Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition

C E Dubé,E Boissin,C R Voolstra,C A -F Bourmaud,S Planes,M Ziegler,A Mercière

doi:10.1038/s41467-021-26543-x

Abstract

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Highlights

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems
To assess the relative contribution of host genotype and environment to microbiome structure, we explored bacterial community composition among genetically identical fire coral colonies that inhabit contrasting reef environments
We found bacterial taxa specific to both host genotype and reef habitat

Summary

Introduction

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Empirical studies differentiating the relative contribution from the host genetic background and surrounding environment on microbiome structure in natural systems remain scarce and are largely limited to the biomedical field and human microbiome studies[20,21,22] Such information is critical to assess how flexible microbial associations are and to what degree they contribute to the physiology of their host organisms[1,5,9,23]. Corals depend on Symbiodiniaceae satisfying their energy requirements via the transfer of photosynthetically fixed carbon[30] and the assimilation of dissolved inorganic nitrogen and phosphorus[31], while the association with bacteria may serve a wide variety of functional roles, including nitrogen fixation, sulfur cycling, protection against pathogens, and stress tolerance[6,32,33,34,35,36,37]

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Conclusion