Gary Trubl, a virologist and postdoc at Lawrence Livermore National Laboratory, is using bioinformatics and isotopes to track how viruses influence the flow of carbon in soil.
The Joint Genome Institute presents the Genome Insider podcast.
Transcript of the episode
ALISON: Hey, I’m Alison Takemura, and this is Genome Insider, a podcast of the US Department of Energy Joint Genome Institute.
When I was in grad school, studying the ecology of bacteria, my advisor used to say that ecology is the hardest subject. I mean, it was our field, so of course he would say that. But I think what he was really getting at is just how many interactions, both seen and unseen, ecology attempts to synthesize, so that we can begin to understand and predict what’s going to happen in a given environment.
In today’s episode, we’ll once more wade into those murky ecological waters. We’re going to catch up with Gary Trubl, a virologist and postdoc at Lawrence Livermore National Lab and JGI collaborator who was our guest in our last episode. If you haven’t listened to that episode yet, no problem. Stick with me and you’ll be fine.
Anyway, talking with Gary about his research at the Ohio State University reminded me of how. much. work, and teamwork, it takes to better understand real ecosystems.
GARY: Let me introduce my advisors. I started with Dr. Virginia Rich, and she is an expert in microbial biogeochemistry. And she’s been focusing over 10 years now at a field site, which is a DOE grant that she got and it’s called IsoGenie, this group.
ALISON: I’m going to jump in here, because IsoGenie is an unusual name! IsoGenie is Virginia’s research program and the name is a mashup of the words “Isotopes” and “Genes.” Isotopes are a way that scientists can study what role microbes, and more specifically, their genes, have in shaping ecosystems. And if you’re not sure how isotopes come into play, don’t worry; we’ll come back to that later in the episode.
Right now, I’m gonna play a clip of Virginia talking about the motivation for IsoGenie which she shared at the 2019 Annual JGI Genomics of Energy & Environment Meeting. At the beginning of the clip, you’ll hear her give a quick shoutout to JGI’s own Susannah Tringe, our Deputy of User Programs. Here’s Virginia.
VIRGINIA RICH: I’d like to thank so much Susannah and the other organizers at the JGI for the opportunity to be here today and to tell you about our project characterizing carbon cycling. Why are we studying Arctic peatlands?
Well, northern latitudes host a lot of wet ecosystems, and indeed about a third to a half of the planet’s soil carbon is stored in these systems. This carbon has been frozen for hundreds to thousands of years, locked out of availability to the biosphere. Conditions in these areas are changing rapidly; as most of us know the poles are heating disproportionately quickly. And they’re also getting wetter. So these carbon rich soils are now thawing. Permafrost thawing acts as a feast for microbes.
ALISON: What that means is microbes can now metabolize the once frozen organic material, releasing greenhouse gases carbon dioxide and methane as waste products, and thus contributing to global warming. The IsoGenie team is trying to tease out all the factors that could influence this process.
GARY: ..And they’re studying every aspect. They’re studying the geology, they’re studying the hydrology…
ALISON: They’re studying the microbes and their metabolisms.. And they’re also studying the impact of viruses, which infect those microbes and can therefore alter net microbial metabolism, and ultimately the global carbon cycle.
GARY: They’re studying everything. Bringing them together and then making a consensus of the fate of carbon in the soil. And then the goal from here is to feed that into models, predictive models to see what’s going to happen as the site transitions and more permafrost thaws.
ALISON: Working with JGI, Gary has been focusing on the role of the viruses. First, he isolated their DNA from samples.
GARY: We optimized ways to really pull out their DNA, clean it up, and actually sequence it. And then the last step is now that we have the data, how to clean up the data to get as much out of it as we can. Bioinformatics is the biggest bottleneck for us right now.
ALISON: So what does Gary do now-that he has lots of data to analyze? Like many a scientist, he applies for funding. Namely, from the DOE Office of Science Graduate Student Research fellowship.
GARY: The DOE SCGSR, where you can go and work at a DOE facility.
ALISON: Gary gets the funding, chooses JGI, and JGI scientists Simon Roux and Emiley Eloe-Fadrosh — take him under their wing.
GARY: Bioinformatics is the biggest bottleneck for us right now. We had 40 different viromes we were looking at, and just analyzing them at different depths, looking at how the microbial communities change with thaw and with depth. And there’s all these, uh, tools that we use that I would have not been able to use had I not been at JGI. So JGI was like the critical means here. We had the expertise of Simon, and Emiley’s metagenomics group,
ALISON: for five-and-a-half months in 2018!
