Dataset Information

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

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.

SUBMITTER: Minich JJ

PROVIDER: S-EPMC9671965 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Minich Jeremiah J JJ Härer Andreas A Vechinski Joseph J Frable Benjamin W BW Skelton Zachary R ZR Kunselman Emily E Shane Michael A MA Perry Daniela S DS Gonzalez Antonio A McDonald Daniel D Knight Rob R Michael Todd P TP Allen Eric E EE

Nature communications 20221117 1

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, represent ...[more]

PMID: 36396943

Similar Datasets

Project description:Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n = 2, FT n = 1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus, while skin and digesta from RAS fish had 2 times the richness of FT fish. Body sites each had unique microbiomes (P < 0.001) and were influenced by hatchery system type (P < 0.001), with RAS being more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin, and digesta communities were more similar to that in the origin tank biofilm than those in all other experimental tanks, suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density were positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome, with the skin microbiome as an important intermediate.IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and, furthermore, how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.

Project description:Multi-use marine protected areas (MUMPAs) are a commonly applied tool for marine conservation in developing countries, particularly where large no-take reserves are not socially or politically feasible. Although MUMPAs have produced benefits around the world, the persistence of moderate fishing pressure reduces the likelihood of achieving the primary objective of these areas, which is the conservation of ecosystems. In this study we used traditional and functional metrics to evaluate how fish assemblages changed through time in a MUMPA, including shifts in species responses and in ecological processes. We conducted visual censuses of fishes at Espíritu Santo Island, México (MUMPA; N = 320; 24°N, 110°W) from 2005 to 2017 to assess fish richness, size-distribution and density. Three functional indices were calculated using six traits (size, mobility, period of activity, aggregation, position in water column and diet): functional richness (volume occupied by species), dispersion (complementarity between species) and originality (inverse of functional redundancy). We compared fish diversity among three management zone types (sustainable fishing, traditional fishing and no-take zones), through a 13-year period, assessing which species increased or decreased in occurrence, density, and biomass, and how indices respond over time. Despite a general increase in biomass and stability in density and originality, we detected a reduction in fish biodiversity in the form of declines in species and functional richness, which could imply the risk of local extinction and decrease in certain ecosystem processes. In addition, changes in functional dispersion showed that some functions are losing representation through time. Although no single cause is apparent, such factors as competitive interactions, habitat loss and persistence of fishing pressure potentially explain these decreases. The rise in biomass was associated with a general increase in the average size, rather than increased biomass of commercial species, as the latter remained stable during the study period. Expansion of no-take areas, enforcement of fishing regulations, and surveillance in core zones, should be implemented to reverse the decline in particular species and to promote conservation of fish functional diversity in this MUMPA.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets