Methane-producing microbial community in a coal bed of the Illinois basin

New insights into the coal-associated methane architect: the ancient archaebacteria

Exploration and marketable exploitation of coalbed methane (CBM) as cleaner fuel has been started globally. In addition, incidence of methane in coal basins is an imperative fraction of global carbon cycle. Significantly, subsurface coal ecosystem contains methane forming archaea. There is a rising attention in optimizing microbial coal gasification to exploit the abundant or inexpensive coal reserves worldwide. Therefore, it is essential to understand the coalbeds in geo-microbial perspective. Current review provides an in-depth analysis of recent advances in our understanding of how methanoarchaea are distributed in coal deposits globally. Specially, we highlight the findings on coal-associated methanoarchaeal existence, abundance, diversity, metabolic activity, and biogeography in diverse coal basins worldwide. Growing evidences indicates that we have arrived an exciting era of archaeal research. Moreover, gasification of coal into methane by utilizing microbial methanogenesis is a considerable way to mitigate the energy crisis for the rising world population.

Culture-independent assessment of the indigenous microbial diversity of Raniganj coal bed methane block, Durgapur

It is widely acknowledged that conventional mining and extraction techniques have left many parts of the world with depleting coal reserves. A sustainable method for improving the recovery of natural gas from coalbeds involves enhancing the production of biogenic methane in coal mines. By taking a culture-independent approach, the diversity of the microbial community present in the formation water of an Indian reservoir was examined using 16S rRNA gene amplification in order to study the potential of microbial-enhanced coal bed methane (CBM) production from the deep thermogenic wells at a depth of 800-1200 m. Physicochemical characterization of formation water and coal samples was performed with the aim of understanding the in situ reservoir conditions that are most favorable for microbial CBM production. Microbial community analysis of formation water showed that bacteria were more abundant than archaea. Proteobacteria, Firmicutes, and Bacteroidetes were found as the most prevalent phyla in all the samples. These phyla play a crucial role in providing substrate for the process of methanogenesis by performing fermentative, hydrolytic, and syntrophic functions. Considerable variation in the abundance of microbial genera was observed amongst the selected CBM wells, potentially due to variable local geochemical conditions within the reservoir. The results of our study provide insights into the impact of geochemical factors on microbial distribution within the reservoir. Further, the study demonstrates lab-scale enhancement in methane production through nutrient amendment. It also focuses on understanding the microbial diversity of the Raniganj coalbed methane block using amplicon sequencing and further recognizing the potential of biogenic methane enhancement through microbial stimulation. The findings of the study will help as a reference for better strategization and implementation of on-site microbial stimulation for enhanced biogenic methane production in the future.

The effect of organics transformation and migration on pore structure of bituminous coal and lignite during biomethane production

Biomethane generation by coal degradation not only can increase coalbed methane (CBM) reserves, namely, microbially enhanced coalbed methane (MECBM), but also has a significant effect on the pore structure of coal which is the key factor in CBM extraction. The transformation and migration of organics in coal are essential to pore development under the action of microorganisms. Here, the biodegradation of bituminous coal and lignite to produce methane and the cultivation with inhibition of methanogenic activity by 2-bromoethanesulfonate (BES) were performed to analyze the effect of biodegradation on coal pore development by determining the changes of the pore structure and the organics in culture solution and coal. The results showed that the maximum methane productions from bituminous coal and lignite were 117.69 μmol/g and 166.55 μmol/g, respectively. Biodegradation mainly affected the development of micropore whose specific surface area (SSA) and pore volume (PV) decreased while the fractal dimension increased. After biodegradation, various organics were generated which were partly released into culture solution while a large number of them remained in residual coal. The content of newly generated heterocyclic organics and oxygen-containing aromatics in bituminous coal was 11.21% and 20.21%. And the content of heterocyclic organics in bituminous coal was negatively correlated with SSA and PV but positively correlated with the fractal dimension which suggested that the retention of organics contributed greatly to the decrease of pore development. But the retention effect on pore structure was relatively poor in lignite. Besides, microorganisms were observed around fissures in both coal samples after biodegradation which would not be conducive to the porosity of coal on the micron scale. These results revealed that the effect of biodegradation on pore development of coal was governed by the combined action of organics degradation to produce methane and organics retention in coal whose contributions were antagonistic and determined by coal rank and pore aperture. The better development of MECBM needs to enhance organics biodegradation and reduce organics retention in coal.

Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin

To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ¹³C_DIC and TDS and lower SO₄^2-, Fe³⁺ and NO₃^- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO₃^- and SO₄^2-, causing a decrease in the content of these two ions in the stagnant areas.

Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China

Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.

