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
Relevent Species:
Related Records:
Mao, WN, Lu, ZM, Li, WX, Ma, HM and Huang, G (2003)
A new species of Sinocyclocheilus (Cyprinidae) from cave of Yunnan, China
Zhou, J, Zhang, CG and He, AY (2004)A new species of the genus Sinocyclocheilus from Guangxi, China (Cypriniformes, Cyprinidae)
Lan, J.H., Zhao, Y.H. and Zhang, C.G. (2004)A new species of the genus Sinocyclocheilus from China (Cypriniformes, Cyprinidae, Barbinae)
Zhao, Y.H. and Zhang, C.G. (2009)Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China - Species diversity, cave adaptation, systematics and zoogeography
Romero, A., Zhao, Y.H. and Chen, X.Y. (2009)The hypogean fishes of China
Zhao, Y.H. and Zhang, C.G. (2009)Endemic fishes of Sinocyclocheilus (Cypriniformes: Cyprinidae) in China - Species diversity, cave adaptation, systematics and zoogeography
Romero, A., Zhao, Y.H. and Chen, X.Y. (2009)The hypogean fishes of China
Zhao, Y.H., Gozlan, R.E. and Zhang, C.G. (2011)Out of sight out of mind: current knowledge of Chinese cave fishes
Zhao, Y.H., Gozlan, R.E. and Zhang, C.G. (2011)Out of sight out of mind: current knowledge of Chinese cave fishes
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Yang,J., Chen,X., Bai,J., Fang,D., Qiu,Y., Jiang,W., Yuan,H., Bian,C., Lu,J., He,S., Pan,X., Zhang,Y., Wang,X., You,X., Wang,Y., Sun,Y., Mao,D., Liu,Y., Fan,G., Zhang,H., Chen,X., Zhang,X., Zheng,L., Wang,J., Cheng,L. (2016)The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Zhang, C.G. and Zhou, Y.H. (2016)Species diversity and distribution of inland fishes in China
Yang,J., Chen,X., Bai,J., Fang,D., Qiu,Y., Jiang,W., Yuan,H., Bian,C., Lu,J., He,S., Pan,X., Zhang,Y., Wang,X., You,X., Wang,Y., Sun,Y., Mao,D., Liu,Y., Fan,G., Zhang,H., Chen,X., Zhang,X., Zheng,L., Wang,J., Cheng,L. (2016)The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Herzog, H., Klein, B. and Ziegler, A. (2017)Form and function of the teleost lateral line revealed using three-dimensional imaging and computational fluid dynamics
Zhang, X.-Y., Huang, Z.-Q., Ning, T., Xiang, X.H. Li, C.-Q. Chen, S.-Y. and Xiao, H. (2018)Microscopic and submicroscopic gradient variation of olfactory systems among six Sinocyclocheilus species living in different environments
Niu, C., Luo, J., Yang, J. and Zhao, Y. (2018)Length–weight relationships of four cavefish species from China
Huang, Z., Titus, T., Postlethwait, J.H. and Meng, F. (2019)Eye degeneration and loss of otx5b expression in the cavefish Sinocyclocheilus tileihornes
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)Morphometrics of eight Chinese cavefish species
Lunghi, E., Zhao, Y., Sun, X. and Zhao, Y. (2019)Morphometrics of eight Chinese cavefish species
Chen, H., Li, C., Liu, T., Chen, S. and Xiao, H. (2019)A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Chen, H., Li, C., Liu, T., Chen, S. and Xiao, H. (2019)A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Chen, H., Li, C., Liu, T., Chen, S. and Xiao, H. (2019)A metagenomic study of intestinal microbial diversity in relation to feeding habits of surface and cave-dwelling Sinocyclocheilus species
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Mao, T.-R., Liu, Y.-W., Meegaskumbura, M., Yang, J., Ellepola, G., Senevirathne, G., Fu, C.-H., Gross, J.B. and Pie, M.R. (2020)Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals and origin of novel traits
Ma, Z., Herzog, H., Jiang, Y., Zhao, Y. and Zhang, D. (2020)Exquisite structure of the lateral line system in eyeless cavefish Sinocyclocheilus tianlinensis contrast to eyed Sinocyclocheilus macrophthalmus (Cypriniformes: Cyprinidae)
Li, C., Chen, H., Zhao, Y., Chen, S. and Xiao, H. (2020)Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Zhao, Y., Zhang, C. and Proudlove, G.S. (2021)Fishes of the Genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in China. Systematics, biology, biogeography and cave adaptation
Yang, N., Li, Y., Liu, Z., Chen, Q. and Shen, Y. (2021)Molecular phylogenetics and evolutionary history of Sinocyclocheilus (Cypriniformes: Cyprinidae) species within Barbinae in China
Chen, B., Mao, T., Liu, Y., Dai, W., Li, X., Rajput, A.P., Yang, J., Gross, J.B. and Meegaskumbura, M. (2021)Sensory convergence in the world’s largest cavefish diversification: patterns of
neuromast evolution, distribution and associated behaviour in Sinocyclocheilus
Zhou, S., Rajput, A.P., Liu, Y., Mao, T., Yang, J., Herath, J. and Meegaskumbura, M. (2021)Adapting to novel environments together: evolutionary and ecological correlates of the
bacterial microbiome of the world’s largest cavefish diversification
Chen, B., Mao, T., Liu, Y., Dai, W., Li, X., Rajput, A.P., Yang, J., Gross, J.B. and Meegaskumbura, M. (2021)Sensory convergence in the world’s largest cavefish diversification: patterns of
neuromast evolution, distribution and associated behaviour in Sinocyclocheilus
Zhou, S., Rajput, A.P., Liu, Y., Mao, T., Yang, J., Herath, J. and Meegaskumbura, M. (2021)Adapting to novel environments together: evolutionary and ecological correlates of the
bacterial microbiome of the world’s largest cavefish diversification
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Wen, H., Luo., T., Wang, Y., Wang, S., Liu, T., Xiao, N. and Zhou, J. (2022)Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China
Yang, Z., Gong, Z., Jiang, Y., Cai, Y., Ma, Z., Xin Na, Dong, Z. and Zhang, D. (2022)Maximized hydrodynamic stimulation strategy for placement of differential pressure and velocity sensors in artificial lateral line systems
Zhou, S., Rajput, A.P., Mao, T., Liu, Y., Ellepola, G., Herath, J., Yang, J. and Meegaskumbura, M. (2022)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. (2022)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. (2022)Adapting to novel environments together: Evolutionary and ecological correlates of the bacterial microbiome of the world’s largest cavefish diversification (Cyprinidae, Sinocyclocheilus)
Jiang, W.-S., Li, J., Xiang, H.-X., Sun, C., Chang, J.B. and Yang, J.X. (2023)Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish (Cypriniformes: Cyprinidae)
Jiang, W.-S., Li, J., Xiang, H.-X., Sun, C., Chang, J.B. and Yang, J.X. (2023)Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish (Cypriniformes: Cyprinidae)
Jiang, W.-S., Li, J., Xiang, H.-X., Sun, C., Chang, J.B. and Yang, J.X. (2023)Comparative analysis and phylogenetic and evolutionary implications of mitogenomes of Chinese Sinocyclocheilus cavefish (Cypriniformes: Cyprinidae)