Archaeal 16S rDNA Research Articles

Exploration and application of microbial method to enhance the effect of hydraulic fracturing on coal seam permeability enhancement and gas extraction

The efficient extraction of gas from low-permeability coal seams is an urgent problem in coal mine safety production. The traditional gas extraction technology generally suffers from problems that limited penetration enhancement or extraction effect, low construction efficiency, large workload, etc. Thus, it is especially urgent and important to explore the new technology applicable to efficient underground gas extraction. In this paper, based on the principle of hydraulic fracturing to increase permeability, we innovatively propose a technique to enhance the effect of hydraulic fracturing to increase permeability and further improve the efficiency of gas extraction using the gas desorption activity of native microorganisms in coal seams. Herein, the composition of the primary microbial community of a coal seam in Xinji No.2 mine was analyzed by bacterial and archaeal 16SrDNA amplicon sequencing, the community structure of the main functional microorganisms was clarified, the optimal combination of functional microorganisms for organic matter degradation in coal seam under anaerobic culture conditions was obtained. Besides the Biolog microplate technology was used to screen the nutrients of the excitation carbon source to stimulate the rapid decomposition of coal organic matter by microorganisms and to define the optimal ratio of the excitation carbon source to microorganisms. Finally, the effect of this technology on the application of coal seam fracturing and gas extraction was tested through field industrial tests, revealing that the extraction effect of this technology was more significant than that of the common coal seam perforation extraction technology. The results of this paper provide a new technical idea for gas extraction from low permeability coal seams, which is an important reference value for subsequent similar studies.

A Single Application of Compost Can Leave Lasting Impacts on Soil Microbial Community Structure and Alter Cross-Domain Interaction Networks

Our current understanding suggests that nutrient management strategies applied to agricultural soils over multiple years are required to cause major and stable shifts in soil microbial communities. However, some studies suggest that agricultural soils can benefit even from sporadic, single additions of organic matter. Here we investigate how single additions of high-quality organic matter can cause significant shifts in microbial soil communities over multiple cropping cycles. We grew radishes in a tropical Oxisol soil for six crop cycles after a single application of a high-nitrogen compost or urea. At planting and before biomass harvest, we sampled soils influenced by the radish rhizosphere and sequenced bacterial and archaeal 16S and fungal ITS rDNA marker genes. We measured microbial richness and diversity, community composition and structure, and constructed correlation networks to predict cross-domain microbial interactions. We found that a single application of compost, compared to urea or control, resulted in a persistent improved plant biomass response and led to sustained changes in the soil microbial community throughout the duration of the 227-day study. Compost altered the structure of both the fungal and prokaryotic microbial communities, introduced new microorganisms that persisted in the resident soil system, and altered soil microbial correlation network structure and hub taxa. In contrast, fertilization with urea did not significantly alter the structure of soil microbial communities compared to the control but reduced network complexity and altered hub taxa. This study highlights the significant impacts that high-quality organic matter fertilization can exert on agricultural soil microbiomes and adds to the growing body of knowledge on using organic fertilizers as a way to steer the soil microbiome toward a healthier soil.

Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment.

There is a growing interest in plant microbiome’s engineering to optimize desired functions such as improved phytoremediation. This study is aimed at examining the microbial communities inhabiting the roots and rhizospheres of two Salix miyabeana cultivars that had been grown in a short-rotation intensive culture (SRIC) system for six years in a soil contaminated with the discharge from a petrochemical factory. DNA was extracted from roots and rhizospheric soils, and fungal ITS and bacterial and archaeal 16S rDNA regions were amplified and sequenced using Illumina MiSeq technology. Cultivars ‘SX61’ and ‘SX64’ were found to harbor a similar diversity of fungal, bacterial, and archaeal amplicon sequence variants (ASVs). As expected, a greater microbial diversity was found in the rhizosphere biotope than in the roots of both cultivars, except for cultivar ‘SX64’, where a similar fungal diversity was observed in both biotopes. However, we found that microbial community structures were cultivar- and biotope-specific. Although the implication of some identified taxa for plant adaptability and biomass production capacity remains to be explored, this study provides valuable and useful information regarding microbes that could potentially favor the implantation and phytoremediation efficiency of Salix miyabeana in mixed contamination sites in similar climatic environments.