A Review of Biogenic Coalbed Methane Experimental Studies in China

Biogenic coalbed methane (CBM) is an important alternative energy that can help achieve carbon neutrality. Accordingly, its exploration and development have become a research hotspot in the field of fossil energy. In this review, the latest detection technologies for and experimental research on biogenic CBM in China in recent decades are summarized. The factors influencing the generation of biogenic CBM and the identification method of biogenic CBM are systematically analyzed. The technologies to detect biogas and the research methods to study microbial diversity are summarized. The literature shows that biogenic CBM is easily produced in the presence of highly abundant organic matter of low maturity, and the organic matter reaching a certain thickness can compensate for the limitation of biogenic CBM gas production due to the small abundance of organic matter to a certain extent. Biogenic CBM production could be increased in an environment with low salinity, medium alkalinity, and rich Fe²⁺ and Ni²⁺ sources. Furthermore, biogenic CBM can be identified by considering three aspects: (1) the presence of gas composition indicators; (2) the content of heavy hydrocarbon; and (3) variation in the abundance of biomarkers. In recent years, research methods to study the microbial community and diversity of CBM-producing environments in China have mainly included 16S rRNA gene library, fluorescence in situ hybridization, and high-throughput sequencing, and the dominant microorganisms have been determined in various basins in China. The results of numerous studies show that the dominant bacterial phyla are commonly Firmicutes and Proteobacteria, while the archaeal fraction mainly includes Methanoculleus, Methanobacterium, Methanocorpusculum, and Methanothrix. This review summarizes and discusses the advances in biogenic CBM production and the associated microbial community in order to promote further development of coal biotransformation and CO₂ bio-utilization to meet energy demands under carbon neutrality.

Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms

Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.

Microbial Community Shifts on Organic Rocks of Different Maturities Reveal potential Catabolisers of Organic Matter in Coal

The global trend of transiting to more renewable energy sources requires transition fuels, such as coal seam gas, to supplement and secure energy needs. In order to optimise strategies and technologies for enhancing gas production, an understanding of the fundamental microbial processes and interactions would be advantageous. Models have recently begun mapping the microbial roles and interactions in coal seam environments, from direct coal degradation to methanogenesis. This study seeks to expand those models by observing community compositional shifts in the presence of differing organic matter by conducting 16S rRNA microbial surveys using formation water from the Surat and Sydney Basins grown on varying types of organic matter (black and brown coal, oil shale, humic acid, and lignin). A total of 135 microbes were observed to become enriched in the presence of added organic matter in comparison to carbon-free treatments. These surveys allowed detailed analysis of microbial compositions in order to extrapolate which taxa favour growth in the presence of differing organic matter. This study has experimentally demonstrated shifts in the microbial community composition due to differing carbon sources and, for the first time, generated a conceptual model to map putative degradation pathways regarding subsurface microbial consortia.

Nutrients Changed the Assembly Processes of Profuse and Rare Microbial Communities in Coals

Nutrient stimulation is considered effective for improving biogenic coalbed methane production potential. However, our knowledge of the microbial assembly process for profuse and rare microbial communities in coals under nutrient stimulation is still limited. This study collected 16S rRNA gene data from 59 microbial communities in coals for a meta-analysis. Among these communities, 116 genera were identified as profuse taxa, and the remaining 1,637 genera were identified as rare taxa. Nutrient stimulation increased the Chao1 richness of profuse and rare genera and changed the compositions of profuse and rare genera based on nonmetric multidimensional scaling with Bray-Curtis dissimilarities. In addition, many profuse and rare genera belonging to Proteobacteria and Acidobacteria were reduced, whereas those belonging to Euryarchaeota and Firmicutes were increased under nutrient stimulation. Concomitantly, the microbial co-occurrence relationship network was also altered by nutrient addition, and many rare genera mainly belonging to Firmicutes, Bacteroides, and Euryarchaeota also comprised the key microorganisms. In addition, the compositions of most of the profuse and rare genera in communities were driven by stochastic processes, and nutrient stimulation increased the relative contribution of dispersal limitation for both profuse and rare microbial community assemblages and that of variable selection for rare microbial community assemblages. In summary, this study strengthened our knowledge regarding the mechanistic responses of coal microbial diversity and community composition to nutrient stimulation, which are of great importance for understanding the microbial ecology of coals and the sustainability of methane production stimulated by nutrients.

