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Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)

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...

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Autores principales: Zhou, Shipeng, Rajput, Amrapali P., Mao, Tingru, Liu, Yewei, Ellepola, Gajaba, Herath, Jayampathi, Yang, Jian, Meegaskumbura, Madhava
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8964274/
https://www.ncbi.nlm.nih.gov/pubmed/35359710
http://dx.doi.org/10.3389/fmicb.2022.823254
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author Zhou, Shipeng
Rajput, Amrapali P.
Mao, Tingru
Liu, Yewei
Ellepola, Gajaba
Herath, Jayampathi
Yang, Jian
Meegaskumbura, Madhava
author_facet Zhou, Shipeng
Rajput, Amrapali P.
Mao, Tingru
Liu, Yewei
Ellepola, Gajaba
Herath, Jayampathi
Yang, Jian
Meegaskumbura, Madhava
author_sort Zhou, Shipeng
collection PubMed
description 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.
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spelling pubmed-89642742022-03-30 Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus) Zhou, Shipeng Rajput, Amrapali P. Mao, Tingru Liu, Yewei Ellepola, Gajaba Herath, Jayampathi Yang, Jian Meegaskumbura, Madhava Front Microbiol Microbiology 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. Frontiers Media S.A. 2022-03-14 /pmc/articles/PMC8964274/ /pubmed/35359710 http://dx.doi.org/10.3389/fmicb.2022.823254 Text en Copyright © 2022 Zhou, Rajput, Mao, Liu, Ellepola, Herath, Yang and Meegaskumbura. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Zhou, Shipeng
Rajput, Amrapali P.
Mao, Tingru
Liu, Yewei
Ellepola, Gajaba
Herath, Jayampathi
Yang, Jian
Meegaskumbura, Madhava
Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title_full Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title_fullStr Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title_full_unstemmed Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title_short Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus)
title_sort adapting to novel environments together: evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification (cyprinidae, sinocyclocheilus)
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8964274/
https://www.ncbi.nlm.nih.gov/pubmed/35359710
http://dx.doi.org/10.3389/fmicb.2022.823254
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