16S rRNA gene analyses of bacterial community structures in the soils of evergreen broad-leaved forests in south-west China.

Bacterial community structure was studied in humus and mineral soils of evergreen broad-leaved forests in Ailaoshan and Xishuangbanna, representing subtropical and tropical ecosystems, respectively, in south-west China using sequence analysis and terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes. Clone sequences affiliated to Acidobacteria were retrieved as the predominant bacterial phylum in both forest soils, followed by those affiliated to members of the Proteobacteria, Planctomycete and Verrucomicrobia. Despite higher floristic richness at the Xishuangbanna forest than at the Ailaoshan forest, soil at Xishuangbanna harbored a distinctly high relative abundance of Acidobacteria-affiliated sequences (80% of the total clones), which led to a lower overall bacterial diversity than at Ailaoshan. Bacterial communities in humus and mineral soils of the two forests appeared to be well differentiated, based on 16S rRNA gene phylogeny, and correlations were found between the bacterial T-RFLP community patterns and the organic carbon and nutrient contents of the soil samples. The data reveal that Acidobacteria dominate soil bacterial communities in the evergreen broad-leaved forests studied here and suggest that bacterial diversity may be influenced by soil carbon and nutrient levels, but is not related to floristic richness along the climatic gradient from subtropical to tropical forests in south-west China.

Vertical distribution of structure and function of the methanogenic archaeal community in Lake Dagow sediment.

Detailed studies on the relation of structure and function of microbial communities in a sediment depth profile scarcely exist. We determined as functional aspect the vertical distribution of the acetotrophic and hydrogenotrophic CH4 production activity by measuring production rates and stable 13C/12C-isotopic signatures of CH4 in the profundal sediment of Lake Dagow. The structural aspect was determined by the composition of the methanogenic community by quantifying the abundance of different archaeal groups using 'real-time' polymerase chain reaction and analysis of terminal restriction fragment length polymorphism (T-RFLP). Methane production rates in the surface sediment (0-3 cm depth) were higher in August than in May, but strongly decreased with depth (down to 20 cm). The delta13C of the produced CH4 and CO2 indicated an increase in isotopic fractionation with sediment depth. The relative contribution of hydrogenotrophic to total methanogenesis, which was calculated from the isotopic signatures, increased with depth from about 22% to 38%. Total numbers of microorganisms were higher in August than in May, but strongly decreased with depth. The increase of microorganisms from May to August mainly resulted from Bacteria. The Archaea, on the other hand, exhibited a rather constant abundance, but also decreased with depth from about 1 x 10(8) copies of the archaeal 16S rRNA gene per gram of dry sediment at the surface to 4 x 10(7) copies per gram at 15-20 cm depth. T-RFLP analysis combined with phylogenetic analysis of cloned sequences of the archaeal 16S rRNA genes showed that the methanogenic community consisted mainly of Methanomicrobiales and Methanosaetaceae. The relative abundance of Methanosaetaceae decreased with depth, whereas that of Methanomicrobiales slightly increased. Hence, the vertical distribution of the functional characteristics (CH4 production from acetate versus H2/CO2) was reflected in the structure of the community consisting of acetotrophic (Methanosaetaceae) versus hydrogenotrophic (Methanomicrobiales) phenotypes.

Microbial community dynamics during start-up of acidogenic anaerobic reactors.

