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Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids
Author(s) -
Shrestha Minita,
Abraham WolfRainer,
Shrestha Pravin Malla,
Noll Matthias,
Conrad Ralf
Publication year - 2008
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2007.01462.x
Subject(s) - rhizosphere , stable isotope probing , biology , microcosm , terminal restriction fragment length polymorphism , anaerobic oxidation of methane , paddy field , microbial population biology , methanotroph , methane , environmental chemistry , population , botany , soil microbiology , restriction fragment length polymorphism , ecology , soil water , microorganism , bacteria , biochemistry , gene , chemistry , polymerase chain reaction , genetics , demography , sociology
Summary Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH 4 into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH 4 flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T‐RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA‐SIP) using 13 C‐labelled CH 4 directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to 13 CH 4 for 8 and 18 days. Both T‐RFLP/cloning and PLFA‐SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA‐SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms.