Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity

A. Cebron, L. Bodrossy, N. Stralis-Pavese, A. C. Singer, I. P. Thompson, James Ivor Prosser, J. C. Murrell

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating C-13-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient C-13 into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of (CH4)-C-13 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of (CH4)-C-13 was slow and some cross-feeding of C-13 occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of (CH4)-C-13 resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of C-13 into active methanotrophs while avoiding the cross-feeding of C-13.

Original languageEnglish
Pages (from-to)798-807
Number of pages9
JournalApplied and Environmental Microbiology
Volume73
Issue number3
DOIs
Publication statusPublished - 2007

Keywords

  • methane-oxidizing bacteria
  • microbial community function
  • functional gene probes
  • molecular characterization
  • atmospheric methane
  • methyl-chloride
  • grassland soil
  • lake-sediments
  • ribosomal-RNA
  • upland soils

Cite this

Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity. / Cebron, A.; Bodrossy, L.; Stralis-Pavese, N.; Singer, A. C.; Thompson, I. P.; Prosser, James Ivor; Murrell, J. C.

In: Applied and Environmental Microbiology, Vol. 73, No. 3, 2007, p. 798-807.

Research output: Contribution to journalArticle

Cebron, A. ; Bodrossy, L. ; Stralis-Pavese, N. ; Singer, A. C. ; Thompson, I. P. ; Prosser, James Ivor ; Murrell, J. C. / Nutrient Amendments in Soil DNA Stable Isotope Probing Experiments Reduce the Observed Methanotroph Diversity. In: Applied and Environmental Microbiology. 2007 ; Vol. 73, No. 3. pp. 798-807.
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AU - Cebron, A.

AU - Bodrossy, L.

AU - Stralis-Pavese, N.

AU - Singer, A. C.

AU - Thompson, I. P.

AU - Prosser, James Ivor

AU - Murrell, J. C.

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AB - Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating C-13-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient C-13 into the DNA of the target organisms. Addition of nutrients can be used to accelerate the processes. However, unnatural concentrations of nutrients may artificially change bacterial diversity and activity. In this study, methanotroph activity and diversity in soil was examined during the consumption of (CH4)-C-13 with three DNA-SIP experiments, using microcosms with natural field soil water conditions, the addition of water, and the addition of mineral salts solution. Methanotroph population diversity was studied by targeting 16S rRNA and pmoA genes. Clone library analyses, denaturing gradient gel electrophoresis fingerprinting, and pmoA microarray hybridization analyses were carried out. Most methanotroph diversity (type I and type II methanotrophs) was observed in nonamended SIP microcosms. Although this treatment probably best reflected the in situ environmental conditions, one major disadvantage of this incubation was that the incorporation of (CH4)-C-13 was slow and some cross-feeding of C-13 occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of (CH4)-C-13 resulting in the labeling of a less diverse population of only type I methanotrophs. DNA-SIP incubations using water-amended microcosms yielded faster incorporation of C-13 into active methanotrophs while avoiding the cross-feeding of C-13.

KW - methane-oxidizing bacteria

KW - microbial community function

KW - functional gene probes

KW - molecular characterization

KW - atmospheric methane

KW - methyl-chloride

KW - grassland soil

KW - lake-sediments

KW - ribosomal-RNA

KW - upland soils

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JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

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ER -