Nutrient amendments in soil DNA stable isotope probing experiments reduce observed methanotroph diversity

Cebron, Aurelie; Bodrossy, Levente; Stralis-Pavese, Nancy; Singer, Andrew C. ORCID:; Thompson, Ian P.; Prosser, James I.; Murrell, J. Colin. 2007 Nutrient amendments in soil DNA stable isotope probing experiments reduce observed methanotroph diversity. Applied and Environmental Microbiology, 73 (3). 798-807.

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Stable isotope probing (SIP) can be used to analyze the active bacterial populations involved in a process by incorporating 13C-labeled substrate into cellular components such as DNA. Relatively long incubation times are often used with laboratory microcosms in order to incorporate sufficient13C 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 13CH4 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 non- amended SIP microcosms. Although this treatment probably best reflected the in situ environmental condi- tions, one major disadvantage of this incubation was that the incorporation of 13CH4 was slow and somecross-feeding of 13C occurred, thereby leading to labeling of nonmethanotroph microorganisms. Conversely, microcosms supplemented with mineral salts medium exhibited rapid consumption of13CH4, 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 13C into active methanotrophs while avoiding the cross-feeding of 13C.

Item Type: Publication - Article
Digital Object Identifier (DOI):
Programmes: CEH Programmes pre-2009 publications > Biogeochemistry
CEH Programmes pre-2009 publications > Biodiversity
UKCEH and CEH Sections/Science Areas: Hails
ISSN: 0099-2240
NORA Subject Terms: Biology and Microbiology
Ecology and Environment
Date made live: 22 Mar 2012 16:27 +0 (UTC)

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