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Bell AG, McMurtrie J, Bolaños LM, Cable J, Temperton B, Tyler CR. Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome. FEMS Microbiol Ecol 2024; 100:fiae021. [PMID: 38366921 PMCID: PMC10903987 DOI: 10.1093/femsec/fiae021] [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: 12/05/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
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Affiliation(s)
- Ashley G Bell
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Luis M Bolaños
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Ben Temperton
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Charles R Tyler
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
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2
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Berggren H, Nordahl O, Yıldırım Y, Larsson P, Tibblin P, Forsman A. Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish. Proc Biol Sci 2023; 290:20231608. [PMID: 38113936 PMCID: PMC10730295 DOI: 10.1098/rspb.2023.1608] [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: 11/11/2022] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Oscar Nordahl
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial model Systems, EEMiS Department of Biology and Environmental Science, Linnaeus University, 391 82 Kalmar, Sweden
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Sadeghi J, Chaganti SR, Johnson TB, Heath DD. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome. MICROBIOME 2023; 11:258. [PMID: 37981701 PMCID: PMC10658978 DOI: 10.1186/s40168-023-01697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/11/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation. RESULTS We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. CONCLUSIONS Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA
| | - Timothy B Johnson
- Ontario Ministry of Natural Resources and Forestry, Glenora Fisheries Station, Picton, ON, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Ochoa-Sánchez M, Acuña Gomez EP, Moreno L, Moraga CA, Gaete K, Eguiarte LE, Souza V. Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns. PeerJ 2023; 11:e16290. [PMID: 37933257 PMCID: PMC10625763 DOI: 10.7717/peerj.16290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023] Open
Abstract
Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lucila Moreno
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Claudio A. Moraga
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Katherine Gaete
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Valeria Souza
- Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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Wang LC, Chen LH, Chiu YC, Liou CY, Chen HC, Lu CY, Chen JL. Teleost skin microbiome: An intimate interplay between the environment and the host immunity. FISH & SHELLFISH IMMUNOLOGY 2023; 139:108869. [PMID: 37285875 DOI: 10.1016/j.fsi.2023.108869] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/22/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The mucosal microbiome plays a role in regulating host health. The research conducted in humans and mice has governed and detailed the information on microbiome-host immunity interactions. Teleost fish, different from humans and mice, lives in and relies on the aquatic environment and is subjected to environmental variation. The growth of teleost mucosal microbiome studies, the majority in the gastrointestinal tract, has emphasized the essential role of the teleost microbiome in growth and health. However, research in the teleost external surface microbiome, as the skin microbiome, has just started. In this review, we examine the general findings in the colonization of the skin microbiome, how the skin microbiome is subjected to environmental change and the reciprocal regulation with the host immune system, and the current challenges that potential study models can address. The information collected from teleost skin microbiome-host immunity research would help future teleost culturing from the potential parasitic infestation and bacterial infection as foreseeing growing threats.
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Affiliation(s)
- Liang-Chun Wang
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Committee of Fisheries Extension Service, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan.
| | - Li-Hsuan Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan; Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Yu-Che Chiu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chung-Yi Liou
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Han-Chung Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chia-Yun Lu
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Jian-Lin Chen
- Marine and Pathogenic Microbiology Laboratory, Department of Marine Biotechnology and Resources, College of Marine Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
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Tsoukalas D, Hoel S, Lerfall J, Jakobsen AN. Photobacterium predominate the microbial communities of muscle of European plaice (Pleuronectes platessa) caught in the Norwegian sea independent of skin and gills microbiota, fishing season, and storage conditions. Int J Food Microbiol 2023; 397:110222. [PMID: 37099863 DOI: 10.1016/j.ijfoodmicro.2023.110222] [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: 02/09/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023]
Abstract
