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.

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

Department of Large Animal Clinical Sciences University of Florida Gainesville FL United States

Department of Physiological Sciences University of Florida Gainesville FL United States

RECETOX Faculty of Science Masaryk University Brno Czechia

Univ Angers Institut Agro INRAE IRHS SFR QUASAV Angers France

Zobrazit více v PubMed

Adamovsky O., Buerger A. N., Vespalcova H., Sohag S. R., Hanlon A. T., Ginn P. E., et al. (2020). Evaluation of microbiome-host relationships in the zebrafish gastrointestinal system reveals adaptive immunity is a target of Bis(2-ethylhexyl) Phthalate (DEHP) exposure. PubMed DOI

Adamovsky O., Buerger A. N., Wormington A. M., Ector N., Griffitt R. J., Bisesi J. H., et al. (2018). The gut microbiome and aquatic toxicology: an emerging concept for environmental health. PubMed DOI

Adamovsky O., Kopp R., Zikova A., Blaha L., Kohoutek J., Ondrackova P., et al. (2011). The effect of peroral administration of toxic cyanobacteria on laboratory rats ( PubMed DOI

Adamovsky O., Moosova Z., Pekarova M., Basu A., Babica P., Svihalkova Sindlerova L., et al. (2015). Immunomodulatory potency of microcystin, an important water-polluting cyanobacterial toxin. PubMed DOI

Akhter N., Wu B., Memon A. M., Mohsin M. (2015). Probiotics and prebiotics associated with aquaculture: a review. PubMed DOI

Annadotter H., Cronberg G., Nystrand R., Rylander R. (2005). Endotoxins from cyanobacteria and gram-negative bacteria as the cause of an acute influenza-like reaction after inhalation of aerosols. DOI

Apprill A., Miller C. A., Moore M. J., Durban J. W., Fearnbach H., Barrett-Lennard L. G. (2017). Extensive core microbiome in drone-captured whale blow supports a framework for health monitoring. PubMed DOI PMC

Apprill A., Mooney T. A., Lyman E., Stimpert A. K., Rappé M. S. (2011). Humpback whales harbour a combination of specific and variable skin bacteria. PubMed DOI

Apprill A., Robbins J., Eren A. M., Pack A. A., Reveillaud J., Mattila D., et al. (2014). Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? PubMed DOI PMC

Arias-Andres M., Klümper U., Rojas-Jimenez K., Grossart H.-P. (2018). Microplastic pollution increases gene exchange in aquatic ecosystems. PubMed DOI

Asakura T., Sakata K., Yoshida S., Date Y., Kikuchi J. (2014). Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches. PubMed DOI PMC

Ashbolt N. J. (2004). Microbial contamination of drinking water and disease outcomes in developing regions. PubMed DOI PMC

Aylagas E., Borja Á, Tangherlini M., Dell’Anno A., Corinaldesi C., Michell C. T., et al. (2017). A bacterial community-based index to assess the ecological status of estuarine and coastal environments. PubMed DOI

Baker M. E., King R. S. (2010). A new method for detecting and interpreting biodiversity and ecological community thresholds. DOI

Banks J. C., Cary S. C., Hogg I. D. (2014). Isolated faecal bacterial communities found for Weddell seals, DOI

Banning E. C., Casciotti K. L., Kujawinski E. B. (2010). Novel strains isolated from a coastal aquifer suggest a predatory role for flavobacteria. PubMed DOI

Bierlich K. C., Miller C., DeForce E., Friedlaender A. S., Johnston D. W., Apprill A. (2018). Temporal and regional variability in the skin microbiome of humpback whales along the Western Antarctic Peninsula. PubMed DOI PMC

Bik E. M., Costello E. K., Switzer A. D., Callahan B. J., Holmes S. P., Wells R. S., et al. (2016). Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. PubMed DOI PMC

Bláha L., Bláhová L., Kohoutek J., Adamovský O., Babica P., Marsálek B. (2010). Temporal and spatial variability of cyanobacterial toxins microcystins in three interconnected freshwater reservoirs. DOI

Blahova L., Adamovsky O., Kubala L. L. L., Svihalkova L., Zounkova R., Blaha L., et al. (2013). The isolation and characterization of lipopolysaccharides from PubMed DOI

Bohmann K., Evans A., Gilbert M. T. P., Carvalho G. R., Creer S., Knapp M., et al. (2014). Environmental DNA for wildlife biology and biodiversity monitoring. PubMed DOI

