Soil microbial communities under model biofuel cropping systems in southern Wisconsin, USA: Impact of crop species and soil properties

► We analyzed microbial lipids and soil properties under corn, switchgrass and prairie. ► Lipid markers showed lower total biomass and greater in situ stress in corn system. ► An increase in fungi to bacteria ratio coincided with a net growth in fungal biomass. ► Lipid % abundance showed a reduced AMF and an increased Gm+ in corn than other systems. ► Effects by physicochemical properties discriminate against different microbial groups.