The aim of this study was to investigate seasonal variations (September, December and April) in the initial microbial communities of skin and gills' external mucosal tissues (EMT) and muscle of European plaice (Pleuronectes platessa). Moreover, a potential relationship between EMT and fresh muscle microbiota was examined. The microbial community succession in plaice muscle as a function of fishing season and storage conditions was also investigated. The selected seasons for the storage experiment were September and April. Investigated storage conditions were; fillets packaged in either vacuum or modified atmosphere (70 % CO2, 20 % N2, 10 % O2) and chilled/refrigerated conditions (4 °C). Whole fish stored on ice (0 °C) was selected as a commercial standard. Seasonal variations were detected in the initial microbial communities of EMT and plaice muscle. The highest microbial diversity was found in EMT and muscle of April-caught plaice, followed by December and September catch indicating the important role of environmental factors in shaping the initial EMT and muscle microbial communities. The EMT microbial communities were more diverse than fresh muscle samples. The low number of shared taxa between EMT and initial muscle microbial communities indicates that only a minor part of the muscle microbiota came from the EMT. Psychrobacter and Photobacterium were the predominant genera in the EMT microbial communities in all seasons. Photobacterium dominated the initial muscle microbial communities with a gradual seasonal reduction of its abundance from September to April. Storage time and storage conditions shaped a less diverse and distinct community compared to the fresh muscle. However, no clear separation was seen between the communities at the middle and end of storage time. Regardless of EMT microbiota, fishing season and storage conditions, Photobacterium dominated the microbial communities of stored muscle samples. The Photobacterium prevalence as the primary specific spoilage organism (SSO) could be attributed to its high relative abundance in the initial microbiota of muscle and its CO2-tolerance. The findings of this study indicate the important contribution of Photobacterium to the microbial spoilage of plaice. Thus, the development of innovative preservation techniques addressing the rapid growth of Photobacterium could contribute to the production of high-quality and shelf-stable convenient retail plaice products.
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Affiliation(s)
- Dionysios Tsoukalas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway.
| | - Sunniva Hoel
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Jørgen Lerfall
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Anita Nordeng Jakobsen
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
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Dragičević P, Bielen A, Žučko J, Hudina S. The mycobiome of a successful crayfish invader and its changes along the environmental gradient. Anim Microbiome 2023; 5:23. [PMID: 37041598 PMCID: PMC10088235 DOI: 10.1186/s42523-023-00245-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/26/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The microbiome plays an important role in biological invasions, since it affects various interactions between host and environment. However, most studies focus on the bacteriome, insufficiently addressing other components of the microbiome such as the mycobiome. Microbial fungi are among the most damaging pathogens in freshwater crayfish populations, colonizing and infecting both native and invasive crayfish species. Invading crayfish may transmit novel fungal species to native populations, but also, dispersal process and characteristics of the novel environment may affect the invaders' mycobiome composition, directly and indirectly affecting their fitness and invasion success. This study analyzes the mycobiome of a successful invader in Europe, the signal crayfish, using the ITS rRNA amplicon sequencing approach. We explored the mycobiomes of crayfish samples (exoskeletal biofilm, hemolymph, hepatopancreas, intestine), compared them to environmental samples (water, sediment), and examined the differences in fungal diversity and abundance between upstream and downstream segments of the signal crayfish invasion range in the Korana River, Croatia. RESULTS A low number of ASVs (indicating low abundance and/or diversity of fungal taxa) was obtained in hemolymph and hepatopancreas samples. Thus, only exoskeleton, intestine, sediment and water samples were analyzed further. Significant differences were recorded between their mycobiomes, confirming their uniqueness. Generally, environmental mycobiomes showed higher diversity than crayfish-associated mycobiomes. The intestinal mycobiome showed significantly lower richness compared to other mycobiomes. Significant differences in the diversity of sediment and exoskeletal mycobiomes were recorded between different river segments (but not for water and intestinal mycobiomes). Together with the high observed portion of shared ASVs between sediment and exoskeleton, this indicates that the environment (i.e. sediment mycobiome) at least partly shapes the exoskeletal mycobiome of crayfish. CONCLUSION This study presents the first data on crayfish-associated fungal communities across different tissues, which is valuable given the lack of studies on the crayfish mycobiome. We demonstrate significant differences in the crayfish exoskeletal mycobiome along the invasion range, suggesting that different local environmental conditions may shape the exoskeletal mycobiome during range expansion, while the mycobiome of the internal organ (intestine) remained more stable. Our results provide a basis for assessing how the mycobiome contributes to the overall health of the signal crayfish and its further invasion success.