Bolyen E., Rideout J. R., Dillon M. R., Bokulich N. A., Abnet C. C., Al-Ghalith G. A., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. PubMed DOI PMC

Boutin S., Bernatchez L., Audet C., Derôme N. (2012). Antagonistic effect of indigenous skin bacteria of brook charr ( PubMed DOI

Bowman J. P., Nichols D. S. (2005). Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including PubMed DOI

Brown R., Wiens G., Salinas I. (2018). Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout ( DOI

Browne M. A., Dissanayake A., Galloway T. S., Lowe D. M., Thompson R. C. (2008). Ingested microscopic plastic translocates to the circulatory system of the mussel, PubMed DOI

Callens M., Watanabe H., Kato Y., Miura J., Decaestecker E. (2018). Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia. PubMed DOI PMC

Carda-Diéguez M., Ghai R., Rodríguez-Valera F., Amaro C. (2017). Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution. PubMed DOI PMC

Carding S., Verbeke K., Vipond D. T., Corfe B. M., Owen L. J. (2015). Dysbiosis of the gut microbiota in disease. PubMed DOI PMC

Caruso G., Pedà C., Cappello S., Leonardi M., La Ferla R., Lo Giudice A., et al. (2018). Effects of microplastics on trophic parameters, abundance and metabolic activities of seawater and fish gut bacteria in mesocosm conditions. PubMed DOI

Chae Y., An Y.-J. (2020). Nanoplastic ingestion induces behavioral disorders in terrestrial snails: trophic transfer effects via vascular plants. DOI

Chen J., Xie P., Lin J., He J., Zeng C., Chen J. (2015). Effects of microcystin-LR on gut microflora in different gut regions of mice. PubMed DOI

Cheng L., Qi C., Fu T., Zhang X. (2020). gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions. PubMed DOI PMC

Chiarello M., Auguet J.-C., Bettarel Y., Bouvier C., Claverie T., Graham N. A. J., et al. (2018). Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. PubMed DOI PMC

Chiarello M., Paz-Vinas I., Veyssière C., Santoul F., Loot G., Ferriol J., et al. (2019). Environmental conditions and neutral processes shape the skin microbiome of European catfish ( PubMed DOI

Chiarello M., Villéger S., Bouvier C., Auguet J. C., Bouvier T. (2017). Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals. PubMed DOI PMC

Chiarello M., Villéger S., Bouvier C., Bettarel Y., Bouvier T. (2015). High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species. PubMed DOI

Christen V., Meili N., Fent K. (2013). Microcystin-LR induces endoplasmatic reticulum stress and leads to induction of NFκB, interferon-alpha, and tumor necrosis factor-alpha. PubMed DOI

Clements K. D., Pasch I. B. Y., Moran D., Turner S. J. (2007). Clostridia dominate 16S rRNA gene libraries prepared from the hindgut of temperate marine herbivorous fishes. DOI

Comizzoli P., Power M. (2019). Reproductive microbiomes in wild animal species: a new dimension in conservation biology. PubMed DOI

Cordier T., Lanzén A., Apothéloz-Perret-Gentil L., Stoeck T., Pawlowski J. (2019). Embracing environmental genomics and machine learning for routine biomonitoring. PubMed DOI

Crespo-Piazuelo D., Estellé J., Revilla M., Criado-Mesas L., Ramayo-Caldas Y., Óvilo C., et al. (2018). Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions. PubMed DOI PMC

Dang H., Lovell C. R. (2016). Microbial surface colonization and biofilm development in marine environments. PubMed DOI PMC

Delport T. C., Power M. L., Harcourt R. G., Webster K. N., Tetu S. G. (2016). Colony location and captivity influence the gut microbial community composition of the Australian sea lion ( PubMed DOI PMC

Dubilier N., Bergin C., Lott C. (2008). Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. PubMed DOI

Duperron S., Halary S., Gallet A., Marie B. (2020). Microbiome-aware ecotoxicology of organisms: relevance, pitfalls, and challenges. PubMed DOI PMC

Duperron S., Halary S., Habiballah M., Gallet A., Huet H., Duval C., et al. (2019). Response of Fish gut microbiota to toxin-containing cyanobacterial extracts: a microcosm study on the medaka ( DOI

Durack P. J., Wijffels S. E., Matear R. J. (2012). Ocean salinities reveal strong global water cycle intensification during 1950 to 2000. PubMed DOI

