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Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the 'greenhouse' effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure-function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate-nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).

Forest and other upland soils are important sinks for atmospheric CH 4 , consuming 20 to 60 Tg of CH 4 per year. Consumption of atmospheric CH 4 by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH 4 oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting the pmoA gene, coding for the ␣ subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The forest soil was a sink for atmospheric CH 4 in situ and in vitro at all times. In winter, atmospheric CH 4 was oxidized in a well-defined subsurface soil layer (6 to 14 cm deep), whereas in summer, the complete soil core was active (0 cm to 26 cm deep). The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with soil depth (0 to 28 cm deep) from about 40 to 1 g DNA per g (dry weight) of soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration of pmoA changed with depth and season. pmoA was detected only in soil layers with active CH 4 oxidation, i.e., 6 to 16 cm deep in winter and throughout the soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH 4 consumption rates also exhibited more bands of pmoA in DGGE, indicating that high CH 4 oxidation activity was positively correlated with the number of methanotrophic populations present. The pmoA sequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH 4 consumption.The atmospheric concentration of CH 4 , one of the most important greenhouse gases, has increased dramatically over the past 200 years. About 80 to 90% of atmospheric CH 4 is of biogenic origin (20). The major sink is the chemical destruction by OH˙and Cl˙radicals in the troposphere and stratosphere, respectively (9, 10). However, the capacity of these atmospheric sinks may decline, since the rising concentrations of other trace gases emitted by anthropogenic activity result in a reduction of OH˙radicals in the troposphere (27).The only biological sink for CH 4 is oxidation in soil. Atmospheric CH 4 is consumed in forest, agricultural, and other upland soils. CH 4 consumption in these soils is caused by methane-oxidizing bacteria. However, the identity of these methanotrophs is still unknown. The apparent half-saturation constant (K m ) for oxidation of atmospheric CH 4 (approximately 1.8 parts per million by volume [ppmv]) in upland soils ranges from 0.8 to 280 nM (6, 7, 13, 16). However, the K m of the common type I or II methanotrophs (0.8 to 66 M), which are available in culture collections, is 1 to 3 orders of magnitude higher, and these common methanotrophs are not abl...

methane in the biosphere is mainly produced by prokaryotic methanogenic archaea, biomass burning, coal and oil extraction, and to a lesser extent by eukaryotic plants. Here we demonstrate that saprotrophic fungi produce methane without the involvement of methanogenic archaea. Fluorescence in situ hybridization, confocal laser-scanning microscopy and quantitative realtime PCR confirm no contribution from microbial contamination or endosymbionts. our results suggest a common methane formation pathway in fungal cells under aerobic conditions and thus identify fungi as another source of methane in the environment. stable carbon isotope labelling experiments reveal methionine as a precursor of methane in fungi. These findings of an aerobic fungus-derived methane formation pathway open another avenue in methane research and will further assist with current efforts in the identification of the processes involved and their ecological implications.

Methane consumption by forest soil was studied in situ and in vitro with respect to responses to nitrogen additions at atmospheric and elevated methane concentrations. Methane concentrations in intact soil decreased continuously from atmospheric levels at the surface to 0.5 ppm at a depth of 14 cm. The consumption rate of atmospheric methane in soils, however, was highest in the 4- to 8-cm depth interval (2.9 nmol per g of dry soil per day), with much lower activities below and above this zone. In contrast, extractable ammonium and nitrate concentrations were highest in the surface layer (0 to 2 cm; 22 and 1.6 μmol per g of dry soil, respectively), as was potential ammonium-oxidizing activity (19 nmol per g of dry soil per day). The difference in zonation between ammonium oxidation and methane consumption suggested that ammonia-oxidizing bacteria did not contribute significantly to atmospheric methane consumption. Exogenous ammonium inhibited methane consumption in situ and in vitro, but the pattern of inhibition did not conform to expectations based on simple competition between ammonia and methane for methane monooxygenase. The extent of ammonium inhibition increased with increasing methane concentration. Inhibition by a single ammonium addition remained constant over a period of 39 days. In addition, nitrite, the end product of methanotrophic ammonia oxidation, was a more effective inhibitor of methane consumption than ammonium. Factors that stimulated ammonium oxidation in soil, e.g., elevated methane concentrations and the availability of cosubstrates such as formate, methanol, or β-hydroxybutyrate, enhanced ammonium inhibition of methane oxidation, probably as a result of enhanced nitrite production.