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Affiliation(s)
- Paula Dragičević
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
| | - Ana Bielen
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Jurica Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, Zagreb, Croatia
| | - Sandra Hudina
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Pereira A, Soares MC, Santos T, Poças A, Pérez-Losada M, Apprill A, Sikkel PC, Xavier R. Reef Location and Client Diversity Influence the Skin Microbiome of the Caribbean Cleaner Goby Elacatinus evelynae. MICROBIAL ECOLOGY 2023; 85:372-382. [PMID: 35275230 DOI: 10.1007/s00248-022-01984-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Fish-associated microorganisms are known to be affected by the environment and other external factors, such as microbial transfer between interacting partners. One of the most iconic mutualistic interactions on coral reefs is the cleaning interactions between cleaner fishes and their clients, during which direct physical contact occurs. Here, we characterized the skin bacteria of the Caribbean cleaner sharknose goby, Elacatinus evelynae, in four coral reefs of the US Virgin Islands using sequencing of the V4 region of the 16S rRNA gene. We specifically tested the relationship between gobies' level of interaction with clients and skin microbiota diversity and composition. Our results showed differences in microbial alpha- and beta-diversity in the skin of gobies from different reef habitats and high inter-individual variation in microbiota diversity and structure. Overall, the results showed that fish-to-fish direct contact and specifically, access to a diverse clientele, influences the bacterial diversity and structure of cleaner gobies' skin. Because of their frequent contact with clients, and therefore, high potential for microbial exchange, cleaner fish may serve as models in future studies aiming to understand the role of social microbial transfer in reef fish communities.
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Affiliation(s)
- Ana Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, 4099-002, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal.
| | - Marta C Soares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Teresa Santos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Ana Poças
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052, USA
| | - Amy Apprill
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Paul C Sikkel
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
- Water Research Group, Unit for Environmental Sciences and Management, Potchefstroom Campus, North West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Raquel Xavier
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
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Gadoin E, Desnues C, Bouvier T, Roque D'orbcastel E, Auguet JC, Crochemore S, Adingra A, Bettarel Y. Tracking spoilage bacteria in the tuna microbiome. FEMS Microbiol Ecol 2022; 98:6702722. [PMID: 36124730 DOI: 10.1093/femsec/fiac110] [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: 03/15/2022] [Revised: 09/03/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022] Open
Abstract
Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.
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Affiliation(s)
- Elsa Gadoin
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
| | - Christelle Desnues
- Campus Technologique et Scientifique de Luminy, 163 avenue de Luminy - Bat. Méditerranée, 13288 Marseille, France
| | - Thierry Bouvier
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
| | - Emmanuelle Roque D'orbcastel
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
| | - Jean-Christophe Auguet
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
| | - Sandrine Crochemore
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
| | - Antoinette Adingra
- Centre de Recherche Océanologiques (CRO)- 29 rue des pêcheurs, Zone 3, Treichville, BP V 18 00225 Abidjan, Cote d'Ivoire
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation and Conservation, Université Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon 34090, Montpellier, France
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Nakatani H, Yamada N, Hashimoto N, Okazaki F, Arakawa T, Tamaru Y, Hori K. Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture. BIOLOGY 2022; 11:biology11081249. [PMID: 36009876 PMCID: PMC9405476 DOI: 10.3390/biology11081249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022]
Abstract
The bacterial flora of the epidermal mucus of fish is closely associated with the host’s health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.
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Affiliation(s)
- Hajime Nakatani
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Aichi, Japan
| | - Naoki Yamada
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Aichi, Japan
| | - Naoki Hashimoto
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Mie, Japan
| | - Fumiyoshi Okazaki
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Mie, Japan
| | - Tomoko Arakawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Aichi, Japan
| | - Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Mie, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Aichi, Japan
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11
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Clavere-Graciette AG, McWhirt ME, Hoopes LA, Bassos-Hull K, Wilkinson KA, Stewart FJ, Pratte ZA. Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari). Anim Microbiome 2022; 4:34. [PMID: 35606841 PMCID: PMC9128078 DOI: 10.1186/s42523-022-00187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 05/09/2022] [Indexed: 11/15/2022] Open
Abstract
Background Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a ‘natural’ host microbiome. Focusing on an endangered elasmobranch species—the whitespotted eagle ray Aetobatus narinari—we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.
Results Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.
Conclusion For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00187-8.
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Affiliation(s)
| | - Mary E McWhirt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lisa A Hoopes
- Department of Research and Conservation, Georgia Aquarium, Atlanta, GA, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. .,Department of Microbiology & Cell Biology, Montana State University, Bozeman, MT, USA.
