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Heys C, Cheaib B, Busetti A, Kazlauskaite R, Maier L, Sloan WT, Ijaz UZ, Kaufmann J, McGinnity P, Llewellyn MS. Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar. Appl Environ Microbiol 2020; 86:e02283-19. [PMID: 32033945 PMCID: PMC7117918 DOI: 10.1128/aem.02283-19] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/18/2020] [Indexed: 01/31/2023] Open
Abstract
In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.
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Affiliation(s)
- C Heys
- Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - B Cheaib
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - A Busetti
- Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - R Kazlauskaite
- Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - L Maier
- Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - W T Sloan
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - U Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - J Kaufmann
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
| | - P McGinnity
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Ireland
- Marine Institute, Newport, Ireland
| | - M S Llewellyn
- Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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Jacobs A, De Noia M, Praebel K, Kanstad-Hanssen Ø, Paterno M, Jackson D, McGinnity P, Sturm A, Elmer KR, Llewellyn MS. Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach. Sci Rep 2018; 8:1203. [PMID: 29352185 PMCID: PMC5775277 DOI: 10.1038/s41598-018-19323-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/17/2017] [Indexed: 12/13/2022] Open
Abstract
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
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Affiliation(s)
- A Jacobs
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M De Noia
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - K Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - M Paterno
- Department of Biology, University of Padova, Padova, Italy
| | | | - P McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - A Sturm
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - K R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
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Llewellyn MS, Leadbeater S, Garcia C, Sylvain FE, Custodio M, Ang KP, Powell F, Carvalho GR, Creer S, Elliot J, Derome N. Parasitism perturbs the mucosal microbiome of Atlantic Salmon. Sci Rep 2017; 7:43465. [PMID: 28266549 PMCID: PMC5339869 DOI: 10.1038/srep43465] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/25/2017] [Indexed: 12/20/2022] Open
Abstract
Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.
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Affiliation(s)
| | - S. Leadbeater
- St Andrew’s Marine Station, Department of Fisheries and Oceans, New Brunswick, Canada
| | | | | | - M. Custodio
- Universidade Federale do Rondonia, Porto Vehlo, Brazil
| | | | | | - G. R. Carvalho
- Marine and Fisheries Genetics Laboratory, University of Wales, Bangor, Wales, UK
| | - S. Creer
- Marine and Fisheries Genetics Laboratory, University of Wales, Bangor, Wales, UK
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Ramírez JD, Llewellyn MS. Response to Tibayrenc and Ayala: reproductive clonality in protozoan pathogens - truth or artefact? Mol Ecol 2015; 24:5782-4. [DOI: 10.1111/mec.13442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/22/2015] [Accepted: 10/27/2015] [Indexed: 01/11/2023]
Affiliation(s)
- J. D. Ramírez
- Grupo de Investigaciones Microbiológicas - UR (GIMUR); Facultad de Ciencias Naturales y Matemáticas; Universidad del Rosario; Bogotá Colombia
| | - M. S. Llewellyn
- Institute of Biodiversity; Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
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