The ecological roles of assembling genomes for Bacillales and Clostridiales in coal seams

Biogenic coalbed methane is produced by biological processes mediated by synergistic interactions of microbial complexes in coal seams. However, the ecological role of functional bacteria in biogenic coalbed methane remains poorly understood. Here, we studied the metagenome assembled genomes (MAGs) of Bacillales and Clostridiales from coal seams, revealing further expansion of hydrogen and acetogen producers involved in organic matter decomposition. In this study, Bacillales and Clostridiales were dominant orders (91.85 ± 0.94%) in cultured coal seams, and a total of 16 MAGs from 6 families, including Bacillus, Paenibacillus, Staphylococcus, Anaerosalibacter, Hungatella and Paeniclostridium, were reconstructed. These microbial groups possessed multiple metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate, β-oxidation, TCA cycle, assimilatory sulfate reduction, nitrogen metabolism and encoding hydrogenase) that provided metabolic substrates (acetate and/or H2) for the methanogenic processes. Therein, the hydrogenase-encoding gene and hydrogenase maturation factors were merely found in all the Clostridiales MAGs. β-oxidation was the main metabolic pathway involved in short-chain fatty acid degradation and acetate production, and most of these pathways were detected and exhibited different operon structures in Bacillales MAGs. In addition, assimilatory sulfate reduction and nitrogen metabolism processes were also detected in some MAGs, and these processes were also closely related to acetate production and/or organic matter degradation according to their operon structures and metabolic pathways. In summary, this study enabled a better understanding of the ecological roles of Bacillales and Clostridiales in biogenic methane in coal seams based on a combination of bioinformatic techniques.

Enhancing Biomethane Production From Lignite by an Anaerobic Polycyclic Aromatic Hydrocarbon Degrading Fungal Flora Enriched From Produced Water

The coal-degrading ability of microorganisms is essential for the formation of biogenic coalbed methane. The ability to degrade the aromatic compound of coal is more important because it is perceived as the main refractory component for bioconversion. In this paper, a polycyclic aromatic hydrocarbon (PAH) degrading fungal community (PF) was enriched from produced water using phenanthrene as sole carbon source. The goal was to improve both the microbial structure of the methanogenic microflora and its coal-degrading ability. Two strategies were pursued. The first used coal pretreatment with PF (PP), followed by methane production by methanogenic microflora; the second used methane production directly from coal by mixed culture of PF and methanogenic microflora (PM). The results showed that methane productions of PP and PM increased by 29.40 and 39.52%, respectively. After 7 days of cultivation, the fungal community has been altered in PP and PM, especially for Penicillium the proportions of which were 67.37 and 89.81% higher than that in methanogenic microflora, respectively. Furthermore, volatile fatty acid accumulations increased by 64.21 and 58.15%, respectively. The ¹³C-NMR results showed that PF addition promoted the transformation of aromatic carbons in coal to carboxyl and carbonyl carbons, which contributed greatly to the production of methane together with oxygen-containing functional groups. These results suggest that methane production can be increased by indigenous PAH-degrading fungi by improving the fermentation of aromatics in coal and the generation of volatile fatty acids. This provided a feasible method for enhancing biomethane generation in the coal seam.

Methane Generation from Anthracite by Fungi and Methanogen Mixed Flora Enriched from Produced Water Associated with the Qinshui Basin in China

Biogenic coalbed methane (CBM) is generally believed to be formed by anaerobic bacteria and methanogens, while a few studies took fungi into account. Here, the microflora consisting of fungi and methanogens was enriched from the produced water associated with the Qinshui Basin using anthracite as the only carbon source. The maximum methane yield of 231 μmol/g coal was obtained after 22 days of cultivation under the optimum temperature of 35 °C, pH of 8, salinity of 0-2%, particle size of 0.075-0.150 mm, and the solid-liquid ratio of 1:30. It could remain active even after exposure to air for 24 h. Miseq results showed that the archaea were mainly composed of Methanocella, a hydrogenotrophic methanogen, followed by acetoclastic methanogen Methanosaeta and Methanosarcina, which could use various methanogenic substrates. The fungal communities mainly included Amorphotheca, Alternaria, Aspergillus, and Penicilium, which are all able to degrade complex organics such as aromatics and lignin. After cultivation, the crystal structure of anthracite became looser, as shown by XRD results, which might be due to the swelling effect caused by the destruction of the aromatic ring structure of coal under the function of fungi. The stretching vibration intensity of each functional group in coal decreased with cultivation, as revealed by FTIR. The GC-MS results showed that the concentration of alkanes and alcohols decreased significantly, which are the products of ring-opening of aromatics by fungi. These results suggested that fungi and methanogens in the coalbed also can syntrophically degrade coal effectively, especially for aromatics in coal.

Design of effective value calculation model for dynamic dataflow of infrared gas online monitoring

The development of "CC30A CH4-CO2 combined analyzer" with infrared gas sensor as the core detection device can be widely used in online gas component analysis. In data analysis, the maximum value and arithmetic mean of the sensor data for each test period are not effective value. The characteristics of the dynamic data are: (1) Each DAW completes one test for one parameter, there is a unique effective value; (2) In test state, the fluctuation of the sensor value gradually decreases when approaching to the end of the test. An effective value calculation model was designed using the method of dimensionality reduction of dynamic data. The model was based on the distribution characteristics of the process data, and consists of 4 key steps: (1) Identify the Data Analysis Window (DAW) and build DAW dataset; (2) Calculate the value of optimal DAW dataset segmentation and build DAW subdataset; (3) Calculate the arithmetic mean (Mc) and count the amount of data in each subdataset (Fc), and build the optimal segmentation statistical set; (4) Effective value calculation and error evaluation. Calculation result with 50 sets of monitor data conformed that the EVC model for dynamic data of gas online monitoring meets the requirements of experimental accuracy requirements and test error. This method can be independently calculated without relying on the feedback information of the monitoring device, and it has positive significance for using the algorithm to reduce the hardware design complexity.

Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL

Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput Fluidigm^TM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N₂ fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.

Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia

Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.

Surface Analysis of Coal Indicating Neutral Red Enhances the Precursor Steps of Methanogenesis

Artificially stimulated, high-yield microbial production of methane from coal is a challenging problem that continues to generate research interest. Decomposition of organic matter and production of methane from coal are the results of multiple redox reactions carried out by different communities of bacteria and archaea. Recent work by our group (Beckmann et al., 2015) demonstrated that the presence of the redox-mediating molecule neutral red, in its crystalline form on a coal surface, can increase methane production. However, hydrolysis and the acetogenesis of the coal surface are essential precursor steps for methane production by archaea. Acetogenesis is the preparation phase of methanogenesis because methanogens can only assimilate acetate, CO₂ and H₂ among the products formed during this process. In the present study, the surface chemical analysis of neutral red treated coal using attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) demonstrate that the acetate production and resulting oxidation of the coal only occurred at few nanometers into the coal surface (at the nanoscale <5 nm). We observed that in the presence of neutral red and groundwater microbes, acetate signals in coal surface chemistry increased. This is the first evidence suggesting that neutral red enhances the biological conversion of coal into acetate. Microscopy demonstrated that neutral red crystals were co-localize with cells at the surface of coal in groundwater. This is consistent with neutral red crystals serving as a redox hub, concentrating and distributing reducing equivalents amongst the microbial community. In this study, the chemical changes of neutral red treated coal indicated that neutral red doubles the concentration of acetate over the control (coal without neutral red), emphasizing the importance of maximizing the fracture surface coverage of this redox mediator. Overall, results suggested that, neutral red not only can benefit acetoclastic methanogens, but also the fermentative and acetogenic bacteria involved in generating acetate.

Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China

Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture-dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confirmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more flexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.

Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments

BACKGROUND

Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood.

RESULTS

Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H₂-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production.

CONCLUSIONS

Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.

The effect of NaOH pretreatment on coal structure and biomethane production

Biogenic CBM is an important component of detected CBM, which is formed by coal biodegradation and can be regenerated by anaerobic microorganisms. One of the rate-limiting factors for microbial degradation is the bioavailability of coal molecules, especially for anthracite which is more condense and has higher aromaticity compared with low-rank coal. In this paper, NaOH solution with different concentrations and treating time was employed to pretreat anthracite from Qinshui Basin to alter the coal structure and facilitate the biodegradation. The results showed that the optimal pretreatment conditions were 1.5 M NaOH treating for 12 h, under which the biomethane production was increased by 17.65% compared with untreated coal. The results of FTIR and XRD showed that NaOH pretreatment mainly reduced the multi-substituted aromatics, increased the C-O in alcohols and aromatic ethers and the branching degree of aliphatic chain, and decreased the aromatic ring structure, resulting in the improvement of coal bioavailability and enhancement of biomethane yield. And some organics with potential to generate methane were released to filtrate as revealed by GC-MS. Our results suggested that NaOH was an effective solution for pretreating coal to enhance biogenic methane production, and anthracite after treating with NaOH could be the better substrate for methanogenesis.

Effect of mixed solutions of heavy metal eluents on soil fertility and microorganisms

This study analyzed the effect of heavy metal eluents (0.3 mol/L C₆H₈O₇, 5 × 10^-4 mol/L EDTA, and 0.01 mol/L Na₂S₂O₃) on the content of organic matter, hydrolytic nitrogen, available phosphorus and potassium, and species composition of bacteria and fungi in vegetable soils. The obtained results documented that the treatment of the soil, consisting of shaking the sample with a mixture of eluents, significantly increased the content of organic matter, hydrolytic nitrogen, and available phosphorus and potassium. The mixed solutions of eluents increase the maximum available P in the soil by 279.3%, and hydrolytic N by 30.7%. The eluents affected, to a certain extent, the dominant species of microorganisms in the soil, but did not increase species richness and evenness in all soil samples.

Bioconversion of coal to methane by microbial communities from soil and from an opencast mine in the Xilingol grassland of northeast China

BACKGROUND

The Xilingol grassland ecosystem has abundant superficial coal reserves. Opencast coal mining and burning of coal for electricity have caused a series of environmental challenges. Biogenic generation of methane from coal possesses the potential to improve economic and environmental outcomes of clean coal utilization. However, whether the microbes inhabiting the grassland soil have the functional potential to convert coal into biomethane is still unclear.

