Metagenomic Exploration of Cover Crop and Amendment Effects on Functional Bacterial Communities in Organic Soil

Final Report Submitted to the Ceres Trust Organic Research Initiative

Craig Sheaffer, Michael Sadowsky, Donald Wyse, Adria Fernandez, and Kristine Moncada

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Agricultural soils are home to an enormous diversity of microbes, which carry out many functions essential to soil and crop health, including nutrient cycling, disease suppression, and building soil organic matter and aggregate structure. Organic farmers recognize the soil as a living system whose health depends upon this diversity of microbial functions and knowing how their management practices such as fertilizers and cover crops affect the soil would be valuable. Previous research has documented that additions of organic matter can affect the structure (“who’s there”) and function (“what are they doing”) of soil microbial communities. However, the detailed effects of particular cover crops and organic amendments on particular soil microbes and their functions, and the relationships between effects on soil community structure and changes in soil function are not well described. The development of high-throughput next-generation sequencing technology now allows a uniquely detailed look at the makeup of soil microbial communities. This project used sequencing of bacterial 16S rDNA, which serves as a “fingerprint” for identifying bacteria, to investigate the effects of cover crops and organic fertility amendments on soil bacterial communities. This information was combined with assays of soil respiration, N mineralization, and nutrient-cycling enzyme activity, as well as routine soil tests and corn yield data, to determine whether changes in crop-relevant soil functions were correlated with changes in bacterial community structure. Treatments used were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted chicken manure, and Sustane 8-2-4, plus a no-amendment control. Cover crops were planted and fertilizers applied in fall 2012 and incorporated in spring 2013. Corn was planted in May 2013. Research was conducted on three organic farms in diverse environments within Minnesota.

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