Host Species and Habitat Shape Fish- associated Bacterial Communities: Phylosymbiosis between Fish and their Microbiome

Abstract

BackgroundWhile many studies have reported that the structure of the gut and skin microbiome 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 (BCs) and assess the extent to which host habitat and phylogeny predict BC 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 BC composition using 16S metabarcoding and tested for community variation. ResultsWe found that the water BC was distinct from the fish microbiome BCs, although the skin BC more closely resembled the water BC. We also found that environmental (sample location), habitat, fish diet and host species factors shape and promote divergence or convergence of the fish BCs. Since host species significantly affected both gut and skin BC (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus BC dissimilarity. We found significant phylogenetic effects on BC dissimilarity, consistent with phylosymbiosis for both the fish skin and gut BCs, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes. ConclusionsAnalyzing the gut content and skin mucus BCs 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.

Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations

“…However, changes in fish gut microbial communities were associated with gradients of turbidity, dissolved oxygen, temperature, total nitrogen, and sampling date throughout the year. Previous research indicates that fish gut microbiomes are influenced both by the environment and host selective factors resulting in differing microbial communities even between closely related species and species reared in the same environment [ 8 , 47 , 48 ]. Our results indicated many notable similarities between the gut microbiomes of the species analyzed.…”

Microbiota associated with meiofaunal nemerteans reveals evidence of phylosymbiosis

“…Most studies investigating patterns of phylosymbiosis have predominantly focused on only a small fraction of animals such as mammals and other vertebrates (Brown et al, 2023;Ley et al, 2008;Moeller et al, 2017;Sadeghi et al, 2022), arthropods, particularly insects (Dunaj et al, 2020;Li et al, 2022;Tinker & Ottesen, 2020), or corals and sponges (Moitinho-Silva et al, 2017;Pushpakumara et al, 2023;Röthig et al, 2016;Sweet & Bulling, 2017;Thomas et al, 2016). Other organisms residing in various ecosystems and distinguished by a range of life histories have received relatively less attention in comparison.…”