Biologist Jeff Blanchard, knee bows in the middle of hat, collects land samples surrounded by students at Harvard Forest in…
Biologist Jeff Blanchard, knee bows in the middle of hat, collects land samples surrounded by students at Harvard Forest in central Massachusetts. He and his Ph.D. student Lauren Alteio unexpectedly discovered the large-scale giabnt virus there. Credit: UMass Amherst
Finally, researchers thought of viruses as the smallest contaminants, small compared to typical bacteria and human cells. So imagine the surprise when biologist Jeff Blanchard and Ph.D. student Lauren Alteio at the University of Massachusetts Amherst, with others at the US Department of Energy (DOE) Joint Genome Institute (JGI), discovered giant viruses ̵
1; to a large extent the size of Macy’s parade balloons – in the field at Harvard Forest in Petersham, Massachusetts.
“We did not look for giant viruses,” Blanchard said. “Our goal was to isolate bacteria directly from the environment to understand how microbial communities change in response to geothermal energy.”
For this work, the researchers suspended microbial cells from the ground in a mild cleaning solution, adding a non-toxic DNA binding dye, then using fluorescence activated cell sorting (FACS) to isolate individual cells, Blanchard explains. Giant virus, up to hundreds of times larger than other viruses, has extremely large genomes and captured by this method because of their similarity in size to bacteria, he notes.
A co-partner and senior researcher at JGI in Walnut Creek, California, Tanja Woyke, suggested that they then use a new strategy, mini-metagenomics, to put the cells into small pools prior to sequencing and assembly of their genomes. This resulted in DNA sequences from over 2000 individual cells and / or particles, Blanchard reports. In the pools, they found 16 new giant viruses, which were “a wonderful surprise and very exciting new science,” he adds.
Author of Alteio of the Paper in Nature Communications JGI Bioinformatics Frederik Schulz, who helped Alteio identify new soil bacteria and archaea in minimal-data data, states that “the fact that we found all these giant viral genoms in soil was special exciting because most of the previously described giant viruses were discovered in the aquatic environment. The metagenomic data generated here from a single sampling site contained much more new giant viruses than any other set of data I’ve seen so far. “
Blanchard adds:” Our research is usually focused on the effects of geothermal heat, but this new meta-genetic method has revealed a virus and bacterial biodiversity faith in species that we do not usually associate with the Earth. There are a number of mysteries to follow. “
Schul z points out : “We recovered 16 different giant viral genes in this study, me n We only cut the surface. If we try more on the same site, this number would easily be double, triple or even quadrupled. “The authors say that the results show that using new methods can lead to key findings.”
The giant virus discovery is related to long-term field warming experiments on site for many years in the research forest about 28 miles northeast of the UMass Amherst campus where heat cables similar to those used to hold soccer and football plans from freezing were buried about 10 inches (10 cm) under several plots. The cables keep the surface 5 degrees Celsius warmer than ambient temperature, creating an outdoor laboratory of artificial climate change, Blanchard says.
In most giant virus research, he says scientists grow a protist or amoeba host that attracts viruses that usually infect it, a labor intensive process. “They are difficult to work with, and only viruses growing in this host will be grown,” he states. “There are millions of potential hosts and I would not be able to use this approach with all of them.” On the other hand, isolation of cells directly from the environment and the use of metagnetic methods with genomic data at a lower cost, he says.
“Tanja is known for sequencing genes of hard to breed organisms from environmental samples and she had the intuition that if we took the new approach, new parts of life would reveal,” Blanchard said. “While we use this method, we do not know what our giant virus looks like , one can try to repeat the experiment in future research to form some particles after sorting. “
Microbiologist UMass Amherst adds,” Not only did we discover only many new giant viruses, but we did it with a narrow soil. It would be nice to characterize these viruses one at a time, there is a lot of skill and art in it. But it would be a year long project. Finding 16 at a time is a bit overwhelming, and none of them are the same. If you think of all the earth in the world, if there are 10,000 bacteria in one gram of soil, about a teaspoon, imagine how many new giant viruses are out there. “
Woyke adds:” To me, the most exciting and eye-opening part of the study was the high number and multiplicity of main capside proteins, which is a barcode for giant viruses, found in the non-composite mass genome. Deep sequencing of soil meta-genoms revolutionizes the understanding of these very important ground-based ecosystems with many exciting soil-environmental initiatives, but our data emphasize that still many missing pieces remain in the puzzle. “
The researchers gave the new species names reflecting the origin of their forest, such as” Dasovirus “Greek” daso “for forest and” Solumvirus “for the Latin” solum “field. They also suggest the naming of a” Harvovirus “in honor of Harvard Forest .
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Frederik Schulz et al., Hidden diversity of soil giant viruses, Nature Communications (2018). DOI: 10,1038 / s41467-018-07335-2