title: Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the beta subdivision of the class proteobacteria in arable soils to nitrogen fertilizer.
abstract: This study examined the effects of NH(4)NO(3) fertilizer on the size and activity of nitrifying, autotrophic, ammonia-oxidizing populations of the beta subdivision of the class Proteobacteria in arable soils. Plots under different long-term fertilizer regimes were sampled before and after NH(4)NO(3) additions, and the rates of nitrification were determined by (15)N isotopic pool dilution assays. Ammonia-oxidizing populations in the plots were quantified by competitive PCR assays based on the amoA and ribosomal 16S genes. Prior to fertilizer addition, ammonium concentrations and nitrification rates in the plots were comparatively low; ammonia-oxidizing populations were present at 10(4) to 10(5) gene copies g of soil(-1). Three days after the application of fertilizer, nitrification rates had risen considerably but the size of the ammonia-oxidizing population was unchanged. Six weeks after fertilizer treatment, ammonium concentrations and nitrification rates had fallen while the ammonia-oxidizing populations in plots receiving fertilizer had increased. The rapidity of the rise in nitrification rates observed after 3 days suggests that it results from phenotypic changes in the ammonia-oxidizing bacterial population. Associated increases in population sizes were only observed after 6 weeks and did not correlate directly with nitrifying activity. Phylogenetic analyses of PCR products from one of the plots revealed a population dominated by Nitrosospira-type organisms, similar to those prevalent in other soils.
authors.affiliation: IACR-Rothamsted, Harpenden, Hertfordshire AL5 2JQ, United Kingdom. tom.mendum@bbsrc.ac.uk
authors.forename: T A
authors.initials: TA
authors.lastname: Mendum
authors.forename: R E
authors.initials: RE
authors.lastname: Sockett
authors.forename: P R
authors.initials: PR
authors.lastname: Hirsch
mesh_terms: D020562:Betaproteobacteria / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D005308:Fertilizers; D020459:Genes, rRNA; D008969:Molecular Sequence Data; D009590:Nitrogen Radioisotopes / Q000378:metabolism; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D000644:Quaternary Ammonium Compounds / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D005308:Fertilizers; D009590:Nitrogen Radioisotopes; D000644:Quaternary Ammonium Compounds; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C045582:ammonia monooxygenase