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Biessy L, Pearman JK, Mertens KN, Réveillon D, Savar V, Hess P, Hampton H, Thompson L, Lebrun L, Terre-Terrillon A, Smith KF. Sudden peak in tetrodotoxin in French oysters during the summer of 2021: Source investigation using microscopy, metabarcoding and droplet digital PCR. Toxicon 2024; 243:107721. [PMID: 38636612 DOI: 10.1016/j.toxicon.2024.107721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
Tetrodotoxin (TTX) is a potent neurotoxin causing human intoxications from contaminated seafood worldwide and is of emerging concern in Europe. Shellfish have been shown to contain varying TTX concentrations globally, with concentrations typically higher in Pacific oysters Crassostrea gigas in Europe. Despite many decades of research, the source of TTX remains unknown, with bacterial or algal origins having been suggested. The aim of this study was to identify potential source organisms causing TTX contamination in Pacific oysters in French coastal waters, using three different techniques. Oysters were deployed in cages from April to September 2021 in an estuary where TTX was previously detected. Microscopic analyses of water samples were used to investigate potential microalgal blooms present prior or during the peak in TTX. Differences in the bacterial communities from oyster digestive glands (DG) and remaining flesh were explored using metabarcoding, and lastly, droplet digital PCR assays were developed to investigate the presence of Cephalothrix sp., one European TTX-bearing species in the DG of toxic C. gigas. Oysters analysed by liquid chromatography-tandem mass spectrometry contained quantifiable levels of TTX over a three-week period (24 June-15 July 2021), with concentrations decreasing in the DG from 424 μg/kg for the first detection to 101 μg/kg (equivalent to 74 to 17 μg/kg of total flesh), and trace levels being detected until August 13, 2021. These concentrations are the first report of the European TTX guidance levels being exceeded in French shellfish. Microscopy revealed that some microalgae bloomed during the TTX peak, (e.g., Chaetoceros spp., reaching 40,000 cells/L). Prokaryotic metabarcoding showed increases in abundance of Rubritaleaceae (genus Persicirhabdus) and Neolyngbya, before and during the TTX peak. Both phyla have previously been described as possible TTX-producers and should be investigated further. Droplet digital PCR analyses were negative for the targeted TTX-bearing genus Cephalothrix.
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Affiliation(s)
- Laura Biessy
- Cawthron Institute, Private Bag 2, Nelson, 7010, New Zealand.
| | - John K Pearman
- Cawthron Institute, Private Bag 2, Nelson, 7010, New Zealand
| | - Kenneth Neil Mertens
- Ifremer, LITTORAL Unit, Place de la Croix, BP40537, 29900, Concarneau CEDEX, France
| | | | | | | | - Hannah Hampton
- Cawthron Institute, Private Bag 2, Nelson, 7010, New Zealand
| | - Lucy Thompson
- Cawthron Institute, Private Bag 2, Nelson, 7010, New Zealand
| | - Luc Lebrun
- Ifremer, LITTORAL Unit, Place de la Croix, BP40537, 29900, Concarneau CEDEX, France
| | | | - Kirsty F Smith
- Cawthron Institute, Private Bag 2, Nelson, 7010, New Zealand
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Zhong KX, Chan AM, Collicutt B, Daspe M, Finke JF, Foss M, Green TJ, Harley CDG, Hesketh AV, Miller KM, Otto SP, Rolheiser K, Saunders R, Sutherland BJG, Suttle CA. The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification. Appl Environ Microbiol 2024; 90:e0005224. [PMID: 38466091 PMCID: PMC11022565 DOI: 10.1128/aem.00052-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/18/2024] [Indexed: 03/12/2024] Open
Abstract
Pacific oysters (Magallana gigas, a.k.a. Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and pCO2 levels (800, 1,600, and 2,800 µatm) in a fully crossed design for 3 weeks. Under all conditions, the microbiome changed over time, with a large decrease in the relative abundance of potentially pathogenic ciliates (Uronema marinum) in all treatments with time. The microbiome composition differed significantly with temperature, but not acidification, indicating that Pacific oyster spat microbiomes can be altered by ocean warming but is resilient to ocean acidification in our experiments. Microbial taxa differed in relative abundance with temperature, implying different adaptive strategies and ecological specializations among