Viral mixing: Kenneth Stedman discusses the discovery of a novel class of viruses

Posted by Biome on 27th May 2013 - 3 Comments

Studying the evolutionary history of viruses has proven difficult due to their high rates of genetic mutation, mosaicism and lateral gene transfer. Current dogma states that viruses fall into three major groups; RNA viruses (believed to have emerged first), DNA viruses and retroviruses that need to be reverse transcribed from RNA into DNA. However, metagenomics – the study of genetic material from microorganisms collected directly from the environment – now tells a different story, as published in a recent study in Biology Direct from Geoffrey Diemer and Kenneth Stedman (Portland State University). This exceptional article won BioMed Central’s 7th Annual Research Award (read about this in Award winning research). In this interview, we asked Dr Stedman to tell us more about how they uncovered a potentially new viral group.

Boiling Springs Lake, Lassen Volcanic National Park, USA. Image source: flickr, LassenNPS


How did you first become interested in studying viruses?

After finishing my PhD with Sydney Kustu at University of California, Berkeley working on transcriptional regulation in Salmonella, I went to Wolfram Zillig’s lab at the Max Planck Institute for Biochemistry in Germany to work on transcriptional regulation in Archaea. Wolfram Zillig was the pioneer in both archael transcription and viruses of Archaea. He was interested in using viruses as tools to understand archaeal molecular biology in a manner analogous to  bacteriophages lambda and T4 for Bacteria or adenovirus for Eukarya. However, I became fascinated by the viruses themselves: what do these novel genes do? How are the unique structures made? How can the viruses survive in the extreme environments in which they are found? Part of this fascination included collecting new viruses in volcanic hot springs throughout the world, first with Wolfram Zillig, then with Mark Young at Montana State University, and finally with my own group.


What led to the study described in the paper and what was the main goal of the research?

The study is part of an NSF-sponsored Microbial Observatories project together with Patricia Siering and Mark Wilson from Humboldt State University and Gordon Wolfe from California State University, Chico. We are studying the ecosystem of an acidic hot lake, Boiling Springs Lake, with a low temperature of 50°C, a high temperature of 95°C and a uniform pH of ~ 2.5. The main goal of the research is to determine the diversity and identity of the viruses in this simple ecosystem. Longer term, we wish to understand the role that viruses play in this ecosystem.


What did you find and why was this exciting?

We were looking for some viruses that we thought would be in this particular Boiling Springs Lake but we couldn’t find those so we took a step back and instead conducted a really high throughput, really massive sequencing approach. We took all of the appropriate fraction we could find from our sample of lake sediment (that should have been about virus-sized) sequenced it like mad, got about 400,000 sequences out of it and lo and behold, among those sequences we found some sequences that looked like the viruses we were looking for. But the real surprise was we found some sequences of viruses that we weren’t looking for at all!

We found a contig (assembly of DNA fragments) that appeared to contain two genes, one derived from DNA viruses, one from RNA viruses. At first we didn’t believe it. I didn’t believe it at all. I told the graduate student to go back and do it again! We confirmed this result and found the whole genome of this ‘RNA-DNA hybrid virus’ in not only samples from Boiling Springs Lake, but also in numerous other metagenomic samples. This result was particularly surprising because it was thought that DNA and RNA viruses do not recombine with each other. We showed that they clearly do. That’s really the big breakthrough that we made; it raises very important issues for the evolution of viruses and the emergence of new viruses.


What impact does ‘openness’ in the form of open access and open peer review have within your field?

I think that open peer review is excellent to have, in particular making the (very helpful) reviewer’s comments available to all readers and not just the authors. Biology Direct do this online and within the PDF of the published article. Open access has allowed our work to be read and commented on by people throughout the world, including Ghana, Peru and Ecuador. In the field of virus ecology and (meta)genomics, I think that many authors prefer to publish in open access journals.

We chose Biology Direct for the very specific reason that we knew it was open access but also has an open peer review process. The open peer review was extremely useful to us. We got lots of wonderful comments from reviewers and I think it greatly increased the value of our research and our analyses. [Editors note: Read more on Biology Direct’s open peer-review system on the BioMed Central blog]


What has happened to the project since the study was published and what’s next?

Now, three other virus genomes similar to our RNA-DNA hybrid (BSL RDHV), which appear to have been formed through interviral RNA-DNA recombination, have been found by other researchers. We have since found similar viruses in a number of other ecosystems both by direct and meta-analyses. Efforts to identify the host for the BSL RDHV and related viruses, as well as determining the mechanism by which the virus arose, are currently underway. Being able to take – literally steal – RNA from an RNA virus and put it into a DNA virus, is amazing and was completely unheard of when we found it was happening. Now the big question is how is it happening? How frequently is it happening? That’s the real area of research that we’re moving into right now.


What difference will winning BioMed Central’s Annual Research Award make?

We feel that winning the award will highlight the potential of viral metagenomics as a powerful research tool. It is our hope that having been selected for such an award will encourage other researchers to venture into this fascinating new territory as well.


More about the author(s)

Kenneth Stedman, Associate Professor of Biology, Portland State University, USA.

Kenneth Stedman is Associate Professor of Biology at Portland State University’s Center for Life in Extreme Environments. Stedman began his scientific career with an undergraduate degree in Chemical Engineering from Stanford University, California, after which he moved to Switzerland to work in biotechnology. Stedman returned to the USA to obtain his PhD in Molecular and Cell Biology at University of California, Berkeley under the supervision of Sydney Kustu, where he worked on the regulation of bacterial transcription. Obtaining a Marie-Curie postdoctoral fellowship, he went on to work with Wolfram Zillig, a pioneer of archaeal transcription and archaeal viruses, at the Max Planck Institute for Biochemistry. It was here that Stedman developed his love of ‘extreme viruses’. He is currently co-Chair of the NASA virus focus group.