Egerton S., Culloty S., Whooley J., Stanton C., Ross R. P. (2018). The gut microbiota of marine fish. PubMed DOI PMC

Eren A. M., Esen O. C., Quince C., Vineis J. H., Morrison H. G., Sogin M. L., et al. (2015). Anvi’o: an advanced analysis and visualization platformfor ’omics data. PubMed DOI PMC

Erwin P. M., Rhodes R. G., Kiser K. B., Keenan-Bateman T. F., McLellan W. A., Pabst D. A. (2017). High diversity and unique composition of gut microbiomes in pygmy ( PubMed DOI PMC

Evariste L., Barret M., Mottier A., Mouchet F., Gauthier L., Pinelli E. (2019). Gut Microbiota of aquatic Organisms: a key endpoint for ecotoxicological studies. PubMed DOI

Ezer A., Matalon E., Jindou S., Borovok I., Atamna N., Yu Z., et al. (2008). Cell surface enzyme attachment is mediated by family 37 carbohydrate-binding modules, unique to PubMed DOI PMC

Fackelmann G., Sommer S. (2019). Microplastics and the gut microbiome: how chronically exposed species may suffer from gut dysbiosis. PubMed DOI

Falcinelli S., Picchietti S., Rodiles A., Cossignani L., Merrifield D. L., Taddei A. R., et al. (2015). PubMed DOI PMC

Frère L., Maignien L., Chalopin M., Huvet A., Rinnert E., Morrison H., et al. (2018). Microplastic bacterial communities in the Bay of Brest: influence of polymer type and size. PubMed DOI

Gehringer M. M., Shephard E. G., Downing T. G., Wiegand C., Neilan B. A. (2004). An investigation into the detoxification of microcystin-LR by the glutathione pathway in Balb/c mice. PubMed DOI

Givens C. E., Ransom B., Bano N., Hollibaugh J. T. (2015). Comparison of the gut microbiomes of 12 bony fish and 3 shark species. DOI

Gomez D., Sunyer J. O., Salinas I. (2013). The mucosal immune system of fish: the evolution of tolerating commensals while fighting pathogens. PubMed DOI PMC

Guardiola F. A., Mabrok M., Machado M., Azeredo R., Afonso A., Esteban M. A., et al. (2019). Mucosal and systemic immune responses in Senegalese sole ( PubMed DOI

Guo X., Ran C., Zhang Z., He S., Jin M., Zhou Z. (2017). The growth-promoting effect of dietary nucleotides in fish is associated with an intestinal microbiota-mediated reduction in energy expenditure. PubMed DOI

Hanning I., Diaz-Sanchez S. (2015). The functionality of the gastrointestinal microbiome in non-human animals. PubMed DOI PMC

Hartmann N. B., Hüffer T., Thompson R. C., Hassellöv M., Verschoor A., Daugaard A. E., et al. (2019). Are we speaking the same language? Recommendations for a definition and categorization framework for plastic debris. PubMed DOI

Hauffe H. C., Barelli C. (2019). Conserve the germs: the gut microbiota and adaptive potential. DOI

Hernandez-Agreda A., Leggat W., Bongaerts P., Ainsworth T. D. (2016). The microbial signature provides insight into the mechanistic basis of coral success across reef habitats. PubMed DOI PMC

Hess S., Wenger A. S., Ainsworth T. D., Rummer J. L. (2015). Exposure of clownfish larvae to suspended sediment levels found on the Great Barrier Reef: impacts on gill structure and microbiome. PubMed DOI PMC

Hooper R., Brealey J., Valk T., Van Der, Alberdi A., Durban J. W., Fearnbach H., et al. (2018). Characterising the microbiome from host shotgun sequencing data: bacterial and diatom community dynamics derived from killer whale skin. DOI

Hooper R., Brealey J. C., Valk T., Alberdi A., Durban J. W., Fearnbach H., et al. (2019). Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin. PubMed DOI PMC

Horton A. A., Newbold L. K., Palacio-Cortés A. M., Spurgeon D. J., Pereira M. G., Carter H., et al. (2020). Accumulation of polybrominated diphenyl ethers and microbiome response in the great pond snail PubMed DOI

Iijima N., Tanimoto N., Emoto Y., Morita Y., Uematsu K., Murakami T., et al. (2003). Purification and characterization of three isoforms of chrysophsin, a novel antimicrobial peptide in the gills of the red sea bream. PubMed DOI

