Diversity and activity of methanotrophs in alkaline soil from a Chinese coal mine

Emerging Ecotone and Microbial Community of a Sulfidic Spring in the Reka River near Škocjanske Jame, Slovenia

During long periods with no precipitation, a sulfidic spring (Smrdljivec) appears in the dry bed of the Reka River before sinking into the karst underground. The study characterizes the area’s geological setting, development of microbial communities and an ecotone, and impact on the vulnerable karst ecosystem. Geological mapping of the area, stable isotopic analyses, field measurements, and physico-chemical and toxicity analyses were applied to elucidate the environmental conditions. The spring’s microbial diversity was assessed using cultivation methods, microscopy, and metagenomics. Sulfur compounds in the spring probably originate from coal layers in the vicinity. Metagenomic analyses revealed 175 distinct operational taxonomic units in spring water and biofilms. Proteobacteria predominated in developed biofilms, and a “core” microbiome was represented by methylotrophs, including Methylobacter, Methylomonas, and Methylotenera. Diatoms represented an important component of biofilm biomass. A combination of environmental factors and climatic conditions allows the formation and accessibility of emerging biodiversity hotspots and ecotones. Details of their dynamic nature, global impact, and distribution should be highlighted further and given more protection.

Methanotroph-microalgae co-culture for greenhouse gas mitigation: Effect of initial biomass ratio and methane concentration

This work evaluated the effect of different initial biomass ratios in a co-culture of an alkaliphilic methanotrophic bacteria consortium (AMB) and the green microalga Scenedesmus obtusiusculus (GM) on the maximum CH₄ specific biodegradation rate and global carbon uptake. The highest maximum specific biodegradation rate was 589 ± 0.01 mg_CH4 g_biomass^-1 d^-1 obtained for a proportion of 3:1 AMB-GM (w w^-1) and 8% of initial CH₄ in the headspace. The methane degradation rate was 1.5 times lower than the value obtained solely by the AMB consortium, and it was associated with pH increases due to the evolved CO₂ consumption by the microalga. Increased activity of the AMB consortium along the experiments was due to progressive adaptation. Massive sequencing revealed the presence of methanotrophic/methylotrophic species such as Methylocystis sp., Methylomicrobium sp., Methylophaga sp., and Hyphomicrobium sp. Successful complete methane and carbon dioxide uptake was obtained with the 3:1, 4:1, and 5:1 AMB-GM biomass ratios, while for the rest of the ratios tested, more than 70% of the initial methane was transformed into biomass and inorganic carbon. This study showed that methanotrophic-microalgal co-cultures lead to a promising strategy for greenhouse gases mitigation in one step.

Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review

Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.

Methanobactin from methanotrophs: genetics, structure, function and potential applications

Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps

BACKGROUND

Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites.

RESULTS

The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using ¹³C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only).

CONCLUSIONS

Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.

Effect of temperature on methane oxidation and community composition in landfill cover soil

Municipal solid waste (MSW) landfills are the third largest anthropogenic source of methane (CH₄) emissions in the United States. The majority of CH₄ generated in landfills is converted to carbon dioxide (CO₂) by CH₄-oxidizing bacteria (MOB) present in the landfill cover soil, whose activity is controlled by various environmental factors including temperature. As landfill temperature can fluctuate substantially seasonally, rates of CH₄ oxidation can also vary, and this could lead to incomplete oxidation. This study aims at analyzing the effect of temperature on CH₄ oxidation potential and microbial community structure of methanotrophs in laboratory-based studies of landfill cover soil and cultivated consortia. Soil and enrichment cultures were incubated at temperatures ranging from 6 to 70 °C, and rates of CH₄ oxidation were measured, and the microbial community structure was analyzed using 16S rRNA gene amplicon sequencing and shotgun metagenome sequencing. CH₄ oxidation occurred at temperatures from 6 to 50 °C in soil microcosm tests, and 6-40 °C in enrichment culture batch tests; maximum rates of oxidation were obtained at 30 °C. A corresponding shift in the soil microbiota was observed, with a transition from putative psychrophilic to thermophilic methanotrophs with increasing incubation temperature. A strong shift in methanotrophic community structure was observed above 30 °C. At temperatures up to 30 °C, methanotrophs from the genus Methylobacter were dominant in soils and enrichment cultures; at a temperature of 40 °C, putative thermophilic methanotrophs from the genus Methylocaldum become dominant. Maximum rate measurements of nearly 195 μg CH₄ g^-1 day^-1 were observed in soil incubations, while observed maximum rates in enrichments were significantly lower, likely as a result of diffusion limitations. This study demonstrates that temperature is a critical factor affecting rates of landfill soil CH₄ oxidation in vitro and that changing rates of CH₄ oxidation are in part driven by changes in methylotroph community structure.

