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The characterization of microbial cell diversity in a handful of soil is so complex that it was considered impossible. To date, only a small fraction of microbes living in, on and around soils have been identified as part of efforts to understand their contributions to the global carbon cycle and other nutrient cycles. . Soils are also home to countless viruses that can infect microbes, affecting their ability to regulate these global cycles.
Posted on November 19, 2018 in Nature Communications, Giant virus genomes were first discovered in a forest soil ecosystem by researchers at the Joint Genome Institute (JGI) of the Department of Energy (DOE), a user facility of the Science Office of the DOE and the University of Massachusetts at Amherst (UMass Amherst). As their name suggests, giant viruses are characterized by genomes and virions of a disproportionate size that harbor the genetic material of viruses. They are frequently found in protists and algae. It is therefore thought that they have a significant impact on the dynamics of their host population and the biogeochemical cycles of the planet.
The 16 new giant viruses discovered in this study have increased the total phylogenetic diversity of giant viruses by more than 20% and belong to different lineages. Half of the new viruses, for example, belong to Klosneuvirinae, making it the largest subfamily of Mimiviridae. Schulz and Woyke have previously reported that they have discovered a new group of giant viruses that they call Klosneuvirus in wastewater metagenomes.
"These giant viruses have probably been neglected in soil ecosystems, but if you look at the major capsid proteins, which are barcodes or barcode fragments, they are ubiquitous," said the program manager. microbial of JGI and its author Tanana Woyke.
Virus in the Harvard Forest
The genomes of the giant virus were discovered by JGI researcher Frederik Schulz as he helped graduate student Lauren Alteio of UMass Amherst in Jeff Blanchard's lab analyze his metagenomic data. "The large number of distinct genomes of giant viruses found at this sampling site is unprecedented compared to other metagenomic datasets I've seen," Schulz said. The data was generated from soil samples collected by Alteio as part of the Blanchard Project as part of the IGJ's Community Science program.
Blanchard generates reference genomes from soils harvested in heated and unheated plots in the Harvard Forest. These data will ultimately provide a better understanding of microbial emission and uptake of greenhouse gases. Alteio spent a year at JGI working on this project in the Woyke Lab through the Graduate Research Program of the DOE Office of Science (SCGSR).
For almost 30 years, the Harvard Forest in Massachusetts has been home to the world's longest ongoing soil warming experiment. Funded by the National Science Foundation's Long-Term Ecological Research Program (LTER), a portion of the 4,000-hectare area includes heating cables buried a few inches underground, regulating the temperature to maintain a constant five-degree temperature to that of the neighboring control areas.
"This is the first time that giant viruses have been discovered in a forest ecosystem," said Blanchard, "and the amazing diversity in just half an inch of soil suggests that we have just begun to understand their biodiversity and their role in soil ecosystems. "
"Based on the size of the genome, many of the new viruses were among the largest viruses discovered to date," concluded Schulz. "One of them, with a genome of 2.4 megabase, was named" Hyperionvirus "by analogy with the world's largest living tree known."
Small pieces of soil diversity
With a myriad of microbial cells in one gram of soil, JGI researchers sought to reduce complexity by sorting microbes into streams in several small groups of 100 cells each before sequencing them separately. When analyzing metagenomic data for this approach, 15 new genomes of giant viruses were discovered. In contrast, a single genome of the giant virus was recovered using the standard shotgun metagenome approach by community on bulk forest soil samples, even though these bulk soil samples have been sequenced much more deeply.
"This non-standard approach was deliberately taken to divide the diversity into smaller pieces, and if we had done it in the usual way, we would have missed these giant viruses completely," said JGI scientist Rex Malmstrom. co-author of the study.
"The richness of giant viruses in the soil is remarkable and highlights the pervasiveness of these enigmatic entities and the fact that these viruses are still largely under-explored," Schulz said.
Woyke agreed that the discovery of these new giant virus genomes was only a beginning. "Soils have been a neglected ecosystem for the diversity of giant viruses, with studies primarily focused on aquatic environments." The data on soils containing unassociated metagenome suggest that the extent of soil virus diversity Harvard forest is far superior to 16 recovered genomes It is difficult to access genomes with traditional approaches This finding suggests that soils should be considered as a target for giant virus co-culture efforts. "
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