Ishii H., Nishijima M., Abe T. (2004). Characterization of degradation process of cyanobacterial hepatotoxins by a gram-negative aerobic bacterium. PubMed DOI

Isobe K., Bouskill N. J., Brodie E. L., Sudderth E. A., Martiny J. B. H. (2020). Phylogenetic conservation of soil bacterial responses to simulated global changes. PubMed DOI PMC

Jacob H., Besson M., Swarzenski P. W., Lecchini D., Metian M. (2020). Effects of virgin micro- and nanoplastics on fish: trends, meta-analysis, and perspectives. PubMed DOI

Jarošová B., Javu̇rek J., Adamovský O., Hilscherová K. (2015). Phytoestrogens and mycoestrogens in surface waters — their sources, occurrence, and potential contribution to estrogenic activity. PubMed DOI

Javu̇rek J., Sychrová E., Smutná M., Bittner M., Kohoutek J., Adamovský O., et al. (2015). Retinoid compounds associated with water blooms dominated by Microcystis species. DOI

Ji P., Parks J., Edwards M. A., Pruden A. (2015). Impact of water chemistry, pipe material and stagnation on the building plumbing microbiome. PubMed DOI PMC

Jin Y., Lu L., Tu W., Luo T., Fu Z. (2019). Impacts of polystyrene microplastic on the gut barrier, microbiota and metabolism of mice. PubMed DOI

Jin Y., Xia J., Pan Z., Yang J., Wang W., Fu Z. (2018). Polystyrene microplastics induce microbiota dysbiosis and inflammation in the gut of adult zebrafish. PubMed DOI

Jonas A., Scholz S., Fetter E., Sychrova E., Novakova K., Ortmann J., et al. (2015). Endocrine, teratogenic and neurotoxic effects of cyanobacteria detected by cellular in vitro and zebrafish embryos assays. PubMed DOI

Jones J., DiBattista J. D., Stat M., Bunce M., Boyce M. C., Fairclough D. V., et al. (2018). The microbiome of the gastrointestinal tract of a range-shifting marine herbivorous fish. PubMed DOI PMC

Juni E., Bøvre K. (2015). DOI

Keeley N., Wood S. A., Pochon X. (2018). Development and preliminary validation of a multi-trophic metabarcoding biotic index for monitoring benthic organic enrichment. DOI

Kim D. H., Brunt J., Austin B. (2007). Microbial diversity of intestinal contents and mucus in rainbow trout ( PubMed DOI

Krotman Y., Yergaliyev T. M., Alexander Shani R., Avrahami Y., Szitenberg A. (2020). Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system. PubMed DOI PMC

Landesman W. J., Dighton J. (2011). Shifts in microbial biomass and the bacteria: fungi ratio occur under field conditions within 3 h after rainfall. PubMed DOI

Langille M. G. I., Zaneveld J., Caporaso J. G., McDonald D., Knights D., Reyes J. A., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. PubMed DOI PMC

Larsen A., Tao Z., Bullard S. A., Arias C. R. (2013). Diversity of the skin microbiota of fishes: evidence for host species specificity. PubMed DOI

Lau K. E. M., Washington V. J., Fan V., Neale M. W., Lear G., Curran J., et al. (2015). A novel bacterial community index to assess stream ecological health. DOI

Lebreton L., Andrady A. (2019). Future scenarios of global plastic waste generation and disposal. DOI

LeBrun E. S., King R. S., Back J. A., Kang S. (2018). Microbial community structure and function decoupling across a phosphorus gradient in streams. PubMed DOI

Legrand T. P. R. A., Catalano S. R., Wos-Oxley M. L., Stephens F., Landos M., Bansemer M. S., et al. (2018). The inner workings of the outer surface: skin and gill microbiota as indicators of changing gut health in Yellowtail Kingfish. PubMed DOI PMC

Lehman P. W., Marr K., Boyer G. L., Acuna S., Teh S. J. (2013). Long-term trends and causal factors associated with microcystis abundance and toxicity in San Francisco Estuary and implications for climate change impacts. DOI

Li B., Ding Y., Cheng X., Sheng D., Xu Z., Rong Q., et al. (2020). Polyethylene microplastics affect the distribution of gut microbiota and inflammation development in mice. PubMed DOI

Li J., Chen C., Zhang T., Liu W., Wang L., Chen Y., et al. (2019). M Evaluation of microcystin-LR absorption using an in vivo intestine model and its effect on zebrafish intestine. PubMed DOI