RESULTS

Microbial communities in an opencast coal mine and in grassland soil covering and surrounding this mine and their biomethane production potential were investigated by Hiseq sequencing and anaerobic cultivation. The microbial communities in covering soil showed high similarity to those in the surrounding soil, according to the pairwise weighted UniFrac distances matrix. The majority of bacterial communities in coal and soil samples belonged to the phyla Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. The dominant bacterial genera in grassland soil included Gaiella, Solirubrobacter, Sphingomonas and Streptomyces; whereas, the most abundant genus in coal was Pseudarthrobacter. In soil, hydrogenotrophic Methanobacterium was the dominant methanogen, and this methanogen, along with acetoclastic Methanosarcina and methylotrophic Methanomassiliicoccus, was detected in coal. Network-like Venn diagram showed that an average of 28.7% of microbial communities in the samples belonged to shared genera, indicating that there is considerable microbial overlap between coal and soil samples. Potential degraders and methanogens in the soil efficiently stimulated methane formation from coal samples by the culturing-based approach. The maximum biogenic methane yields from coal degradation by the microbial community cultured from grassland soil reached 22.4 μmol after 28 day.

CONCLUSION

The potential microbial coal degraders and methanogenic archaea in grassland soil were highly diverse. Significant amounts of biomethane were generated from coal by the addition of grassland soil microbial communities. The unique species present in grassland soil may contribute to efficient methanogenic coal bioconversion. This discovery not only contributes to a better understanding of global microbial biodiversity in coal mine environments, but also makes a contribution to our knowledge of the synthetic microbiology with regard to effective methanogenic microbial consortia for coal degradation.

Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation

Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.

Potential of biogenic methane for pilot-scale fermentation ex situ with lump anthracite and the changes of methanogenic consortia

Pilot-scale fermentation is one of the important processes for achieving industrialization of biogenic coalbed methane (CBM), although the mechanism of biogenic CBM remains unknown. In this study, 16 samples of formation water from CBM production wells were collected and enriched for methane production, and the methane content was between 3.1 and 21.4%. The formation water of maximum methane production was used as inoculum source for pilot-scale fermentation. The maximum methane yield of the pilot-scale fermentation with lump anthracite amendment reached 13.66 μmol CH₄/mL, suggesting that indigenous microorganisms from formation water degraded coal to produce methane. Illumina high-throughput sequencing analysis revealed that the bacterial and archaeal communities in the formation water sample differed greatly from the methanogic water enrichment culture. The hydrogenotrophic methanogen Methanocalculus dominated the formation water. Acetoclastic methanogens, from the order Methanosarcinales, dominated coal bioconversion. Thus, the biogenic methanogenic pathway ex situ cannot be simply identified according to methanogenic archaea in the original inoculum. Importantly, this study was the first time to successfully simulate methanogenesis in large-capacity fermentors (160 L) with lump anthracite amendment, and the result was also a realistic case for methane generation in pilot-scale ex situ.

Differentiating between biogenic and thermogenic sources of natural gas in coalbed methane reservoirs from the Illinois Basin using noble gas and hydrocarbon geochemistry

While coalbed methane (CBM) is a significant source of natural gas production globally, uncertainties regarding the proportions of biogenic and thermogenic natural gas in CBM reservoirs still remain. We integrate major gases, hydrocarbon composition, hydrocarbon stable isotopes and noble gases in fluids from 20 producing CBM wells to more accurately constrain the genetic source of natural gases in the eastern Illinois Basin, USA. Previous studies have indicated primarily biogenic production of methane (>99.6%) with negligible contributions from thermogenic natural gases. However, by integrating noble gases, we identify quantifiable (up to 19.2%) contributions of exogenous thermogenic gas in produced gases from the Seelyville and Springfield coal seams. Thermogenic gases are distinguished by a positive relationship between methane, ethane and helium-4, lower C1/C2+, heavier δ13C-CH4, more radiogenic noble gases (4He, 21Ne*, 40Ar*), and lower abundances of atmospherically derived gases (20Ne, 36Ar). Biogenic gases displayed lighter δ13C-CH4, higher C1/C2+, higher levels of atmospheric gases and lower abundances of radiogenic noble gases. Our data suggest that natural gases from a deeper, exogenous thermogenic source likely migrated to the Pennsylvanian-aged coals at an unknown time and later mixed with biogenic methane diluting the geochemical signature of the thermogenic methane within the Springfield and Seelyville coal seams.

