The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge.

Autor: Doane MP; Sydney Institute of Marine Science, Mosman, NSW, Australia.; Biology Department, San Diego State University, San Diego, CA, USA., Morris MM; Biology Department, San Diego State University, San Diego, CA, USA.; Department Biology, Stanford University, Stanford, California, USA., Papudeshi B; National Center for Genome Analysis Support, Indiana University, San Diego, Indiana, USA., Allen L; Biology Department, San Diego State University, San Diego, CA, USA., Pande D; Computer Sciences Department, San Diego State University, San Diego, CA, USA., Haggerty JM; Biology Department, San Diego State University, San Diego, CA, USA., Johri S; Biology Department, San Diego State University, San Diego, CA, USA.; Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA., Turnlund AC; Biology Department, San Diego State University, San Diego, CA, USA.; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, Queens, USA., Peterson M; Biology Department, San Diego State University, San Diego, CA, USA., Kacev D; Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA., Nosal A; Scripps Institute of Oceanography, University of California-San Diego, La Jolla, California, USA.; Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA, USA., Ramirez D; Whale Shark Mexico, ConCiencia Mexico AC, La Paz, BC, USA., Hovel K; Biology Department, San Diego State University, San Diego, CA, USA., Ledbetter J; Biology Department, San Diego State University, San Diego, CA, USA., Alker A; Biology Department, San Diego State University, San Diego, CA, USA., Avalos J; Biology Department, San Diego State University, San Diego, CA, USA., Baker K; Biology Department, San Diego State University, San Diego, CA, USA., Bhide S; Biology Department, San Diego State University, San Diego, CA, USA., Billings E; Biology Department, San Diego State University, San Diego, CA, USA., Byrum S; Department of Biology, University of Florida, Gainesville, FL, USA., Clemens M; Biology Department, San Diego State University, San Diego, CA, USA., Demery AJ; Biology Department, San Diego State University, San Diego, CA, USA., Lima LFO; Biology Department, San Diego State University, San Diego, CA, USA., Gomez O; Biology Department, San Diego State University, San Diego, CA, USA., Gutierrez O; Biology Department, San Diego State University, San Diego, CA, USA., Hinton S; Biology Department, San Diego State University, San Diego, CA, USA., Kieu D; Biology Department, San Diego State University, San Diego, CA, USA., Kim A; Biology Department, San Diego State University, San Diego, CA, USA., Loaiza R; Biology Department, San Diego State University, San Diego, CA, USA., Martinez A; Biology Department, San Diego State University, San Diego, CA, USA., McGhee J; Biology Department, San Diego State University, San Diego, CA, USA., Nguyen K; Biology Department, San Diego State University, San Diego, CA, USA., Parlan S; Biology Department, San Diego State University, San Diego, CA, USA., Pham A; Biology Department, San Diego State University, San Diego, CA, USA., Price-Waldman R; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA., Edwards RA; Biology Department, San Diego State University, San Diego, CA, USA.; Viral Information Institute, San Diego State University, San Diego, CA, USA., Dinsdale EA; Biology Department, San Diego State University, San Diego, CA, USA. Elizabeth_dinsdale@hotmail.com.; Viral Information Institute, San Diego State University, San Diego, CA, USA. Elizabeth_dinsdale@hotmail.com.
Jazyk: angličtina
Zdroj: Microbiome [Microbiome] 2020 Jun 13; Vol. 8 (1), pp. 93. Date of Electronic Publication: 2020 Jun 13.
DOI: 10.1186/s40168-020-00840-x
Abstrakt: Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.
Results: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.
Conclusion: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.
Databáze: MEDLINE
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