GARY: .. where I could shoot out ideas and get feedback, also had the hands-on training from Simon, and then the access to NERSC and the super-computing power that came along with it. That just allowed me to go down every rabbit hole and really go through my data and analyze it. This is something that I would have never had otherwise.
ALISON: Gary mentioned this really quickly, but I’ll zoom in on it because it’s — it’s actually pretty neat: NERSC, N-E-R-S-C. This stands for the National Energy Research Scientific Computing Center. It’s one of DOE’s supercomputing centers, operated by Berkeley Lab, and time on it is a coveted resource by environmental genomics researchers.
Gary was first an experimental scientist, but now he had to start diving into bioinformatics. Here’s Gary.
GARY: So what I’ve learned is in the lab, you can have people working next to you, and you can look up protocols and download them. But when you’re doing bioinformatics, a lot of the work is actually googling stuff. Like, Hey, I got this error, what is this error? What do I do now? I mean, the number one thing I would say to people learning bioinformatics is, everyone starts off googling everything; you got to learn the basic language, and then when errors come out—when something isn’t going right—you Google; you’ll Google, you’ll Google, you’ll Google. And you’ll just start finding people who you can follow and pay attention to that can provide feedback.
ALISON: Did you Simon? Simon, Simon?
GARY: Haha, “Simon says.” He has a great name for that. So..that.. that’s part of what my experience at JGI was. He’s such a great mentor; he gave me the space to explore, and he said, come to me with ideas, and come to me when you have questions. And I would write out a script to do work. And it would do- I would have to move it from A to B to C to D. And I would have a script for each individual one and it would probably take a week. And then I’d go and show it to Simon and say, “Hey, I have A running now, I’ll get to B tomorrow. And then by next week, I’ll have D.” And he’ll say, “Send me your code.” And he’ll come and talk with me. And he said, “Okay, here’s a code that will do ABC and D, and it’ll do them in tandem. And you’ll have it done in two days. And you’ll use half the resources.” And I thought, “Oh. so this is fantastic.”
And that’s actually a lot of it is that once you learn things, you’ll start using it, but it’s actually not the most efficient way. Part of my training assignment with Simon is not just learning bioinformatics; I had somewhat of a handle — but being more efficient at it. And that has helped out so much in my postdoc work. There’s stuff I’ve done now in a month or two, that took me almost a whole year to do in my PhD.
ALISON: But when Gary and Simon were working on this project, they found that it was still slow-going, because existing analysis pipelines were just scratching the surface of their data.
GARY: An example would be, before when we looked at viruses, we maybe (sigh) used 10% of our data, which is actually not too bad for viruses at this stage. And then from that data, we got, let’s say, a made-up number 100 viral contigs. And these are contiguous sequence of when the reads come together. And we think one contig is one virus, right, so let’s say we have 100 viruses. Just by doing some simple trimming and stuff along the way, we can increase that five to 10-fold.
ALISON: Wow that’s such a big jump!
GARY: And the best analogy for this would be like you get a whole watermelon. And then you just cut out the red center, but then you skim around the rind to get that last bit, right? Now with that, you can feed more people watermelon. So that’s kind of what our tools do: we get everything we can out of our data.
ALISON: The data are fragmented DNA sequences, which Gary and Simon are reconstructing into viral genomes. It’s like putting together hundreds of tiny sweaters from little bits of yarn.
Now a computer can knit the pieces together for Gary and Simon, but only if they first give the computer good quality instructions, or algorithms. The computer needs these instructions to sort the yarn bits, determine which are of good enough quality to even use, and then to reassemble them into sweaters — i.e. to go from DNA fragments to whole viral genomes. Gary and Simon experimented with several sets of instructions to find which worked best, and that took a lot of computing time.
GARY: And I was able to do that because I was at JGI. Now, if I had been anywhere else, you’re allocated so many resource units or computing hours. And then once you hit that limit, you have to write another proposal, so you have to stop everything you’re doing, write this proposal, wait for it to get funded, and then resume your research.
ALISON: Gary and Simon published a paper, with Simon as lead author. We’ll have it in the show notes. Based on his work, Gary had this to say to fellow virome hunters:
GARY: If you are looking at something that has low coverage,
ALISON: —whether that’s because of sequencing trouble or low DNA inputs—
GARY: this pipeline worked really well compared to the other ones we assessed. So this is something to try, to see if you can increase the amount of data you see.
