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Bruto M, Oger PM, Got P, Bernard C, Melayah D, Cloarec LA, Duval C, Escalas A, Duperron S, Guigard L, Leboulanger C, Ader M, Sarazin G, Jézéquel D, Agogué H, Troussellier M, Hugoni M. Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome. Mol Ecol 2023; 32:6824-6838. [PMID: 37901963 DOI: 10.1111/mec.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
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Affiliation(s)
- Maxime Bruto
- VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | - Philippe M Oger
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Patrice Got
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Delphine Melayah
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Lilian A Cloarec
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Arthur Escalas
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Ludivine Guigard
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | | | - Magali Ader
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon, France
| | - Hélène Agogué
- LIENSs, UMR7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Mylène Hugoni
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
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Oyanedel D, Lagorce A, Bruto M, Haffner P, Morot A, Labreuche Y, Dorant Y, de La Forest Divonne S, Delavat F, Inguimbert N, Montagnani C, Morga B, Toulza E, Chaparro C, Escoubas JM, Gueguen Y, Vidal-Dupiol J, de Lorgeril J, Petton B, Degremont L, Tourbiez D, Pimparé LL, Leroy M, Romatif O, Pouzadoux J, Mitta G, Le Roux F, Charrière GM, Travers MA, Destoumieux-Garzón D. Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus. Proc Natl Acad Sci U S A 2023; 120:e2305195120. [PMID: 37751557 PMCID: PMC10556616 DOI: 10.1073/pnas.2305195120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/10/2023] [Indexed: 09/28/2023] Open
Abstract
Polymicrobial infections threaten the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease affecting oyster production worldwide. In the French Atlantic coast, the disease involves coinfection with ostreid herpesvirus 1 (OsHV-1) and virulent Vibrio. However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with OsHV-1 during pathogenesis. By connecting field-based approaches in a Mediterranean ecosystem, laboratory infection assays and functional genomics, we uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We show that Vibrio harveyi and Vibrio rotiferianus are predominant in OsHV-1-diseased oysters and that OsHV-1 drives the partition of the Vibrio community observed in the field. However only V. harveyi synergizes with OsHV-1 by promoting mutual growth and accelerating oyster death. V. harveyi shows high-virulence potential and dampens oyster cellular defenses through a type 3 secretion system, making oysters a more favorable niche for microbe colonization. In addition, V. harveyi produces a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus, which cooccurs with V. harveyi in diseased oysters, and behaves as a cheater by benefiting from V. harveyi metabolite sharing. Our data show that cooperative behaviors contribute to synergy between bacterial and viral coinfecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling cooperative behaviors or countering their effects opens avenues for mitigating polymicrobial diseases.
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Affiliation(s)
- Daniel Oyanedel
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Arnaud Lagorce
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Maxime Bruto
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Philippe Haffner
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Amandine Morot
- Université de Bretagne Occidentale, CNRS, Institut de recherche pour le développement (IRD), Ifremer, Laboratoire des sciences de l'environnement marin (LEMAR), Plouzané,F-29280, France
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, Institut Universitaire Européen de la Mer, LorientF-56100, France
| | - Yannick Labreuche
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Yann Dorant
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Sébastien de La Forest Divonne
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - François Delavat
- Nantes Université, CNRS, Unité en Sciences Biologiques et Biotechnologies (US2B), UMR6286, Nantes,F-44000, France
| | - Nicolas Inguimbert
- Centre de Recherches Insulaires et OBservatoire de l’Environnement (CRIOBE), UAR3278, Ecole Pratique des Hautes Etudes (EPHE), Université de Perpignan Via Domitia, CNRS, PerpignanF-66860, France
| | - Caroline Montagnani
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Benjamin Morga
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Eve Toulza
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Cristian Chaparro
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Jean-Michel Escoubas
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Yannick Gueguen
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- MARine Biodiversity, Exploitation and Conservation (MARBEC) Univ Montpellier, CNRS, Ifremer, IRD, SèteF-34200, France
| | - Jeremie Vidal-Dupiol
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Julien de Lorgeril
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, ENTROPIE, Nouméa, Nouvelle-Calédonie,F-98800, France
| | - Bruno Petton
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Université de Bretagne Occidentale, CNRS, Institut de recherche pour le développement (IRD), Ifremer, Laboratoire des sciences de l'environnement marin (LEMAR), Plouzané,F-29280, France
| | - Lionel Degremont
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Delphine Tourbiez
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Léa-Lou Pimparé
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Marc Leroy
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Océane Romatif
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Juliette Pouzadoux
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Guillaume Mitta
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- Ifremer, Université de Polynésie Française, IRD, Institut Louis Malardé (ILM), Ecosystèmes Insulaires Océaniens (EIO), VairaoF-98719, Polynésie Française
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Guillaume M. Charrière
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Marie-Agnès Travers
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Delphine Destoumieux-Garzón
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
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Melayah D, Bontemps Z, Bruto M, Nguyen A, Oger P, Hugoni M. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems. Methods Mol Biol 2022; 2605:17-35. [PMID: 36520387 DOI: 10.1007/978-1-0716-2871-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.