Li X., Yan Q., Xie S., Hu W., Yu Y., Hu Z. (2013). Gut microbiota contributes to the growth of fast-growing transgenic common carp ( PubMed DOI PMC

Lin J., Chen J., He J., Chen J., Yan Q., Zhou J., et al. (2015). Effects of microcystin-LR on bacterial and fungal functional genes profile in rat gut. PubMed DOI

Ling F., Whitaker R., LeChevallier M. W., Liu W. T. (2018). Drinking water microbiome assembly induced by water stagnation. PubMed DOI PMC

Liu Z., Yu P., Cai M., Wu D., Zhang M., Chen M., et al. (2019). Effects of microplastics on the innate immunity and intestinal microflora of juvenile Eriocheir sinensis. PubMed DOI

Lowrey L., Woodhams D. C., Tacchi L., Salinas I. (2015). Topographical mapping of the rainbow trout ( PubMed DOI PMC

Lu L., Wan Z., Luo T., Fu Z., Jin Y. (2018). Polystyrene microplastics induce gut microbiota dysbiosis and hepatic lipid metabolism disorder in mice. PubMed DOI

Lumsden J. S., Ostland V. E., MacPhee D. D., Ferguson H. W. (1995). Production of gill-associated and serum antibody byrainbow trout ( DOI

Lusher A. L., McHugh M., Thompson R. C. (2013). Occurrence of microplastics in the gastrointestinal tract of pelagic and demersal fish from the English Channel. PubMed DOI

Macke E., Callens M., De Meester L., Decaestecker E. (2017). Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria. PubMed DOI PMC

Marón C. F., Kohl K. D., Chirife A., Di Martino M., Fons M. P., Navarro M. A., et al. (2019). Symbiotic microbes and potential pathogens in the intestine of dead southern right whale ( PubMed DOI

Martiny J. B. H., Jones S. E., Lennon J. T., Martiny A. C. (2015). Microbiomes in light of traits: a phylogenetic perspective. PubMed DOI

McKenney E. A., Koelle K., Dunn R. R., Yoder A. D. (2018). The ecosystem services of animal microbiomes. PubMed DOI

Merson S. D., Ouwerkerk D., Gulino L. M., Klieve A., Bonde R. K., Burgess E. A., et al. (2014). Variation in the hindgut microbial communities of the PubMed DOI

Minich J. J., Morris M. M., Brown M., Doane M., Edwards M. S., Michael T. P., et al. (2018). Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. PubMed DOI PMC

Miyake S., Ngugi D. K., Stingl U. (2015). Diet strongly influences the gut microbiota of surgeonfishes. PubMed DOI

Moosova Z., Hrouzek P., Kapuscik A., Blaha L., Adamovsky O. (2018). Immunomodulatory effects of selected cyanobacterial peptides in vitro. PubMed DOI

Moosova Z., Pekarova M., Sindlerova L. S., Vasicek O., Kubala L., Blaha L., et al. (2019). Immunomodulatory effects of cyanobacterial toxin cylindrospermopsin on innate immune cells. PubMed DOI

Moran M. A. (2015). The global ocean microbiome. PubMed DOI

Mouchet M. A., Bouvier C., Bouvier T., Troussellier M., Escalas A., Mouillot D. (2012). Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints. PubMed DOI

Mowe M. A. D., Porojan C., Abbas F., Mitrovic S. M., Lim R. P., Furey A., et al. (2017). Corrigendum to “rising temperatures may increase growth rates and microcystin production in tropical Microcystis species” [Harmful Algae 50 88–98]. PubMed DOI

Murray H. M., Gallant J. W., Douglas S. E. (2003). Cellular localization of pleurocidin gene expression and synthesis in winter flounder gill using immunohistochemistry and in situ hybridization. PubMed DOI

Nayak S. K. (2010). Role of gastrointestinal microbiota in fish. DOI

Nelson T., Wallen M., Bunce M., Oskam C., Lima N., Clayton L., et al. (2019). Detecting respiratory bacterial communities of wild dolphins: implications for animal health. DOI

Nelson T. M., Rogers T. L., Carlini A. R., Brown M. V. (2013). Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. PubMed DOI

Neuman C., Hatje E., Zarkasi K. Z., Smullen R., Bowman J. P., Katouli M. (2016). The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic Salmon ( DOI