Characterization of the archaeal and fungal diversity associated with gypsum efflorescences on the walls of the decorated Sorcerer’s prehistoric cave

This study focuses on analysis of the archaeal and fungal diversity associated with gypsum efflorescences damaging the walls of the Sorcerer’s prehistoric cave registered as a world cultural heritage site. Archaeal 16S rDNA and fungal internal transcribed spacer (ITS) clone libraries were constructed and analysed. Two thaumarchaeotal OTUs belonging to the Nitrososphaeraceae family dominated the archaeal community (100% of clones). Nitrososphaeraceae are obligate aerobic, chemolithoautotrophic organisms that derive their energy from the oxidation of ammonia and may contribute to primary productivity in the cave. Seven fungal OTUs belonging to Ascomycota and one belonging to Basidiomycota were present. The Cordycipitaceae family, mainly represented by entomophilous fungi, dominated the analysis (66.7% of clones). We show that archaeal and fungal OTUs are associated with gypsum efflorescences damaging the walls of the Sorcerer’s cave. The role of these microorganisms in the deterioration of the walls of the cave remains to be determined.

Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment.

This study describes, for the first time, the water chemistry and microbial diversity in Dziani Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6–14.5 g L-1 eq. CO32-, i.e. 160–220 mM compare to around 2–2.5 in seawater), with salinity up to 52 psu, 1.5 higher than seawater. Hierarchical clustering discriminated Dziani Dzaha water from other alkaline, saline lakes, highlighting its thalassohaline nature. The phytoplankton biomass was very high, with a total chlorophyll a concentration of 524 to 875 μg chl a L-1 depending on the survey, homogeneously distributed from surface to bottom (4 m). Throughout the whole water column the photosynthetic biomass was dominated (>97% of total biovolume) by the filamentous cyanobacteria Arthrospira sp. with a straight morphotype. In situ daily photosynthetic oxygen production ranged from 17.3 to 22.2 g O2 m-2 d-1, consistent with experimental production / irradiance measurements and modeling. Heterotrophic bacterioplankton was extremely abundant, with cell densities up to 1.5 108 cells mL-1 in the whole water column. Isolation and culture of 59 Eubacteria strains revealed the prevalence of alkaliphilic and halophilic organisms together with taxa unknown to date, based on 16S rRNA gene analysis. A single cloning-sequencing approach using archaeal 16S rDNA gene primers unveiled the presence of diverse extremophilic Euryarchaeota. The water chemistry of Dziani Dzaha Lake supports the hypothesis that it was derived from seawater and strongly modified by geological conditions and microbial activities that increased the alkalinity. Dziani Dzaha has a unique consortium of cyanobacteria, phytoplankton, heterotrophic Eubacteria and Archaea, with very few unicellular protozoa, that will deserve further deep analysis to unravel its uncommon diversity. A single taxon, belonging to the genus Arthrospira, was found responsible for almost all photosynthetic primary production.

Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane.

Hydrogenotrophic methanogens can use gaseous substrates, such as H2 and CO2, in CH4 production. H2 gas is used to reduce CO2. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH4 production from CO2 and H2. CO2 and H2 were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5–5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH4 production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp., restricted the development of acetoclastic methanogens in the acidic CH4 production process. The results show that acidic operation of a CH4 production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens.

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage.

We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity) under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.

Eubacterial and archaeal community characteristics in the man-made pit mud revealed by combined PCR-DGGE and FISH analyses

