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Microbial Ecology of Atlantic Salmon (Salmo salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Appl Environ Microbiol 2020; 86:AEM.00411-20. [PMID: 32303543 DOI: 10.1128/aem.00411-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 12/19/2022] Open
Abstract
Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
Aquaculture is the fastest-growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crop and livestock production, aquaculture production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.
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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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Horlick J, Booth MA, Tetu SG. Alternative dietary protein and water temperature influence the skin and gut microbial communities of yellowtail kingfish ( Seriola lalandi). PeerJ 2020; 8:e8705. [PMID: 32219022 PMCID: PMC7085898 DOI: 10.7717/peerj.8705] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/06/2020] [Indexed: 01/21/2023] Open
Abstract
Fish skin and gut microbiomes contribute to host health and growth and are often significantly different in aquaculture-reared fish compared to wild fish. Determining how factors associated with aquaculture, including altered diet and abiotic conditions, affect the microbiome will assist with optimizing farming practices and non-invasively assessing fish health. Here, juvenile yellowtail kingfish (Seriola lalandi) housed at optimal (22 °C) and non-optimal (26 °C) water temperature were fed a fishmeal control diet or the same diet substituted with 30% soy-protein concentrate (SPC) in order to investigate impacts on host health and the microbial community composition of the skin mucosa, gut mucosa and digesta. Each of these sites was observed to have a distinct microbiome composition. The combination of SPC and housing at 26 °C significantly reduced weight gain in yellowtail kingfish and affected immune parameters. The overall microbial composition and relative abundance of specific operational taxonomic units (OTUs) was also significantly altered by inclusion of SPC at 26 °C, with a notable increase in an OTU identified as Photobacterium in the skin mucosa and digesta. Increased relative abundance of Photobacterium sp. was significantly correlated with reduced levels of digesta myeloperoxidase in yellowtail kingfish; a recognized innate immunity defense mechanism. The changes in the microbial communities of yellowtail kingfish fed a diet containing 30% SPC at 26 °C highlights the importance of considering the interactive effects of diet and environmental factors on microbiome health in farmed yellowtail kingfish.
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Affiliation(s)
- Jack Horlick
- Department of Molecular Science, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Mark A Booth
- NSW Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, NSW, Australia
| | - Sasha G Tetu
- Department of Molecular Science, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
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54
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Uren Webster TM, Rodriguez-Barreto D, Castaldo G, Gough P, Consuegra S, Garcia de Leaniz C. Environmental plasticity and colonisation history in the Atlantic salmon microbiome: A translocation experiment. Mol Ecol 2020; 29:886-898. [PMID: 32011775 PMCID: PMC7078932 DOI: 10.1111/mec.15369] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 01/11/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for nonmammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between artificial and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for 6 weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterized the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive microbiome plasticity for both the gut and skin, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable effects of fish origin, and there was also a near-complete turnover in microbiome structure. However, we also identified, for the first time in fish, evidence of historical colonisation effects reflecting early-life experience, including ASVs characteristic of captive rearing. These results have important implications for host adaptation to local selective pressures, and highlight how conditions experienced during early life can have a long-term influence on the microbiome and, potentially, host health.
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Affiliation(s)
- Tamsyn M Uren Webster
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | | | - Giovanni Castaldo
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Peter Gough
- Cynrig Fish Culture Unit, Natural Resources Wales, Llanfrynach, UK
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, College of Science, Swansea University, Swansea, UK
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55
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Krotman Y, Yergaliyev TM, Alexander Shani R, Avrahami Y, Szitenberg A. Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system. MICROBIOME 2020; 8:9. [PMID: 32005134 PMCID: PMC6995075 DOI: 10.1186/s40168-020-0784-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/05/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. RESULTS Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. CONCLUSIONS Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.
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Affiliation(s)
| | - Timur M Yergaliyev
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel
| | | | - Yosef Avrahami
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel
| | - Amir Szitenberg
- Dead Sea and Arava Science Center, Dead Sea Branch, 8693500, Masada, Israel.
