Researchers sample soils to track microbes’ contribution to climate warming

December 19, 2012

Biologist Jeffrey Blanchard and microbiologist Kristen DeAngelis, with other New England researchers, recently received a $500,000 grant from the Joint Genome Institute at the U.S. Department of Energy to identify soil microbes in Harvard Forest and track how they break down forest litter in a simulated warmer climate. The goal is to determine the impact of a warmer climate on microbes and their production of greenhouse gases.
 
The study takes advantage of three long-term soil-warming experiments already in place in the forest, where heating coils similar to those used to keep football and soccer fields from freezing are buried about 4 inches (10 cm) deep in several plots. They keep the soil surface exactly 5 degrees Celsius warmer than the ambient temperature, creating an outdoor laboratory of artificial climate change. The three patches have been kept warm for six, nine and 20 years, corresponding to three distinct phases of projected CO2 emissions, to provide a timeline of soil changes, the researchers say.
 
“This study will help us to understand how climate change affects the composition and activities of soil microbial communities over time, in particular changes that go beyond what one would expect from normal temperature variation,” says Blanchard.
 
He and DeAngelis began collecting microbes in the Harvard Forest soils in north central Massachusetts near Petersham about two years ago. The high-throughput DNA sequencing grant, shared with researchers at the University of New Hampshire and the Marine Biological Laboratory, Woods Hole, will support analysis and experiments to test the hypothesis that specialized microbial communities have emerged in the soil plots in response to warming and that they reduce organic materials in the topsoil faster than in soil at current temperatures, thus emitting more CO2 and contributing to higher greenhouse gas levels.
 
DeAngelis, a microbial ecologist, says many bacteria found in soil can’t be grown in the laboratory, in part because their nutritional and other growth requirements are not yet known and in part because they have symbiotic or interconnected relationships with others. So the availability of natural soil samples from the differently warmed plots is a key to exploring the microbial role in a warmer forest ecology. For this study, the researchers collected soil cores to about 10 inches (15 cm) depth.
 
The researchers say about 10,000 microbe species can usually be found in a gram of soil, about the size of a sugar cube. To identify the specific organisms present, Blanchard, a genome scientist, and the research team will sequence three terabases (3,000,000,000,000) of extracted DNA and RNA. This is equivalent to sequencing 500,000 bacterial genomes or about 1,000 human genomes, he points out. Each investigator will train undergraduate and graduate students to assist in the research and analysis.
 
Blanchard explains, “RNA analysis will show us the activated genes, the fingerprint of what these microbes have been up to, such as whether they’re eating the woodier parts of plant litter faster in the warm plots, as we suspect.”
 
Normal topsoil may be 3 inches deep, but in some of the long-term warm patches it is half that depth, he adds. “We think this is because certain communities of microbes have emerged who can digest that material and turn it into CO2 more readily than others. We’d like to know which microbes are responding to warming. We expect to find that a particular group is becoming more active, that is the guys who can eat up the cellulose and lignin, the hard-to-digest fibrous parts.”
 
The sequencing analysis will take two to three years, setting up “an amazing foundation for further experiments,” says Blanchard. DeAngelis adds that in the future they hope to identify which ecological processes are changing with warming and which specific pathways the microbes are using to turn lignin and cellulose into CO2.
 
She adds, “One of the interesting stories will be the one about adaptation. Warming is changing not just the community, but how the communities respond to other stress, to each other and to the changing environment.”