The aim of this study was to investigate the shift of eubacterial and archaeal communities in various man-made pit muds (PMs) with different pit ages (the use time of cellar) by combining denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) approaches. Analysis of the diversity index calculated from the eubacterial and archaeal DGGE profiles showed that the 4-year-PMs exhibited higher Shannon–Wiener index than that in other man-made PMs. Results of eubacterial DGGE pattern of the 16S rDNA gene fragment analysis illustrated that nine families including Leuconostocaceae, Clostridiaceae, Lactobacillaceae, Moraxellaceae, Enterococcaceae, Lachnospiraceae, Comamonadaceae, Sphingomonadaceae and Ruminococcaceae were identified, and Clostridiaceae was the dominant, accounting for 46.2%. Specially, Ruminococcaceae was only found in 4-year-PMs. Also, archaeal 16S rDNA gene fragment identification demonstrated that Methanobrevibacter, Methanobacterium and Methanoculleus were the majority of archaea. Validation of the result was performed by FISH experiment, and FISH analysis showed that the number of live eubacteria and archaea in the man-made PMs increased with pit age. The proportions of Methanobacteriales and Methanomicrobiales were decreased from 45.1% and 54.9% to 22.7% and 27.9%, respectively, after the cellars were used for 2years continuously. However, no significant change was observed in 3- and 4-year-PMs. Knowledge of the eubacterial and archaeal communities studied in the man-made PMs is essential to exploit the metabolic regulation during fermentation process and consequently develop appropriate strategies for liquor quality improvement.

Active Methanotrophs in Two Contrasting North American Peatland Ecosystems Revealed Using DNA-SIP

The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phylogenetic diversity of organisms that had assimilated (13)C, including methanotrophs from both the Alpha- and Gammaproteobacteria classes and other potentially non-methanotrophic organisms that were similar to bacteria detected in a UK and Finnish fen. Based on similarities between bacteria in our sites and those in Europe, including Russia, we conclude that site physicochemical characteristics rather than biogeography controlled the phylogenetic diversity of active methanotrophs and that differences in phylogenetic diversity between the bog and fen did not relate to measured CH(4) oxidation rates. A single crenarchaeon in the bog site appeared to be assimilating (13)C in 16S rDNA; however, its phylogenetic similarity to other CO(2)-utilizing archaea probably indicates that this organism is not directly involved in CH(4) oxidation in peat.

Assimilation of glucose-derived carbon into methanogenic archaea in soil under unflooded condition

Ecology of methanogenic archaea, one of the obligate anaerobes, in soil under unflooded condition has not been well documented. To elucidate whether methanogenic archaea assimilate carbon derived from easily decomposable organic matters in soil even under unflooded condition, we analyzed bacterial and methanogenic archaeal communities in a soil incubated with 0.5% 12C- and 13C-glucose under upland condition (60% of maximum water holding capacity) by DNA-stable isotope probing (DNA-SIP) and denaturing gradient gel electrophoresis (DGGE). The added glucose was rapidly decomposed within 7days of the incubation and the bacterial community immediately responded to the added glucose. Clone analysis of the 13C-enriched bacterial 16S rRNA genes (16S rDNA) on the days 2 and 7 showed that not only aerobic and facultative anaerobic bacteria closely related to Bacillus spp., Ammoniphilus spp. (or Oxalophagus spp.), Paenibacillus spp. and Azotobacter spp. but also obligate anaerobes such as Clostridium spp. and Anaerobacter spp. assimilated glucose-derived carbon. By contrast, DGGE band patterns of methanogenic archaeal 16S rDNA obtained from the incubated soil did not change during the incubation period. However, when DGGE band patterns were compared between the 12C- and 13C-glucose treatments after fractionation by isopycnic centrifugation, some DGGE bands were observed from the heavy DNA fractions in the 13C-glucose treatment on the days 7 and 14. The sequences of these DGGE bands were closely related to Methanocella spp., Methanosaeta spp., Methanosarcina spp., the ZC-I group in Methanosarcinales and Methanobacterium spp. The present study showed that a part of glucose-derived C flows to methanogenic archaea in the soil during the glucose decomposition even under unflooded condition.

Diversity of Achaea Communities in Deep Sea Sediments from the Sulu Sea

To study the archaeal diversity of deep-sea sediments in the tropical Western Pacific,we investigated the archaeal community structure in six sediments subsamples along the MD3059 sediment core collected during the IMAGES ⅪⅤ cruise with 16S rDNA analysis. A total of 543 archaeal 16S rDNA clones were examined and a total of 137 OTUs were obtained. Phylogenetic results showed that the archaeal diversity in the collected samples was very diverse,and the obtained OTUs were grouped into Crenarchaeota and Euryarchaeota,with the former dominated by Miscellaneous Crenarchaeotic Group ( MCG,54% of total archaeal clones) and the latter dominated by Marine Benthic Group D ( MBG-D) ,South African Gold Mine Euryarchaeotic Group ( SAGMEG) and Marine Benthic Group B ( MBG-B). These data have important implications for our understanding of archaeal community in deep-sea sediments of the tropical Western Pacific.