microorganisms. Additionally, a small proportion (~0.2% of the total taxa) of the relatively abundant microbial taxa were core constituents (>50% occurrence among samples) across different temperatures, pCO2 levels, or time. Some taxa, including A4b bacteria and members of the family Saprospiraceae in the phyla Chloroflexi (syn. Chloroflexota) and Bacteroidetes (syn. Bacteroidota), respectively, as well as protists in the genera Labyrinthula and Aplanochytrium in the class Labyrinthulomycetes, and Pseudoperkinsus tapetis in the class Ichthyosporea were core constituents across temperatures, pCO2 levels, and time, suggesting that they play an important, albeit unknown, role in maintaining the structural and functional stability of the Pacific oyster spat microbiome in response to ocean warming and acidification. These findings highlight the flexibility of the spat microbiome to environmental changes.IMPORTANCEPacific oysters are the most economically important and widely farmed species of oyster, and their production depends on healthy oyster spat. In turn, spat health and productivity are affected by the associated microbiota; yet, studies have not scrutinized the effects of temperature and pCO2 on the prokaryotic and eukaryotic microbiomes of spat. Here, we show that both the prokaryotic and, for the first time, eukaryotic microbiome of Pacific oyster spat are surprisingly resilient to changes in acidification, but sensitive to ocean warming. The findings have potential implications for oyster survival amid climate change and underscore the need to understand temperature and pCO2 effects on the microbiome and the cascading effects on oyster health and productivity.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy M. Chan
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Maxim Daspe
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan F. Finke
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Megan Foss
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Timothy J. Green
- Centre for Shellfish Research, Vancouver Island University, Nanaimo, British Columbia, Canada
- Department of Fisheries and Aquaculture, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Christopher D. G. Harley
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amelia V. Hesketh
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Sarah P. Otto
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Ben J. G. Sutherland
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia, Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada
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Clerissi C, Huot C, Portet A, Gourbal B, Toulza E. Covariation between microeukaryotes and bacteria associated with Planorbidae snails. PeerJ 2023; 11:e16639. [PMID: 38144201 PMCID: PMC10740603 DOI: 10.7717/peerj.16639] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/19/2023] [Indexed: 12/26/2023] Open
Abstract
Background Microbial communities associated with macroorganisms might affect host physiology and homeostasis. Bacteria are well studied in this context, but the diversity of microeukaryotes, as well as covariations with bacterial communities, remains almost unknown. Methods To study microeukaryotic communities associated with Planorbidae snails, we developed a blocking primer to reduce amplification of host DNA during metabarcoding analyses. Analyses of alpha and beta diversities were computed to describe microeukaryotes and bacteria using metabarcoding of 18S and 16S rRNA genes, respectively. Results Only three phyla (Amoebozoa, Opisthokonta and Alveolata) were dominant for microeukaryotes. Bacteria were more diverse with five dominant phyla (Proteobacteria, Bacteroidetes, Tenericutes, Planctomycetes and Actinobacteria). The composition of microeukaryotes and bacteria were correlated for the Biomphalaria glabrata species, but not for Planorbarius metidjensis. Network analysis highlighted clusters of covarying taxa. Among them, several links might reflect top-down control of bacterial populations by microeukaryotes, but also possible competition between microeukaryotes having opposite distributions (Lobosa and Ichthyosporea). The role of these taxa remains unknown, but we believe that the blocking primer developed herein offers new possibilities to study the hidden diversity of microeukaryotes within snail microbiota, and to shed light on their underestimated interactions with bacteria and hosts.
