Microbiomes of Caribbean Octocorals Vary Over Time but Are Resistant to Environmental Change

Abstract

The bacterial microbiome is an essential component of many corals, although knowledge of the microbiomes in scleractinian corals far exceeds that for octocorals. This study characterized the bacterial communities present in shallow water Caribbean gorgonian octocorals over time and space, in addition to determining the bacterial assemblages in gorgonians exposed to environmental perturbations. We found that seven shallow water Caribbean gorgonian species maintained distinct microbiomes and predominantly harbored two bacterial genera, Mycoplasma and Endozoicomonas. Representatives of these taxa accounted for over 70% of the sequences recovered, made up the three most common operational taxonomic units (OTUs), and were present in most of the gorgonian species. Gorgonian species sampled in different seasons and/or in different years, exhibited significant shifts in the abundances of these bacterial OTUs, though there were few changes to overall bacterial diversity, or to the specific OTUs present. These shifts had minimal impact on the relative abundance of inferred functional proteins within the gorgonian corals. Sequences identified as Escherichia were ubiquitous in gorgonian colonies sampled from a lagoon but not in colonies sampled from a back reef. Exposure to increased temperature and/or ultraviolet radiation (UVR) or nutrient enrichment led to few significant changes in the gorgonian coral microbiomes. While there were some shifts in the abundance of the prevalent bacteria, more commonly observed was "microbial switching" between different OTUs identified within the same bacterial genus. The relative stability of gorgonian coral bacterial microbiome may potentially explain some of the resistance and resilience of Caribbean gorgonian corals against changing environmental conditions.

Keywords: UVR; bacteria; coral; gorgonian; microbiome; nitrogen; phosphorus; temperature.

FIGURE 1

The bacterial microbiome of seven Caribbean gorgonian species in the back reef and lagoon. (A) Bacterial beta diversity, shown as non-metric multidimensional scaling ordination (stress = 0.18) based on Bray-Curtis dissimilarity between gorgonians. Ellipses depict 95% confidence intervals and strong (>0.75) Spearman Operational Taxonomic Unit (OTU) correlations included for each significantly correlated OTU. (B) Branches are clustered based on Bray-Curtis dissimilarity, and displayed as a hierarchical clustering dendrogram. (C) Relative bacterial phyla and class abundance (%) within the gorgonian corals. Each column represents data from 3 to 6 gorgonian coral colonies and from 4,007 to 30,706 sequence reads. The gorgonian species are Pseudoplexaura crucis (Pc), Eunicea tourneforti (Et), Eunicea flexuosa (Ef), Pseudoplexaura flagellosa (Pf), Pseudoplexaura porosa (Pp), Pterogorgia anceps (Pa), and Plexaurella nutans (Pn). Numbers in parentheses denote sampling years: 2012 (12), 2014 (14), and 2015 (15), with letters indicating summer (S) or winter (W).

FIGURE 2

The most abundant bacterial Operational Taxonomic Units (OTUs) in seven Caribbean gorgonian species. Prominent bacterial OTUs (1–8) are listed to the lowest bacterial taxonomic level. OTU presence in gorgonian branches (0–100% of branches sampled) is depicted by different shades of blue. The mean contribution (% of sequences) of each OTU to the microbiome of a gorgonian species is listed in each cell, with the total contribution in the final column. The prevalence (%) of each bacterial OTU in the bacteria obtained from all the gorgonian species combined appears in the bottom row. The gorgonian species are Plexaurella nutans, Pterogorgia anceps, Pseudoplexaura flagellosa, Pseudoplexaura porosa, Pseudoplexaura crucis, Eunicea tourneforti, and Eunicea flexuosa; Summer = July, Winter = December.

FIGURE 3

The bacterial microbiome in the two Caribbean gorgonian species Pseudoplexaura crucis and Eunicea tourneforti sampled from a back reef and after 7 days of experimental exposure to ambient or elevated (+3°C) temperature without (–) or with (+) ultraviolet radiation, in the summer and winter. (A) Bacterial beta diversity, shown as non-metric multidimensional scaling ordination (stress = 0.13) based on Bray-Curtis dissimilarity between samples. Ellipses depict the 95% confidence intervals. (B) Branches are clustered based on Bray-Curtis dissimilarity, and displayed as a hierarchical clustering dendrogram. (C) Relative bacterial phyla and class abundance (%) within the gorgonian coral species. Each column includes from 3,619 to 28,111 sequence reads and represents data from 3 to 4 gorgonian coral colonies.

FIGURE 4

The bacterial microbiome in the two Caribbean gorgonian species Pseudoplexaura crucis and Eunicea tourneforti sampled from a lagoon and after 7 days of experimental exposure to phosphorous (4 μM) and nitrogen (10 μM and 50 μM) nutrient enrichment. (A) Bacterial beta diversity, shown as non-metric multidimensional scaling ordination (stress = 0.09) based on Bray-Curtis dissimilarity between samples. Ellipses depict the 95% confidence intervals. (B) Branches are clustered based on Bray-Curtis dissimilarity, and displayed as a hierarchical clustering dendrogram. (C) Relative bacterial phyla and class abundance (% of sequences) within the gorgonian corals. Each column includes from 7,525 to 27,886 sequence reads and represents data from 4 to 6 gorgonian coral colonies exposed for 7 days to either no nutrient enrichment (Control), 4 μM phosphate (4 μM P), and 10 μM (10 μM A), or 50 μm (50 μM A) ammonium enrichment.

FIGURE 5

Heat map of the relative abundances of major bacterial Operational Taxonomic Units (OTUs) in the microbiome of Caribbean gorgonian corals. (A) Eunicea tourneforti and Pseudoplexaura crucis after 7 days exposure to ambient or increased (+3°C) temperatures, without (–) or with (+) ultraviolet radiation (UVR). (B) Eunicea tourneforti and Pseudoplexaura porosa after 7 days exposure to either no nutrient enrichment (Control), 4 μM phosphate, and 10 μM or 50 μM ammonium enrichment. The heat map presents the bacterial orders for OTUs that significantly changed with treatments. Each bacterial order depicted contributed at least 1% of the gorgonian coral’s microbiome assemblage with the OTU number appearing in parentheses. Color strength represents the relative abundance of the OTU, whereby darker blue represents a greater abundance.

FIGURE 6

Heat map and dendrogram of the relative abundances (%) of major KEGG (Kyoto Encyclopedia of Genes and Genomes) representative protein pathways present in six Caribbean gorgonian species sampled from a lagoon. The gorgonian species are: Pseudoplexaura flagellosa (Pf), Pseudoplexaura porosa (Pp), Eunicea tourneforti (Et), Eunicea flexuosa (Ef), Pterogorgia anceps (Pa) and Plexaurella nutans (Pn). Numbers in parentheses denote sampling years: 2012 (12), 2014 (14), and 2015 (15). Arrows indicate values significantly higher or lower in relative abundance of the inferred protein pathways present (p < 0.05).