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56
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Bird S, Prewer E, Kutz S, Leclerc L, Vilaça ST, Kyle CJ. Geography, seasonality, and host-associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal. Ecol Evol 2019; 9:13202-13217. [PMID: 31871639 PMCID: PMC6912892 DOI: 10.1002/ece3.5768] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022] Open
Abstract
The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture, and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007-2016), and host genetic structure on population-level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters. These clusters are defined by Arctic Mainland and Island populations, including the following: (a) two mainland sampling locations of the Northwest Territories and Nunavut and (b) four locations of Victoria Island. Between these geographic populations, we found that differences in the microbiome reflected host-associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population-level structure in driving fecal microbiome differences in a large Arctic mammal.
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Affiliation(s)
- Samantha Bird
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
| | - Erin Prewer
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
| | - Susan Kutz
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
- Canadian Wildlife Health CooperativeAlberta NodeFaculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
| | | | - Sibelle T. Vilaça
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
- Biology DepartmentTrent UniversityPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science ProgramTrent UniversityPeterboroughONCanada
- Environmental and Life Sciences Graduate ProgramTrent UniversityPeterboroughONCanada
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57
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Fonseca F, Cerqueira R, Fuentes J. Impact of Ocean Acidification on the Intestinal Microbiota of the Marine Sea Bream ( Sparus aurata L.). Front Physiol 2019; 10:1446. [PMID: 31849701 PMCID: PMC6893888 DOI: 10.3389/fphys.2019.01446] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/08/2019] [Indexed: 02/06/2023] Open
Abstract
Within a scenario of increasing atmospheric CO2 and ocean acidification (OA), it is highly relevant to investigate its impacts not only on fish performance but also on fish intestinal microbiome and how that reflects on host performance and health. The main objective of this study was to establish if the intestinal microbiota of the sea bream (Sparus aurata) was affected by high level of CO2 in line with the predictions for this century. The bacterial communities of the intestinal fluid were characterized in animals kept at the present-day level of CO2 (400 μatm) and in animals switched to high CO2 (1200 μatm) for 1 month. Bacterial taxa identification was based on molecular methods, using the DNA coding for the 16S ribosomal RNA and primers targeting the regions V1-V3. Amplicons obtained from DNA samples of animals in the same tank were combined, cloned to obtain a bacterial DNA library, and the clones were sequenced. No significant differences were found between the two treatments for alpha diversity. However, beta diversity analysis revealed distinct dysbiosis in response to hypercapnia, with phylum Firmicutes absent from the bacterial communities of fish exposed to 1200 μatm CO2, whereas Proteobacteria relative abundance was increased at elevated CO2, due to the presence of Gammaproteobacteria (Vibrionaceae and Alteromonadaceae), a class not present in the control samples. This study provides a first glimpse at the impact of OA in fish intestinal microbiota and highlights potential downstream effects to the general condition of fishes under hypercapnia.
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Affiliation(s)
- Filomena Fonseca
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
| | - Ricardo Cerqueira
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Juan Fuentes
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
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58
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Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ, Preziosi RF. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 2019; 88:1684-1695. [PMID: 31325164 PMCID: PMC6899969 DOI: 10.1111/1365-2656.13065] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
Abstract
Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.
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Affiliation(s)
- Sarah M. Griffiths
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Donald C. Behringer
- Fisheries and Aquatic SciencesUniversity of FloridaGainesvilleFLUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Mark J. Butler
- Department of Biological SciencesOld Dominion UniversityNorfolkVAUSA
| | - Richard F. Preziosi
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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Chiarello M, Paz-Vinas I, Veyssière C, Santoul F, Loot G, Ferriol J, Boulêtreau S. Environmental conditions and neutral processes shape the skin microbiome of European catfish (Silurus glanis) populations of Southwestern France. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:605-614. [PMID: 31162878 DOI: 10.1111/1758-2229.12774] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/03/2019] [Indexed: 05/22/2023]
Abstract
Teleost fishes interact with diverse microbial communities, playing crucial functions for host fitness. While gut microbiome has been extensively studied, skin microbiome has been overlooked. Specifically, there is no assessment of the relative impact of host and environmental factors on microbiome variability as well as neutral processes shaping fish skin microbiome. Here, we assessed the skin microbiome of a Siluriforme, the European catfish (Silurus glanis) sampled in four sites located in Southwestern France. We assessed the relative roles of individual features (body size and genetic background), local environment and neutral processes in shaping skin microbiome. Catfish skin microbiome composition was distinct to that of other freshwater fish species previously studied with high abundances of Gammaproteobacteria and Bacteroidetes. We found no effect of catfish individual genotype and body size on the structure of its associated skin microbiome. Geographical location was the best catfish skin microbiome structure predictor, together with neutral models of microbiome assembly.
