Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Applied and Environmental Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
General Microbial Ecology

Characterization of Methanotrophic Bacterial Populations in Soils Showing Atmospheric Methane Uptake

Andrew J. Holmes, Peter Roslev, Ian R. McDonald, Niels Iversen, Kaj Henriksen, J. Colin Murrell
Andrew J. Holmes
Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom;
Commonwealth Key Centre for Biodiversity and Bioresources, School of Biological Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia; and
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter Roslev
Environmental Engineering Laboratory, Aalborg University, DK-9000 Aalborg, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ian R. McDonald
Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Niels Iversen
Environmental Engineering Laboratory, Aalborg University, DK-9000 Aalborg, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kaj Henriksen
Environmental Engineering Laboratory, Aalborg University, DK-9000 Aalborg, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Colin Murrell
Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AEM.65.8.3312-3318.1999
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Fig. 1.
    • Open in new tab
    • Download powerpoint
    Fig. 1.

    14C-PLFA fingerprints for MOB. (A) Unknown methanotrophs that metabolized atmospheric methane in two forest soils in Denmark (Rold) and the United States (Maine). (B) Type I methanotroph Methylomicrobium album BG8 and type II methanotroph Methylosinus trichosporium OB3b. Each bar represents the amount of radiolabel in a fraction as a percentage of the radioactivity in all fractions. The following reference standard PLFAs coeluted with the 14C-PLFAs: 14:0, i15:1, and a15:1 in fraction 2; 16:1w9 and 16:1w8 in fraction 4; 16:1w7, 16:1w5, and 16:0 in fraction 5; i17:0, a17:0, and 17:1w8 in fraction 7; and 18:1w9, 18:1w8, and 18:1w7 in fraction 11.

  • Fig. 2.
    • Open in new tab
    • Download powerpoint
    Fig. 2.

    Alignment of predicted peptide sequences of PmoA and AmoA from representative methanotrophic and nitrifying bacteria with soil clone RA14 and RA21 sequences. Residues which are universally conserved in extant MOB are highlighted with black. Putative MMO signatures are highlighted with dots, and putative AMO signatures are highlighted with grey. The horizontal lines indicate predicted hydrophilic domains conserved in all of the peptides (15). The sequences shown (and their accession numbers) are as follows: Ms.tri, Methylosinus trichosporium (U31650 ); Mc. M,Methylocystis sp. strain M (U81596 ); Mc.par,Methylocystis parvus (U31651 ); Nc.oce, Nitrosococcus oceanus (U31652 ); Mb.alb, Methylomicrobium album BG8 (U31654 ); Mm.met, Methylomonas methanica S1 (U31653 ); LK6,Methylocaldum tepidum LK6 (U89304 ); Mc.cap,Methylococcus capsulatus Bath (L40804 ); Nm.eur,Nitrosomonas europaea (L08050 ); Nl.mul, Nitrosolobus multiformis (U31649 ); AHB1, Nitrosospira sp. strain AHB1 (X90821 ); Nspira, Nitrosospira sp. strain Np22 (U31655 ).

  • Fig. 3.
    • Open in new tab
    • Download powerpoint
    Fig. 3.

    Unrooted phylogenetic trees showing relationships of RA14 and RA21 to representative methanotrophs and ammonia-oxidizing bacteria. (A) Tree constructed by using a 171-amino-acid segment of the 27-kDa subunit of MMO (PmoA or AmoA). (B) Tree constructed by using a restricted sequence alignment (125 amino acids) in which putative signature residues (see Fig. 2) were omitted from the analysis. On the basis of the bacterial phylogeny derived from rRNA (10, 26, 42), the root of the trees is predicted to lie on the branch indicated by a dot. The numbers at the nodes indicate the numbers of times the groups occurred in 100 bootstrap replicates. ApproximateKm values for CH4(Km CH4) of the holoenzymes are indicated as micromolar concentrations (Table 1). For the sequence accession numbers see the legend to Fig. 2. Abbreviations: Mb,Methylomicrobium; Mm., Methylomonas; Nc.,Nitrosococcus; Mc., Methylocystis; Ms.,Methylosinus; Nm., Nitrosomonas; Nl.,Nitrosolobus; Nspira, Nitrosospira.