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12
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Chiarello M, Bucholz JR, McCauley M, Vaughn SN, Hopper GW, Sánchez González I, Atkinson CL, Lozier JD, Jackson CR. Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species ( Corbicula fluminea). Front Microbiol 2022; 13:800061. [PMID: 35444631 PMCID: PMC9014210 DOI: 10.3389/fmicb.2022.800061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Abstract
The Asian clam Corbicula fluminea (Family: Cyneridae) has aggressively invaded freshwater habitats worldwide, resulting in dramatic ecological changes and declines of native bivalves such as freshwater mussels (Family: Unionidae), one of the most imperiled faunal groups. Despite increases in our knowledge of invasive C. fluminea biology, little is known of how intrinsic and extrinsic factors, including co-occurring native species, influence its microbiome. We investigated the gut bacterial microbiome across genetically differentiated populations of C. fluminea in the Tennessee and Mobile River Basins in the Southeastern United States and compared them to those of six co-occurring species of native freshwater mussels. The gut microbiome of C. fluminea was diverse, differed with environmental conditions and varied spatially among rivers, but was unrelated to host genetic variation. Microbial source tracking suggested that the gut microbiome of C. fluminea may be influenced by the presence of co-occurring native mussels. Inferred functions from 16S rRNA gene data using PICRUST2 predicted a high prevalence and diversity of degradation functions in the C. fluminea microbiome, especially the degradation of carbohydrates and aromatic compounds. Such modularity and functional diversity of the microbiome of C. fluminea may be an asset, allowing to acclimate to an extensive range of nutritional sources in invaded habitats, which could play a vital role in its invasive success.
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Affiliation(s)
- Marlène Chiarello
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Jamie R Bucholz
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Mark McCauley
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Stephanie N Vaughn
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | - Garrett W Hopper
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | | | - Carla L Atkinson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Jeffrey D Lozier
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Colin R Jackson
- Department of Biology, University of Mississippi, Oxford, MS, United States
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13
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Scheifler M, Sanchez-Brosseau S, Magnanou E, Desdevises Y. Diversity and structure of sparids external microbiota (Teleostei) and its link with monogenean ectoparasites. Anim Microbiome 2022; 4:27. [PMID: 35418308 PMCID: PMC9009028 DOI: 10.1186/s42523-022-00180-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/03/2022] [Indexed: 12/31/2022] Open
Abstract
Background Animal-associated microbial communities appear to be key factors in host physiology, ecology, evolution and its interactions with the surrounding environment. Teleost fish have received relatively little attention in the study of surface-associated microbiota. Besides the important role of microbiota in homeostasis and infection prevention, a few recent studies have shown that fish mucus microbiota may interact with and attract some specific parasitic species. However, our understanding of external microbial assemblages, in particular regarding the factors that determine their composition and potential interactions with parasites, is still limited. This is the objective of the present study that focuses on a well-known fish-parasite interaction, involving the Sparidae (Teleostei), and their specific monogenean ectoparasites of the Lamellodiscus genus. We characterized the skin and gill mucus bacterial communities using a 16S rRNA amplicon sequencing, tested how fish ecological traits and host evolutionary history are related to external microbiota, and assessed if some microbial taxa are related to some Lamellodiscus species. Results Our results revealed significant differences between skin and gill microbiota in terms of diversity and structure, and that sparids establish and maintain tissue and species-specific bacterial communities despite continuous exposure to water. No phylosymbiosis pattern was detected for either gill or skin microbiota, suggesting that other host-related and environmental factors are a better regulator of host-microbiota interactions. Diversity and structure of external microbiota were explained by host traits: host species, diet and body part. Numerous correlations between the abundance of given bacterial genera and the abundance of given Lamellodiscus species have been found in gill mucus, including species-specific associations. We also found that the external microbiota of the only unparasitized sparid species in this study, Boops boops, harbored significantly more Fusobacteria and three genera, Shewenella, Cetobacterium and Vibrio, compared to the other sparid species, suggesting their potential involvement in preventing monogenean infection. Conclusions This study is the first to explore the diversity and structure of skin and gill microbiota from a wild fish family and present novel evidence on the links between gill microbiota and monogenean species in diversity and abundance, paving the way for further studies on understanding host-microbiota-parasite interactions. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00180-1.
