Publications & Resources
Opening New Areas of Biology—
Metagenomic study initiates the field of coral virology
Assistant Professor of Biology at Florida International University & former San Diego State University post-doc
Study Summary: Herpes-like viruses may contribute to pandemic decline of tropical reefs. Little is known about the causative agents of coral disease, a major contributor to the deterioration of reefs which has put nearly one-third of all coral species in the threat of extinction. In an effort to determine the influence of viral pathogens in declining coral health, researchers at San Diego State University used metagenomic analysis with the Genome Sequencer system to sequence Porites compressa coral samples under varying environmental stressors. The purpose of the study, led by Drs. Forest Rohwer and Rebecca Vega Thurber, was to replicate current ecological changes in tropical reef habitats such as reduced pH, elevated nutrients and increased temperatures to determine their effects on viral populations within the coral. The experiments found highly-abundant levels of a herpes-like viruses in stressed Porites compressa corals. Interestingly, the viral sequences were rarely detected in un-stressed, healthy samples. While further studies are needed to understand how these viruses affect coral physiology, it is clear that environmental stressors not only result in coral symbiont loss and bacterial and fungal diseases but also in increased herpes-like virus production that together may explain the devastating death of coral reefs as ocean temperatures rise and pollution increases.
What was the role of 454 Sequencing in the coral-virus study?
Although corals are extremely important ecosystem engineers in tropical reef systems little is known about their microbiology. As a result, studies on coral disease have mostly been limited to bacteria and fungus that can be easily cultivated. 454 Sequencing has eliminated this barrier. Using the Genome Sequencer System I have identified over 15,000 coral associated viral sequences and found that herpesviruses are the most common viruses. The shear number of available sequences has also allowed me to demonstrate that the similarities have broad and deep coverage across the a-herpesvirus genomes and are not due to bias in the database (e.g. more herpesviruses genomes than other eukaryotic viral genomes). Most importantly these sequences have allowed me to use alternative measures to test and confirm the hypothesis that stress causes production of these herpes-like viruses.
What has been your most exciting discovery using 454 Sequencing?
The most exciting discovery in this study was that herpesvirus-like sequences constitute about 30% of all similarities in stressed corals. Using this data we hypothesized that other Cnidarians may also have herpes-like genes. After evaluating the reference libraries for the Nematostella genome and the Hydra EST library we found that dozens of genes were similar to herpesviral sequences. This suggests that herpes-like viruses are commonly found in Cnidarians, one of the oldest metazoan phyla. This has important implications in the evolution of herpesviruses, and may serve as source of novel therapies for human disease.
What have been the implications of this discovery in your field of research?
This is the first study of its kind in many ways. First, this is the first major paper on viruses in corals. Second, this is one of just a handful of studies that used an empirical approach and 454 Sequencing to test hypotheses. Many sequencing projects to date have compared and contrasted different habitats, but our study used DNA from 5 different temporal studies. This allowed us to show that not only does the viral consortia change, but shows how it changes in response to different stressors over time.
All in all, this discovery has created the field of coral virology. It has also provided scientists a foundation of genomic data on viruses from corals, a tool we did not previously have. Future testable hypotheses can be created from this study and sequence based tools are now available for searches.
How has 454 Sequencing changed the way you approach your research?
454 Sequencing has opened up many avenues of research that were previously restricted due to technical feasibility, cost, and time. Coral viruses are a great example. Investigations of previously unexplored viral consortia require a cloning independent and high throughput based approach. The system's long reads enable accurate assignment with metagenomic databases.
What's your next step? How do you plan to use 454 Sequencing in the future?
Currently I have two other manuscripts that use 454 Sequencing to investigate the changing community of phage, bacteria, fungi, and micro-eukayotes that inhabit, and potentially cause, disease in corals. Also, I have collected samples of coral tumors that we believe maybe the result of these viruses. We have preliminary data that show that herpes-like viruses are more abundant in these tumors than in healthy tissue. We hope to sequence these libraries in the future to confirm this finding and to assemble the complete coral herpesvirus genome. This method is, of course, applicable to fields outside of marine biology and I am beginning collaborations for similar viral disease studies involving farm animal species.
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