Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise

Abstract

SummaryReef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and amplification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are diverse, with double-and singlestranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association.

Reef invertebrate viromics: diversity, host specificity and functional capacity

“…). Herpes‐like viruses have previously been reported to infect bleached, diseased and stressed corals (Vega Thurber et al ., ; Soffer et al ., ; Correa et al ., ) but were not identified in any of the coral samples from the present study, possibly reflecting species specific, health state or methodological differences (Weynberg et al ., ; Wood‐Charlson et al ., ).…”

“…Up to 40 Circoviridae OTUs were also evident across the GBR sponge, coral and seawater samples. The presence of ssDNA Microviruses in coral virome data sets has been reported elsewhere (reviewed in (Wood‐Charlson et al ., )), although it was previously assumed their prominence was due to Phi29‐based multiple displacement amplification methods preferentially enriching ssDNA molecules (Wood‐Charlson et al ., ). Members of the Microviridae have also been identified in the human gut, where they are responsible for increased variability in comparison to temperate phages (Minot et al ., ).…”

“…Hosts: Ar, archaea; B, bacteria; F, fungi; I, invertebrate; P, plant; Pr, protist; V, vertebrate. This table is a modification of the results presented in Wood‐Charlson and colleagues (). OTU‐based analysis is displayed in red, and viral RefSeq taxonomic assignment from these results is displayed in pink (Wood‐Charlson et al ., ).…”

Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle

“…This profile differs from those of pristine coral reefs in the Pacific, where respiration and virulence were the most abundant functions (Dinsdale et al, 2008a,b). These differences may, however, be a result of method variability, from DNA extraction to sequencing (Wood-Charlson et al, 2015). …”

Viruses in corals: hidden drivers of coral bleaching and disease?

“…Coral-associated virus communities are highly diverse and comprise bacteriophages, archaeal and eukaryotic viruses [10][11][12] . Despite this diversity, only a smaller subset of taxonomic groups are commonly found in corals, including bacteriophages belonging to the order of the Caudovirales, and eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) belonging to the families Phycodnaviridae, Mimiviridae, Poxviridae and Iridoviridae, as well as…”