Ralf Conrad

Microbial Ecology of Methanogens and Methanotrophs

Rice agriculture feeds about a third of the worlds population. However, rice fields are also an important source in the global budget of the greenhouse gas methane. The emission of methane from flooded rice fields is the result of the activity of methanogenic archaea that produce the methane and of methanotrophic bacteria that oxidize part of it, so that the ecology of these two physiological groups of microorganisms is key for the understanding of methane cycling in rice fields and for possible mitigation of emission from this important agro-ecosystem. In this chapter I will describe the ecology of methanogens and methanotrophs and will give examples where production and emission of methane on the field scale can be understood on the basis of processes on the microscale.

Kinetics of methane oxidation in oxic soils

We investigated the kinetics of CH4 oxidation in three different soils (cutivated cambisol, forest cambisol, meadow cambisol) under oxic conditions. CH4 oxidation was apparently due to aerobic microorganisms which were inhibited by autoclaving, and followed a Michaelis-Menten kinetic with a half saturation constant (Km) of about 20–45 ppmv and a maximum oxidation rate (Vmax) of about 0.6–3.6 nmol CH4 h−1g−1 dry weight soil. The determined Km values were much smaller than those known from previous experiments with soil or methanotrophic bacteria. Extrapolation of the linear part of the Michaelis-Menten kinetic (range of first- order kinetics) to zero CH4 oxidation usually resulted in threshold mixing ratios (Tha) of about 0.2–0.3 ppmv CH4, i.e. lower than the atmospheric mixing ratio. CH4 was oxidized even below these threshold mixing ratios, but at a rate that was much lower than expected from the first-order rate constant of CH4 oxidation. These results show that oxidation of atmospheric CH4 in soil is not a simple first-order reaction emphasizing careful interpretation of kinetic data with respect to field conditions.

Activity and community structure of methane-oxidising bacteria in a wet meadow soil

The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137-300 nM CH(4), a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (10(5)-10(7) cells g(-1) d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses.

Mechanisms Controlling Methane Emission from Wetland Rice Fields

Wetland rice fields are an important source in the global budget of atmospheric CH4 and, thus, have a significant impact on climate and on atmospheric photochemistry. Methane emission rates from rice fields vary greatly with field site, management, time of day, and season. Field and laboratory studies of CH4 turnover in paddy soil are reviewed with respect to the mechanisms that control the emission of CH4 into the atmosphere, i.e., CH4 production, CH4 diffusion, CH4 oxidation, and interaction of CH4 turnover with nutrients such as nitrogen, iron, and sulfur compounds. Methane production involves a complex anaerobic microbial community that degrades organic matter via various intermediates to CO2 and CH4. The rice aerenchyma allows the diffusion of O2 into the rhizosphere and, thus, provides oxic microsites within the anoxic submerged soil. This allows the oxidation of CH4 and makes the involvement of other aerobic bacteria in the turnover of CH4 possible. The rice aerenchyma also provides the predominant route for escape of CH4 from the soil into the atmosphere and may tap bubbles that constitute CH4 reservoirs in the submerged soil.

Methane and hydrogen in seawater (Atlantic Ocean)

Abstract Measurements of dissolved methane and hydrogen from the Atlantic Ocean, between 50°N and 35°S, showed the surface water to be supersaturated, while the deep ocean water was in equilibrium or slightly undersaturated with respect to atmospheric CH4 and H2. Dissolved H2 was highest in surface water and decreased within the upper 100 m of the water column, whereas dissolved CH4 remained high within the entire euphotic water layer. There is evience for a diurnal variation of dissolved H2, with higher amplitudes at the water surface compared to 20m depth. Dissolved CH4 at 4 m depth also was measured using a continuously working equilibration technique which procided information on short-term fluctuations. The dissolved CH4 showed no diurnal variations and was independent of wind speed. Highest CH4 concentrations were observed in areas with high nutrient input, e.g. in the upwelling areas off West Africa, and correlated well with the observed chorophyll a concentrations. Based on an average CH4 saturation factor of about 1.1, the total source strength for atmospheric CH4 is calculated to about 1.5 Tg y−1.

Diversity of methanotrophic bacteria in tropical upland soils under different land uses

ABSTRACT Three upland soils from Thailand, a natural forest, a 16-year-old reforested site, and an agricultural field, were studied with regard to methane uptake and the community composition of methanotrophic bacteria (MB). The methane uptake rates were similar to rates described previously for forest and farmland soils of the temperate zone. The rates were lower at the agricultural site than at the native forest and reforested sites. The sites also differed in the MB community composition, which was characterized by denaturing gradient gel electrophoresis (DGGE) of pmoA gene fragments (coding for a subunit of particulate methane monooxygenase) that were PCR amplified from total soil DNA extracts. Cluster analysis based on the DGGE banding patterns indicated that the MB communities at the forested and reforested sites were similar to each other but different from that at the farmland site. Sequence analysis of excised DGGE bands indicated that Methylobacter spp. and Methylocystis spp. were present. Sequences of the “forest soil cluster” or “upland soil cluster α,” which is postulated to represent organisms involved in atmospheric methane consumption in diverse soils, were detected only in samples from the native forest and reforested sites. Additional sequences that may represent uncultivated groups of MB in the Gammaproteobacteria were also detected.

Measurement and Research Techniques

The geographical distribution and increasing trend of trace gas concentrations in the global atmosphere are determined by a complex interplay of the geographical distribution of natural and human sources, biogeochemical and ecosystem dynamics, human agricultural and industrial practices, and atmospheric chemistry and dynamics. For an understanding of the global methane cycle, it is necessary to develop and apply methods that are suitable for measuring methane and its isotopes and that can be used for research on the many facets of the budget of atmospheric methane.

Mikrobielle Methanproduktion: Treibhausgas aus Archaeen

ZusammenfassungDie wichtigsten Quellen für Methan, ein Treibhausgas in der Atmosphäre, sind der Pansen von Wiederkäuern, geflutete Reisfelder und Feuchtgebiete. Methan wird dort beim anaeroben Abbau von organischem Material auf unterschiedlichen Wegen und durch verschiedene methanogene Archaeen gebildet.AbstractThe most important sources of the atmospheric greenhouse gas methane are ruminants, flooded rice fields, and wetlands. At these sites methane is produced by anaerobic degradation of organic matter involving different pathways and methanogenic archaea.