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Affiliation(s)
- Camille Clerissi
- Current Affiliation: PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France
| | - Camille Huot
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Anaïs Portet
- Current Affiliation: MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Benjamin Gourbal
- 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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The Porifera microeukaryome: Addressing the neglected associations between sponges and protists. Microbiol Res 2022; 265:127210. [PMID: 36183422 DOI: 10.1016/j.micres.2022.127210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
While bacterial and archaeal communities of sponges are intensively studied, given their importance to the animal's physiology as well as sources of several new bioactive molecules, the potential and roles of associated protists remain poorly known. Historically, culture-dependent approaches dominated the investigations of sponge-protist interactions. With the advances in omics techniques, these associations could be visualized at other equally important scales. Of the few existing studies, there is a strong tendency to focus on interactions with photosynthesizing taxa such as dinoflagellates and diatoms, with fewer works dissecting the interactions with other less common groups. In addition, there are bottlenecks and inherent biases in using primer pairs and bioinformatics approaches in the most commonly used metabarcoding studies. Thus, this review addresses the issues underlying this association, using the term "microeukaryome" to refer exclusively to protists associated with an animal host. We aim to highlight the diversity and community composition of protists associated with sponges and place them on the same level as other microorganisms already well studied in this context. Among other shortcomings, it could be observed that the biotechnological potential of the microeukaryome is still largely unexplored, possibly being a valuable source of new pharmacological compounds, enzymes and metabolic processes.
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Paillard C, Gueguen Y, Wegner KM, Bass D, Pallavicini A, Vezzulli L, Arzul I. Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture. Curr Opin Biotechnol 2022; 73:225-232. [PMID: 34571318 DOI: 10.1016/j.copbio.2021.07.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 02/08/2023]
Abstract
In bivalves, no clear-cut functional role of microbiota has yet been identified, although many publications suggest that they could be involved in nutrition or immunity of their host. In the context of climate change, integrative approaches at the crossroads of disciplines have been developed to explore the environment-host-pathogen-microbiota system. Here, we attempt to synthesize work on (1) the current methodologies to analyse bivalve microbiota, (2) the comparison of microbiota between species, between host compartments and their surrounding habitat, (3) how the bivalve microbiota are governed by environmental factors and host genetics and (4) how host-associated microorganisms act as a buffer against pathogens and/or promote recovery, and could thereby play a role in the prevention of disease or mortalities.
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Affiliation(s)
| | - Yannick Gueguen
- IHPE, Univ Montpellier, CNRS, Ifremer, UPVD, Montpellier, France.
| | - K Mathias Wegner
- Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research, Coastal Ecology, Waddensea Station Sylt, D-25992 List, Germany
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, DT4 8UB Dorset, UK; Centre for Sustainable Aquaculture Futures, University of Exeter, College of Life and Environmental Sciences, University of Exeter, EX4 4QD Exeter, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, SW7 5BD London, UK
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgeri 5, 34126 Trieste, Italy; National Institute of Oceanography and Applied Geophysics, via Piccard 54, 34151 Trieste, Italy
| | - Luigi Vezzulli
- Department of Earth, Environmental and Life Sciences (DISTAV), University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| | - Isabelle Arzul
- Ifremer, RBE-SG2M-LGPMM, Station de La Tremblade, Avenue de Mus de Loup, F-17390 La Tremblade, France.
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Zhong KX, Cho A, Deeg CM, Chan AM, Suttle CA. Revealing the composition of the eukaryotic microbiome of oyster spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS). MICROBIOME 2021; 9:230. [PMID: 34823604 PMCID: PMC8620255 DOI: 10.1186/s40168-021-01180-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The microbiome affects the health of plants and animals, including humans, and has many biological, ecological, and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. RESULTS To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that > 96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. CONCLUSION CCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences. Video Abstract.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Anna Cho
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christoph M Deeg
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Botany, The University of British Columbia, Vancouver, British Columbia, Canada.
- Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada.
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