Meta-analysis of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations.

Abstract

Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. Our objective was to unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocessed 12,010 cnidarian microbiome samples from 186 studies, alongside 4,002 poriferan, cultured Symbiodiniaceae, and environmental samples, unifying ~6.5 billion sequence reads. This meta-analysis uncovered an incredible diversity of 86 archaeal and bacterial phyla. Globally, cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body. Host phylogeny and sampling depth also influenced the Cnidaria ‘core microbiome’. We identified host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This meta-analysis forms a framework for understanding factors governing cnidarian microbiomes, creating a baseline to help elucidate the impact of stress associated dysbiosis.

Chlamydiae in cnidarians: Shared functional potential despite broad taxonomic diversity

“…By analyzing datasets from186 cnidarian and Symbiodiniaceae microbiome studies [7], we found that reads assigned to the phylum Chlamydiota are widespread in these host taxa, being detected in 1,925 individual samples out of 10,255, although usually at a low relative abundance (< 2% for all families except Psammocoridae, Figure 1). The highest relative abundance was in the scleractinian family, Psammocoridae (32% chlamydiae), although this data came from only one study (seven samples).…”

“…Here, we analyzed previously published data from cnidarian and Symbiodiniaceae microbiome studies and eight chlamydial MAGs sequenced from cnidarian hosts (corals), to increase our understanding of both chlamydial and cnidarian biology, and lay the foundations for further studies on cnidarian-chlamydiae interactions. The sequences derived from 186 cnidarian and Symbiodiniaceae microbiome studies [7] enabled a comprehensive overview of the presence, prevalence, and diversity of chlamydiae in cnidarian holobionts. Cnidarian-associated chlamydiae were highly diverse; with the exception of members of the chordate-infecting Piscichlamydiaceae, Parilichlamydiaceae, and Chlamydiaceae, members of all other chlamydial families occur in cnidarian microbiomes.…”

“…Six out of eight MAGs were members of the Simkaniaceae and Parasimkaniaceae families, which are often found to be highly abundant in cnidarian metabarcoding studies [7,11,14].…”

“…Five databases were obtained from a previously published meta-analysis of 186 cnidarian and cultured Symbiodiniaceae microbiome studies [7]. The five datasets each group metabarcoding based on the hypervariable region of the 16S rRNA gene that was targeted (V1-V2, V3, V4, V5-V6, and V7-V8, respectively).…”

“…Among them, bacteria have important functions, including protection against pathogens, and nitrogen and sulfur cycling [3][4][5]. Although the bacterial microbiome is highly diverse [6][7][8], most functional and genomic studies have focused on a few bacterial taxa, such as Proteobacteria, leaving most other taxa understudied. This includes the Chlamydiota (also known as chlamydiae), a phylum of obligate intracellular bacteria that infect a broad spectrum of eukaryotic hosts [9,10].…”