Effects of agronomic treatments on structure and function of ammonia-oxidizing communities

The aim of this study was to determine the effects of different agricultura l treatments and plant communities on the diversity of ammonia oxidizer pop ulations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled w ith specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the beta subgroup of the division Proteobac teria by use of DNA extracted from cultivated, successional, and native dec iduous forest soils. Community profiles of the different soil types were co mpared with nitrification rates and most-probable-number (MPN) counts. Desp ite significant variation in measured nitrification rates among communities , there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incuba tions, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA, Nitrosomonas-like band s were seen in the MPN DNA but were not detected in the DNA extracted direc tly from soils. These bands were detected in some samples taken from MPN in cubations carried out with medium containing 1,000 mug of NH4+-N ml(-1), to the exclusion of bands detected in the native DNA, Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lo wer than those determined by competitive PCR (cPCR), Although no difference s were seen in ammonia oxidizer MPN counts from the different soil treatmen ts, cPCR revealed higher numbers in fertilized soils. The use of a combinat ion of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine- scale compositions among treatments that may be associated with changes in population size and function.