Ni J., Yan Q., Yu Y., Zhang T. (2014). Factors influencing the grass carp gut microbiome and its effect on metabolism. PubMed DOI

Nováková K., Babica P., Adamovský O., Bláha L. (2011). Modulation of gap-junctional intercellular communication by a series of cyanobacterial samples from nature and laboratory cultures. PubMed DOI

Nováková K., Kohoutek J., Adamovský O., Brack W., Krauss M., Bláha L. (2013). Novel metabolites in cyanobacterium Cylindrospermopsis raciborskii with potencies to inhibit gap junctional intercellular communication. PubMed DOI

Pacheco-Sandoval A., Schramm Y., Heckel G., Brassea-Pérez E., Martínez-Porchas M., Lago-Lestón A. (2019). The Pacific harbor seal gut microbiota in Mexico: its relationship with diet and functional inferences. PubMed DOI PMC

Païssé S., Goñi-Urriza M., Coulon F., Duran R. (2010). How a bacterial community originating from a contaminated coastal sediment responds to an oil input. PubMed DOI

Palikova M., Adamovsky O., Blaha L., Mares J., Kopp R., Navratil S., et al. (2013). Fish tapeworm Khawia sinensis: an indicator of environmental microcystins? PubMed

Palikova M., Papezikova I., Kopp R., Mares J., Markova Z., Navratil S., et al. (2015). Effect of arsenic and cyanobacterial co-exposure onpathological, haematological and immunological parameters of rainbow trout ( PubMed

Pascoe E. L., Hauffe H. C., Marchesi J. R., Perkins S. E. (2017). Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies the dawn of modern microbiota research. PubMed DOI PMC

Pérez-Pascual D., Lunazzi A., Magdelenat G., Rouy Z., Roulet A., Lopez-Roques C., et al. (2017). The complete genome sequence of the fish pathogen PubMed DOI PMC

Pinto A. J., Schroeder J., Lunn M., Sloan W., Raskin L. (2014). Spatial-temporal survey and occupancy-abundance modeling to predict bacterial community dynamics in the drinking water microbiomez. PubMed DOI PMC

Pinto A. J., Xi C., Raskin L. (2012). Bacterial community structure in the drinking water microbiome is governed by filtration processes. PubMed DOI

Pratte Z. A., Besson M., Hollman R. D., Stewarta F. J. (2018). The gills of reef fish support a distinct microbiome influenced by hostspecific factors. PubMed DOI PMC

Proctor C. R., Hammes F. (2015). Drinking water microbiology-from measurement to management. PubMed DOI

Qiao R., Sheng C., Lu Y., Zhang Y., Ren H., Lemos B. (2019). Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish. PubMed DOI

Raverty S. A., Rhodes L. D., Zabek E., Eshghi A., Cameron C. E., Hanson M. B., et al. (2017). Respiratory microbiome of endangered Southern resident killer whales and microbiota of surrounding sea surface microlayer in the Eastern North Pacific. PubMed DOI PMC

Rawls J. F., Samuel B. S., Gordon J. I. (2004). Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. PubMed DOI PMC

Ray A. K., Ghosh K., Ringø E. (2012). Enzyme-producing bacteria isolated from fish gut: a review. DOI

Rees H. C., Maddison B. C., Middleditch D. J., Patmore J. R. M., Gough K. C. (2014). The detection of aquatic animal species using environmental DNA - a review of eDNA as a survey tool in ecology. DOI

Reverter M., Sasal P., Tapissier-Bontemps N., Lecchini D., Suzuki M. (2017). Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems. PubMed DOI

Riiser E. S., Haverkamp T. H. A., Varadharajan S., Borgan Ø, Jakobsen K. S., Jentoft S., et al. (2020). Metagenomic shotgun analyses reveal complex patterns of intra- and interspecific variation in the intestinal microbiomes of codfishes. PubMed DOI PMC

Risely A. (2020). Applying the core microbiome to understand host-microbe systems. PubMed DOI

Roberts S. D., Powell M. D. (2003). Comparative ionic flux and gill mucous cell histochemistry: effects of salinity and disease status in Atlantic salmon ( PubMed DOI

Robertson P. A. W., O’Dowd C., Burrells C., Williams P., Austin B. (2000). Use of DOI

Rocca J. D., Simonin M., Blaszczak J. R., Ernakovich J. G., Gibbons S. M., Midani F. S., et al. (2019). The microbiome stress project: toward a global meta-analysis of environmental stressors and their effects on microbial communities. PubMed DOI PMC

