Open AccessBiochemical and molecular characterization of methanotrophs in soil from a pristine New Zealand beech forest
Author(s) -
Singh Brajesh K.,
Tate Kevin
Publication year - 2007
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1111/j.1574-6968.2007.00885.x
Subject(s) - biology , methanotroph , library , beech , terminal restriction fragment length polymorphism , restriction fragment length polymorphism , anaerobic oxidation of methane , botany , bacteria , ecology , gene , 16s ribosomal rna , biochemistry , polymerase chain reaction , genetics , methane
Methane (CH 4 ) oxidation and the methanotrophic community structure of a pristine New Zealand beech forest were investigated using biochemical and molecular methods. Phospholipid‐fatty acid‐stable‐isotope probing (PLFA‐SIP) was used to identify the active population of methanotrophs in soil beneath the forest floor, while terminal‐restriction fragment length polymorphism (T‐RFLP) and cloning and sequencing of the pmoA gene were used to characterize the methanotrophic community. PLFA‐SIP suggested that type II methanotrophs were the predominant active group. T‐RFLP and cloning and sequencing of the pmoA genes revealed that the methanotrophic community was diverse, and a slightly higher number of type II methanotrophs were detected in the clone library. Most of the clones from type II methanotrophs were related to uncultured pmoA genes obtained directly from environmental samples, while clones from type I were distantly related to Methylococcus capsulatus . A combined data analysis suggested that the type II methanotrophs may be mainly responsible for atmospheric CH 4 consumption. Further sequence analysis suggested that most of the methanotrophs detected shared their phylogeny with methanotrophs reported from soils in the Northern Hemisphere. However, some of the pmoA sequences obtained from this forest had comparatively low similarity (<97%) to known sequences available in public databases, suggesting that they may belong to novel groups of methanotrophic bacteria. Different methods of methanotrophic community analysis were also compared, and it is suggested that a combination of molecular methods with PLFA‐SIP can address several shortcomings of stable isotope probing.