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Affiliation(s)
- Marlène Chiarello
- EcoLab, Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Ivan Paz-Vinas
- EcoLab, Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Charlotte Veyssière
- EDB, Laboratoire Évolution et Diversité Biologique, Université de Toulouse, CNRS, ENSFEA, IRD, Toulouse, France
| | - Frédéric Santoul
- EcoLab, Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Géraldine Loot
- EDB, Laboratoire Évolution et Diversité Biologique, Université de Toulouse, CNRS, ENSFEA, IRD, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
| | - Jessica Ferriol
- EcoLab, Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Stéphanie Boulêtreau
- EcoLab, Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
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Räihä V, Sundberg L, Ashrafi R, Hyvärinen P, Karvonen A. Rearing background and exposure environment together explain higher survival of aquaculture fish during a bacterial outbreak. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ville Räihä
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
| | - Lotta‐Riina Sundberg
- Department of Biological and Environmental Science and Nanoscience Center Centre of Excellence in Biological Interactions University of Jyväskylä Jyväskylä Finland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
| | - Pekka Hyvärinen
- Aquatic Population Dynamics Natural Resources Institute Finland (Luke) Paltamo Finland
| | - Anssi Karvonen
- Department of Biological and Environmental Science University of Jyväskylä Jyväskylä Finland
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61
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Tarnecki AM, Brennan NP, Schloesser RW, Rhody NR. Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild. MICROBIAL ECOLOGY 2019; 77:770-781. [PMID: 30191255 PMCID: PMC6469608 DOI: 10.1007/s00248-018-1252-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/29/2018] [Indexed: 05/22/2023]
Abstract
The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.
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Affiliation(s)
- Andrea M Tarnecki
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA.
| | - Nathan P Brennan
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Ryan W Schloesser
- Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA
| | - Nicole R Rhody
- Mote Aquaculture Research Park, 874 WR Mote Way, Sarasota, FL, 34240, USA
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62
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Brown RM, Wiens GD, Salinas I. Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). FISH & SHELLFISH IMMUNOLOGY 2019; 86:497-506. [PMID: 30513381 PMCID: PMC8040288 DOI: 10.1016/j.fsi.2018.11.079] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/25/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
Commensal microorganisms present at mucosal surfaces play a vital role in protecting the host organism from bacterial infection. There are multiple factors that contribute to selecting for the microbiome, including host genetics. Flavobacterium psychrophilum, the causative agent of Bacterial Cold Water Disease in salmonids, accounts for acute losses in wild and farmed rainbow trout (Oncorhynchus mykiss). The U.S. National Center for Cool and Cold Water Aquaculture has used family-based selective breeding to generate a line of rainbow trout with enhanced resistance to F. psychrophilum. The goal of this study is to determine whether selective breeding impacts the gut and gill microbiome of the F. psychrophilum-resistant as compared to a background matched susceptible trout line. Mid-gut and gill samples were collected from juvenile fish maintained at high or low stocking densities and microbial diversity assessed by 16S rDNA amplicon sequencing. Results indicate that alpha diversity was significantly higher in the mid-gut of the susceptible line compared to the resistant line, while no significant differences in alpha diversity were observed in the gills. Mycoplasma sp. was the dominant taxon in the mid-gut of both groups, although it was present at a decreased abundance in the susceptible line. We also observed an increased abundance of the potential opportunistic pathogen Brevinema andersonii in the susceptible line. Within the gills, both lines exhibited similar microbial profiles, with Candidatus Branchiomonas being the dominant taxon. Together, these results suggest that selectively bred F. psychrophilum-resistant trout may harness a more resilient gut microbiome, attributing to the disease resistant phenotype. Importantly, interactions between host genetics and environmental factors such as stocking density have a significant impact in shaping trout microbial communities.
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Affiliation(s)
- Ryan M Brown
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agriculture Research Service, United States Department of Agriculture Kearneysville, WV, USA
| | - Irene Salinas
- University of New Mexico, Department of Biology, Center for Evolutionary and Theoretical Immunology (CETI), Albuquerque, NM, USA.
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63
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Houston RD, Macqueen DJ. Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding. Anim Genet 2019; 50:3-14. [PMID: 30426521 PMCID: PMC6492011 DOI: 10.1111/age.12748] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Atlantic salmon (Salmo salar L.) is among the most iconic and economically important fish species and was the first member of Salmonidae to have a high-quality reference genome assembly published. Advances in genomics have become increasingly central to the genetic improvement of farmed Atlantic salmon as well as conservation of wild salmon stocks. The salmon genome has also been pivotal in shaping our understanding of the evolutionary and functional consequences arising from an ancestral whole-genome duplication event characterising all Salmonidae members. Here, we provide a review of the current status of Atlantic salmon genetics and genomics, focussed on progress made from genome-wide research aimed at improving aquaculture production and enhancing understanding of salmonid ecology, physiology and evolution. We present our views on the future direction of salmon genomics, including the role of emerging technologies (e.g. genome editing) in elucidating genetic features that underpin functional variation in traits of commercial and evolutionary importance.
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Affiliation(s)
- R. D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghMidlothianEH25 9RGUK
| | - D. J. Macqueen
- School of Biological SciencesUniversity of AberdeenAberdeenAB24 2TZUK
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Gupta S, Fečkaninová A, Lokesh J, Koščová J, Sørensen M, Fernandes J, Kiron V. Lactobacillus Dominate in the Intestine of Atlantic Salmon Fed Dietary Probiotics. Front Microbiol 2019; 9:3247. [PMID: 30700981 PMCID: PMC6343587 DOI: 10.3389/fmicb.2018.03247] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Probiotics, the live microbial strains incorporated as dietary supplements, are known to provide health benefits to the host. These live microbes manipulate the gut microbial community by suppressing the growth of certain intestinal microbes while enhancing the establishment of some others. Lactic acid bacteria (LAB) have been widely studied as probiotics; in this study we have elucidated the effects of two fish-derived LAB types (RII and RIII) on the distal intestinal microbial communities of Atlantic salmon (Salmo salar). We employed high-throughput 16S rRNA gene amplicon sequencing to investigate the bacterial communities in the distal intestinal content and mucus of Atlantic salmon fed diets coated with the LABs or that did not have microbes included in it. Our results show that the supplementation of the microbes shifts the intestinal microbial profile differentially. LAB supplementation did not cause any significant alterations in the alpha diversity of the intestinal content bacteria but RIII feeding increased the bacterial diversity in the intestinal mucus of the fish. Beta diversity analysis revealed significant differences between the bacterial compositions of the control and LAB-fed groups. Lactobacillus was the dominant genus in LAB-fed fish. A few members of the phyla Tenericutes, Proteobacteria, Actinobacteria, and Spirochaetes were also found to be abundant in the LAB-fed groups. Furthermore, the bacterial association network analysis showed that the co-occurrence pattern of bacteria of the three study groups were different. Dietary probiotics can modulate the composition and interaction of the intestinal microbiota of Atlantic salmon.
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Affiliation(s)
- Shruti Gupta
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Adriána Fečkaninová
- Department of Food Hygiene and Technology, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Jep Lokesh
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jana Koščová
- Department of Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Mette Sørensen
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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