Roeselers G., Mittge E. K., Stephens W. Z., Parichy D. M., Cavanaugh C. M., Guillemin K., et al. (2011). Evidence for a core gut microbiota in the zebrafish. PubMed DOI PMC

Rosado D., Pérez-Losada M., Severino R., Cable J., Xavier R. (2019). Characterization of the skin and gill microbiomes of the farmed seabass ( DOI

Russo C. D., Weller D. W., Nelson K. E., Chivers S. J., Torralba M., Grimes D. J. (2018). Bacterial species identified on the skin of bottlenose dolphins off Southern California via next generation sequencing techniques. PubMed DOI

Salguero M., Al-Obaide M., Singh R., Siepmann T., Vasylyeva T. (2019). Dysbiosis of Gram-negative gut microbiota and the associated serum lipopolysaccharide exacerbates inflammation in type 2 diabetic patients with chronic kidney disease. PubMed DOI PMC

Sanders J. G., Beichman A. C., Roman J., Scott J. J., Emerson D., McCarthy J. J., et al. (2015). Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. PubMed DOI PMC

Sarkar S., Alhasson F., Kimono D., Albadrani M., Seth R. K., Xiao S., et al. (2020). Microcystin exposure worsens nonalcoholic fatty liver disease associated ectopic glomerular toxicity via NOX-2-MIR21 axis. PubMed DOI PMC

Schmidt V. T., Smith K. F., Melvin D. W., Amaral-Zettler L. A. (2015). Community assembly of a euryhaline fish microbiome during salinity acclimation. PubMed DOI

Shade A., Jones S. E., Gregory Caporaso J., Handelsman J., Knight R., Fierer N., et al. (2014). Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. PubMed DOI PMC

Shah S., Akhter N., Auckloo B., Khan I., Lu Y., Wang K., et al. (2017). Structural diversity, biological properties and applications of natural products from Cyanobacteria. A review. PubMed DOI PMC

Simonin M., Dasilva C., Terzi V., Ngonkeu E. L. M., Diouf D., Kane A., et al. (2020). Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils. PubMed DOI

Simonin M., Voss K. A., Hassett B. A., Rocca J. D., Wang S., Bier R. L., et al. (2019). In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient. PubMed DOI

Sison-Mangus M. P., Mushegian A. A., Ebert D. (2015). Water fleas require microbiota for survival, growth and reproduction. PubMed DOI PMC

Smriga S., Sandin S. A., Azam F. (2010). Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces. PubMed DOI

Soares-Castro P., Araújo-Rodrigues H., Godoy-Vitorino F., Ferreira M., Covelo P., López A., et al. (2019). Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring. PubMed DOI PMC

Sokoronin J. I. (1966).

Sovadinova I., Babica P., Adamovský O., Alpatová A., Tarabara V., Upham B. L., et al. (2017). Chlorination and ozonation reduce microcystin content and tumour promoting activity of complex cyanobacterial extract. DOI

Steinum T., Sjåstad K., Falk K., Kvellestad A., Colquhoun D. J. (2009). An RT PCR-DGGE survey of gill-associated bacteria in Norwegian seawater-reared Atlantic salmon suffering proliferative gill inflammation. DOI

Sullam K. E., Essinger S. D., Lozupone C. A., O’Connor M. P., Rosen G. L., Knight R., et al. (2012). Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. PubMed DOI PMC

Sun M.-L., Zhao F., Chen X.-L., Zhang X.-Y., Zhang Y.-Z., Song X.-Y., et al. (2020). Promotion of wound healing and prevention of frostbite injury in rat skin by exopolysaccharide from the arctic marine Bacterium PubMed DOI PMC

Sunagawa S., Coelho L. P., Chaffron S., Kultima J. R., Labadie K., Salazar G., et al. (2015). Structure and function of the global ocean microbiome. PubMed DOI

Suzuki A., Segawa T., Sawa S., Nishitani C., Ueda K., Itou T., et al. (2019a). Comparison of the gut microbiota of captive common bottlenose dolphins PubMed DOI

Suzuki A., Ueda K., Segawa T., Suzuki M. (2019b). Fecal microbiota of captive Antillean manatee PubMed DOI

Sylvain F. É, Holland A., Audet-Gilbert É, Luis Val A., Derome N. (2019). Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients. PubMed DOI