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Affiliation(s)
- Delphine Melayah
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Zélia Bontemps
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | | | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Mylène Hugoni
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France.
- Institut Universitaire de France (IUF), Paris, France.
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Escalas A, Troussellier M, Melayah D, Bruto M, Nicolas S, Bernard C, Ader M, Leboulanger C, Agogué H, Hugoni M. Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiol Ecol 2021; 97:6464137. [PMID: 34918080 DOI: 10.1093/femsec/fiab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Marc Troussellier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Delphine Melayah
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Sébastien Nicolas
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, CP 39, 75005 Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, 75005 Paris, France
| | - Christophe Leboulanger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Hélène Agogué
- Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS -La Rochelle Université, 17000 La Rochelle, France
| | - Mylène Hugoni
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.,Institut Universitaire de France (IUF)
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Lasa A, Auguste M, Lema A, Oliveri C, Borello A, Taviani E, Bonello G, Doni L, Millard AD, Bruto M, Romalde JL, Yakimov M, Balbi T, Pruzzo C, Canesi L, Vezzulli L. A deep-sea bacterium related to coastal marine pathogens. Environ Microbiol 2021; 23:5349-5363. [PMID: 34097814 PMCID: PMC8519021 DOI: 10.1111/1462-2920.15629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 11/29/2022]
Abstract
Evolution of virulence traits from adaptation to environmental niches other than the host is probably a common feature of marine microbial pathogens, whose knowledge might be crucial to understand their emergence and pathogenetic potential. Here, we report genome sequence analysis of a novel marine bacterial species, Vibrio bathopelagicus sp. nov., isolated from warm bathypelagic waters (3309 m depth) of the Mediterranean Sea. Interestingly, V. bathopelagicus sp. nov. is closely related to coastal Vibrio strains pathogenic to marine bivalves. V. bathopelagicus sp. nov. genome encodes genes involved in environmental adaptation to the deep-sea but also in virulence, such as the R5.7 element, MARTX toxin cluster, Type VI secretion system and zinc-metalloprotease, previously associated with Vibrio infections in farmed oysters. The results of functional in vitro assays on immunocytes (haemocytes) of the Mediterranean mussel Mytilus galloprovincialis and the Pacific oyster Crassostrea gigas, and of the early larval development assay in Mytilus support strong toxicity of V. bathopelagicus sp. nov. towards bivalves. V. bathopelagicus sp. nov., isolated from a remote Mediterranean bathypelagic site, is an example of a planktonic marine bacterium with genotypic and phenotypic traits associated with animal pathogenicity, which might have played an evolutionary role in the origin of coastal marine pathogens.
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Affiliation(s)
- Aide Lasa
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
- Department of Microbiology and ParasitologyCIBUS‐Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - Manon Auguste
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Alberto Lema
- Department of Microbiology and ParasitologyCIBUS‐Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - Caterina Oliveri
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Alessio Borello
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Elisa Taviani
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Guido Bonello
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Lapo Doni
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Andrew D. Millard
- Department of Genetics and Genome BiologyUniversity of LeicesterUniversity Road, LeicesterUK
| | - Maxime Bruto
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff CS 90074Roscoff CedexF‐29688France
| | - Jesus L. Romalde
- Department of Microbiology and ParasitologyCIBUS‐Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de CompostelaSantiago de Compostela15782Spain
| | - Michail Yakimov
- Institute of Biological Resources and Marine Biotechnology, National Research Council (IRBIM‐CNR)Messina98122Italy
| | - Teresa Balbi
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Carla Pruzzo
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Laura Canesi
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaCorso Europa 26, 16132Italy
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Hugoni M, Galland W, Lecomte S, Bruto M, Barakat M, Piola F, Achouak W, Haichar FEZ. Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome. Microorganisms 2021; 9:1406. [PMID: 34209897 PMCID: PMC8306639 DOI: 10.3390/microorganisms9071406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/04/2022] Open
Abstract
Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.
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Affiliation(s)
- Mylène Hugoni
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
- Institut Universitaire de France (IUF), CEDEX 05, F-75231 Paris, France
| | - William Galland
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Solène Lecomte
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Maxime Bruto
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon, Université Lyon 1, CNRS, UMR5558, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France;
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Florence Piola
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France;
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Feth el Zahar Haichar
- Microbiologie, Adaptation, Pathogénie, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, 10 rue Raphaël Dubois, F-69622 Villeurbanne, France
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7
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Oyanedel D, Labreuche Y, Bruto M, Amraoui H, Robino E, Haffner P, Rubio T, Charrière GM, Le Roux F, Destoumieux-Garzón D. Vibrio splendidus O-antigen structure: a trade-off between virulence to oysters and resistance to grazers. Environ Microbiol 2020; 22:4264-4278. [PMID: 32219965 DOI: 10.1111/1462-2920.14996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/13/2020] [Accepted: 03/22/2020] [Indexed: 01/19/2023]
Abstract
A major debate in evolutionary biology is whether virulence is maintained as an adaptive trait and/or evolves to non-virulence. In the environment, virulence traits of non-obligatory parasites are subjected to diverse selective pressures and trade-offs. Here, we focus on a population of Vibrio splendidus that displays moderate virulence for oysters. A MARTX (Multifunctional-autoprocessing repeats-in-toxin) and a type-six secretion system (T6SS) were found to be necessary for virulence toward oysters, while a region (wbe) involved in O-antigen synthesis is necessary for resistance to predation against amoebae. Gene inactivation within the wbe region had major consequences on the O-antigen structure, conferring lower immunogenicity, competitive advantage and increased virulence in oyster experimental infections. Therefore, O-antigen structures that favour resistance to environmental predators result in an increased activation of the oyster immune system and a reduced virulence in that host. These trade-offs likely contribute to maintaining O-antigen diversity in the marine environment by favouring genomic plasticity of the wbe region. The results of this study indicate an evolution of V. splendidus towards moderate virulence as a compromise between fitness in the oyster as a host, and resistance to its predators in the environment.
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Affiliation(s)
- Daniel Oyanedel
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Yannick Labreuche
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Maxime Bruto
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Hajar Amraoui
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Etienne Robino
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Philippe Haffner
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Tristan Rubio
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France.,Molecular Microbiology and Structural Biochemistry (UMR 5086). CNRS, University of Lyon, 69367, Lyon, France
| | - Guillaume M Charrière
- IHPE, Univ Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
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8
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Wegner KM, Piel D, Bruto M, John U, Mao Z, Alunno-Bruscia M, Petton B, Le Roux F. Molecular Targets for Coevolutionary Interactions Between Pacific Oyster Larvae and Their Sympatric Vibrios. Front Microbiol 2019; 10:2067. [PMID: 31555250 PMCID: PMC6742746 DOI: 10.3389/fmicb.2019.02067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
Bacteria of the Vibrio genus are the most predominant infectious agents threatening marine wildlife and aquaculture. Due to the large genetic diversity of these pathogens, the molecular determinants of Vibrio virulence are only poorly understood. Furthermore, studies tend to ignore co-evolutionary interactions between different host populations and their locally encountered Vibrio communities. Here, we explore the molecular targets of such co-evolutionary interactions by analyzing the genomes of nine Vibrio strains from the Splendidus-clade showing opposite virulence patterns towards two populations of Pacific oysters introduced into European Wadden Sea. By contrasting Vibrio phylogeny to their host specific virulence patterns, we could identify two core genome genes (OG1907 and OG 3159) that determine the genotype by genotype (G × G) interactions between oyster larvae and their sympatric Vibrio communities. Both genes show positive selection between locations targeting only few amino acid positions. Deletion of each gene led to a loss of the host specific virulence patterns while complementation with OG3159 alleles from both locations could recreate the wild type phenotypes matching the origin of the allele. This indicates that both genes can act as a genetic switch for Vibrio-oyster coevolution demonstrating that local adaptation in distinct Vibrio lineages can rely on only few genes independent of larger pathogenicity islands or plasmids.
