Vertical distribution of the methanotrophic community after drainage of rice field soil

Abstract

Anoxic soils, such as flooded rice fields, are major sources of the greenhouse gas CH(4) while oxic upland soils are major sinks of atmospheric CH(4). Nevertheless, CH(4) is also consumed in rice fields where up to 90% of the produced CH(4) is oxidized in a narrow oxic zone around the rice roots and in the soil surface layer before it escapes into the atmosphere. After 1 day drainage of rice field soil, CH(4) oxidation was detected in the top 2-mm soil layers, but after 8 days drainage the zone of CH(4) oxidation extended to 8 mm depth. Simultaneously, the potential for CH(4) production decreased, but some production was still detectable after 8 days drainage throughout the soil profile. The vertical distribution of the methanotrophic community was also monitored after 1 and 8 days drainage using denaturing gradient gel electrophoresis after PCR amplification with primer sets targeting two regions on the 16S rRNA gene that are relatively specific for methylotrophic alpha- and gamma-Proteobacteria, and targeting two functional genes encoding subunits of key enzymes in all methanotrophs, i.e. the genes for the particulate methane monooxygenase (pmoA) and the methanol dehydrogenase (mxaF). Drainage stimulated the methanotrophic community. Eight days after drainage, new methanotrophic populations appeared and a distinct methanotrophic community developed. The population structure of type I and II methanotrophs was differently affected by drainage. Type II methanotrophs (alpha-Proteobacteria) were present throughout the soil core directly after drainage (1 day), and the community composition remained largely unchanged with depth. Only two new type II populations appeared after 8 days of drainage. Drainage had a more pronounced impact on the type I methanotrophic community (gamma-Proteobacteria). Type I populations were not or only weakly detected 1 day after drainage. However, after 8 days of drainage, a large diversity of type I methanotrophs were detected, altough they were not evenly distributed throughout the soil core but dominated at different depths. A distinct type I community structure had developed within each soil section between 0 and 20 mm soil depth, indicating the widening of suitable habitats for methanotrophs in the rice field soil within 1 week of drainage.

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

“…It is possible that the conflicting results reported may be due to different communities with different activity (i.e., different MMO expression) having a competitive advantage under different wetting regimes. Such a hypothesis is supported from the findings of Henckel, et al (2001). In this study, drainage of rice field soils revealed that Type I and II methanotrophs were differentially affected by reducing water content.…”

Diversity of Aerobic Methanotrophic Bacteria in a Permafrost Active Layer Soil of the Lena Delta, Siberia

“…In all studies discussed, the MOB community is exposed to environmental extremes such as freeze-thaw cycles, low pH values, or low substrate concentrations and was found to be restricted to certain taxonomic groups of MOB. In contrast to that, a wide range of MOB genera of both type I and type II MOB was reported for more moderate environments such as landfill soils [59], rice field soils [22,24,28], freshwater sediments [8,42,44], and subarctic tundra soils [31]. This points at a trend toward a restricted diversity or a selection for certain groups of MOB in more extreme environments, which is in accordance with the results obtained in the present study.…”

“…Members of the Methylocystaceae and Beijerinckiaceae are termed type II MOB and belong to the α-subdivision of the Proteobacteria phylum [10][11][12][13][14][15][16][17][18][19][20][21]. The diversity and composition of MOB have been investigated in several environments such as freshwater sediments [8,42], landfill soils [59], rice field soils [22,24], habitats with only atmospheric methane concentrations [29,33,35], and peat bogs with very low pH values [39,40].…”

Bacteriohopanepolyols in tropical soils and sediments from the Congo River catchment area

“…A study by van Winden et al (2012a) found CH 4 oxidation markers in peatlands, specifically at the oxic-anoxic boundary where AMO is thought to occur. Additionally, Henckel et al (2001) found that AMO increased during the drying out of methane-producing wetland type environments, presumably due to the extension of the oxic-anoxic boundary. Lastly, the apparent lack of CH 4 oxidation markers in the soil samples could be due to a lack in our understanding of the source organisms of aminopentol and related compounds.…”