  • Fig. 4.
    • Open in new tab
    • Download powerpoint
    Fig. 4.

    Phylogenetic analysis of the derived amino acid sequences encoded by the pmoA genes of methanotrophs, nitrifiers, and Rold, Maine, and Pantanal soil DNA samples. The dendrogram shows the results of an analysis in which PROTDIST was used. Bootstrap values greater than 50% derived from 100 replicates are also shown. The bar represents 10% sequence divergence, as determined by measuring the lengths of the horizontal lines connecting any two species.

Tables

  • Figures
  • Table 1.

    Some characteristics of AAOB (nitrifying bacteria), methanotrophic bacteria, and unknown high-affinity methane oxidizers in soila

    BacteriaPhylogenetic affiliationMembrane typeMajor fatty acidsbKey enzymeApparent Km for CH4 (μM)cVmax for CH4 (mmol · g of cells−1· h−1)Oxidation inhibited by C2H2, C2H4, DME, and COdGrowth inhibited by elevated NH3 concnCH4 required to maintain activity% Assimilation of oxidized CH4e
    MAB
     Group 1γ-ProteobacteriaStacked, central14:0, 16:0, and 16:1 speciespMMO (+ some sMMO)0.8–3210–31+++29–62
     Group 2α-ProteobacteriaFlat, peripheral18:1 speciespMMO (+ some sMMO)0.8–3210–31+++29–62
     Soil high affinity??18:1 species?0.01–0.06?+++20–54
    AAOB
     Group 3β-ProteobacteriaFlat, peripheral16:0 and 16:1 speciesAMO2,000  0.03–0.59+−−0–17
     Group 4γ-ProteobacteriaStacked, central16:0 and 16:1 speciesAMO    6.60.01–0.08+−−1–47
    • ↵a Data from references 1, 2, 5, 9, 12, 17, 19, 20, 22, 28, 30, 31, 39, and40.

    • ↵b A major fatty acid is present at a concentration of >10% in at least one member of each group.

    • ↵c The values for nitrifiers were based on theKi of CH4 for ammonia oxidation.

    • ↵d DME, dimethyl ether.

    • ↵e The fate of labelled methane in nitrifiers is not known. The apparent assimilation could be due to nonspecific labelling by formaldehyde or assimilation at the level of CO2.

PreviousNext
Back to top
Download PDF
Citation Tools
Characterization of Methanotrophic Bacterial Populations in Soils Showing Atmospheric Methane Uptake
Andrew J. Holmes, Peter Roslev, Ian R. McDonald, Niels Iversen, Kaj Henriksen, J. Colin Murrell
Applied and Environmental Microbiology Aug 1999, 65 (8) 3312-3318; DOI: 10.1128/AEM.65.8.3312-3318.1999

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Applied and Environmental Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Characterization of Methanotrophic Bacterial Populations in Soils Showing Atmospheric Methane Uptake
(Your Name) has forwarded a page to you from Applied and Environmental Microbiology
(Your Name) thought you would be interested in this article in Applied and Environmental Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Characterization of Methanotrophic Bacterial Populations in Soils Showing Atmospheric Methane Uptake
Andrew J. Holmes, Peter Roslev, Ian R. McDonald, Niels Iversen, Kaj Henriksen, J. Colin Murrell
Applied and Environmental Microbiology Aug 1999, 65 (8) 3312-3318; DOI: 10.1128/AEM.65.8.3312-3318.1999
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • MATERIALS AND METHODS
    • RESULTS
    • DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

methane
Methylococcaceae
soil microbiology

Related Articles

Cited By...

About

  • About AEM
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AppEnvMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

 

Print ISSN: 0099-2240; Online ISSN: 1098-5336