Deciphering the bacterial microworld in corals: structure, variability and persistence

Abstract

Decades of research have defined the coral meta-organism as a complex microbial system due to the diversity, abundance and variability of the associated microorganisms. Bacteria are the most studied group of coral-associated prokaryotes, and they are located within the mucus, skeleton, tissues and cellular spaces. Abiotic factors including light irradiance, current, pH, and oxygen generate distinct micro-niches that differ between coral species, depths, reefs, and bioregions. This variety in microhabitats leads to enormous configurations of hundred of thousand bacteria, from tens of thousand phylotypes, associated with each coral species. The variability, diversity and richness of these bacterial communities have undermined the capacity to identify bacterial phylotypes in symbiosis with corals, to describe their functional roles and to establish the characteristics of a healthy bacterial community in corals. Herein, I dissect the variability, diversity and richness of bacterial communities in healthy corals. I aim to (1) define the characteristics of a healthy coral microbiome, (2) evaluate the presence of universal bacterial symbionts in coral-associated bacterial assemblages, and (3) identify factors generating variability in assessments of the coral-associated bacterial communities. In doing so, I developed a conceptual framework that extends on the core microbiome concept, attempting to structure and understand the high diversity observed in coral-associated microbial communities. Initially, I compared sample preservation and preparation methodologies with samples from the corals Goniastrea edwardsi and Isopora palifera collected from Heron Island (Southern Great Barrier Reef, Australia). I showed that preservation in DMSO and 4% paraformaldehyde solution generate comparable composition results to traditional snap freezing in liquid nitrogen for generating 16S microbiome datasets. Furthermore, I showed that homogenization with beat beating is the most reliable, reproducible and practical method for rapid sample preparation. I further evaluated the bacterial communities associated with the coral polyp and coenosarcs from the widely distributed coral Pocillopora damicornis. Although overall bacterial communities appeared similar between microhabitats, differences were evident when comparing diversity, dispersion and core, low-abundance bacteria. These results highlight the importance of considering rare bacteria in the coral microbiome, and the efficiency of core microbiome concept in detecting fine-scale differences. To address variability across broad geographic and ecological scales, I identified and quantified the bacterial community of three depth generalist corals, Pachyseris speciosa, Mycedium elephantotus and Acropora aculeus, at distinct depth intervals (10, 20, 40, and 60-80 m), across a broad latitudinal range in two distinct bioregions (the Great Barrier Reef and the western Coral Sea). I demonstrated that bacterial communities are comparable in richness, diversity and taxonomic structure. In the three coral species, the response of bacterial communities structure is reflective of differences in reef location and bioregion. I further identified ubiquitous bacterial phylotypes (core microbiome) for each species, and determined bacteria consistently associated with both shallow and mesophotic reefs. Coupling the core microbiome framework with an analysis of beta-diversity, taxonomic breadth, taxonomic redundancy and functional prediction on the databases of the three species, I further identified and quantified the variability associated to species, bioregions, reefs and individuals. I demonstrated that bacterial communities in corals show taxonomical, and potentially functional, redundancy in both the resident community and the core microbiome. Based on these results, I propose a conceptual framework defining bacterial communities in healthy corals as three layers: an environmentally responsive community (thousands of phylotypes, transient and variable), an individual microbiome (~500-600 OTUs, variable between reefs but with consistent taxonomy and function) and a core microbiome (few bacteria likely to be in symbiosis showing functional redundancy). This conceptual framework provides structure to the observed high levels of diversity and indicates that bacterial communities in corals are not as complex as previously considered. Given the ongoing degradation of reef environments and the increasing frequency and severity of anthropogenic stressors, future research should be directed towards identifying direct links of microbial contributions to coral resistance and resilience, including an understanding of their individual roles, functional redundancy, and their localization within coral niches.