Microbial community distribution in sediments from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

We studied the microbial communities collected from hydrate-bearing sediments on the North Slope of Alaska to determine how abiotic variables (e.g., grain size, hydrate presence, formation fluid gases) may correspond to the type and distribution of microbes in the sediments. The cores were acquired from sub-permafrost, Eocene (46–55 million year old) sediments in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well within which hydrates are believed to have formed 1.5 mya. Forty samples, eight of which originally contained hydrates, were acquired from depths of ca. 606–666 m below land surface. Five drilling fluid samples acquired from the same depth range were included in the analysis as a control for possible contamination by drilling fluid microbes during the drilling and handling of cores. DNA was extracted from 15 samples (typically <1 ng DNA/g sediment was recovered) and then amplified using polymerase chain reaction with primers specific for bacterial and archaeal 16S rDNA genes, which indicates the likelihood that microbes were present in all analyzed samples. Only bacterial DNA amplicons were detected. Terminal-restriction fragment length polymorphism (T-RFLP) was used to measure bacterial diversity in the respective samples. Non-metric multidimensional scaling (NMS) was used to determine the abiotic variables that may have influenced bacterial diversity. NMS analysis revealed that the microbial taxa present in the sediment were distinct from the taxa present in the drilling fluids suggesting that the sediments were not contaminated by the drilling fluids. Multi-response permutation procedures (MRPP) found no significant difference between three sample groups identified a priori as being from within a hydrate zone, outside of hydrate zone, or on the edge of a hydrate/non-hydrate zone according to downhole nuclear magnetic resonance spectroscopy logs. However, among the several other abiotic parameters that were evaluated mud gas methane concentration and variables related to hydrate presence (e.g., chloride concentration, salinity, and resistivity) appeared to define the arrangement of microbial community signatures in plots resulting from NMS analysis. Communities from hydrate and non-hydrate layers each contained unique taxa as determined by the T-RFLP assay.

Diversity and Community Structure of Archaea in Deep Subsurface Sediments from the Tropical Western Pacific

Archaeal 16S rRNA gene clone libraries using PCR amplicons from eight different layers of the MD06-3051 core were obtained from the tropical Western Pacific sediments. A total of 768 clones were randomly selected, and 264 representative clones were sequenced by restriction fragment length polymorphism. Finally, 719 valid clones and 104 operational taxonomic units were identified after chimera-check and > or =97% similarity analysis. The phylogenetic analysis of 16S rDNA sequences obtained from sediment samples were very diverse and showed stratification with depth. Majority of the members were most closely related to uncultivated groups and physiologically uncharacterized assemblages. All phylotypes were affiliated with Crenarchaeota (76%) and Euryarchaeota (24%), respectively. Deep-sea archaeal group (DSAG, 41% of total clones) and miscellaneous crenarchaeotic group (MCG, 29% of total clones) belonging to Crenarchaeota were the most predominant archaeal 16S rDNA phylotypes in clone libraries. Phylotypes in this study shared high similarity with those in subsurface sediments from Peru Margin sites, which indicated that different geographical zones might host similar members of archaeal populations based on similar sedimentary environments. In our study, members of DSAG and MCG seemed to dominate certain layers of the nonhydrate sediments, suggesting a wide ecophysiological adaptation than previously appreciated. The spatial distribution and community structure of these groups might vary with the different geochemical gradients of the environment.