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be "hot spots" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ¹³C- or ¹⁵N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50-2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell-targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well

Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source. We tracked cell counts, methane production, acetate concentration and geochemical parameters for 25 months in one amended and one unamended coal well in Australia. Additionally, the microbial community was analysed with 16S rRNA gene amplicon sequencing at 17 and 25 months after amendment and complemented by metagenome sequencing at 25 months. We found that cell numbers increased rapidly from 3.0 × 10⁴ cells ml^-1 to 9.9 × 10⁷ in the first 7 months after amendment. However, acetate depletion with concomitant methane production started only after 12-19 months. The microbial community was dominated by complex organic compound degraders (Anaerolineaceae, Rhodocyclaceae and Geobacter spp.), acetoclastic methanogens (Methanothrix spp.) and fungi (Agaricomycetes). Even though the microbial community had the functional potential to convert coal to methane, we observed no indication that coal was actually converted within the time frame of the study. Our results suggest that even though nutrient and acetate amendment stimulated relevant microbial species, it is not a sustainable way to transform non-producing coal wells into bioenergy factories.

Changes in pore structure of coal caused by coal-to-gas bioconversion

Microbial enhanced coalbed methane (ME-CBM) recovery is critically examined as a viable technology for natural gas recovery from coalbed methane (CBM) reservoirs. Since the majority of gas-in-place (GIP) is stored as an adsorbed phase in fine pores of coal matrix, the nano-pore structure directly influences gas storage and transport properties. Only limited studies have quantified the alteration of the nano-pore structure due to ME-CBM treatment. This study examines the evolution of the pore structure using a combination of small angle X-ray scattering (SAXS), low-pressure N₂ and CO₂ adsorption (LPGA) and high-pressure methane adsorption methods. The results show that the surface fractal dimension decreases for the two bioconverted coals compared to the untreated coal. After bio-treatment, the mesopore surface area and pore volume decrease with the average pore diameter increases, while the micropore surface area increases with pore volume decreases. Both inaccessible meso-/micropore size distributions decrease after bioconversion, while the accessible micropore size distribution increases, making a portion of closed micropore network accessible. In addition, the methane adsorption capacities increase after bio-treatment, which is confirmed by the increase of micropore surface area. A conceptual physical model of methanogenesis is proposed based on the evolution of the pore structure.

Elucidation of the methanogenic potential from coalbed microbial communities amended with volatile fatty acids

The potential for modern coalfield methanogenesis was assessed using formation water from the Illinois Basin, Powder River Basin and Cook Inlet gas field as inocula for nutrient-replete incubations amended with C1-C5 fatty acids as presumed intermediates formed during anaerobic coal biodegradation. Instead of the expected rapid mineralization of these substrates, methanogenesis was inordinately slow (∼1 μmol day-1), following long lag periods (>100 days), and methane yields typically did not reach stoichiometrically expected levels. However, a gene microarray confirmed the potential for a wide variety of microbiological functions, including methanogenesis, at all sites. The Cook Inlet incubations produced methane at a relatively rapid rate when amended with butyrate (r = 0.98; p = 0.001) or valerate (r = 0.84; p = 0.04), a result that significantly correlated with the number of positive mcr gene sequence probes from the functional gene microarray and was consistent with the in situ detection of C4-C5 alkanoic acids. This finding highlighted the role of syntrophy for the biodegradation of the softer lignite and subbituminous coal in this formation, but methanogenesis from the harder subbituminous and bituminous coals in the other fields was less apparent. We conclude that coal methanogenesis is probably not limited by the inherent lack of metabolic potential, the presence of alternate electron acceptors or the lack of available nutrients, but more likely restricted by the inherent recalcitrance of the coal itself.

Thermodynamic and hydrochemical controls on CH4 in a coal seam gas and overlying alluvial aquifer: new insights into CH4 origins

Using a comprehensive data set (dissolved CH₄, δ¹³C-CH₄, δ²H-CH₄, δ¹³C-DIC, δ³⁷Cl, δ²H-H₂O, δ¹⁸O-H₂O, Na, K, Ca, Mg, HCO₃, Cl, Br, SO₄, NO₃ and DO), in combination with a novel application of isometric log ratios, this study describes hydrochemical and thermodynamic controls on dissolved CH₄ from a coal seam gas reservoir and an alluvial aquifer in the Condamine catchment, eastern Surat/north-western Clarence-Moreton basins, Australia. δ¹³C-CH₄ data in the gas reservoir (−58‰ to −49‰) and shallow coal measures underlying the alluvium (−80‰ to −65‰) are distinct. CO₂ reduction is the dominant methanogenic pathway in all aquifers, and it is controlled by SO₄ concentrations and competition for reactants such as H₂. At isolated, brackish sites in the shallow coal measures and alluvium, highly depleted δ²H-CH₄ (<310‰) indicate acetoclastic methanogenesis where SO₄ concentrations inhibit CO₂ reduction. Evidence of CH₄ migration from the deep gas reservoir (200–500 m) to the shallow coal measures (<200 m) or the alluvium was not observed. The study demonstrates the importance of understanding CH₄ at different depth profiles within and between aquifers. Further research, including culturing studies of microbial consortia, will improve our understanding of the occurrence of CH₄ within and between aquifers in these basins.