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Affiliation(s)
- Mathilde Scheifler
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France.
| | - Sophie Sanchez-Brosseau
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Elodie Magnanou
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
| | - Yves Desdevises
- Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, Sorbonne Université - CNRS, 66650, Banyuls/Mer, France
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14
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Chiarello M, McCauley M, Villéger S, Jackson CR. Ranking the biases: The choice of OTUs vs. ASVs in 16S rRNA amplicon data analysis has stronger effects on diversity measures than rarefaction and OTU identity threshold. PLoS One 2022; 17:e0264443. [PMID: 35202411 PMCID: PMC8870492 DOI: 10.1371/journal.pone.0264443] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline’s effect, OTU threshold and rarefaction had a minimal impact on all measurements.
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Affiliation(s)
- Marlène Chiarello
- Department of Biology, University of Mississippi, University, MS, United States of America
- * E-mail:
| | - Mark McCauley
- Department of Biology, University of Mississippi, University, MS, United States of America
| | - Sébastien Villéger
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Colin R. Jackson
- Department of Biology, University of Mississippi, University, MS, United States of America
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15
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Sultana S, Khan MN, Hossain MS, Dai J, Rahman MS, Salimullah M. Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis. Front Microbiol 2022; 13:856014. [PMID: 35295300 PMCID: PMC8918984 DOI: 10.3389/fmicb.2022.856014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/08/2022] [Indexed: 12/03/2022] Open
Abstract
The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.
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Affiliation(s)
- Shirin Sultana
- Aquatic Animal Health Group, Department of Fisheries, University of Dhaka, Dhaka, Bangladesh
- Fisheries Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Md. Nasir Khan
- Fisheries Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Jingcheng Dai
- School of Life Sciences and Technology, Wuhan Polytechnique University, Wuhan, China
| | - Mohammad Shamsur Rahman
- Aquatic Animal Health Group, Department of Fisheries, University of Dhaka, Dhaka, Bangladesh
| | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
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16
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Yu C, Zhang C, Salisu A, Wang Y. Comparison of the Intestinal Bacteria Between Black Seabass Centropristis striata Reared in Recirculating Aquaculture System and Net Pen. Curr Microbiol 2022; 79:109. [PMID: 35175391 DOI: 10.1007/s00284-022-02789-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/26/2022] [Indexed: 11/03/2022]
Abstract
Determination of diversity and function of the bacteria in fish gut is essential to understanding the interaction between intestinal bacteria and their host organism. This study compared intestinal bacterial community of black seabass (Centropristis striata) hatched by the same breeding farm but reared in different aquaculture systems, an indoor recirculating aquaculture system (RAS) and an inshore net pen (INP). The fish were fed with formulated feed manufactured by same feed company. Bacteria in fish gut, formulated feed and seawater were identified by 16S rRNA high throughout sequencing (HTS). Total 1484 OTUs, which belonged to 34 phyla and 79 genera, were identified from fish gut, formulated feed and seawater. In fish gut, 24 phyla and 43 genera were identified. Proteobacteria, Fusobacteria, and Firmicutes dominated at the phylum level in fish gut in INP, while Proteobacteria and Firmicutes dominated in fish gut in RAS. Photobacterium, Vibrio, and Cetobacterium dominated at the genus level in fish gut in both INP and RAS. One OTU of Photobacterium occurred in all the fish gut samples, suggesting this bacterium might be the main component of the core microbiota. No significant difference was found in bacterial diversity in fish gut between INP and RAS, suggesting genetic background should be a primary factor determining intestinal bacterial community of black seabass. Bacterial diversity in seawater was high relative to that in fish gut and formulated feed, regardless in INP or RAS. The common OTU between fish gut and seawater was more than that between fish gut and formulated feed in INP, while the common OTU between fish gut and seawater was slightly less than that between fish gut and formulated feed in RAS. These results reveal that the bacteria in formulated feed and seawater could influence the bacteria in fish gut, and their priority in shaping intestinal bacterial community depended on the bacterial composition in feed and seawater. This study reveals that intestinal bacterial community of black seabass was influenced by both genetic background and environmental factors.
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Affiliation(s)
- Cong Yu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Chen Zhang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Abba Salisu
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China.,Department of Biological Sciences, Bayero University, Kano, PMB 3011, Nigeria
| | - Yan Wang
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, People's Republic of China.