Long-chain fatty acids inhibition and adaptation process in anaerobic thermophilic digestion: Batch tests, microbial community structure and mathematical modelling

Biomass samples taken during the continuous operation of thermophilic anaerobic digestors fed with manure and exposed to successive inhibitory pulses of long-chain fatty acids (LCFA) were characterized in terms of specific metabolic activities and 16S rDNA DGGE profiling of the microbial community structure. Improvement of hydrogenotrophic and acidogenic (β-oxidation) activity rates was detected upon successive LCFA pulses, while different inhibition effects over specific anaerobic trophic groups were observed. Bioreactor recovery capacity and biomass adaptation to LCFA inhibition were verified. Population profiles of eubacterial and archaeal 16S rDNA genes revealed that no significant shift on microbial community composition took place upon biomass exposure to LCFA. DNA sequencing of predominant DGGE bands showed close phylogenetic affinity to ribotypes characteristic from specific β-oxidation bacterial genera ( Syntrophomonas and Clostridium), while a single predominant syntrophic archaeae was related with the genus Methanosarcina. The hypothesis that biomass adaptation was fundamentally of physiological nature was tested using mathematical modelling, taking the IWA ADM1 as general model. New kinetics considering the relation between LCFA inhibitory substrate concentration and specific biomass content, as an approximation to the adsorption process, improved the model fitting and provided a better insight on the physical nature of the LCFA inhibition process.

Evaluation of extraction and purification methods for obtaining PCR-amplifiable DNA from aged refuse for microbial community analysis

In order to develop and establish a method for isolation of PCR-amplifiable DNA from aged refuse, the orthogonal experiment was conducted to evaluate systematically the effects of various steps within each method in terms of DNA yield, purity, fragment size, humus contamination, PCR amplifiability using universal eubacterial and archaeal 16S rDNA prime pairs, and genetic diversity estimate from denaturing gradient gel electrophoresis. The inclusion of the pretreatment step was demonstrated to be crucial for the recovery of high-quality DNA preparations from the aged refuse and the pre-washing with TENP-PBS buffer was recommended. Satisfactory DNA yields and unbiased DNA extraction required the introduction of lysis by bead-beating treatment. The modified Sephadex G-200 spin column was effective in obtaining relatively stable DNA preparations from the aged refuse. It was established that a combination of pre-washes with TENP-PBS buffer plus gentle bead lysis and proteinase K treatment followed by SDS-based extraction and subsequent modified Sephadex G-200 spin column purification could ensure the acquisition of PCR-amplifiable DNA from the aged refuse expediently and cheaply.

Predominance of Methanolobus spp. and Methanoculleus spp. in the Archaeal Communities of Saline Gas Field Formation Fluids

The microbial communities in sulfate-rich, saline formation fluids of a natural gas reservoir in Lower Saxony, Germany were investigated to enhance the knowledge about microbial communities in potential carbon dioxide sequestration sites. This investigation of the initial state of the deep subsurface microbiota is necessary to predict their influence on the long-term stability and storage capacity of such sites. While the bacterial 16S rDNA gene library was comprised of sequences affiliating with the Firmicutes, the Alphaproteobacteria, the Gammaproteobacteria and the Thermotogales, the archaeal 16S rDNA libraries were simply dominated by two phylotypes related to the genera Methanolobus and Methanoculleus. The monitoring of the archaeal communities in different formation fluid samples by T-RFLP and Real-Time-PCR indicated that these two methanogenic genera dominated at all, whereas the proportion of the two groups varied. Thus, methylotrophic and autotrophic methanogenesis seems to be of importance in the reservoir fluids, dependent on the provided reduction equivalents and substrates and it also may influence the fate of CO2 in the subsurface.

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

The phylogenetic structure of the microbial community residing in a fermentation sample from a production-scale biogas plant fed with maize silage, green rye and liquid manure was analysed by an integrated approach using clone library sequences and metagenome sequence data obtained by 454-pyrosequencing. Sequencing of 109 clones from a bacterial and an archaeal 16S-rDNA amplicon library revealed that the obtained nucleotide sequences are similar but not identical to 16S-rDNA database sequences derived from different anaerobic environments including digestors and bioreactors. Most of the bacterial 16S-rDNA sequences could be assigned to the phylum Firmicutes with the most abundant class Clostridia and to the class Bacteroidetes, whereas most archaeal 16S-rDNA sequences cluster close to the methanogen Methanoculleus bourgensis. Further sequences of the archaeal library most probably represent so far non-characterised species within the genus Methanoculleus. A similar result derived from phylogenetic analysis of mcrA clone sequences. The mcrA gene product encodes the α-subunit of methyl-coenzyme-M reductase involved in the final step of methanogenesis. BLASTn analysis applying stringent settings resulted in assignment of 16S-rDNA metagenome sequence reads to 62 16S-rDNA amplicon sequences thus enabling frequency of abundance estimations for 16S-rDNA clone library sequences. Ribosomal Database Project (RDP) Classifier processing of metagenome 16S-rDNA reads revealed abundance of the phyla Firmicutes, Bacteroidetes and Euryarchaeota and the orders Clostridiales, Bacteroidales and Methanomicrobiales. Moreover, a large fraction of 16S-rDNA metagenome reads could not be assigned to lower taxonomic ranks, demonstrating that numerous microorganisms in the analysed fermentation sample of the biogas plant are still unclassified or unknown.