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot

Caves in Mizoram, Northeast India, are potential hotspot diversity regions due to the historical significance of the formation of the Indo-Burman plateau and also because of their unexplored and unknown diversity. High-throughput paired end Illumina sequencing of the V4 region of 16S rRNA was performed to study the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (OTUs) (based on 97 % cutoff) comprising of 21 major and 21 candidate phyla with a sequencing depth of 1,140,013 were found in this study. The overall taxonomic profile obtained by the RDP classifier and Greengenes OTU database revealed high diversity within the bacterial communities. Communities were dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of Archaea were less varied and mostly comprising of Eukaryoarchea. Analysis revealed that Farpuk (CFP) cave sediment has low microbial diversity and is mainly dominated by Actinobacteria (80 % reads), whereas different bacterial communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis also revealed that a major portion of the identified OTUs was classified under rare biosphere. Importantly, all these caves recorded a high number of unclassified OTUs, which might represent new species. Further analysis with whole genome sequencing is needed to validate the unknown species as well as to determine their functional role.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA

Microorganisms have contributed significantly to subsurface energy resources by converting organic matter in hydrocarbon reservoirs into methane, the main component of natural gas. In this study, we consider environmental controls on microbial populations in coal-bearing strata of the Cherokee basin, an unconventional natural gas resource in southeast Kansas, USA. Pennsylvanian-age strata in the basin contain numerous thin (0.4–1.1 m) coalbeds with marginal thermal maturities (0.5–0.7% R_o) that are interbedded with shale and sandstone. We collected gas, water, and microbe samples from 16 commercial coalbed methane wells for geochemical and microbiological analysis. The water samples were Na–Cl type with total dissolved solids (TDS) content ranging from 34.9 to 91.3 g L⁻¹. Gas dryness values [C₁/(C₂ + C₃)] averaged 2640 and carbon and hydrogen isotope ratios of methane differed from those of carbon dioxide and water, respectively, by an average of 65 and 183‰. These values are thought to be consistent with gas that formed primarily by hydrogenotrophic methanogenesis. Results from cultivation assays and taxonomic analysis of 16S rRNA genes agree with the geochemical results. Cultivable methanogens were present in every sample tested, methanogen sequences dominate the archaeal community in each sample (avg 91%), and few archaeal sequences (avg 4.2%) were classified within Methanosarcinales, an order of methanogens known to contain methylotrophic methanogens. Although hydrogenotrophs appear dominant, geochemical and microbial analyses both indicate that the proportion of methane generated by acetoclastic methanogens increases with the solute content of formation water, a trend that is contrary to existing conceptual models. Consistent with this trend, beta diversity analyses show that archaeal diversity significantly correlates with formation water solute content. In contrast, bacterial diversity more strongly correlates with location than solute content, possibly as a result of spatial variation in the thermal maturity of the coalbeds.

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.

Methanogenic archaea in marcellus shale: a possible mechanism for enhanced gas recovery in unconventional shale resources

Marcellus Shale occurs at depths of 1.5-2.5 km (5000 to 8000 feet) where most geologists generally assume that thermogenic processes are the only source of natural gas. However, methanogens in produced fluids and isotopic signatures of biogenic methane in this deep shale have recently been discovered. This study explores whether those methanogens are indigenous to the shale or are introduced during drilling and hydraulic fracturing. DNA was extracted from Marcellus Shale core samples, preinjected fluids, and produced fluids and was analyzed using Miseq sequencing of 16s rRNA genes. Methanogens present in shale cores were similar to methanogens in produced fluids. No methanogens were detected in injected fluids, suggesting that this is an unlikely source and that they may be native to the shale itself. Bench-top methane production tests of shale core and produced fluids suggest that these organisms are alive and active under simulated reservoir conditions. Growth conditions designed to simulate the hydrofracture processes indicated somewhat increased methane production; however, fluids alone produced relatively little methane. Together, these results suggest that some biogenic methane may be produced in these wells and that hydrofracture fluids currently used to stimulate gas recovery could stimulate methanogens and their rate of producing methane.

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport.

