Bacterial and archaeal ammonia oxidizers respond differently to long-term tillage and fertilizer management at a continuous maize site

•Ammonia oxidizing archaea (AOA) and bacteria (AOB) were measured in cropped soil.•AOA greatly outnumbered AOB and varied over time within a maize cropping system.•AOB were almost 10-fold lower in disk plots, but AOA did not differ.•N rate had no or minimal effect on ammonia oxidizer abundance.•Microbial community biomass was dynamic and responsive to date, tillage and N rate.

Fertilizer use and tillage affect both the general soil microbial community and specific N-utilizing microbial groups, but likely to varying degrees. To assess these impacts, soil was collected on three key dates from a long-term (26+ years), rainfed, continuous maize site where tillage (no-till and disk) and N fertilizer rates (0, 40, 80, 120, and 160 kg ha−1 yr−1) were applied. Microbial community changes were assessed using fatty acid methyl esters (FAME), and ammonia oxidizer (AO) changes were followed using quantitative PCR. Ammonia-oxidizing archaea (AOA) greatly outnumbered ammonia-oxidizing bacteria (AOB) based upon amoA gene copy (108 versus 104 g−1 soil, respectively), and both populations were dynamic across sampling dates. Over the long term, tillage had a differential effect; AOB were almost 10-fold lower in disk tillage plots, but AOA did not differ. N rate had no effect on ammonia-oxidizers abundance, but a moderate correlation (r = 0.423) between AOB and N rate was observed. AOA correlated moderately (r = 0.552) with water-filled pore space. In contrast, the biomass of various microbial groups was highly responsive to sample date, tillage, and N rate. This study found that long-term agronomic practices affected the overall microbial community more than the AO community, while short-term changes over a growing season were surprisingly dynamic for both AO and select groups within the general soil community.