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Affiliation(s)
- K Mathias Wegner
- Coastal Ecology, Waddensea Station Sylt, Alfred Wegener Institut - Helmholtz-Zentrum für Polar- und Meeresforschung, List, Germany
| | - Damien Piel
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer, Plouzané, France.,Integrative Biology of Marine Models, UPMC Paris 06, CNRS, UMR 8227, Sorbonne Universités, Station Biologique de Roscoff, Roscoff, France
| | - Maxime Bruto
- Integrative Biology of Marine Models, UPMC Paris 06, CNRS, UMR 8227, Sorbonne Universités, Station Biologique de Roscoff, Roscoff, France
| | - Uwe John
- Ecolgical Chemistry, Alfred Wegener Institut - Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Zhijuan Mao
- Biological and Environmental College, Zhejiang Wanli University, Ningbo, China
| | - Marianne Alunno-Bruscia
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer, Plouzané, France.,LEMAR UMR 6539, Ifremer, Argenton-en-Landunvez, France
| | - Bruno Petton
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer, Plouzané, France.,LEMAR UMR 6539, Ifremer, Argenton-en-Landunvez, France
| | - Frédérique Le Roux
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer, Plouzané, France.,Integrative Biology of Marine Models, UPMC Paris 06, CNRS, UMR 8227, Sorbonne Universités, Station Biologique de Roscoff, Roscoff, France
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9
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Piel D, Bruto M, James A, Labreuche Y, Lambert C, Janicot A, Chenivesse S, Petton B, Wegner KM, Stoudmann C, Blokesch M, Le Roux F. Selection of
Vibrio crassostreae
relies on a plasmid expressing a type 6 secretion system cytotoxic for host immune cells. Environ Microbiol 2019; 22:4198-4211. [DOI: 10.1111/1462-2920.14776] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Damien Piel
- Unité Physiologie Fonctionnelle des Organismes Marins ZI de la Pointe du Diable, CS 10070 Ifremer F‐29280 Plouzané France
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Maxime Bruto
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Adèle James
- Unité Physiologie Fonctionnelle des Organismes Marins ZI de la Pointe du Diable, CS 10070 Ifremer F‐29280 Plouzané France
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Yannick Labreuche
- Unité Physiologie Fonctionnelle des Organismes Marins ZI de la Pointe du Diable, CS 10070 Ifremer F‐29280 Plouzané France
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Christophe Lambert
- Laboratoire des Sciences de l'Environnement Marin UMR 6539 CNRS UBO IRD IFREMER, Institut Universitaire Européen de la Mer, Technopôle Brest‐Iroise – Rue Dumont d'Urville F‐29280 Plouzané France
| | - Adrian Janicot
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Sabine Chenivesse
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
| | - Bruno Petton
- Unité Physiologie Fonctionnelle des Organismes Marins ZI de la Pointe du Diable, CS 10070 Ifremer F‐29280 Plouzané France
- Laboratoire des Sciences de l'Environnement Marin UMR 6539 CNRS UBO IRD IFREMER, Institut Universitaire Européen de la Mer, Technopôle Brest‐Iroise – Rue Dumont d'Urville F‐29280 Plouzané France
| | - K. Mathias Wegner
- AWI ‐ Alfred Wegener Institut, Helmholtz‐Zentrum für Polar und Meeresforschung, Coastal Ecology, Wadden Sea Station Sylt, 25992, Hafenstrasse 43, List Germany
| | - Candice Stoudmann
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences Ecole Polytechnique Fédérale de Lausanne CH‐1015 Lausanne Switzerland
| | - Melanie Blokesch
- Laboratory of Molecular Microbiology, Global Health Institute, School of Life Sciences Ecole Polytechnique Fédérale de Lausanne CH‐1015 Lausanne Switzerland
| | - Frédérique Le Roux
- Unité Physiologie Fonctionnelle des Organismes Marins ZI de la Pointe du Diable, CS 10070 Ifremer F‐29280 Plouzané France
- Sorbonne Universités UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074 F‐29688 Roscoff cedex France
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10
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Luis P, Saint-Genis G, Vallon L, Bourgeois C, Bruto M, Marchand C, Record E, Hugoni M. Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments. Environ Microbiol 2019; 21:1407-1424. [PMID: 30807675 DOI: 10.1111/1462-2920.14571] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/20/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022]
Abstract
Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.