ALISON: It definitely worked for Gary. He was able to peek into the world of viruses in arctic peatland. For example, he found that, especially in bogs — which are these soggy, partially-thawed peatland habitats — that viruses infect an abundant group of microbes belonging to the phylum called Acidobacteria. In short, he linked these soil viruses to their hosts. And that finding released a torrent of questions.
GARY: Are they persisting in the soil? Do they degrade? Are the hosts persisting? Are they being lysed? Is this nutrients going into other hosts? Is it being respired? Is it being captured in the soil? What’s happening? What is the fate of the carbon? And the viruses and the microbes are kind of the, the controllers of where this is going to go.
ALISON: These questions propelled Gary to take on the next phase of his research — what he’s working on now. And this brings us back to isotopes. Gary’s using them to track the fate of carbon and oxygen through the environment.
So.. how do isotopes work?
GARY: The idea is you have elements, and then you have different numbers of neutrons, these different numbers of neutrons create a different mass, but it’s still the same element. And the neutrons are kind of inert, they don’t really do anything. So an example would be for carbon, we have 12 carbon; it’s like 99% of everything we see out there. Then you have 13C carbon, it has that extra neutron. And we actually see that as well. Now life is super cool. Where when it uses a compound, or a chemical, let’s say, it wants to use the lighter isotope, and it’ll preferentially use this. So if there’s compounds that have 13C and 12C, it will want to use 12C. Now, with stable isotopes, we add plant material, which has been enriched in 13 C, and we
— that’s all we feed it.
ALISON: So the microbes are like, well, I guess there’s nothing else to eat… So they get labelled with 13C. And then viruses infect and lyse those microbes!.. There’s just all this messy life happening at the same time: eating over here, bursting over there, and — dying all over the place. And the isotopes are letting Gary track where the carbon is flowing.
GARY: So we can see the 13C in the organisms.
ALISON: Gary’s doing these experiments at Lawrence Livermore National Lab, where he’s working with microbial ecologists Steve Blazewicz and Jennifer Pett-Ridge. But that does not mean that he’s left his friends at JGI behind. Oh no. He’s still collaborating with Simon, who mentioned another reason why these experiments are so neat.
SIMON: One of the very cool things, and one of the remaining questions has been, when you see a virus in the soil, is this virus here because it was infecting a host here, and it was active, and it just got created. Or has it been here for 10,000 years? And it’s just kind you know of an empty shell and it’s not doing anything. That’s a question that’s really basic, but it’s really hard to understand.
ALISON: And Gary’s helping to solve that mystery. So this is where we leave Gary for now — in the midst of these super cool experiments; trying to decipher who’s alive?, who’s eating what?, and what metabolisms are affecting the fate of carbon in soil. Alright, until next time!
ALISON: This episode was directed and produced by me, Alison Takemura, with editorial and technical assistance from Massie Ballon and David Gilbert. Genome Insider is a production of the Joint Genome Institute, a user facility of the US Department of Energy Office of Science, located at Lawrence Berkeley National Lab in beautiful Berkeley, California. Thanks today to our guests Gary Trubl and Simon Roux for sharing their research. If you enjoyed the podcast and want to help others find us, leave us a review on Apple Podcasts, Google Play, or wherever you get your podcasts. If you have a question or want to give us feedback, Tweet us @JGI or record a voice memo and email us at jgi dash comms at L-B-L.gov. That’s jgi dash c-o-m-m-s at l-b-l dot g-o-v. And because we’re a user facility, if you’re interested in partnering with us, we want to hear from you! We have projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. If you want to collaborate, let us know! Find out more at jgi.doe.gov slash user dash programs. That’s it for now!
Additional information related to the episode
- Simon Roux and Gary Trubl’s paper on assembling genomes, including viral, from metagenomes: Optimizing de novo genome assembly from PCR-amplified metagenomes
- Gary acknowledges his funding sources: “This IsoGenie work was funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research (grants DE-SC0010580 and DE-SC0016440), The Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program. The SCGSR program is administered by the Oak Ridge Institute for Science and Education (ORISE) for the DOE. ORISE is managed by ORAU under contract number DE-SC0014664. Work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract no. DE-AC52-07NA27344.”
- A talk by microbial ecologist Virginia Rich at the Ohio State University on microbial metabolism in thawing permafrost at the JGI Annual Meeting in 2019
- Emiley Eloe-Fadrosh’s Environmental Genomics Group
- The JGI Metagenome Program
- Our contact info:
- Twitter: @JGI
- Email: jgi-comms at lbl dot gov