Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil. By analyzing key functional genes (nifH, bacterial amoA, archaeal amoA and nosZ) and 16S rRNA genes, we monitored changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of diazotrophic bacteria, ammonia-oxidizing bacteria (AOB) and archaea (AOA), denitrifying bacteria and the overall bacterial/archaeal community over two years after crop establishment. Over time, the quantities of these N-cycling genes were relatively stable in all the crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months, and denitrifier abundance increased in comparison to the other crops in the second season. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 10899, 3187, 3945, 11242 and 19824 unique nucleotide sequences observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize significantly decreased in the second year. Among the observed bacterial genera, covering nine phyla, 31.8% were significantly changed in at least one crop. Unifrac PCoA analysis showed that the N-transforming microbial community structures in the soil under these crops changed following different trajectories. Thus far, our two year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that application of fertilizer increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and significant changes in the structure of these N-transforming populations.