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Affiliation(s)
- Patricia Luis
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Geoffroy Saint-Genis
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Laurent Vallon
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
| | - Carine Bourgeois
- IMPMC, Institut de Recherche pour le Développement (IRD), UPMC, CNRS, MNHN, Noumea, New Caledonia, France
| | - Maxime Bruto
- UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Universités, CS 90074, F-29688, Roscoff Cedex, France
| | - Cyril Marchand
- IMPMC, Institut de Recherche pour le Développement (IRD), UPMC, CNRS, MNHN, Noumea, New Caledonia, France.,ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851, Noumea, New Caledonia, France
| | - Eric Record
- INRA, Aix-Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France
| | - Mylène Hugoni
- CNRS, UMR5557; Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, 69220, Villeurbanne Cedex, France
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11
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Almario J, Bruto M, Vacheron J, Prigent-Combaret C, Moënne-Loccoz Y, Muller D. Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism. Front Microbiol 2017; 8:1218. [PMID: 28713346 PMCID: PMC5491608 DOI: 10.3389/fmicb.2017.01218] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/15/2017] [Indexed: 11/13/2022] Open
Abstract
Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+Pseudomonas strains in the "P. corrugata" and "P. protegens" subgroups of the "Pseudomonas fluorescens" group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+Pseudomonas include species of the "P. fluorescens" group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the "P. fluorescens" group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.
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Affiliation(s)
- Juliana Almario
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Maxime Bruto
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Jordan Vacheron
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Claire Prigent-Combaret
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Yvan Moënne-Loccoz
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Daniel Muller
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
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12
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Almario J, Bruto M, Vacheron J, Prigent-Combaret C, Moënne-Loccoz Y, Muller D. Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism. Front Microbiol 2017; 8:1218. [PMID: 28713346 DOI: 10.3389/fmibc.2017.01218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/15/2017] [Indexed: 05/26/2023] Open
Abstract
Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+Pseudomonas strains in the "P. corrugata" and "P. protegens" subgroups of the "Pseudomonas fluorescens" group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+Pseudomonas include species of the "P. fluorescens" group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the "P. fluorescens" group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.
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Affiliation(s)
- Juliana Almario
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Maxime Bruto
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Jordan Vacheron
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Claire Prigent-Combaret
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Yvan Moënne-Loccoz
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
| | - Daniel Muller
- Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lyon, Université Claude Bernard Lyon1, VetAgro Sup, UMR Ecologie MicrobienneVilleurbanne, France
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13
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Petton B, Bruto M, James A, Labreuche Y, Alunno-Bruscia M, Le Roux F. Crassostrea gigas mortality in France: the usual suspect, a herpes virus, may not be the killer in this polymicrobial opportunistic disease. Front Microbiol 2015. [PMID: 26217318 PMCID: PMC4491618 DOI: 10.3389/fmicb.2015.00686] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Successive disease outbreaks in oyster (Crassostrea gigas) beds in France have resulted in dramatic losses in production, and subsequent decline in the oyster-farming industry. Deaths of juvenile oysters have been associated with the presence of a herpes virus (OsHV-1 μvar) and bacterial populations of the genus Vibrio. Although the pathogenicity of OsHV-1 μvar, as well as several strains of Vibrio has been demonstrated by experimental infections, our understanding of the complexity of infections occurring in the natural environment remains limited. In the present study, we use specific-pathogen-free (SPF) oysters infected in an estuarine environment to study the diversity and dynamics of cultured microbial populations during disease expression. We observe that rapid Vibrio colonization followed by viral replication precedes oyster death. No correlation was found between the vibrio concentration and viral load in co-infected animals. We show that the quantity of viral DNA is a predictor of mortality, however, in the absence of bacteria, a high load of herpes virus is not sufficient to induce the full expression of the disease. In addition, we demonstrate that juvenile mortalities can occur in the absence of herpes virus, indicating that the herpes virus appears neither essential nor sufficient to cause juvenile deaths; whereas bacteria are necessary for the disease. Finally, we demonstrate that oysters are a reservoir of putative pathogens, and that the geographic origin, age, and cultivation method of oysters influence disease expression.
