title: Application of cation-exchange membranes for characterisation and imaging ammonia-oxidising bacteria in soils.
abstract: A new approach, in which ammonia-oxidizing bacteria (AOB) are entrapped from soil onto cation-exchange membranes, was applied to identify terrestrial AOB by fluorescence in situ hybridization (FISH). An experimental hot spot of ammonia oxidation was developed by establishing a gradient of ammonium substrate (200 to <20 mg NH4+-N l(-1)) diffused through the cation-exchange membranes incubated in soil for 6 months. By this approach we were able to characterise and image indigenous AOB populations growing in heavily oil-polluted soil using FISH and sequence analysis of PCR-amplified 16S rRNA genes, respectively. The FISH results revealed that Nitrosospira-like AOB were dominant on the ammonium-enriched membranes incubated in the soil. Fourteen unique Nitrosospira-like 16S rRNA gene sequences belonging to clusters 2 and 3 were recovered from the soil-incubated membranes and from the soil, suggesting the importance of Nitrosospira-like AOB in the oil-polluted landfarming soil.
authors.affiliation: Department of Biological and Environmental Sciences, Division of General Microbiology, FIN-00014 University of Helsinki, Finland. Jukka.Kurola@Helsinki.fi
authors.forename: Jukka
authors.initials: J
authors.lastname: Kurola
authors.forename: Christoph
authors.initials: C
authors.lastname: Wittmann
authors.forename: Mirja
authors.initials: M
authors.lastname: Salkinoja-Salonen
authors.forename: Tuula
authors.initials: T
authors.lastname: Aarnio
authors.forename: Martin
authors.initials: M
authors.lastname: Romantschuk
mesh_terms: D000641:Ammonia / Q000378:metabolism*; D020562:Betaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D002411:Cation Exchange Resins; D015169:Colony Count, Microbial; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D005387:Finland; D017404:In Situ Hybridization, Fluorescence; D007220:Industrial Waste; D008567:Membranes, Artificial; D010084:Oxidation-Reduction; D010578:Petroleum; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D012989:Soil Pollutants / Q000378:metabolism*
chemical_list: D002411:Cation Exchange Resins; D004269:DNA, Bacterial; D007220:Industrial Waste; D008567:Membranes, Artificial; D010578:Petroleum; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; D000641:Ammonia