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Joint Genome Institute Study Reveals Diversity of Giant Viruses Worldwide

An artistic illustration of a giant virus and a strand of DNA

(Credit: Zosia Rostomian/Berkeley Lab)

A team led by the U.S. Department of Energy Joint Genome Institute (JGI) at Berkeley Lab has reconstructed the genomes of 2,074 large and giant viruses found across the globe, drastically increasing the number of known viruses and providing a resource for future studies on this poorly understood group of viruses, called nucleocytoplasmic large DNA viruses (NCLDVs).

The work, recently published in Nature, drew from more than 8,500 publicly available metagenome datasets generated from samples of microbial communities, many of which were from freshwater ecosystems. (A metagenome is the entire collection of genetic information captured in a sample.)

The genomes of the large and giant viruses – which carry between 10 and 100 times more genes than most well-studied viruses – were digitally extracted from the other genetic information by filtering for a NCLDV-specific protein and then organized into distinct genomes known as metagenome-assembled genomes (MAGs). This process was performed, in part, using capabilities of the National Energy Research Scientific Computing Center (NERSC), also located at Berkeley Lab.

“This is the first study to take a more global look at giant viruses by capturing genomes of uncultivated giant viruses from environmental sequences across the globe, then using these sequences to make inferences about the biogeographic distribution of these viruses in the various ecosystems, their diversity, their predicted metabolic features and putative hosts,” said Tanja Woyke, senior author of the study and head of JGI’s Microbial Genomics Program.

After analyzing the genes identified in the viral MAGs, Woyke and her colleagues found that NCLDVs have evolved strategies to alter the metabolism of their host organisms (primarily single-celled eukaryotes, but also multicellular eukaryotic organisms) in order to optimize conditions for viral replication. Because eukaryotic microbes are known to play a big part in biogeochemical processes such as carbon and nitrogen cycling, the findings suggest that NCLDVs are a key part of understanding how ecosystems function.

Read the full release by JGI