Giant viruses discovered for the first time in the soil of a forest

One of the heated plots at the Harvard Forest (Photo courtesy Jeff Blanchard. All rights reserved)
One of the heated plots at the Harvard Forest (Photo courtesy Jeff Blanchard. All rights reserved)

An article published in the journal “Nature Communications” reports the discovery of giant viruses in a forest soil ecosystem. Researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the University of Massachusetts-Amherst (UMass Amherst) discovered 16 new giant viruses and described their genome. A genomic analysis on their capsid, the protein structure that contains DNA or RNA of a virus, indicates a genetic diversity of giant viruses still unknown.

This study began with the aim of examining the changes in microbe communities in response to forest soil warming but focused in particular on bacteria. The UMass Amherst graduate student Lauren Alteio was working in an area about 45 kilometers (28 miles) from the campus, in a forest area that belongs to the University of Harvard, where cables were placed in the ground to heat it to simulate certain phenomena that are happening more and more frequently.

Often microorganisms are grown in the laboratory but the JGI researcher Tanja Woyke, an expert in this kind of genomic research, suggested the strategy of mini-metagenomics, based on stimulating their growth in their habitat and then taking samples to be submitted to genomic analysis. In this way DNA sequences were obtained from over 2,000 individual cells or fragments. The discovery of 16 new giant viruses was a stroke of luck that biologist Jeff Blanchard of UMass Amherst defined a wonderful surprise and very exciting new science.

The bioinformatics Frederik Schulz, who contributed to the identification of new bacteria and archaea in the mini-metagenomic data, stated that the discovery of genomes of giant viruses in the soil was particularly intriguing as most of those described previously were discovered in aquatic habitats. The metagenomic data generated during the new study by a single sampling on the site contained more newer genomes of giant viruses than any other data set seen by Schulz. He and the other researchers just scratched the surface and taking more samples at the same site could easily double, triple or even quadruple those genomes.

Half of the new giant viruses discovered belong to the subfamily Klosneuvirinae, which includes the Klosneuviruses whose discovery was reported by a JGI team that included Tanja Woyke and Frederik Schulz in an article published in the journal “Science” in April 2017. One year and half later that subfamily became the largest within the big Mimiviridae family.

Genetic testing of the new giant viruses also revealed the diversity in their capsids, which Tanja Woyke compared to barcodes. She pointed out that metagenomics studies are revolutionizing our understanding of very important ecosystems thanks to a series of researches focused on the microbiome existing in the soil. In this case it was a forest but different ecosystems can contain equally different microbiomes.

Fully understanding an ecosystem helps to predict its evolution and its reactions to climate change and that was the original purpose of this research. The discovery of giant viruses was an extra that can provide further information on these microorganisms whose origin is not yet clear and offers a greater completeness on our knowledge of their ecosystem.

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