Taking a Metagenomics Approach to Soil's Reaction to Rainfall

What do large umbrellas covering a part of the Kansas prairie have to do with climate change?

Current scientific knowledge tells us that the environmental pressures leading to climate change will result in less frequent rainfall. However, the rainfall events will be more intense, and drop larger amounts of precipitation. The effect of changing precipitation patterns on agriculture is a main cause for concern among researchers in the Department of Crop and Soil Science at Oregon State University.

David Myrold and Peter Bottomley, soil scientists in the department, are concerned with climate change's effect on soil, specifically carbon (C) cycling. Our societies depend on soil to grow the crops needed to feed people and animals, and to produce clothing and fuel, among other things, and understanding the effect of climate change on soil is key to weathering the change.

The ability of soils to perform its many functions depends greatly on soil microbes. For example, soil microbes play a critical role in decomposing crop residue and recycling mineral nutrients that helps crop grow again. Soil microbial biomass can be substantial and is responsible for retaining some of the plant carbon in the soil each year. Microbial biomass helps to stabilize the soil and withstand the disturbances associated with cultivation and crop production.

To what extent might changes in rainfall pattern affect the balance between plant carbon inputs and carbon retention in soil?  One possibility is that the composition of the soil microbial community will shift and be dominated by members more adept at dealing with the longer drought intervals and more intense rewet events. This “adaptive behavior” might include shifts in the physiological behavior of the adapted microbial community which will differ from the original community, and might affect the balance between plant carbon input and the fraction that is retained in soil.        

Myrold and Bottomley are taking an "-omics" approach to studying soil C cycling—studying the cycle collectively. Metagenomics, which is the study of DNA from a community rather than a single organism, allows scientists to have a big picture view of the soil community's composition. Taking this whole picture approach allows Myrold and Bottomley to create climate change scenarios and predict how the carbon cycling soil microbial community responds to these scenarios and to determine what kinds of changes in soil activities might be occurring in response to the shifts in precipitation.

"You go into a house and watch what one person does once the sun sets," explains Myrold. "Does that person turn on the kitchen light first? Lower the blinds in the living room? Turn on the TV? That's looking at the things one person does." Using a satellite to look at what a whole city does when the sun goes down and how all those processes add up to a whole, that's metagenomics, says Myrold.

That's where the umbrellas in Kansas come in.

"We're studying the long term effects of different patterns of rainfall on the prairie," explains Myrold. "And we're manipulating that rainfall to see how the microbial community and its activities respond."

The umbrellas that are stretched over portions of the field catch the natural rain, but the scientists are giving the soil the same amount of rainfall in different pulses. Some areas are allowed to go longer between rainfall events, but the volume dispersed is more, while other areas have more frequent, less heavy, rewetting.

"We know that soil has a flush, or pulse, of activity when it is rewet," says Myrold. "This pulse of activity sets off many different reactions and activities, some of which create carbon dioxide, a major contributor to climate change."

Myrold and his group are measuring a variety of responses, including if the microbial communities behave differently when the water comes at different intervals. Do the variety of organisms react differently or is there a change in how the whole community behaves?

What they've found, Myrold explains, is that the soil becomes more stressed during the drier intervals. "The bacteria and fungi adjust to the 'droughtier' conditions by forming spores or going into resting stages."

This "-omics" research project is sponsored by the Department of Energy's Office of Biological and Environmental Research and is a collaboration between Oregon State University, Kansas State University, Lawrence Berkeley National Laboratory, the Joint Genome Institute, and Oak Ridge National Laboratory.

More research is planned to see how other environments respond to this precipitation manipulation. The research group is planning on expanding the project to test a wetter soil in Wisconsin, and a dry summertime soil in Oregon, allowing the group to generalize their results and be able to offer theories on how soil microbes are affected by change in weather.