A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum , six were closely related but not identical to those of strains of Methanosaeta concilii , two grouped with members of the genus Methanosarcina , and two were related to the methanogenic endosymbiont of Plagiopyla nasuta . The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10 ⁷ per g of dry soil for the H ₂ -CO ₂ -utilizing methanogens and of up to 10 ⁶ for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H ₂ -CO ₂ , grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium -like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta -like group and the Methanobacterium -like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 μM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.

Summary: Cultivation‐independent techniques were applied to assess the succession and phylogenetic composition of bacterial communities in a vertical oxygen gradient in flooded, unplanted paddy soil microcosms. Microsensor measurements showed that within 6 h of flooding, oxygen was depleted from 200 µM at the floodwater‐soil interface to undetectable amounts at a depth of approximately 2 mm and below. The gradient was quite stable over time, although the oxygen depletion was less pronounced 84 days than 6 h after flooding. Community fingerprint patterns were obtained by terminal restriction fragment length polymorphism (T‐RFLP) analysis from the oxic, transition, and anoxic zones of triplicate soil microcosms at 0, 1 and 6 h, and 1, 2, 7, 21, 30, 42, 84, and 168 days after flooding. Correspondence analyses revealed that T‐RFLP patterns obtained using either community DNA or RNA were affected by time and oxygen zone, and that there was a significant interaction between the effects of time and oxygen zone. The temporal dynamics of bacterial populations were resolved more clearly using RNA than using DNA. At the RNA level, successional community dynamics were most pronounced from 1 h to 2 days and less pronounced from 2 to 21 days after flooding, for both oxic and anoxic zones. No effect of time or oxygen zone on the community dynamics was observed from 21 to 168 days after flooding. Dominant early successional populations were identified by cloning and comparative sequence analysis of environmental 16S rRNA and 16S rRNA genes as members of the Betaproteobacteria (oxic zone) and the clostridial cluster I (anoxic zone). Dominant late successional populations belonged to the Verrucomicrobia and Nitrospira (detected mainly in the oxic zone), and to the Myxococcales (detected mainly in the anoxic zone). In conclusion, the bacterial community developed through successional stages, leading at the RNA level to almost stable community patterns within 21 days after flooding. This principal finding, in combination with the phylogenetic identity of early‐ and late‐appearing populations, suggests that the community dynamics can be explained by the principles of r‐ and K‐selection.

A molecular ecological study was performed on an Australian soil sample to unravel a substantial portion of the bacterial diversity. A large fragment of the 16S rRNA gene was amplified, using DNA isolated by lysing the microorganisms directly within the soil matrix, and a clone library was generated. Comparative sequence analysis of 30 clones and dot blot hybridization of 83 additional clones with defined oligonucleotide probes revealed the presence of three major groups of prokaryotes of the domain Bacteria. The first one comprises 57 clones that indicate relatives of nitrogen-fixing bacteria of the alpha-2 subclass of the class Proteobacteria; the second group of 7 clones originates from members of the order Planctomycetales that, however, reveal no close relationship to any of the described Planctomycetales species; 22 clones of the third group are indicative of members of a novel main line of descent, sharing a common ancestry with members of planctomycetes and chlamydiae.

The Bacteria community composition in an acidic Sphagnum peat bog (pH 3.9 to 4.5) was characterized by a combination of 16S rRNA gene clone library analysis, rRNA-targeted fluorescence in situ hybridization (FISH), and cultivation. Among 84 environmental 16S rRNA gene clones, a set of only 16 cloned sequences was closely related (≥95% similarity) to taxonomically described organisms. Main groups of clones were affiliated with the Acidobacteria (24 clones), Alphaproteobacteria (20), Verrucomicrobia (13), Actinobacteria (8), Deltaproteobacteria (4), Chloroflexi (3), and Planctomycetes (3). The proportion of cells that hybridized with oligonucleotide probes specific for members of the domains Bacteria (EUB338-mix) and Archaea (ARCH915 and ARC344) accounted for only 12 to 22% of the total cell counts. Up to 24% of the EUB338-positive cells could be assigned by FISH to specific bacterial phyla. Alphaproteobacteria and Planctomycetes were the most numerous bacterial groups (up to 1.3 × 10 ⁷ and 1.1 × 10 ⁷ cells g ⁻¹ peat, respectively). In contrast to conventional plating techniques, a novel biofilm-mediated enrichment approach allowed us to isolate some representatives of predominant Bacteria groups, such as Acidobacteria and Planctomycetes . This novel strategy has great potential to enable the isolation of a significant proportion of the peat bog bacterial diversity.