In the present study, bacterial communities in 200-liter biogas reactors containing liquid manure consecutively fed with casein, starch, and cream were investigated over a period of up to 33 days. A 16S rRNA gene clone library identifiedBacteroidetesandFirmicutesas the most abundant bacterial groups in the starting material, at 58.9% and 30.1% of sequences, respectively. The community development of both groups was monitored by real-time PCR and single-strand conformation polymorphism (SSCP) analysis. TheFirmicutesandBacteroidetescommunities were unexpectedly stable and hardly influenced by batch-feeding events. The continuous feeding of starch led to community shifts that nevertheless contributed to a stable reactor performance. A longer starving period and a change in the pH value resulted in further community shifts within theBacteroidetesbut did not influence theFirmicutes. Predominant DNA bands from SSCP gels were cloned and sequenced. Sequences related toPeptococcaceae,Cytophagales, andPetrimonas sulfuriphilawere found in all samples from all experiments. Real-time PCR demonstrated the abundance of members of the phylumBacteroidetesand also reflected changes in gene copy numbers in conjunction with a changing pH value and acetate accumulation.

Forest and other upland soils are important sinks for atmospheric CH₄, consuming 20 to 60 Tg of CH₄per year. Consumption of atmospheric CH₄by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH₄oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting thepmoAgene, coding for the α 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 CH₄in situ and in vitro at all times. In winter, atmospheric CH₄was 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 μg 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 ofpmoAchanged with depth and season.pmoAwas detected only in soil layers with active CH₄oxidation, 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 CH₄consumption rates also exhibited more bands ofpmoAin DGGE, indicating that high CH₄oxidation activity was positively correlated with the number of methanotrophic populations present. ThepmoAsequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH₄consumption.