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17
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Berggren H, Tibblin P, Yıldırım Y, Broman E, Larsson P, Lundin D, Forsman A. Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals. Front Microbiol 2022; 12:767770. [PMID: 35126324 PMCID: PMC8813977 DOI: 10.3389/fmicb.2021.767770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fish skin-associated microbial communities are highly variable among populations and species and can impact host fitness. Still, the sources of variation in microbiome composition, and particularly how they vary among and within host individuals, have rarely been investigated. To tackle this issue, we explored patterns of variation in fish skin microbiomes across different spatial scales. We conducted replicate sampling of dorsal and ventral body sites of perch (Perca fluviatilis) from two populations and characterized the variation of fish skin-associated microbial communities with 16S rRNA gene metabarcoding. Results showed a high similarity of microbiome samples taken from the left and right side of the same fish individuals, suggesting that fish skin microbiomes can be reliably assessed and characterized even using a single sample from a specific body site. The microbiome composition of fish skin differed markedly from the bacterioplankton communities in the surrounding water and was highly variable among individuals. No ASV was present in all samples, and the most prevalent phyla, Actinobacteria, Bacteroidetes, and Proteobacteria, varied in relative abundance among fish hosts. Microbiome composition was both individual- and population specific, with most of the variation explained by individual host. At the individual level, we found no diversification in microbiome composition between dorsal and ventral body sites, but the degree of intra-individual heterogeneity varied among individuals. To identify how genetic and phenotypic characteristics of fish hosts impact the rate and nature of intra-individual temporal dynamics of the skin microbiome, and thereby contribute to the host-specific patterns documented here, remains an important task for future research.
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Affiliation(s)
- Hanna Berggren
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Daniel Lundin
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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18
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OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6517683. [DOI: 10.1093/femsec/fiac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/13/2021] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
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19
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Gomez JA, Primm TP. A Slimy Business: the Future of Fish Skin Microbiome Studies. MICROBIAL ECOLOGY 2021; 82:275-287. [PMID: 33410931 DOI: 10.1007/s00248-020-01648-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/16/2020] [Indexed: 05/10/2023]
Abstract
Fish skin contains a mucosal microbiome for the largest and oldest group of vertebrates, a location ideal for microbial community ecology and practical applications in agriculture and veterinary medicine. These selective microbiomes are dominated by Proteobacteria, with compositions different from the surrounding water. Core taxa are a small percentage of those present and are currently functionally uncharacterized. Methods for skin sampling, DNA extraction and amplification, and sequence data processing are highly varied across the field, and reanalysis of recent studies using a consistent pipeline revealed that some conclusions did change in statistical significance. Further, the 16S gene sequencing approaches lack quantitation of microbes and copy number adjustment. Thus, consistency in the field is a serious limitation in comparing across studies. The most significant area for future study, requiring metagenomic and metabolomics data, is the biochemical pathways and functions within the microbiome community, the interactions between members, and the resulting effects on fish host health being linked to specific nutrients and microbial species. Genes linked to skin colonization, such as those for attachment or mucin degradation, need to be uncovered and explored. Skin immunity factors need to be directly linked to microbiome composition and individual taxa. The basic foundation has been laid, and many exciting future discoveries remain.
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Affiliation(s)
- Javier A Gomez
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77320, USA
| | - Todd P Primm
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, 77320, USA.
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20
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Fishing for the Virome of Tropical Tuna. Viruses 2021; 13:v13071291. [PMID: 34372497 PMCID: PMC8310200 DOI: 10.3390/v13071291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022] Open
Abstract
While planktonic viruses have received much attention in recent decades, knowledge of the virome of marine organisms, especially fish, still remains rudimentary. This is notably the case with tuna, which are among the most consumed fish worldwide and represent considerable economic, social and nutritional value. Yet the composition of the tuna virome and its biological and environmental determinants remain unknown. To begin to address this gap, we investigated the taxonomic diversity of viral communities inhabiting the skin mucus, gut and liver of two major tropical tuna species (skipjack and yellowfin) in individuals fished in the Atlantic and Indian Oceans. While we found significant differences in the virome composition between the organs, this was totally independent of the tuna species or sex. The tuna virome was mainly dominated by eukaryotic viruses in the digestive organs (gut and liver), while bacteriophages were predominant in the mucus. We observed the presence of specific viral families in each organ, some previously identified as fish or human pathogens (e.g., Iridoviridae, Parvoviridae, Alloherpesviridae, Papillomaviridae). Interestingly, we also detected a ‘core virome’ that was shared by all the organs and was mainly composed of Caudovirales, Microviridae and Circoviridae. These results show that tuna host a mosaic of viral niches, whose establishment, role and circulation remain to be elucidated.