A novel methanotrophic co-metabolic system with high soluble methane monooxygenase activity to biodegrade refractory organics in pulping wastewater

Pulping wastewater still contains massive refractory organics after biotreatment, with high colority, low biodegradability, and lasting biotoxicity. To eliminate refractory organics in pulping wastewater, a methanotrophic co-metabolic system in a gas cycle Sequencing Batch Biofilm Reactor (gcSBBR) seeded by soil at a ventilation opening of coal mine was quickly built on the 92nd day. The removal rate of COD, colority and TOC was 53.28%, 50.59% and 51.60%, respectively. Analysis of 3D-EEM indicated that glycolated protein-like, melanoidin-like or lignocellulose-like, and humic acid-like decreased by 7.85%, 5.02% and 1.74%, respectively. Moreover, this system exhibited high activity of soluble methane monooxygenase (sMMO) and mmoX encoding sMMO reached up to 7.89 × 10⁵ copies/μL. Methanotrophs, namely, Methylocaldum (8.28%), Methylococcus (6.06%) and Methylomonas (0.07%), were detected by 16S rRNA sequencing. And other bacteria were dominated by Denitratisoma, Anaerolineaceae_uncultured and Methylophilaceae_uncultured. Refractory organics was biodegraded through the synergy among microorganisms, and a postulated synergy pathway was put forward.

Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing

Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.

Differential assemblage of functional units in paddy soil microbiomes

Flooded rice fields are not only a global food source but also a major biogenic source of atmospheric methane. Using metatranscriptomics, we comparatively explored structural and functional succession of paddy soil microbiomes in the oxic surface layer and anoxic bulk soil. Cyanobacteria, Fungi, Xanthomonadales, Myxococcales, and Methylococcales were the most abundant and metabolically active groups in the oxic zone, while Clostridia, Actinobacteria, Geobacter, Anaeromyxobacter, Anaerolineae, and methanogenic archaea dominated the anoxic zone. The protein synthesis potential of these groups was about 75% and 50% of the entire community capacity, respectively. Their structure-function relationships in microbiome succession were revealed by classifying the protein-coding transcripts into core, non-core, and taxon-specific transcripts based on homologous gene distribution. The differential expression of core transcripts between the two microbiomes indicated that structural succession is primarily governed by the cellular ability to adapt to the given oxygen condition, involving oxidative stress, nitrogen/phosphorus metabolism, and fermentation. By contrast, the non-core transcripts were expressed from genes involved in the metabolism of various carbon sources. Among those, taxon-specific transcripts revealed highly specialized roles of the dominant groups in community-wide functioning. For instance, taxon-specific transcripts involved in photosynthesis and methane oxidation were a characteristic of the oxic zone, while those related to methane production and aromatic compound degradation were specific to the anoxic zone. Degradation of organic matters, antibiotics resistance, and secondary metabolite production were detected to be expressed in both the oxic and anoxic zones, but by different taxonomic groups. Cross-feeding of methanol between members of the Methylococcales and Xanthomonadales was suggested by the observation that in the oxic zone, they both exclusively expressed homologous genes encoding methanol dehydrogenase. Our metatranscriptomic analysis suggests that paddy soil microbiomes act as complex, functionally coordinated assemblages whose taxonomic composition is governed by the prevailing habitat factors and their hierarchical importance for community succession.

