The Use of Microscopy and Metagenomics to Understand the Viral Community Associated with Acroporid Corals

Research on the holobiont of coral is becoming increasingly important as coral reef are in decline. This requires not only knowledge on the microbial community but also the viral community as well, as it is thought that the diverse array of viruses found in corals play multiple roles that dictate the health of coral reefs. Usually one of two methods are used to identify any virus-like particles (VLPs), these are microscopy and metagenomics. However, there is downfalls of using these methods individually when looking at VLPs. Microscopy can only show morphological characteristics of a viral group, this can present a problem with grouping similar viral groups together as viral families can encompass a range of sizes and shapes. Metagenomics, the problem lies with many viral groups share significantly similarities in there genomic sequences and this can make it difficult to group the viruses together as well. It is also difficult to rule out contamination with metagenomics alone which can be a problem.  Therefore, the investigation looked at using both techniques (microscopy and metagenomics) to gain a finer taxonomic resolution by characterizing the viruses associated with the pacific acroporid corals.

It was found that, although there was a diverse array of viruses present in the acroporid corals, four main eukaryotic viruses dominate (Two nucleocytoplasmic large DNA viruses (NCLDVs), an atypical herpes-like virus and a gamma-retrovirus).  The two NCLDVs that were commonly identified in the investigation varied greatly. One variant was ~150 nm in size and was found within the host tissues. The second variant was ~300nm in size and located within or near Symbiodium. It is also thought that the second variant is a new relative of the megaviruses.  The atypical herpes-like viruses found were morphologically similar to herpesviruses however, it differed biologically. Typically herpesviruses replicate in the nuclei of cells, the herpes-like virus found in the investigation were not identified within the nuclei of the corals cells so I thought not to be a true herpesvirus.

Overall, the investigation has shown the benefits of combining both microscopy and metagenomics to look at viral communities as the data collected by both methods can complement the other dataset and improve confidence in the overall results. In this investigation it specifically used coral fragments as an example, however it would be easily transferred into investigations looking at more viral communities in different ecosystems.

Reviewed paper: Correa, AMS; Ainsworth, TD; Rosales, SM; Thurber, AR; Butler, CR; Thurber, RLV. (2016). 'Viral outbreak in corals associated with an in situ bleaching event: Atypical herpes-like viruses and a new megavirus infecting Symbiodium'. Frontiers In Microbiology. 7.