Growing viral

PETERSHAM – Ordinarily when folks think of a virus this time of year, it’s a common cold or the flu – nothing to rejoice over.

But a team of researchers at Harvard Forest, looking closely at thimbleful of soil taken from an experimental plot of artificially warmed soil duplicating the impact of climate change, found 16 giant viruses that were previously unknown.

“This is one of the most exciting finds I’ve had in my career,” said Jeff Blanchard, associate professor of microbiology at the University of Massachusetts in Amherst.

He added, “This find is akin to discovering a whole new continent, like discovering Africa with all its diversity, but only seeing a few of the animals at first glance.”

Mr. Blanchard said his first exposure to Harvard Forest came during a sabbatical in 2010 and 2011 working with the research team that in 1991 began the long-term climate-change experiment.

“At that point there had been no analysis of the microbial community, and we had no idea of what microbes or other microscopic organisms were in the soil,” he said.

Working with Ph.D. student Lauren Alteio and others at the U.S. Department of Energy Joint Genome Institute in California, Mr. Blanchard characterized finding giant viruses (when they weren't looking for them) as groundbreaking.

“We were not looking for giant viruses. Our goal was to isolate bacteria directly from the environment to understand how microbial communities are changing in response to soil warming,” the researcher said.

Describing the process by which the discovery was made, Mr. Blanchard said the team isolated and suspended microbial cells from the soil in a solution of dish soap to which they added a nontoxic DNA-binding dye.

He further explained the team used fluorescence-activated cell sorting to isolate individual cells.

Because some giant viruses are hundreds of times larger than other viruses, have extremely large genomes and are similar in size to bacteria, they are captured by the same method used to find bacteria.

For comparison purposes, the microbiologist said the influenza virus has about 10 genes.

“Some of the giant viruses we found in the soil have more than 2,500 genes. There are some bacteria that have 1,000 genes, so the viruses are bigger in size and genetic complexity than many bacteria,” he explained.

According to information provided by UMass in a press release, Tanja Woyke, a collaborator and senior scientist at the Joint Genome Institute, suggested using a new strategy, mini-metagenomics, for putting the cells into small pools before sequencing and assembling their genomes.

The result was DNA sequences from over 2,000 individual cells and/or particles. It was in these pools that 16 new giant viruses were found.

The team’s discovery has recently been published in the journal Nature Communications.

Frederik Schulz, a bioinformaticist at the Joint Genome Institute, co-authored the article with Ms. Alteio and helped the researcher identify new soil bacteria and archaea in the mini-metagenomic data.

Archaea are a group of microorganisms that resemble bacteria but are different from them in their genetic makeup.

“The fact that we found all these giant virus genomes in soil was especially intriguing, as most of the previously described giant viruses were discovered in aquatic habitats. The metagenomic data generated here from a single sampling site contained far more new giant virus genomes than any other data set I have seen to date,” Mr. Schulz said.

In Mr. Blanchard's work, heating cables similar to those used to keep football and soccer fields from freezing are buried about 4 inches under the surface of several soil plots. The cables keep the soil surface 5 degrees Celsius (41 degrees Fahrenheit) warmer than the ambient temperature, creating an outdoor laboratory of artificial climate change, he said.

“This new mini-metagenomic approach has uncovered a trove of viral and bacterial biodiversity in species groups we don't typically associate with the soil. There are a number of mysteries we'll be following up on,” he said.

The professor said there are no known cases of giant viruses infecting humans or any animal.

“As far as we know giant viruses only invade protists, single-celled eukaryotic microbes, but they were only discovered recently and we don't have any evidence as to the hosts of our giant viruses at Harvard Forest,” he said.

Mr. Schulz said, “We recovered 16 distinct giant virus genomes in this study, but we are merely scratching the surface. If we sample more at the same site this number would easily double, triple or even quadruple.”

Mr. Blanchard said that at some point in the future this discovery of giant viruses in soil could have biotechnology applications, but it’s too early to know what they might be.

The microbiologist said, “It would be nice to characterize these viruses one at a time, there's a lot of skill and art in that. But it would be a years-long project. Finding 16 at once is kind of overwhelming, and none of them are the same. If you think of all the soil in the world, if there are 10,000 species of bacteria in a gram of soil, about a teaspoon, imagine how many new giant viruses are out there.”