HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Radajewski, S. Articles by Murrell, J. C. Search for Related Content PubMed PubMed Citation Articles by Radajewski, S. Articles by Murrell, J. C. Agricola Articles by Radajewski, S. Articles by Murrell, J. C.

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

Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK¹
Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK²
Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK³
Department of Biology, University of York, PO Box 373, YO10 5YW, UK⁴

Author for correspondence: J. Colin Murrell. Tel: +44 24 7652 2553. Fax: +44 24 7652 3568. e-mail: cmurrell{at}bio.warwick.ac.uk

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 ¹³CH₃OH or ¹³CH₄. Distinct ¹³C-labelled DNA (¹³C-DNA) fractions were resolved from total community DNA by CsCl density-gradient centrifugation. Analysis of 16S rDNA sequences amplified from the ¹³C-DNA revealed that bacteria related to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the ¹³C-labelled substrates, which suggested that moderately acidophilic methylotroph populations were active in the microcosms. Enrichments targeted towards the active proteobacterial CH₃OH 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 ß-subclass of the Proteobacteria. Analysis of AOB-selective 16S rDNA amplification products identified Nitrosomonas and Nitrosospira sequences in the ¹³C-DNA fractions, suggesting certain AOB assimilated a significant proportion of ¹³CO₂, possibly through a close physical and/or nutritional association with the active methylotrophs. Other sequences retrieved from the ¹³C-DNA were related to the 16S rDNA sequences of members of the Acidobacterium division, the ß-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 ¹³CH₃OH and ¹³CH₄ SIP experiments thus provide a rational basis for further investigations into the ecology of methylotroph populations in situ.

Keywords: methanotrophs, community structure, culture-independent techniques, ¹³C, functional genes

Abbreviations: AOB, ammonia-oxidizing bacteria; DGGE, denaturing gradient gel electrophoresis; g.d.w.,g dry weight; OTU, operational taxonomic unit; SIP, stable-isotope probing

^c The GenBank accession numbers for the sequences reported in this paper are AY080911–AY080961.

^a Present address: Cardiff School of Biosciences, Cardiff University, Main Building, Cardiff CF10 3TL, UK.

^b Present address: Institute of Ecology and Resource Management, University of Edinburgh, Darwin Building, Edinburgh EH9 3JU, UK.

This article has been cited by other articles:

				I. R. McDonald, L. Bodrossy, Y. Chen, and J. C. Murrell Molecular Ecology Techniques for the Study of Aerobic Methanotrophs Appl. Envir. Microbiol., March 1, 2008; 74(5): 1305 - 1315. [Full Text] [PDF]

				S. N. Dedysh, S. E. Belova, P. L. E. Bodelier, K. V. Smirnova, V. N. Khmelenina, A. Chidthaisong, Y. A. Trotsenko, W. Liesack, and P. F. Dunfield Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing 'signature' fatty acids of type I methanotrophs Int J Syst Evol Microbiol, March 1, 2007; 57(3): 472 - 479. [Abstract] [Full Text] [PDF]

				A. Cebron, L. Bodrossy, N. Stralis-Pavese, A. C. Singer, I. P. Thompson, J. I. Prosser, and J. C. Murrell Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity Appl. Envir. Microbiol., February 1, 2007; 73(3): 798 - 807. [Abstract] [Full Text] [PDF]

				P. J. Maxfield, E. R. C. Hornibrook, and R. P. Evershed Estimating High-Affinity Methanotrophic Bacterial Biomass, Growth, and Turnover in Soil by Phospholipid Fatty Acid 13C Labeling. Appl. Envir. Microbiol., June 1, 2006; 72(6): 3901 - 3907. [Abstract] [Full Text] [PDF]

				A. Chauhan and A. Ogram Fatty Acid-Oxidizing Consortia along a Nutrient Gradient in the Florida Everglades Appl. Envir. Microbiol., April 1, 2006; 72(4): 2400 - 2406. [Abstract] [Full Text] [PDF]

				S. N. Dedysh, T. A. Pankratov, S. E. Belova, I. S. Kulichevskaya, and W. Liesack Phylogenetic analysis and in situ identification of bacteria community composition in an acidic sphagnum peat bog. Appl. Envir. Microbiol., March 1, 2006; 72(3): 2110 - 2117. [Abstract] [Full Text] [PDF]