Microbial diversity in surface sediments of the Xisha Trough, the South China Sea

Microbial communities were obtained from the surface sediments of the Xisha Trough using the culture-independent technique. The characteristics of the 16S rDNA gene amplified from the sediments indicated that archaeal clones could be grouped into Euryarchaeota and Crenarchaeota, respectively. Two archaeal groups, Marine Crenarchaeotic Group I and Terrestrial Miscellaneous Euryarchaeotal Group, were the most dominant archaeal 16S rDNA gene components in the sediments. The remaining components were related to the members of Marine Benthic Group B, Marine Benthic Group A, Marine Benthic Group D, Novel Euryarchaeotic Group and C3. The bacterial clones exhibited greater diversity than the archaeal clones with the 16S rDNA gene sequences from the members of Proteobacteria, Planctomycetes, Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, candidate division OP8, Bacterioidetes/Chlorobi and Verrucomicrobia. Most of these lineages represented uncultured microorganisms. The result suggests that a vast amount of microbial resource in the surface sediments of the South China Sea has not been known.

Phylogenetic Diversity of the Archaeal Community in a Continental High-Temperature, Water-Flooded Petroleum Reservoir

The diversity of an archaeal community was analyzed in the water from a continental high-temperature, long-term water-flooded petroleum reservoir in Huabei Oilfield in China. The archaea were characterized by their 16S rRNA genes. An archaeal 16S rDNA clone library was constructed from the DNA isolated from the formation water, and 237 randomly selected positive clones were clustered in 28 phylotypes by sequencing analyses. Phylogenetic analysis of these sequences indicated that the dominant members of the archaeal phylotypes were affiliated with the order Methanomicrobiales. Totally, the archaeal community was composed of methanogens belonging to four orders: Methanobacteriales, Methanococcales, Methanomicrobiales, and Methanosarcinales. Most of the clones clustered with sequences previously described for methanogens, but there was a difference in the relative distribution of sequences detected here as compared to that of previous studies. Some thermophilic methanogens detected had been previously isolated from a number of high-temperature petroleum reservoirs worldwide; thus, they might exhibit adaptations to the environments and be the common habitants of geothermally heated subsurface environments.

Archaeal Communities in a Tropical Estuarine Ecosystem: Guanabara Bay, Brazil

Guanabara Bay is an eutrophic estuarine system located in a humid tropical region surrounded by the second largest metropolitan area of Brazil. This study explores the contrasting environmental chemistry and microbiological parameters that influence the archaeaplankton diversity in a pollution gradient in Guanabara Bay ecosystem. The environments sampled ranged from completely anoxic waters in a polluted inner channel to the adjacent, relatively pristine, coastal Atlantic Ocean. Partial archaeal 16S rDNA sequences in water samples were retrieved by polymerase chain reaction (PCR) and analyzed using denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Sequences were subjected to phylogenetic and diversity analyses. Community structure of the free-living archaeal assemblages was different from that of the particle-attached archaea according to DGGE. Gene libraries revealed that phylotype identification was consistent with environmental setting. Archaeal phylotypes found in polluted anoxic waters and in more pristine waters were closely related to organisms that have previously been found in these environments. However, inner bay archaea were related to organisms found in oil, industrial wastes, and sewage, implying that water pollution controls archaea communities in this system. The detection of a substantial number of uncultured phylotypes suggests that Guanabara Bay harbors a pool of novel archaeaplankton taxa.