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21
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Minich JJ, Nowak B, Elizur A, Knight R, Fielder S, Allen EE. Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi. FRONTIERS IN MARINE SCIENCE 2021; 8:676731. [PMID: 36248701 PMCID: PMC9563383 DOI: 10.3389/fmars.2021.676731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fish gut microbiome is impacted by a number of biological and environmental factors including fish feed formulations. Unlike mammals, vertical microbiome transmission is largely absent in fish and thus little is known about how the gut microbiome is initially colonized during hatchery rearing nor the stability throughout growout stages. Here we investigate how various microbial-rich surfaces from the built environment "BE" and feed influence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine fish, yellowtail kingfish, Seriola lalandi, over time. For the first experiment, we sampled gill and skin microbiomes from 36 fish reared in three tank conditions, and demonstrate that the gill is more influenced by the surrounding environment than the skin. In a second experiment, fish mucous (gill, skin, and digesta), the BE (tank side, water, inlet pipe, airstones, and air diffusers) and feed were sampled from indoor reared fish at three ages (43, 137, and 430 dph; n = 12 per age). At 430 dph, 20 additional fish were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in fish from the ocean net pen compared to indoor fish. The gill and skin are most influenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut "allochthonous" microbiome becomes increasingly differentiated from the environment over time. Feed had a relatively low impact on driving microbial communities. Our findings suggest that S. lalandi mucosal microbiomes are differentially influenced by the BE with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine fish. In addition, results demonstrate how early life (larval) exposure to biofouling in the rearing environment may influence fish microbiome development which is important for animal health and aquaculture production.
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Affiliation(s)
- Jeremiah J. Minich
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Barbara Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Abigail Elizur
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Stewart Fielder
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, NSW, Australia
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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22
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Sehnal L, Brammer-Robbins E, Wormington AM, Blaha L, Bisesi J, Larkin I, Martyniuk CJ, Simonin M, Adamovsky O. Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health. Front Microbiol 2021; 12:567408. [PMID: 33776947 PMCID: PMC7995652 DOI: 10.3389/fmicb.2021.567408] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/05/2021] [Indexed: 01/03/2023] Open
Abstract
Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
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Affiliation(s)
- Ludek Sehnal
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Elizabeth Brammer-Robbins
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States.,Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Alexis M Wormington
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Joe Bisesi
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States.,Department of Environmental and Global Health, University of Florida, Gainesville, FL, United States
| | - Iske Larkin
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL, United States
| | - Christopher J Martyniuk
- Department of Physiological Sciences, University of Florida, Gainesville, FL, United States.,Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, United States
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
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23
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Rosado D, Pérez-Losada M, Pereira A, Severino R, Xavier R. Effects of aging on the skin and gill microbiota of farmed seabass and seabream. Anim Microbiome 2021; 3:10. [PMID: 33499971 PMCID: PMC7934244 DOI: 10.1186/s42523-020-00072-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background Important changes in microbial composition related to sexual maturation have been already reported in the gut of several vertebrates including mammals, amphibians and fish. Such changes in fish are linked to reproduction and growth during developmental stages, diet transitions and critical life events. We used amplicon (16S rRNA) high-throughput sequencing to characterize the skin and gill bacterial microbiota of farmed seabass and seabream belonging to three different developmental age groups: early and late juveniles and mature adults. We also assessed the impact of the surrounding estuarine water microbiota in shaping the fish skin and gill microbiota. Results Microbial diversity, composition and predicted metabolic functions varied across fish maturity stages. Alpha-diversity in the seabass microbiota varied significantly between age groups and was higher in older fish. Conversely, in the seabream, no significant differences were found in alpha-diversity between age groups. Microbial structure varied significantly across age groups; moreover, high structural variation was also observed within groups. Different bacterial metabolic pathways were predicted to be enriched in the microbiota of both species. Finally, we found that the water microbiota was significantly distinct from the fish microbiota across all the studied age groups, although a high percentage of ASVs was shared with the skin and gill microbiotas. Conclusions We report important microbial differences in composition and potential functionality across different ages of farmed seabass and seabream. These differences may be related to somatic growth and the onset of sexual maturation. Importantly, some of the inferred metabolic pathways could enhance the fish coping mechanisms during stressful conditions. Our results provide new evidence suggesting that growth and sexual maturation have an important role in shaping the microbiota of the fish external mucosae and highlight the importance of considering different life stages in microbiota studies. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-020-00072-2.
