In a new national effort, UMass Amherst scientists led by Jeff Blanchard, biology, have received a two-year, renewable resource grant from the Department of Energy (DOE) to apply – for the first time – new genomics and omics-related techniques to microbial communities at 15 to 20 established NSF research sites across the United States, Hawaii and Puerto Rico.
The new soil data will be integrated with older soil sample data to assess how these communities are responding over time to climate change and their role in respiring carbon dioxide from soil, which is the major repository of terrestrial carbon, Blanchard says.
The work will take advantage of his lab’s soil-warming and microbe population experiments at Harvard Forest in Petersham and the National Science Foundation’s (NSF) National Ecological Observatory Network (NEON). Researchers will use advanced -omics capabilities at the DOE’s Joint Genome Institute (JGI) and its Environmental Molecular Sciences Laboratory (EMSL). “We are fortunate to be able to work with top-notch laboratory and computational scientists at JGI and EMSL,” Blanchard says.
In addition to Blanchard, the national research team includes co-leader Janet Jansson and Jason McDermott of Pacific Northwest National Lab, Lee Stanish of NEON, Jorge Rodriguez of the University of California, Davis, Will Wieder of the National Center for Atmospheric Research and Stuart Grandy of the University of New Hampshire.
Blanchard, who is principal investigator of an NSF Long Term Ecological Research synthesis working group, says, “I’m excited to be working on a national level and to be coordinating with other groups doing similar projects across the network. This establishes us as leaders in this new area on a national scale.”
“There’s a lot of basic soil data that’s been collected by NEON staff over the years, and those samples, with temperature and moisture measurements, are archived,” he explains. “We’re requesting samples from that archive, and we’ll do additional measurements for analysis with more soil-omics – genomics and mass spectroscopy – tools.”
The team will supply the JGI with microbial samples, where they will be analyzed using three advanced tests: a DNA-, nucleotide-based analysis, an mRNA-based meta-transcriptomics analysis – which identifies products from gene expression – and a very new approach that isolates single microbes and sequences that cell’s whole genome.
“In the past, we had very little knowledge about what microbes were there, little understanding of who lived there and what happened to soil communities living with different conditions,” Blanchard notes. “Before we had these DNA-based techniques, soil scientists cultured the soil samples and looked for microbes with microscopes. Those methods were rough, but there is some useful data from those old measurements.”
He and colleagues will track how microbial communities vary with varied natural temperature and moisture conditions at the same NEON sites years later. They will also measure major microbe metabolites in each environment with spectroscopy and chromatography. Microbes produce different amino acids, lipids and carbohydrates under different conditions, “and from that we can get a picture of the active metabolic pathways happening. Those should correspond to the genes being expressed,” he says.
Rather than research dollars, each participating lab receives state-of-the-art DNA- and RNA-based analyses from the government labs, plus services they would not ordinarily have access to, in return for soil samples and other activities, Blanchard notes.
“We receive this rich data back. It’s a boon to our lab, and it should lead to several papers in the next few years. We’ll also be able to use results as preliminary data for our next round of proposed research. We’ll come out with more knowledge on how microbial communities change in response to climate, moisture and temperature variation.”