Changes in the population structure of β-group autotrophic ammonia oxidising bacteria in arable soils in response to agricultural practice

Autotrophic ammonia oxidising bacteria of the β-group proteobacteria are important in the global nitrogen cycle, as they are responsible for the majority of ammonia oxidation in arable soil. This study examined the effects of agricultural practices on the community structure of autotrophic ammonia oxidising populations in arable plots that receive either NH4NO3, farmyard manure plus NH4NO3, or no nitrogen. The 16S rRNA genes of autotrophic ammonia oxidisers were PCR amplified from DNA extracted from these soils, and the products hybridised to oligonucleotide probes specific for each of the previously recognised phylogenetically distinct groups of autotrophic ammonia oxidising bacteria. Only 16S rDNA sequences from group 3 and group 4 organisms were detected in the PCR products. Products from the plot that received NH4NO3 fertiliser were dominated by group 3 sequences, while those that received no nitrogen fertiliser were dominated by group 4 sequences. Ploughing of the plots was associated with an increased abundance of group 3 organisms particularly in plots that had previously received NH4NO3 fertiliser. These data were related to both the size and activity of the ammonia oxidising populations, as determined by a competitive PCR assay based upon the amoA gene, and by 15N isotopic pool dilution, respectively.