Soil microbial communities of biofuel crops as evaluated by lipid and pyrosequencing analyses of 16/18S and 28S rRNA genes and of nifH genes

Understanding how the cultivation of biofuel crops impacts microbial soil communities is important for productive and sustainable management of these crops and their ecosystem services. We evaluated the effects of corn, switchgrass, and prairie and two spatial designs (intensive, i.e. contiguously located, and extensive, i.e. regionally distributed) on soil microbial communities. Bacterial and fungal communities were compared by both lipid analysis and pyrosequencing of their rRNA genes, and nitrogen fixation gene diversities were compared by pyrosequencing of part of the nifH gene. Extensive sites under long-term management of the crops were contrasted to intensive sites with recently planted crops (2 seasons) on replicated plots at two sites, one each in Michigan and another in Wisconsin. The sites in the two states were selected to be representative of the soil and climate of the Great Lakes region. For the young, intensive sites, rRNA and nifH analyses indicated that location and soil type, but not vegetation type, were important in determining microbial community structure, while the lipid analysis was able to detect a significant interaction between vegetation and location in Wisconsin. For the extensive sites, vegetation cover was more important, with communities under corn clearly differentiated from those under perennial grasses. Lipids and nifH also showed a clear distinction between locations. Bacterial and fungal biomass, and especially arbuscular mycorrhizal fungi, were favored under switchgrass and prairie, suggesting a more active carbon pool and greater microbial processing potential which is thought to be beneficial for biofuel crops and microbially-based services.