carbon fluxes in this region.

Published
2020

18. 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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