The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage

Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

Identification and characterization of a novel phosphodiesterase from the metagenome of an Indian coalbed

Phosphoesterases are involved in the degradation of organophosphorus compounds. Although phosphomonoesterases and phosphotriesterases have been studied in detail, studies on phosphodiesterases are rather limited. In our search to find novel phosphodiesterases using metagenomic approach, we cloned a gene encoding a putative phosphodiesterase (PdeM) from the metagenome of the formation water collected from an Indian coal bed. Bioinformatic analysis showed that PdeM sequence possessed the characteristic signature motifs of the class III phosphodiesterases and phylogenetic study of PdeM enabled us to identify three distinct subclasses (A, B, and C) within class III phosphodiesterases, PdeM clustering in new subclass IIIB. Bioinformatic, biochemical and biophysical characterization of PdeM further revealed some of the characteristic features of the phosphodiesterases belonging to newly described subclass IIIB. PdeM is a monomer of 29.3 kDa, which exhibits optimum activity at 25°C and pH 8.5, but low affinity for bis(pNPP) as well as pNPPP. The recombinant PdeM possessed phosphodiesterase, phosphonate-ester hydrolase and nuclease activity. It lacked phosphomonoesterase, phosphotriesterase, and RNAse activities. Overexpression of PdeM in E.coli neither affected catabolite respression nor did the recombinant protein hydrolyzed cAMP in vitro, indicating its inability to hydrolyze cAMP. Although Mn²⁺ was required for the activity of PdeM, but addition of metals (Mn²⁺ or Fe³⁺) did not induce oligomerization. Further increase in concentration of Mn²⁺ upto 3 mM, increased α-helical content as well as the phosphodiesterase activity. Structural comparison of PdeM with its homologs showed that it lacked critical residues required for dimerization, cAMP hydrolysis, and for the high affinity binding of bis(pNPP). PdeM, thus, is a novel representative of new subclass of class III phosphodiesterases.

Fe-oxide grain coatings support bacterial Fe-reducing metabolisms in 1.7-2.0 km-deep subsurface quartz arenite sandstone reservoirs of the Illinois Basin (USA)

The Cambrian-age Mt. Simon Sandstone, deeply buried within the Illinois Basin of the midcontinent of North America, contains quartz sand grains ubiquitously encrusted with iron-oxide cements and dissolved ferrous iron in pore-water. Although microbial iron reduction has previously been documented in the deep terrestrial subsurface, the potential for diagenetic mineral cementation to drive microbial activity has not been well studied. In this study, two subsurface formation water samples were collected at 1.72 and 2.02 km, respectively, from the Mt. Simon Sandstone in Decatur, Illinois. Low-diversity microbial communities were detected from both horizons and were dominated by Halanaerobiales of Phylum Firmicutes. Iron-reducing enrichment cultures fed with ferric citrate were successfully established using the formation water. Phylogenetic classification identified the enriched species to be related to Vulcanibacillus from the 1.72 km depth sample, while Orenia dominated the communities at 2.02 km of burial depth. Species-specific quantitative analyses of the enriched organisms in the microbial communities suggest that they are indigenous to the Mt. Simon Sandstone. Optimal iron reduction by the 1.72 km enrichment culture occurred at a temperature of 40°C (range 20-60°C) and a salinity of 25 parts per thousand (range 25-75 ppt). This culture also mediated fermentation and nitrate reduction. In contrast, the 2.02 km enrichment culture exclusively utilized hydrogen and pyruvate as the electron donors for iron reduction, tolerated a wider range of salinities (25-200 ppt), and exhibited only minimal nitrate- and sulfate-reduction. In addition, the 2.02 km depth community actively reduces the more crystalline ferric iron minerals goethite and hematite. The results suggest evolutionary adaptation of the autochthonous microbial communities to the Mt. Simon Sandstone and carries potentially important implications for future utilization of this reservoir for CO2 injection.

Metagenomic scaffolds enable combinatorial lignin transformation

Engineering the microbial transformation of lignocellulosic biomass is essential to developing modern biorefining processes that alleviate reliance on petroleum-derived energy and chemicals. Many current bioprocess streams depend on the genetic tractability of Escherichia coli with a primary emphasis on engineering cellulose/hemicellulose catabolism, small molecule production, and resistance to product inhibition. Conversely, bioprocess streams for lignin transformation remain embryonic, with relatively few environmental strains or enzymes implicated. Here we develop a biosensor responsive to monoaromatic lignin transformation products compatible with functional screening in E. coli. We use this biosensor to retrieve metagenomic scaffolds sourced from coal bed bacterial communities conferring an array of lignin transformation phenotypes that synergize in combination. Transposon mutagenesis and comparative sequence analysis of active clones identified genes encoding six functional classes mediating lignin transformation phenotypes that appear to be rearrayed in nature via horizontal gene transfer. Lignin transformation activity was then demonstrated for one of the predicted gene products encoding a multicopper oxidase to validate the screen. These results illuminate cellular and community-wide networks acting on aromatic polymers and expand the toolkit for engineering recombinant lignin transformation based on ecological design principles.

Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed

A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C(15 : 0) and C(18 : 1)ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBM(T) ( = DSM 28127(T) = JCM 19826(T)). Desulfocarbo is the second genus of the order Desulfarculales.