Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts

Abstract

Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group.Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle | 3769 O'BRIEN Et al.

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

“…Across Cnidaria, host phylogeny plays a key role in microbial assembly, influencing the structure, complexity, and diversity of cnidarian microbiomes. Our cnidarian-wide comparisons greatly expand previous findings of phylogenetic influence on coral microbiomes 44,45,46 , and are similar to processes identified in poriferan holobionts 47,48 . We posit that increasing body plan complexity, e.g., the evolution of skeletons in Alcyonacea, Antipatharia, Helioporacea, Scleractinia, increased the number of internal niches, driving niche partitioning, and facilitating increases in the richness and/or diversity of specific microbial communities (Fig.…”

“…8-9), suggesting that phylosymbiosis (microbial patterns that mirror host phylogeny) may have occurred multiple times in cnidarian holobiont evolution. While bacterial coevolution and phylosymbiosis of Scleractinia and Octocorallia has been documented throughout the South-West Pacific 44,45,46 we posit that these processes may have occurred not only throughout Cnidaria, but repeatedly across geographically distinct ocean basins.…”

“…Further, comparing the Illumina Mi-Seq subset of sequences (V4 library), demonstrated that octocorals in the Caribbean, Mediterranean, and Indo-Pacific not only hosted the greatest absolute abundance of Endozoicomonas, but these sequences were shared across more samples, compared to any other cnidarian. Both specialist and generalist strains of Endozoicomonas exist within Anthozoa, suggesting a variable genetic component that has the potential for coevolution with their hosts 37,44,45,46,53 similar to that of Symbiodiniaceae 59 . We expanded this observation and revealed patterns of switching in host specificity between Anthozoa and non-Anthozoa (including Cubozoa, Hydrozoa, Scyphozoa, and Porifera; Fig.…”

High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata

“…These sequences also shared a basal clade with P. damicornis –associated Endozoicomonas , which along with S. pistillata belong in the Pocilloporidae family and are commonly recognized as also having prevalent CAMAs within their tissues ( 14 , 25 , 49 ). These close host-bacterial phylogenetic relationships provide further evidence for patterns of phylosymbiosis across coral species and the potential for cophylogeny ( 48 , 50 , 51 ).…”

Intracellular Bacterial Symbionts in Corals: Challenges and Future Directions

“…As such, endosymbionts have been vertically transmitted over the course of many speciation events within insect groups-co-diversification, resulting in phylogenetic congruence or cophylogeny between hosts and endosymbionts. Correlations between the phylogeny of hosts and their associated bacteria have been reported in corals, in particular for tissueand skeleton-associated bacteria, i.e., closely associated symbionts [142][143][144]. However, as symbiont stability and mode of transmission are mostly unknown, co-evolution cannot be assumed.…”