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Akter S, Wos-Oxley ML, Catalano SR, Hassan MM, Li X, Qin JG, Oxley AP. Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves. MICROBIAL ECOLOGY 2023; 86:1755-1772. [PMID: 36811710 PMCID: PMC10497454 DOI: 10.1007/s00248-023-02192-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.
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Affiliation(s)
- Shirin Akter
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Sarah R Catalano
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Md Mahbubul Hassan
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Hillarys, WA, Australia
| | - Xiaoxu Li
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Jian G Qin
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Andrew Pa Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
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King NG, Smale DA, Thorpe JM, McKeown NJ, Andrews AJ, Browne R, Malham SK. Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02083-9. [PMID: 35881247 DOI: 10.1007/s00248-022-02083-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.
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Affiliation(s)
- Nathan G King
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK.
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK.
| | - Dan A Smale
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth, PL1 2PB, UK
| | - Jamie M Thorpe
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
| | - Niall J McKeown
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Adam J Andrews
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Ronan Browne
- Bord Iascaigh Mhara, Dún Laoghaire, County Dublin, Ireland
| | - Shelagh K Malham
- Centre of Applied Marine Sciences, School of Ocean Sciences, Bangor University, Menai Bridge, LL59 5AB, UK
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Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound. Microbiol Spectr 2022; 10:e0198221. [PMID: 35536036 PMCID: PMC9241838 DOI: 10.1128/spectrum.01982-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Olympia oyster (Ostrea lurida) of the Puget Sound suffered a dramatic population crash, but restoration efforts hope to revive this native species. One overlooked variable in the process of assessing ecosystem health is association of bacteria with marine organisms and the environments they occupy. Oyster microbiomes are known to differ significantly between species, tissue type, and the habitat in which they are found. The goals of this study were to determine the impact of field site and habitat on the oyster microbiome and to identify core oyster-associated bacteria in the Puget Sound. Olympia oysters from one parental family were deployed at four sites in the Puget Sound both inside and outside of eelgrass (Zostera marina) beds. Using 16S rRNA gene amplicon sequencing of the oyster gut, shell, and surrounding seawater and sediment, we demonstrate that gut-associated bacteria are distinct from the surrounding environment and vary by field site. Furthermore, regional differences in the gut microbiota are associated with the survival rates of oysters at each site after 2 months of field exposure. However, habitat type had no influence on microbiome diversity. Further work is needed to identify the specific bacterial dynamics that are associated with oyster physiology and survival rates. IMPORTANCE This is the first exploration of the microbial colonizers of the Olympia oyster, a native oyster species to the West Coast, which is a focus of restoration efforts. The patterns of differential microbial colonization by location reveal microscale characteristics of potential restoration sites which are not typically considered. These microbial dynamics can provide a more holistic perspective on the factors that may influence oyster performance.
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Clerissi C, de Lorgeril J, Petton B, Lucasson A, Escoubas JM, Gueguen Y, Dégremont L, Mitta G, Toulza E. Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome. Front Microbiol 2020; 11:311. [PMID: 32174904 PMCID: PMC7056673 DOI: 10.3389/fmicb.2020.00311] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/12/2020] [Indexed: 01/01/2023] Open
Abstract
Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from each family were either sampled for individual microbiota analyses using 16S rRNA gene-metabarcoding or transferred into facilities to record their survival using controlled condition. As expected, all oysters from susceptible families died, and all oysters from the resistant family survived. Quantification of OsHV-1 and bacteria showed that 5 days of transplantation were long enough to contaminate oysters by POMS, but not for entering the pathogenesis process. Thus, it was possible to compare microbiota characteristics between resistant and susceptible oysters families at the early steps of infection. Strikingly, we found that microbiota evenness and abundances of Cyanobacteria (Subsection III, family I), Mycoplasmataceae, Rhodobacteraceae, and Rhodospirillaceae were significantly different between resistant and susceptible oyster families. We concluded that these microbiota characteristics might predict oyster mortalities.
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Affiliation(s)
- Camille Clerissi
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France.,PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | - Julien de Lorgeril
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Bruno Petton
- Ifremer, LEMAR UMR 6539 (Université de Bretagne Occidentale, CNRS, IRD, Ifremer), Argenton-en-Landunvez, France
| | - Aude Lucasson
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Jean-Michel Escoubas
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Yannick Gueguen
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | | | - Guillaume Mitta
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
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Lasa A, di Cesare A, Tassistro G, Borello A, Gualdi S, Furones D, Carrasco N, Cheslett D, Brechon A, Paillard C, Bidault A, Pernet F, Canesi L, Edomi P, Pallavicini A, Pruzzo C, Vezzulli L. Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy. Environ Microbiol 2019; 21:4548-4562. [PMID: 31325353 PMCID: PMC7379488 DOI: 10.1111/1462-2920.14750] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 02/05/2023]
Abstract
Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.
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Affiliation(s)
- Aide Lasa
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
- Department of Microbiology and ParasitologyUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Andrea di Cesare
- National Research Council‐Water Research Institute (CNR‐IRSA), Largo Tonolli 50, 28822VerbaniaItaly
| | - Giovanni Tassistro
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Alessio Borello
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Stefano Gualdi
- Department of Plant and Microbial BiologyUniversity of ZürichZürichSwitzerland
| | | | | | - Deborah Cheslett
- Fish Health UnitThe Marine Institute, Rinville OranmoreGalwayIreland
| | - Amanda Brechon
- Fish Health UnitThe Marine Institute, Rinville OranmoreGalwayIreland
| | - Christine Paillard
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la MUniversité de Bretagne Occidentale – UMR6539 CNRS/UBO/IRD/IfremerPlouzanéFrance
| | - Adeline Bidault
- Laboratoire des sciences de l'Environnement Marin, Institut Universitaire Européen de la MUniversité de Bretagne Occidentale – UMR6539 CNRS/UBO/IRD/IfremerPlouzanéFrance
| | - Fabrice Pernet
- Ifremer, Physiologie Fonctionnelle des Organismes MarinsUMR 6539 LEMAR (CNRS/Ifremer/IRD/UBO) Technopole Iroise, CS 1007029280PlouzaneFrance
| | - Laura Canesi
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Paolo Edomi
- Department of Life SciencesUniversity of TriesteTriesteItaly
| | | | - Carla Pruzzo
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV)University of GenoaGenoaItaly
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Jaiteh M, Taly A, Hénin J. Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PLoS One 2016; 11:e0151934. [PMID: 26986966 PMCID: PMC4795631 DOI: 10.1371/journal.pone.0151934] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/07/2016] [Indexed: 01/27/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such “Cys-less” receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the “Cys-loop” proline is absolutely conserved, suggesting the more fitting name “Pro loop” for that motif, and “Pro-loop receptors” for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.
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Affiliation(s)
- Mariama Jaiteh
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
| | - Antoine Taly
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France
- * E-mail:
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