Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species

Jeremiah J. Minich (), Andreas Härer, Joseph Vechinski, Benjamin W. Frable, Zachary R. Skelton, Emily Kunselman, Michael A. Shane, Daniela S. Perry, Antonio Gonzalez, Daniel McDonald, Rob Knight, Todd P. Michael and Eric E. Allen
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Jeremiah J. Minich: The Salk Institute for Biological Studies
Andreas Härer: University of California San Diego
Joseph Vechinski: University of California San Diego
Benjamin W. Frable: University of California San Diego
Zachary R. Skelton: University of California San Diego
Emily Kunselman: University of California San Diego
Michael A. Shane: Hubbs-SeaWorld Research Institute
Daniela S. Perry: University of California, San Diego
Antonio Gonzalez: University of California, San Diego
Daniel McDonald: University of California, San Diego
Rob Knight: University of California, San Diego
Todd P. Michael: The Salk Institute for Biological Studies
Eric E. Allen: University of California San Diego

Nature Communications, 2022, vol. 13, issue 1, 1-19

Abstract: Abstract Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.

Date: 2022
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DOI: 10.1038/s41467-022-34557-2

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