Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils

Autotrophic ammonia oxidizer (AAO) populations in soils from native, tilled , and successional treatments at the Kellogg Biological Station Long-Term E cological Research site in southwestern Michigan were compared to assess ef fects of disturbance on these bacteria. N fertilization effects on AAO popu lations were also evaluated with soils from fertilized microplots within th e successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group -specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes w ere estimated by using most-probable-number (MPN) media containing varied c oncentrations of ammonium sulfate. Tilled soils contained higher numbers th an did native soils of culturable AAOs that were less sensitive to differen t ammonium concentrations in MPN media. Compared to sequences from native s oils, partial 16S rDNA sequences from tilled soils were less diverse and gr ouped exclusively within Nitrosospira cluster 3. Native soils yielded seque nces representing three different AAO clusters. Probes for Nitrosospira clu ster 3 hybridized with DGGE blots from tilled and fertilized successional s oils but not with blots from native or unfertilized successional soils. Hyb ridization results thus suggested a positive association between the Nitros ospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly iden tical for tilled and native soils in both sampling years, indicating spatia l and temporal reproducibility based on treatment.