Taberlet P., Coissac E., Pompanon F., Brochmann C., Willerslev E. (2012). Towards next-generation biodiversity assessment using DNA metabarcoding. PubMed DOI

Tarnecki A. M., Patterson W. F., Arias C. R. (2016). Microbiota of wild-caught Red snapper PubMed DOI PMC

Thompson L. R., Sanders J. G., McDonald D., Amir A., Ladau J., Locey K. J., et al. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. PubMed DOI PMC

Uchii K., Matsui K., Yonekura R., Tani K., Kenzaka T., Nasu M., et al. (2006). Genetic and physiological characterization of the intestinal bacterial microbiota of bluegill ( PubMed DOI

Uren Webster T. M., Consuegra S., Hitchings M., Garcia de Leaniz C. (2018). Interpopulation variation in the atlantic salmon microbiome reflects environmental and genetic diversity. PubMed DOI PMC

USEPA, (2020).

van Kessel M. A. H. J., Mesman R. J., Arshad A., Metz J. R., Spanings F. A. T., van Dalen S. C. M., et al. (2016). Branchial nitrogen cycle symbionts can remove ammonia in fish gills. PubMed DOI

Vandenkoornhuyse P., Quaiser A., Duhamel M., Le Van A., Dufresne A. (2015). The importance of the microbiome of the plant holobiont. PubMed DOI

Vasemägi A., Visse M., Kisand V. (2017). Effect of environmental factors and an emerging parasitic disease on gut microbiome of wild salmonid fish. PubMed DOI PMC

Vendl C., Ferrari B. C., Thomas T., Slavich E., Zhang E., Nelson T., et al. (2019). Interannual comparison of core taxa and community composition of the blow microbiota from East Australian humpback whales. PubMed DOI

Wan X.-L., Mclaughlin R. W., Zheng J.-S., Hao Y.-J., Fan F., Tian R.-M., et al. (2018). Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises ( PubMed DOI PMC

Wan Z., Wang C., Zhou J., Shen M., Wang X., Fu Z., et al. (2019). Effects of polystyrene microplastics on the composition of the microbiome and metabolism in larval zebrafish. PubMed DOI

Wang W., Zhou Z., He S., Liu Y., Cao Y., Shi P., et al. (2010). Identification of the adherent microbiota on the gills and skin of poly-cultured gibel carp ( DOI

Ward N. L., Steven B., Penn K., Methé B. A., Detrich W. H. (2009). Characterization of the intestinal microbiota of two Antarctic notothenioid fish species. PubMed DOI

Watts A. J. R., Lewis C., Goodhead R. M., Beckett S. J., Moger J., Tyler C. R., et al. (2014). Uptake and retention of microplastics by the shore crab PubMed DOI

Westerdahl A., Olsson J. C., Kjelleberg S., Conway P. L. (1991). Isolation and characterization of turbot PubMed DOI PMC

White E. M., Clark S., Manire C. A., Crawford B., Wang S., Locklin J., et al. (2018). Ingested micronizing plastic particle compositions and size distributions within stranded post-hatchling sea turtles. PubMed DOI

Wilson B., Danilowicz B. S., Meijer W. G. (2008). The diversity of bacterial communities associated with Atlantic cod Gadus morhua. PubMed DOI

Wong S., Rawls J. F. (2012). Intestinal microbiota composition in fishes is influenced by host ecology and environment. PubMed DOI PMC

Wood S. A., Borges H., Puddick J., Biessy L., Atalah J., Hawes I., et al. (2017). Contrasting cyanobacterial communities and microcystin concentrations in summers with extreme weather events: insights into potential effects of climate change. DOI

Wright S. L., Rowe D., Thompson R. C., Galloway T. S. (2013). Microplastic ingestion decreases energy reserves in marine worms. PubMed DOI

Xing M., Hou Z., Yuan J., Liu Y., Qu Y., Liu B. (2013). Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot ( PubMed DOI

Zhang Y., Li Z., Kholodkevich S., Sharov A., Feng Y., Ren N., et al. (2020). Microcystin-LR-induced changes of hepatopancreatic transcriptome, intestinal microbiota, and histopathology of freshwater crayfish ( PubMed DOI

Zhu D., Chen Q.-L., An X.-L., Yang X.-R., Christie P., Ke X., et al. (2018). Exposure of soil collembolans to microplastics perturbs their gut microbiota and alters their isotopic composition. DOI

Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome