Soil microbes in organic vegetable production: New insights from pyrosequencing

The response of soil microbial communities to organic and conventional fertilization

Principle Investigators: Dr. Karen Garrett, Dr. Ari Jumpponen, Dr. Megan Kennelly

Collaborators: Lorena Gomez-Montano, M.S.

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Technologies for studying the composition of microbial communities are developing at a very rapid pace. A challenge for agriculture is how to use these technologies to support sustainable production. Soil microbial communities play fundamental roles in the productivity of agricultural systems. Organic methods may foster more diverse soil microbial communities beneficial for crop production that may reduce losses to pathogens and increase plant productivity.

We evaluated bacterial and fungal community responses in an established long-term experimental system comparing organic vs. conventional nutrient management for tomato production. This experiment was designed in collaboration with organic growers to represent current management practices. We used 454 pyrosequencing to simultaneouslyevaluate DNA from hundreds of thousands of microbes in soil samples, including species that could not be cultured using traditional techniques. We also compared the microbial communities recovered from analysis of DNA, rapidly becoming a standard technique, and from RNA, a new approach. Comparing communities recovered through DNA and RNA allowed comparison of the general pool of microbes (DNA) and the microbes that were actively metabolizing (RNA). We recovered a large number of taxa known to have important agroecological roles, and other taxa whose roles are yet to be known.

Our first hypothesis was that microbial diversity would be higher in organic compared to conventional agriculture, and the results supported this hypothesis. Our second hypothesis was that microbial diversity would be higher in DNA than in RNA samples, but higher diversity was sometimes observed in RNA samples. This may have occurred because DNA samples were dominated by a smaller number of taxa with tough dormant structures.

We are building on these analyses in a second Ceres Trust project evaluating organic management effects on microbial communities. Both these projects are the PhD research of Lorena Gomez-Montano, and the projects have also engaged two undergraduate students so far. In addition to a journal article we have published about new experiments that may contribute to understanding microbial community function (Garrett et al, 2012), the results presented in this report will be published in a peer-reviewed journal.

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