Gary Trubl is finishing his PhD in Microbiology at The Ohio State University, co-advised by Drs. Virginia Rich and Matthew Sullivan. He shared a few thoughts on his summer at JGI through a program that provides graduate thesis research opportunities at DOE laboratories.
Gary Trubl (right) with mentor Simon Roux
My dissertation work is on characterizing soil viruses via viral metagenomics (viromics) along a permafrost thaw gradient in Arctic Sweden. Over the past two decades we have learned viruses are major players in ocean biogeochemical cycling and we know virtually nothing about them in soil ecosystems. It has been my job to develop methods to access and characterize soil viruses and make them available and easy to do for other scientists researching soil systems.
I am part of a large DOE-funded collaboration called IsoGenie (https://isogenie.osu.edu/) that brought together 13 principal investigators and more than 30 research scientists, postdocs, lab techs, and graduate and undergraduate students from several disciplines to better understand permafrost thaw, specifically what is going to happen to the newly-thawed carbon. Last year I heard about the DOE Office of Science Graduate Student Research (SCGSR) Program that lets you work at a DOE user facility for 3–12 months to improve your dissertation work, and applied. The DOE is a science agency with a goal to promote scientific innovation to better understand carbon transformations in terrestrial systems and if soil viruses are as important for these transformations as their marine counterparts, then soil virus research should be a cornerstone for DOE research. Knowing this, I submitted a proposal for the DOE SCGSR with some of our preliminary results — happy to say they felt the same way and my proposal was funded.
For my DOE SCGSR fellowship, I am working at JGI (from June through October 2018) with Dr. Simon Roux as my mentor, bioinformatically processing and characterizing 20 viromes that I spent the last year generating. This is the perfect place for me to be doing this kind of research because JGI has been on the forefront of promoting terrestrial virus research by creating the largest viral database, IMG/VR, (which is available for the public and easy to use) and benchmarking the tools to analyze viruses. Additionally, I had already been working with JGI and Dr. Roux for the past two years optimizing protocols to extract DNA from viruses so we could characterize them. With the development of all these new methods and tools and the ending of my graduate career (defense set for November 2018), this is the opportune moment to be at JGI.
The DOE Office of Science Graduate Student Research (SCGSR) Program is currently accepting applications. The deadline to submit is November 15, 2018 at 5:00PM Eastern Time.
Photos by JGI Communications & outreach intern Elise Schiappacasse.