Community structure of coral microbiomes is dependent on host morphology

Abstract

Background: The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities.

Results: The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community.

Conclusions: The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.

Keywords: 16S rRNA gene; Coral; Diazotroph; Microbiome; Nitrogen fixation; Symbiodiniaceae; nifH.

Fig. 1

Estimates of beta diversity from 16S rRNA gene microbiome communities across coral species. A Relative abundances of microbial classes averaged for each coral species. Note that only microbial classes representing > 1% of all reads were included for visualization. Principal coordinates of coral samples colored by coral life history traits based on 16S rRNA gene microbial composition for B ecological life history characteristics, C morphology, D phylogenetic clade, E spawning mode, and F reproductive strategy. Significance testing was based on nested PERMANOVA analyses to account for variation due to coral species, which was highly significant (Table 1). Seawater samples are shown in black and sampling location is denoted by shape

Fig. 2

ASVs with differential enrichment with respect to coral morphology. Significant ASVs determined using Wald tests, adjusted P values < 0.05. A Boulder vs branching; B boulder vs plating; C solitary vs boulder; D plating vs branching; E solitary vs plating; F branching vs solitary. Relative enrichment (log2 scale) shown for ASVs, grouped by assigned genus and colored by microbial class

Fig. 3

A Relative abundance of each nifH phylotype (unique sequence variant) according to placement in either nitrogen-fixing or non-nitrogenase clades. Average abundances calculated after combining samples for each species. B Relative abundance of nifH phylotypes according to their nitrogen-fixing orders. Average abundances calculated after combining samples for each species and only include variants belonging to nifH clusters I and Ill. C Relative abundance of 16S rRNA orders containing candidate diazotrophs. Average abundances calculated after combining samples for each species

Fig. 4

nifH diversity across coral species. A Average relative abundances of nifH phylotypes (unique sequence variants) belonging to nitrogen-fixing clusters I and III. Bar segments are colored according to placement in B phylogeny of nifH amplicons. Peptide translations for de novo nifH and best-match NCBI nifH sequences were aligned with MAFFT along with nitrogenase-like chlorophyllide reductases. De novo nifH that placed within the chlorophyllide/ferrodoxin clades were excluded. Only nifH phylotypes with phylogenetic relationships to established nitrogen-fixing nifH clades (e.g., clusters I and III) were subsequently analyzed. Taxonomic affinity of nifH variants is based on phylogenetic placement using published sequences. Note: only phylotypes representing at least 1% of all reads were included

Fig. 5

Principal coordinate analysis of nifH communities using Euclidean distances on CLR-transformed read counts. Data points are labelled according to A host species, B clade, C reproductive strategy, D morphology, E life history characteristics, and F spawning mode

Fig. 6

Co-inertia analysis (CIA) for the relationship between nifH and 16S rRNA microbial communities. CIA ordinations project 16S rRNA gene (dots) and nifH (arrow tips) samples on axes after maximizing covariation among datasets. Length of arrows corresponds to dissimilarity among communities while shared directionality represents positive correlation between 16S rRNA gene and nifH relative abundances. RV coefficient (with values 0 to 1) indicating the overall correlation between 16S rRNA and nifH gene community compositions, where 0 is no correlation and 1 is maximum correlation

Fig. 7

Symbiodiniaceae diversity across coral species including two-color morphologies of Montastraea cavernosa, orange (OR) and brown (BR). Average relative abundances for each Symbiodiniaceae genus (A) and top-matching NCBI hit for the ITS2 marker across coral species. B Principal coordinate ordination of zooxanthellate communities across coral samples using Bray-Curtis distance on rarefied ITS2 counts