title: Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments.
abstract: ABSTRACT Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kgNha(-1)year(-1)) and cattle manure (75 and 150 kgNha(-1)year(-1)) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different. Also, these sites significantly differed from the control plot (no fertilizer treatment), whereas the patterns for low and high N-additions were barely separable from each other. Sequencing and phylogenetic analysis of 54 nirK clones revealed that the major part of the nirK-containing bacteria investigated belonged to a yet uncultivated cluster of denitrifying bacteria.
authors.affiliation: Department of Microbiology, Copenhagen University, Sølvgade 83H, Copenhagen K, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Wolsing
authors.forename: Anders
authors.initials: A
authors.lastname: Priemé
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D001426:Bacterial Proteins / Q000235:genetics; D044822:Biodiversity; D002417:Cattle; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005308:Fertilizers; D008372:Manure; D008969:Molecular Sequence Data; D009572:Nitrite Reductases / Q000235:genetics; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D012621:Seasons; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005308:Fertilizers; D008372:Manure; D009572:Nitrite Reductases