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Affiliation(s)
- Bruno Petton
- LEMAR UMR 6539, Ifremer Argenton-en-Landunvez, France
| | - Maxime Bruto
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer Plouzané, France ; CNRS, Equipe Génomique des Vibrios, LBI2M, UPMC Paris 06, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités Roscoff, France
| | - Adèle James
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer Plouzané, France ; CNRS, Equipe Génomique des Vibrios, LBI2M, UPMC Paris 06, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités Roscoff, France
| | - Yannick Labreuche
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer Plouzané, France ; CNRS, Equipe Génomique des Vibrios, LBI2M, UPMC Paris 06, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités Roscoff, France
| | | | - Frédérique Le Roux
- Unité Physiologie Fonctionnelle des Organismes Marins, Ifremer Plouzané, France ; CNRS, Equipe Génomique des Vibrios, LBI2M, UPMC Paris 06, UMR 8227, Integrative Biology of Marine Models, Sorbonne Universités Roscoff, France
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14
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Bruto M, Prigent-Combaret C, Luis P, Moënne-Loccoz Y, Muller D. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes. Proc Biol Sci 2015; 281:20140848. [PMID: 24990676 DOI: 10.1098/rspb.2014.0848] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes-as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.
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Affiliation(s)
- Maxime Bruto
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Patricia Luis
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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Bruto M, Prigent-Combaret C, Muller D, Moënne-Loccoz Y. Analysis of genes contributing to plant-beneficial functions in Plant Growth-Promoting Rhizobacteria and related Proteobacteria. Sci Rep 2014; 4:6261. [PMID: 25179219 PMCID: PMC4151105 DOI: 10.1038/srep06261] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/11/2014] [Indexed: 01/22/2023] Open
Abstract
The positive effects of root-colonizing bacteria cooperating with plants lead to improved growth and/or health of their eukaryotic hosts. Some of these Plant Growth-Promoting Rhizobacteria (PGPR) display several plant-beneficial properties, suggesting that the accumulation of the corresponding genes could have been selected in these bacteria. Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria. Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied. However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains. This suggests that the PGPR-plant cooperation could have established separately in various taxa, yielding PGPR strains that use different gene assortments. The number of genes contributing to plant-beneficial functions increased along the continuum -animal pathogens, phytopathogens, saprophytes, endophytes/symbionts, PGPR- indicating that the accumulation of these genes (and possibly of different plant-beneficial traits) might be an intrinsic PGPR feature. This work uncovered preferential associations occurring between certain genes contributing to phytobeneficial traits and provides new insights into the emergence of PGPR bacteria.
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Affiliation(s)
- Maxime Bruto
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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Walker V, Bruto M, Bellvert F, Bally R, Muller D, Prigent-Combaret C, Moënne-Loccoz Y, Comte G. Unexpected phytostimulatory behavior for Escherichia coli and Agrobacterium tumefaciens model strains. Mol Plant Microbe Interact 2013; 26:495-502. [PMID: 23360460 DOI: 10.1094/mpmi-12-12-0298-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Plant-beneficial effects of bacteria are often underestimated, especially for well-studied strains associated with pathogenicity or originating from other environments. We assessed the impact of seed inoculation with the emblematic bacterial models Agrobacterium tumefaciens C58 (plasmid-cured) or Escherichia coli K-12 on maize seedlings in nonsterile soil. Compared with the noninoculated control, root biomass (with A. tumefaciens or E. coli) and shoot biomass (with A. tumefaciens) were enhanced at 10 days for 'PR37Y15' but not 'DK315', as found with the phytostimulator Azospirillum brasilense UAP-154 (positive control). In roots as well as in shoots, Agrobacterium tumefaciens and E. coli triggered similar (in PR37Y15) or different (in DK315) changes in the high-performance liquid chromatography profiles of secondary metabolites (especially benzoxazinoids), distinct from those of Azospirillum brasilense UAP-154. Genome sequence analysis revealed homologs of nitrite reductase genes nirK and nirBD and siderophore synthesis genes for Agrobacterium tumefaciens, as well as homologs of nitrite reductase genes nirBD and phosphatase genes phoA and appA in E. coli, whose contribution to phytostimulation will require experimental assessment. In conclusion, the two emblematic bacterial models had a systemic impact on maize secondary metabolism and resulted in unexpected phytostimulation of seedlings in the Azospirillum sp.-responsive cultivar.
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