Journal Article
Adapting to novel environments together: Evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification (Cyprinidae, Sinocyclocheilus)
Zhou, S., Rajput, A.P., Mao, T., Liu, Y., Ellepola, G., Herath, J., Yang, J. and Meegaskumbura, M.
Record Number:
5733
Year:
2022
Journal:
Frontiers in Microbiology
Pages:
1-17
Volume:
13:823254
Abstract:
The symbiosis between a host and its microbiome is essential for host fitness, and this
association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the
largest cavefish diversification of the world, an emerging multi-species model system
for evolutionary novelty, provides an excellent opportunity for examining correlates
of host evolutionary history, habitat, and gut-microbial community diversity. From the
diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D),
geographic distribution, and knowledge from captive-maintained Sinocyclocheilus
populations, we hypothesize habitat to be the major determinant of microbiome
diversity, with phylogeny playing a lesser role. For this, we subject environmental water
samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus
species, both from the wild and after being in captivity for 6 months, to bacterial
16S rRNA gene profiling using Illumina sequencing. We see significant differences in
the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types;
gut microbiomes too, were influenced by host-related factors. There is no significant
association between the gut microbiomes and host phylogeny. However, there is some
microbiome related structure at the clade level, with the most geographically distant
clades (A and D) being the most distinct, and the two overlapping clades (B and
C) showing similarities. Microbes inhabiting water were not a cause for significant
differences in fish-gut microbiota, but water quality parameters were. Transferring from
wild to captivity, the fish microbiomes changed significantly and became homogenized,
signifying plastic changes and highlighting the importance of environmental factors
(habitat) in microbiome community assembly. The core microbiome of this group, at
higher taxonomic scale, resembled that of other teleost fishes. Our results suggest
that divergent natural environments giving rise to evolutionary novelties underlying host
adaptations, also includes the microbiome of these fishes.
Keywords: fecal microbiome, Sinocyclocheilus, 16S rRNA, phylosymbiosis, core-microbiome, habitat, captive, wild
Times Cited:
3