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Affiliation(s)
- Daniela Rosado
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
| | - Marcos Pérez-Losada
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.,Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, 20052-0066, USA
| | - Ana Pereira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal
| | - Ricardo Severino
- Piscicultura Vale da Lama, Sapal do Vale da Lama, Odiáxere, 8600-258, Lagos, Portugal
| | - Raquel Xavier
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Porto, Portugal.
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24
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Doane MP, Morris MM, Papudeshi B, Allen L, Pande D, Haggerty JM, Johri S, Turnlund AC, Peterson M, Kacev D, Nosal A, Ramirez D, Hovel K, Ledbetter J, Alker A, Avalos J, Baker K, Bhide S, Billings E, Byrum S, Clemens M, Demery AJ, Lima LFO, Gomez O, Gutierrez O, Hinton S, Kieu D, Kim A, Loaiza R, Martinez A, McGhee J, Nguyen K, Parlan S, Pham A, Price-Waldman R, Edwards RA, Dinsdale EA. The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. MICROBIOME 2020; 8:93. [PMID: 32534596 PMCID: PMC7293782 DOI: 10.1186/s40168-020-00840-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/15/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. RESULTS We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. CONCLUSION Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.
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Affiliation(s)
- Michael P Doane
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Megan M Morris
- Biology Department, San Diego State University, San Diego, CA, USA
- Department Biology, Stanford University, Stanford, California, USA
| | - Bhavya Papudeshi
- National Center for Genome Analysis Support, Indiana University, San Diego, Indiana, USA
| | - Lauren Allen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Dnyanada Pande
- Computer Sciences Department, San Diego State University, San Diego, CA, USA
| | - John M Haggerty
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shaili Johri
- Biology Department, San Diego State University, San Diego, CA, USA
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Abigail C Turnlund
- Biology Department, San Diego State University, San Diego, CA, USA
- Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queens, USA
| | | | - Dovi Kacev
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
| | - Andy Nosal
- Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA, USA
| | - Deni Ramirez
- Whale Shark Mexico, ConCiencia Mexico AC, La Paz, BC, USA
| | - Kevin Hovel
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Julia Ledbetter
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Alker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Jackeline Avalos
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristi Baker
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Shruti Bhide
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Emma Billings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Steven Byrum
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Molly Clemens
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | | | - Oscar Gomez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Omar Gutierrez
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Selena Hinton
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Donald Kieu
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Angie Kim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rebeca Loaiza
- Biology Department, San Diego State University, San Diego, CA, USA
| | | | - Jordan McGhee
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Kristine Nguyen
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Sabrina Parlan
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Amanda Pham
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Rosalyn Price-Waldman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Robert A Edwards
- Biology Department, San Diego State University, San Diego, CA, USA
- Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, San Diego, CA, USA.
- Viral Information Institute, San Diego State University, San Diego, CA, USA.
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25
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Chiarello M, Auguet JC, Graham NAJ, Claverie T, Sucré E, Bouvier C, Rieuvilleneuve F, Restrepo-Ortiz CX, Bettarel Y, Villéger S, Bouvier T. Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes. Proc Biol Sci 2020; 287:20200642. [PMID: 32396801 DOI: 10.1098/rspb.2020.0642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However, the diversity of such microbiomes is mostly described in a few coral species and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species. Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic richness was specific and not recovered in surrounding plankton. Estimate of the total richness associated with coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.
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Affiliation(s)
- Marlène Chiarello
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | - Nicholas A J Graham
- Lancaster Environment Centre, Lancaster University, Library Avenue, Lancaster LA1 4YQ, UK
| | - Thomas Claverie
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Département Sciences et Technologie, Centre Universitaire de Formation et de Recherche de Mayotte, Route nationale 3, BP53, 97660 Dembeni, France
| | - Elliott Sucré
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France.,Département Sciences et Technologie, Centre Universitaire de Formation et de Recherche de Mayotte, Route nationale 3, BP53, 97660 Dembeni, France
| | - Corinne Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | | | | | - Yvan Bettarel
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Sébastien Villéger
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Thierry Bouvier
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
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26
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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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