Medic Shapes the Crop Rotation Soil Microbiome.

Fertilizer N increases crop yields, but excess N has deleterious environmental effects.  Replacing some of the crop N requirements with legume N can reduce the environmental effects.  We evaluated the effects of adding medic (Medigaco lupalina L.) to a crop rotation on the soil microbiome.  The experimental treatments consisted of (a) black medic or no medic, (b) three crops (flax, oat and wheat) grown in rotation, with all crops grown each year, and (c) three fertilizer N rates (20, 60, and 100% of soil test recommendations).  The medic was seeded in 2003 and it re-established itself every year.  In 2011, we determined soil bacterial composition by pyrosequencing.  The most abundant bacterial phyla were Actinobacteria (38%), Proteobacteria (33%), Acidobacteria (12%), Bacteroidetes (6.4%), Chloroflexi (2.4%), Planctomycetes (1.7%), Gemmatimonadetes (1.4%), and Firmicutes (1.1%).  Medic increased the Shannon, Simpson and Chao 1 indices of bacterial diversity, and fertilizer N increased Shannon and Simpson indices linearly.  However, principal component analysis (PCA) revealed that the community structures of the bacteria in the different treatments were mainly shaped by medic.  The bacterial phyla that were most associated with treatments that contained medic included Proteobacteria and Bacteoidetes, and those associated with no-medic treatments included Actinobacteria, Chloroflexi and Planctomycetes.  The crop grown, as a main factor, only affected the relative abundance of Gemmatinodetes, which was greater in wheat than in oat or flax. Therefore, although both medic and fertilizer N increased bacterial diversity, medic altered the composition, and presumably the functioning, of the soil microbiome more than fertilizer N.