Start-up of two acidogenic reactors under mesophilic (37 degrees C) and thermophilic (55 degrees C) conditions was carried out with methanogenic granular sludge as an inoculum and dairy wastewater as feed. During these 71 days of the start-up period, microbial community dynamics in these two acidogenic reactors, as monitored by denaturing gradient gel electrophoresis (DGGE) and dot-blot hybridization with group-specific oligonucleotide probes, was correlated to reactor performance. Due to pH drop to 5.5, DGGE community fingerprints for domains Bacteria and Archaea populations showed significant shifts after 13 days of operation, and this change was accompanied with an increase in volatile fatty acid production, a decrease in methane formation, and rapid sludge disintegration. Dot-blot hybridization results further indicated that the decrease in methane production was related to the decrease in Archaea population in particular with methanogens from 34.1% of total 16S-rRNA in the seed sludge to 8% within the first 13 days, and to 2-5% at day 71. Among the methanogens monitored, the class Methanomicrobiales was the most abundant followed up by Methanobacteriales and Methanococcales. Due to an elevated temperature, the microbial community change was more significant and rapid in the thermophilic reactor than in the mesophilic reactor. Significant microbial population changes took place at the first 13 days for both reactors, but a longer period up to 71 days was required to establish a microbial community with a stable metabolic activity.

Characterization of microbial community in granular sludge treating brewery wastewater.

The diversity and distribution of microbes within brewery-degrading anaerobic sludge granules were studied using various molecular techniques. Molecular cloning of small-subunit rRNA gene sequences indicated that all archaeal clones were affiliated with Methanosaeta concillii (>99% sequence similarity), and the bacterial clones were mostly affiliated with a not-yet-cultured Clostridium cluster (48 out of 99 clones) in the low G + C gram-positive group, Xanthomonas spp. in the gamma-subclass of Proteobacteria (30 clones), and Desulfovibrio spp. (16 clones) in the delta-subclass of Proteobacteria. Slot-blot hybridization indicated that archaeal cells from the Methanomicrobiales (58.4% of total rRNA), Methanobacterials (3.3%) and Methanococcales (1.0%) accounted for 62.4% of the total community rRNA. The rest of the microbial populations were the clostridial cluster (27.3% of total rRNA) and Desulfovibrio spp. (9.4%). Fluorescence in-situ hybridization with domain and group-specific oligonucleotide probes further revealed a multi-layer granular architecture. On the surface layer, the hydrolytic clostridial species and hydrogenotrophic Methanobacteriales were the predominant. In the middle layer, mostly H2-producing acetogens from the delta-Proteobacteria (i.e., Desulfovibrio spp.), hydrogenotrophic Methanobacteriales and aceticlastic Methanosaeta were observed to presumably form a syntrophic association. Finally, the center core consisted of microcolonies of Methanosaeta cells.

Methanogenic archaeal community in the sediment of an artificially partitioned acidic bog lake.

Abstract The methanogenic archaeal communities in the sediment of two basins of an artificially partitioned acidic bog lake were studied. In the northeast basin, which was separated from a peat bog, a high methane production rate was measured only in the upper layers of the sediment. In contrast, methane production was detected at various depths of the sediment in the southwest basin, which continuously receiving humic acids from the bog. Ten bands were observed in the denaturing gradient gel electrophoresis (DGGE) fingerprint of the 16S rDNA archaeal amplicons from the NE basin top (0-5 cm) sediment layer, which reflected the presence of at least 10 ribotypes. Seventy clones of the 16S rDNA amplicons were obtained from the NE basin top sediment layer, and were grouped into 10 operational taxonomy units (OTUs) according to their positions on the DGGE gel. Seven of these OTUs could be matched with the bands of the community fingerprint. Phylogenetic analyses indicated that the sequences clustered into three groups: five of the OTUs were related to Methanosaeta, four OTUs to Methanomicrobiales and one OTU to Methanobacterium. Among the OTUs, sequences with high similarities (>96%) were retrieved. The sequence data suggested that the diversity of the methanogenic archaeal community was limited. Bands corresponding to those three phylogenetic groups were found in the DGGE fingerprints of both NE and SW basins, which reflected the presence of the same dominant methanogenic archaeal groups in both basins. However, differences in the distribution of the ribotypes that had high 16S rRNA sequence identities were observed in the fingerprints between the two basins at various depths. The microdiversity decreased along the sediment depth in the NE basin, and vice versa in the SW basin. The greater variety of the archaeal ribotypes, apparently, correlated with the higher methanogenesis rate.