Molecular characterization of microbial communities in bioaerosols of a coal mine by 454 pyrosequencing and real-time PCR

Microbial diversity and abundance in bioaerosols of a coal mine were analyzed based on 454 pyrosequencing and real-time polymerase chain reaction (PCR). A total of 37,191 high quality sequences were obtained and could be classified into 531, 1730 and 448 operational taxonomic units respectively for archaea, bacteria and fungi at 97% sequence similarity. The Shannon diversity index for archaea, bacteria and fungi was respectively 4.71, 6.29 and 3.86, indicating a high diversity in coal mine bioaerosols. Crenarchaeota, Proteobacteria and Ascomycota were the dominant phyla for archaea, bacteria and fungi, respectively. The concentrations of total archaea, bacteria and fungi were 1.44×10(8), 1.02×10(8) and 9.60×10(4) cells/m3, respectively. Methanotrophs observed in bioaerosols suggested possible methane oxidation in the coal mine. The identified potential pathogens to coal miners, such as Acinetobacter schindleri, Aeromonas cavernicola, Alternaria alternata, Aspergillus penicillioides, Cladosporium cladosporioides, and Penicillium brevicompactum were also observed. This was the first investigation of microbial diversity and abundance in coal mine bioaerosols. The investigation of microbial communities would be favorable in promoting the progress of methane control based on microbial technique and concern on coal miners' health.

Association of Growth Substrates and Bacterial Genera with Benzo[a]pyrene Mineralization in Contaminated Soil

Benzo[a]pyrene (BaP) is a carcinogenic polycyclic aromatic hydrocarbon (PAH) that is not known to be a bacterial growth substrate. Organisms capable of cometabolizing BaP in complex field-contaminated systems have not previously been identified. We evaluated BaP mineralization by a bacterial community from a bioreactor treating PAH-contaminated soil during coincubation with or after pre-enrichment on various PAHs as growth substrates. Pyrosequence libraries of 16S rRNA genes were used to identify bacteria that were enriched on the added growth substrate as a means of associating specific organisms with BaP mineralization. Coincubating the bioreactor-treated soil with naphthalene, phenanthrene, or pyrene inhibited BaP mineralization, whereas pre-enriching the soil on the same three PAHs enhanced BaP mineralization. Combined, these results suggest that bacteria in the bioreactor community that are capable of growing on naphthalene, phenanthrene, and/or pyrene can metabolize BaP, with coincubation competitively inhibiting BaP metabolism. Anthracene, fluoranthene, and benz[a]anthracene had little effect on BaP mineralization compared to incubations without an added growth substrate under either coincubation or pre-enrichment conditions. Substantial increases in relative abundance after pre-enrichment with phenanthrene, naphthalene, or pyrene, but not the other PAHs, suggest that members of the genera Cupriavidus and Luteimonas may have been associated with BaP mineralization.

Aerobic and nitrite-dependent methane-oxidizing microorganisms in sediments of freshwater lakes on the Yunnan Plateau

Both aerobic methane-oxidizing bacteria (MOB) and nitrite-dependent anaerobic methane oxidation (n-damo) bacteria can play an important role in mitigating the methane emission produced in anoxic sediment layers to the atmosphere. However, the environmental factors regulating the distribution of these methane-oxidizing microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the distribution of aerobic MOB and n-damo bacteria in sediments of various freshwater lakes on the Yunnan Plateau (China). Quantitative PCR assay and clone library analysis illustrated the spatial variations in the abundances and structures of aerobic MOB and n-damo bacterial communities. Type I MOB (Methylosoma and Methylobacter) and type II MOB (Methylocystis) were detected, while type I MOB was more abundant than type II MOB. Lake sediments n-damo bacterial communities were composed of novel Methylomirabilis oxyfera-like pmoA genes. Lake sediments in the same geographic region could share a relatively similar aerobic MOB community structure. Moreover, Pearson's correlation analysis indicated that n-damo pmoA gene diversity showed a positive correlation with the ratio of organic matter to total nitrogen in lake sediment.

Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils

Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment ecosystems.

Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

Aerobic methanotroph diversity in Riganqiao peatlands on the Qinghai-Tibetan Plateau

The Zoige Plateau is characterized by its high altitude, low latitude and low annual mean temperature of approximately 1°C and is a major source of atmospheric methane in the Qinghai-Tibetan Plateau. Methanotrophs play an important role in the global cycling of CH4, but the diversity, identity and activity of methanotrophs in this region are poorly characterized. Soils were collected from hummocks and hollows in the Riganqiao peatland and the methanotroph community was analysed by qPCR and sequencing methane monooxygenase (pmoA and mmoX) genes. The pmoA genes ranged between 10(7) and 10(8) copies g(-1) fresh soil, with a somewhat greater abundance in hummocks than hollows. The pmoA genes were analysed by amplicon pyrosequencing and the mmoX genes by cloning and sequencing. Methylocystis species were found to be the most abundant methanotrophs, but numerous clades were present including three novel pmoA and three novel mmoX clusters. There were differences between the methanotroph communities in the hummocks and hollows, with the most significant being an increased abundance of uncultivated type Ib methanotrophs in the hollows. The results indicate that aerobic methanotrophs are abundant in Riganqiao peatland and include previously undetected clades in this geographically isolated and distinctive environment.

Methanotrophic bacteria in oilsands tailings ponds of northern Alberta

We investigated methanotrophic bacteria in slightly alkaline surface water (pH 7.4-8.7) of oilsands tailings ponds in Fort McMurray, Canada. These large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. They are primarily anoxic and produce methane but have an aerobic surface layer. Aerobic methane oxidation was measured in the surface water at rates up to 152 nmol CH4 ml(-1) water d(-1). Microbial diversity was investigated via pyrotag sequencing of amplified 16S rRNA genes, as well as by analysis of methanotroph-specific pmoA genes using both pyrosequencing and microarray analysis. The predominantly detected methanotroph in surface waters at all sampling times was an uncultured species related to the gammaproteobacterial genus Methylocaldum, although a few other methanotrophs were also detected, including Methylomonas spp. Active species were identified via (13)CH4 stable isotope probing (SIP) of DNA, combined with pyrotag sequencing and shotgun metagenomic sequencing of heavy (13)C-DNA. The SIP-PCR results demonstrated that the Methylocaldum and Methylomonas spp. actively consumed methane in fresh tailings pond water. Metagenomic analysis of DNA from the heavy SIP fraction verified the PCR-based results and identified additional pmoA genes not detected via PCR. The metagenome indicated that the overall methylotrophic community possessed known pathways for formaldehyde oxidation, carbon fixation and detoxification of nitrogenous compounds but appeared to possess only particulate methane monooxygenase not soluble methane monooxygenase.

Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments

Soda lakes constitute extreme aquatic ecosystems with remarkably high primary productivity rates, but information on the diversity and activity of methanogens in such environments is sparse. Using 16S rRNA and functional genes, we investigated the diversity of methanogens in the sediments of Lonar Lake, a unique saline and alkaline ecosystem formed by meteorite impact in the Deccan basalts. Although domain and phylum level 16S rRNA gene libraries were dominated by phylotypes related to Halobacteriales, sequences related to potentially novel Archaea within the orders Methanosarcinales and Methanomicrobiales were obtained together with a significant fraction of sequences representing uncultivated Euryarchaeota [Correction added after online publication 16 April 2012: orders 'Methanosarcina and Methanomicrobiaceae' changed to 'Methanosarcinales and Methanomicrobiales']. To identify the active methylotrophic Archaea involved in methanogenesis, mRNA transcripts of mcrA were retrieved from methanol consuming and methane emitting sediment microcosms at two different time points. Reverse-transcription PCR, qPCR, DGGE fingerprint, and clone library analysis showed that the active Archaea were closely related to Methanolobus oregonensis. To our knowledge, this is the first study identifying active methylotrophic methanogens in such an environment.

Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray

Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe the protocol used to develop and validate an MDM method for the semiquantification of a range of functional genes--in this case, particulate methane monooxygenase (pmoA)--and we give an example of its application to the study of the community structure of methanotrophs and functionally related bacteria in the environment. The development and validation of an MDM, following this protocol, takes ∼6 months. The pmoA MDM described in detail comprises 199 probes and addresses ∼50 different species-level clades. An experiment comprising 24 samples can be completed, from DNA extraction to data acquisition, within 3 d (12-13 h bench work).

Acetogens and acetoclastic methanosarcinales govern methane formation in abandoned coal mines

In abandoned coal mines, methanogenic archaea are responsible for the production of substantial amounts of methane. The present study aimed to directly unravel the active methanogens mediating methane release as well as active bacteria potentially involved in the trophic network. Therefore, the stable-isotope-labeled precursors of methane, [(13)C]acetate and H(2)-(13)CO(2), were fed to liquid cultures from hard coal and mine timber from a coal mine in Germany. Guided by methane production rates, samples for DNA stable-isotope probing (SIP) with subsequent quantitative PCR and denaturing gradient gel electrophoretic (DGGE) analyses were taken over 6 months. Surprisingly, the formation of [(13)C]methane was linked to acetoclastic methanogenesis in both the [(13)C]acetate- and the H(2)-(13)CO(2)-amended cultures of coal and timber. H(2)-(13)CO(2) was used mainly by acetogens related to Pelobacter acetylenicus and Clostridium species. Active methanogens, closely affiliated with Methanosarcina barkeri, utilized the readily available acetate rather than the thermodynamically more favorable hydrogen. Thus, the methanogenic microbial community appears to be highly adapted to the low-H(2) conditions found in coal mines.

Molecular characterization and geological microenvironment of a microbial community inhabiting weathered receding shale cliffs

Shales play an important role in many earth system processes including coastal erosion, and they form the foundations of many engineering structures. The geobiology of the interior of pyrite-containing receding shale cliffs on the coast of northeast England was examined. The surface of the weathered shales was characterised by a thin layer of disordered authigenic iron oxyhydroxides and localised acicular, platy and aggregated gypsum, which was characterised by Raman spectroscopy, XAS and SEM. These chemical changes are likely to play an important role in causing rock weakening along fractures at the micron scale, which ultimately lead to coastal retreat at the larger scale. The surface of the shale hosts a novel, low-diversity microbial community. The bacterial community was dominated by Proteobacteria, with phylotypes closely associating with Methylocella and other members of the γ-subdivision. The second largest phylogenetic group corresponded to Nitrospira. The archaeal 16S rRNA phylotypes were dominated by a single group of sequences that matched phylotypes reported from South African gold mines and possessed ammonia monooxygenase (amoA) genes. Both the phylogenetic and the mineral data show that acidic microenvironments play an important role in shale weathering, but the shale has a higher microbial diversity than previously described pyritic acid mine drainage sites. The presence of a potentially biogeochemically active microbial population on the rock surface suggests that microorganisms may contribute to early events of shale degradation and coastal erosion.

Environmental distribution and abundance of the facultative methanotroph Methylocella

Methylocella spp. are facultative methanotrophs, which are able to grow not only on methane but also on multicarbon substrates such as acetate, pyruvate or malate. Methylocella spp. were previously thought to be restricted to acidic soils such as peatlands, in which they may have a key role in methane oxidation. There is little information on the abundance and distribution of Methylocella spp. in the environment. New primers were designed, and a real-time quantitative PCR method was developed and validated targeting Methylocella mmoX (encoding the α-subunit of the soluble methane monooxygenase) that allowed the quantification of Methylocella spp. in environmental samples. We also developed and validated specific PCR assays, which target 16S rRNA genes of known Methylocella spp. These were used to investigate the distribution of Methylocella spp. in a variety of environmental samples. It was revealed that Methylocella species are widely distributed in nature and not restricted to acidic environments.