Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences

Abstract

The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species' preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.

Keywords: coral reef; ecological niche; holobiont; metaorganism; microbiome; symbiosis.

Figure 1

Map of study sites. Offshore (Abu Roma and Shib Nazar) and nearshore (Al Quad and Inner Fsar) coral reef sites were sampled from exposed (i.e. ocean facing) and sheltered (i.e. land facing) habitats (indicated by stars) on two sampling occasions (i.e. summer and winter). Replicate numbers are shown for each sampling event and site. Open symbols: offshore, closed symbols: nearshore, circles: exposed reef sites, squares: sheltered reef sites; grey: summer, black: winter.

Figure 2

Substrate cover composition (coloured bars) and abundance (black bars) of the coral Ctenactis echinata at different habitats. Offshore sheltered habitats are the species’ preferred habitat and represent distinct environmental conditions. Error bars indicate SE.

Figure 3

Nonmetric multidimensional scaling plot of bacterial communities associated with Ctenactis echinata samples. Bray–Curtis distances between samples illustrate differences between nearshore and offshore sites as well as between offshore sheltered and offshore exposed environments. Open symbols: offshore, closed symbols: nearshore, circles: exposed reef sites, squares: sheltered reef sites, grey: summer, black: winter.

Figure 4

Phylogenetic distribution and operational taxonomic units (OTU) richness of bacteria associated with the coral Ctenactis echinata across different habitats. Stacked bars: phylogenetic affiliation of abundant OTUs. Numbers next to phylum and genus denote bootstrap values of classification. Black bars: average number of OTUs associated with C. echinata. Error bars: SE.