				K. Stoecker, B. Bendinger, B.ör. Schöning, P. H. Nielsen, J. L. Nielsen, C. Baranyi, E. R. Toenshoff, H. Daims, and M. Wagner From the Cover: Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase PNAS, February 14, 2006; 103(7): 2363 - 2367. [Abstract] [Full Text] [PDF]

				C. M. DeRito, G. M. Pumphrey, and E. L. Madsen Use of Field-Based Stable Isotope Probing To Identify Adapted Populations and Track Carbon Flow through a Phenol-Degrading Soil Microbial Community Appl. Envir. Microbiol., December 1, 2005; 71(12): 7858 - 7865. [Abstract] [Full Text] [PDF]

				O. Nercessian, M. G. Kalyuzhnaya, S. B. Joye, M. E. Lidstrom, and L. Chistoserdova Analysis of fae and fhcD Genes in Mono Lake, California Appl. Envir. Microbiol., December 1, 2005; 71(12): 8949 - 8953. [Abstract] [Full Text] [PDF]

				O. Nercessian, E. Noyes, M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova Bacterial Populations Active in Metabolism of C1 Compounds in the Sediment of Lake Washington, a Freshwater Lake Appl. Envir. Microbiol., November 1, 2005; 71(11): 6885 - 6899. [Abstract] [Full Text] [PDF]

				J.-L. Lin, S. B. Joye, J. C. M. Scholten, H. Schafer, I. R. McDonald, and J. C. Murrell Analysis of Methane Monooxygenase Genes in Mono Lake Suggests That Increased Methane Oxidation Activity May Correlate with a Change in Methanotroph Community Structure Appl. Envir. Microbiol., October 1, 2005; 71(10): 6458 - 6462. [Abstract] [Full Text] [PDF]

				E. Gallagher, L. McGuinness, C. Phelps, L. Y. Young, and L. J. Kerkhof 13C-Carrier DNA Shortens the Incubation Time Needed To Detect Benzoate-Utilizing Denitrifying Bacteria by Stable-Isotope Probing Appl. Envir. Microbiol., September 1, 2005; 71(9): 5192 - 5196. [Abstract] [Full Text] [PDF]

				D. R. Singleton, S. N. Powell, R. Sangaiah, A. Gold, L. M. Ball, and M. D. Aitken Stable-Isotope Probing of Bacteria Capable of Degrading Salicylate, Naphthalene, or Phenanthrene in a Bioreactor Treating Contaminated Soil Appl. Envir. Microbiol., March 1, 2005; 71(3): 1202 - 1209. [Abstract] [Full Text] [PDF]

				T. Lueders, B. Pommerenke, and M. W. Friedrich Stable-Isotope Probing of Microorganisms Thriving at Thermodynamic Limits: Syntrophic Propionate Oxidation in Flooded Soil Appl. Envir. Microbiol., October 1, 2004; 70(10): 5778 - 5786. [Abstract] [Full Text] [PDF]

				G. Webster, R. J. Parkes, J. C. Fry, and A. J. Weightman Widespread Occurrence of a Novel Division of Bacteria Identified by 16S rRNA Gene Sequences Originally Found in Deep Marine Sediments Appl. Envir. Microbiol., September 1, 2004; 70(9): 5708 - 5713. [Abstract] [Full Text] [PDF]

				V. J. Denef, J. Park, T. V. Tsoi, J.-M. Rouillard, H. Zhang, J. A. Wibbenmeyer, W. Verstraete, E. Gulari, S. A. Hashsham, and J. M. Tiedje Biphenyl and Benzoate Metabolism in a Genomic Context: Outlining Genome-Wide Metabolic Networks in Burkholderia xenovorans LB400 Appl. Envir. Microbiol., August 1, 2004; 70(8): 4961 - 4970. [Abstract] [Full Text] [PDF]

				J. Adamczyk, M. Hesselsoe, N. Iversen, M. Horn, A. Lehner, P. H. Nielsen, M. Schloter, P. Roslev, and M. Wagner The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function Appl. Envir. Microbiol., November 1, 2003; 69(11): 6875 - 6887. [Abstract] [Full Text] [PDF]

				M. Tchawa Yimga, P. F. Dunfield, P. Ricke, J. Heyer, and W. Liesack Wide Distribution of a Novel pmoA-Like Gene Copy among Type II Methanotrophs, and Its Expression in Methylocystis Strain SC2 Appl. Envir. Microbiol., September 1, 2003; 69(9): 5593 - 5602. [Abstract] [Full Text] [PDF]