Effect of switching bioenergy crops on rhizosphere N-cycling bacteria/archaea in different soils

Cultivation of perennial grass (e.g. switchgrass [PV] and miscanthus [MG]) instead of maize (ZM) for bioenergy production could reduce fertilizer utilization and environmental pollution, and may also change the belowground ecosystem function through altering soil microbial community. To understand the impact of different bioenergy cropping systems on microorganisms, the compositions and quantities of rhizosphere microbial communities (16S rRNA gene) and N-cycling functional groups (nifH, bacterial amoA, archaeal amoA and nosZ genes) under switchgrass and miscanthus were compared to maize at eight sites representing a latitudinal gradient of temperature and precipitation in Illinois (USA). High phylogenetic diversity of microbial community was observed by high-throughput sequencing, with 12219, 612, 415, 350 and 773 OTUs for 16S rRNA, archaeal amoA, bacterial amoA, nifH and nosZ genes. The environmental factors that determines the abundance of each quantitatively important phylotypes were identified, which revealed a high physiological diversity of rhizosphere microbial community. Plant-specific bacteria were observed, e.g. a Novosphingobium OTU was uniquely observed in switchgrass at all the sites, indicating the species-specific selection of microbes. On the other hand, the significantly lower quantities of ammonia-oxidizers and denitrifiers in the rhizosphere than bulk soil suggests the competition of nutrition (NH4+ and NO3-) between microbes and plants. The microbial composition, diversity and quantity of these genes were significantly affected by plants types, with different microbial group responded differently. For instance, quantity and diversity of nifH was significantly higher, while quantity of bacterial amoA was significantly lower in MG and PV than ZM at most sites, indicating a higher natural N-input and lower potential nitrate leaching in these perennial grasses. Thus, we conclude using miscanthus and switchgrass as the second-generation bioenergy crops instead of maize could increase the soil nitrogen sustainability.