Because microorganisms are the principal agents of organic matter turnover and soil fertility, understanding how microbial communities respond to different cropping systems and management practices provides a foundation for sustainable agriculture. Here we investigate the hypothesis that different cropping systems consistently select for different assemblages of soil microorganisms. Further, we seek to predict the impact on soil microbial communities of two potential second-generation biofuel crops, switchgrass (Panicum virgatum) and Miscanthus X giganteus, in relation to the currently dominant corn-soy rotation and to remnant prairies (e.g. natural condition). Bulk soils from corn, Miscanthus, switchgrass, and prairie were collected from seven locations along a N-S gradient in Illinois, representing a range of soil types. Bacterial community composition was assessed using automated ribosomal intergenic spacer analysis (ARISA), and the site- and plant-specific variation in ARISA peak distribution (i.e. beta-diversity) was assessed using Canonical Correspondence Analysis (CCA).

Results/Conclusions

Overall, bacterial communities from each of the seven Illinois sites were distinct, although at each site the prairie communities were clearly different from the three agricultural soils. The geographic location of samples explained 17.3% of the variation in ARISA profiles, indicating that regional factors and/or soil type can influence soil bacterial composition. Accounting for this site-specific variation with partial CCA, the cropping system explained a further 6.3% of the variation in ARISA profiles, with prairie sites being most distinct from the other three. ARISA profiles from the three cropping systems were judged significantly different (p > 0.005) by permutation test. Thus, bulk soils harbored some bacterial species unique to each of the three crops, although regional differences may play a much larger role in shaping overall community composition.