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PMID: 12177327 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing.

Microbiology (Reading, England) ·Vol. 148 ·No. Pt 8 ·2002-08-00 ·Pages 2331-2342

Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB, Prosser JI, Murrell JC

Abstract

Stable-isotope probing (SIP) is a culture-independent technique that enables the isolation of DNA from micro-organisms that are actively involved in a specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 3.5) microcosms that were exposed to (13)CH(3)OH or (13)CH(4). Distinct (13)C-labelled DNA ((13)C-DNA) fractions were resolved from total community DNA by CsCl density-gradient centrifugation. Analysis of 16S rDNA sequences amplified from the (13)C-DNA revealed that bacteria related to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the (13)C-labelled substrates, which suggested that moderately acidophilic methylotroph populations were active in the microcosms. Enrichments targeted towards the active proteobacterial CH(3)OH utilizers were successful, although none of these bacteria were isolated into pure culture. A parallel analysis of genes encoding the key enzymes methanol dehydrogenase and particulate methane monooxygenase reflected the 16S rDNA analysis, but unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the beta-subclass of the PROTEOBACTERIA: Analysis of AOB-selective 16S rDNA amplification products identified Nitrosomonas and Nitrosospira sequences in the (13)C-DNA fractions, suggesting certain AOB assimilated a significant proportion of (13)CO(2), possibly through a close physical and/or nutritional association with the active methylotrophs. Other sequences retrieved from the (13)C-DNA were related to the 16S rDNA sequences of members of the Acidobacterium division, the beta-Proteobacteria and the order Cytophagales, which implicated these bacteria in the assimilation of reduced one-carbon compounds or in the assimilation of the by-products of methylotrophic carbon metabolism. Results from the (13)CH(3)OH and (13)CH(4) SIP experiments thus provide a rational basis for further investigations into the ecology of methylotroph populations in situ.

MeSH Terms
Ammonia/metabolism Bacteria/classification,genetics,metabolism Betaproteobacteria/classification,genetics,metabolism Carbon Isotopes/metabolism Carbon Radioisotopes/metabolism DNA, Bacterial/analysis Molecular Sequence Data Oxygenases/genetics Phylogeny RNA, Ribosomal, 16S/analysis Soil Microbiology Trees
Chemicals
Carbon Isotopes Carbon Radioisotopes DNA, Bacterial RNA, Ribosomal, 16S Ammonia Oxygenases methane monooxygenase
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Radajewski Stefan
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK1.
Webster Gordon
Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK2.
Reay David S
Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK3.
Morris Samantha A
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK1.
Ineson Philip
Department of Biology, University of York, PO Box 373, YO10 5YW, UK4.
Nedwell David B
Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK3.
Prosser James I
Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK2.
Murrell J Colin
Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK1.
Article Info
Journal
Microbiology (Reading, England)
Abbr.
Microbiology (Reading)
ISSN
1350-0872
DOI
10.1099/00221287-148-8-2331
Published
2002-08-00
Pages
2331-2342
Language
English
Region
England
NLM ID
9430468
Subset
IM
Databases
GENBANK
AY080911, AY080912, AY080913, AY080914, AY080915, AY080916, AY080917, AY080918, AY080919, AY080920, AY080921, AY080922, AY080923, AY080924, AY080925, AY080926, AY080927, AY080928, AY080929, AY080930, AY080931, AY080932, AY080933, AY080934, AY080935, AY080936, AY080937, AY080938, AY080939, AY080940, AY080941, AY080942, AY080943, AY080944, AY080945, AY080946, AY080947, AY080948, AY080949, AY080950, AY080951, AY080952, AY080953, AY080954, AY080955, AY080956, AY080957, AY080958, AY080959, AY080960, AY080961
External Links
PubMed source DOI: 10.1099/00221287-148-8-2331 View journal details
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