Rare and diverse giant viruses found unexpectedly in a forest floor ecosystem

Until recently, scientists considered viruses to be essentially small, tiny infectious agents compared to bacteria and typical human cells. So imagine the surprise when biologist Jeff Blanchard and Ph.D. student Lauren Alteio of the University of Massachusetts at Amherst, as well as other members of the Joint Genome Institute (JGI) of the Department of Energy (DOE), have discovered giant viruses – relatively speaking the size of Macy's parade balloons – in Harvard Forest soil in Petersham, Massachusetts.

"We were not looking for giant viruses," says Blanchard. "Our goal was to directly isolate bacteria from the environment to understand how microbial communities are evolving in response to soil warming."

For this work, the researchers suspended the soil microbial cells in a mild detergent solution, added a non-toxic dye binding to the DNA, and then used FACF cell sorting (fluorescence activation) to isolate the individual cells, Blanchard explains. Giant viruses, up to hundreds of times larger than other viruses, have extremely large genomes and are captured by this method because of their similar size to that of bacteria, he notes.

Tanja Woyke, collaborator and senior scientist at JGI in Walnut Creek, Calif., Suggested using a new strategy, the mini-metagenomics, to place cells in small pools before sequencing and assembling their genomes. This has resulted in DNA sequences of more than 2,000 cells and / or individual particles, reports Blanchard. In the pools, they found 16 new giant viruses, which was "a wonderful surprise and a new science very exciting," he adds.

Co-first author with Alteio of the newspaper in Nature CommunicationsJGI's bioinformatician Frederik Schulz, who helped Alteio identify new soil bacteria and archaea in the mini-metagenomic data, explains: "The fact that we found all these gigantic viral genomes in the soil was particularly intriguing, as the Most of the giant viruses described previously have been discovered in aquatic habitats.The metagenomic data generated here from a single sampling site contained many more new genomes of the giant virus than any other dataset that I've seen so far. "

Blanchard adds, "Our research is generally focused on the effects of soil warming, but this new mini-metagenomic approach has uncovered a treasure trove of viral and bacterial biodiversity in species groups that we associate with. generally not on the ground.There are many mysteries we will follow. "

Schulz points out: "In this study, we have collected 16 distinct giant virus genomes, but we are only scratching the surface, so if we take more from the same site, that number will double, triple or even quadruple." The authors say that the results illustrate that the use of new methods "can lead to key discoveries".

The discovery of the giant virus is linked to long-term soil warming experiments in place for many years in the research forest about 28 miles northeast of the UMass Amherst campus, where heating cables similar to those used to prevent Football freezes and football pitches are buried about 4 inches (10 cm) under several parcels. Cables keep the floor surface warmer by 5 degrees Celsius from room temperature, creating an outdoor laboratory on artificial climate change, Blanchard says.

In most research on giant viruses, he says, researchers cultivate a protist host or amoeba attracting viruses that usually infect it, a process that requires a lot of work. "They are hard to work with and only the viruses that grow in that host will be grown," he says. "There are millions of potential host species and it would be impossible to use this approach with all of them." On the other hand, isolating cells directly from the environment and using mini-metagenomics methods can provide genomic data at lower cost, he said.

"Tanja is famous for sequencing genomes of organisms difficult to grow from environmental samples and she has the intuition that if we adopt this new approach, new branches of life would be revealed" said Blanchard. "Using this method, we do not know what our giant viruses look like, we could try repeating the experiment in future searches to image some particles after sorting them."

UMass' microbiologist Amherst adds, "Not only did we discover many new giant viruses, but we did it using a tiny amount of soil. It would be nice to characterize these viruses one by one, there is a lot of talent and art in this area. It would be a project that would last for years. Finding 16 at one time is rather 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 one gram of soil, about a teaspoon, imagine how many new giant viruses are out there. "

Woyke adds, "For me, the most intriguing and revealing part of the study was the high number and diversity of major capsid proteins, which is like a bar code for giant viruses, found in the metagenome unmixed bulk soil Deep soil sequencing Metagenomes are revolutionizing our understanding of this very important terrestrial ecosystem with many interesting soil microbiome initiatives, but our data underscore that many missing pieces remain to be solved. "

Scientists gave the new species names that reflect their forest origins, such as "Dasovirus", Greek "daso" for forests and "Solumvirus" for Latin soils "solum". They also propose to name a "Harvovirus" to honor Harvard Forest.

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More information:
Frederik Schulz et al, The hidden diversity of giant soil viruses, Nature Communications (2018). DOI: 10.1038 / s41467-018-07335-2