Helen Webster Genomics Course Page

This web page was produced as an assignment for an undergraduate course at Davidson College.

Helen Webster's Genomics Home Page

Goseong Bay location and the six sites of virus collection.Hwang et al.

What was the research project?
According to Hwang et al., viruses are the most abundant microbes in large bodies of water, accounting for 106 to109 particles per mL of seawater. A study conducted by Dr. Hwang and collaborators, published in 2017, takes a look at the genomic diversity of marine viruses, and the effect of seasons on the structure of the marine viral community, and therefore implications on the rest of the marine ecosystem. It has previously been found that viral communities in oceans vary according to latitude, temperature, oxygen concentration, biome, and microbial concentrations (Brum et al.). Knowing this about niche structure, these researchers conducted a mass metagenomic characterization of the molecular diversity of DNA viruses in Goseong Bay, South Korea. The researchers examined the viral distribution, abundance, and ecosystem role of marine viruses with the changing of seasons. Modern techniques, including next generation sequencing, made this metagenomic study possible, as large fragments were able to be read and sequencing, which was a previous limitation of this type of study. The researchers hoped to gain insight into the taxonomic make up of marine viruses themselves and in the context of the entire ecosystem.

Were they testing a hypothesis or doing discovery science?
They were doing discovery science. Hwang et al. conducted a "metagenomic study," which means a large amount of data was collected from the environment and surveyed in order to draw conclusions and predict patterns. Researchers gathered samples from six sites in the Goseong Bay, and reported their findings through organizing and interpreting the data.

What genomic technology was used?
The researchers analyzed multiple DNA libraries from samples collected during each of the four seasons. Illumina HiSeq2000 was then implemented for sequencing. Illumina entails synthesis by sequencing (SBS), mass parallel sequencing DNA and detecting bases one by one in order to build one big strand. Process was made more efficiently by combining the ligation and fragmentation steps into a single step (known as "tagmentation"). The pieces were then amplified using PCR.

What was the take home message?
Viral communities are similar in the different seasons. 108 viruses were present during all seasons, and the breakdown of which viruses and their abundance per season was found. The viral community is an important and influential part of marine ecosystems. From knowing the viral composition, we can further investigate the role of different viruses and how they contribute to the overall marine habitat in terms of infection, gene exchange, and more.

What is your evaluation of the project?
This project is useful because it offers a comprehensive breakdown of viruses in a particular body of water. It is important because it shows that this is most likely occurring in all bodies of water. It might not necessarily be previously known just how much of marine ecosystems is made up by the viral community. The study is well laid out and easy for a non-expert to understand. Clear results and discussion help the reader to fully understand the results and implications of the study, and how further research can and should build on this information.

References
Hwang et al. 2017. Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea. PLoS ONE. 12(1). Available from PLoS ONE.

Brum et al. 2015. Patterns and ecological drivers of ocean viral communities. Science. 348(6237). Available from Science.

HiSeq 2500 Sequencing Technology. 2017. Illumina, Inc. Available from Illumina.

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Email Questions or Comments: hewebster@davidson.edu