Microbial ecology and stable isotope biogeochemistry of methane oxidation

Methane-oxidizing bacteria (methanotrophs) consume a variable but significant fraction of the methane produced in flooded soils, and therefore represent an important sink for greenhouse-active methane gas that would otherwise be emitted to the atmosphere. Information about factors limiting methanotrophs in flooded soils will be essential in efforts to reduce methane emissions from rice paddies and other managed wetlands. Primary factors influencing methanotroph population growth and competition between methanotroph groups in laboratory cultures are methane, oxygen, nitrogen, and copper availability. The objective of this study is to identify which of these factors control the population structure and dynamics of methanotrophs in rice paddies.; Quantitative, depth-resolved measurements of Type I and Type II methanotroph populations in straw-burned and straw-incorporated rice paddies were made by measuring polar lipid fatty acid (PLFA) biomarkers for Type I and Type II methane-oxidizing bacteria. The PLFA biomarker approach was validated using a soil 13CH₄ tracer incubation followed by compound-specific isotope analysis of soil polar lipid fatty acids, testing the link between active methane-consuming organisms and biomarker fatty acids used to quantify methanotroph populations. Methanotroph populations increased during the rice growing season by a factor of 3 to 5, with Type II methanotrophs showing more growth than Type I. Higher belowground methane concentrations in the straw-incorporated rice paddy did not influence methanotroph population structure or dynamics. These results suggest that methanotrophs in the rice paddies are not limited by methane availability. Further experiments conducted in the laboratory showed that methanotrophs in the same soil are not limited by copper. Nitrogen and/or oxygen limitation of methanotroph growth are both consistent with the abundance of Type II relative to Type I methanotrophs.; Previous studies have strongly emphasized the role of methane oxidation occurring in rice rhizospheres. Methanotroph growth in this study occurred almost exclusively near the soil/water interface, and was not correlated with rice root mass distributions with depth. This result indicates that rhizosphere methane oxidation was of minor importance relative to oxidation at the soil/water interface, and suggests that the importance of rice rhizospheres as a niche for methanotrophs may be largely dependent on cultivar or soil characteristics.