Methane production from coal by a single methanogen
Microbes make methane from coal
Methane associated with coal beds is an important global resource of natural gas. Much of the methane in coal comes from microbial methanogenesis. Mayumi et al. characterized a strain of Methermicoccus shengliensis that, unexpectedly, is capable of making methane from the dozens of methoxylated aromatic compounds found in a variety of coal types (see the Perspective by Welte). Isotope tracer experiments showed that this organism could also incorporate carbon dioxide into methane.
Abstract
Coal-bed methane is one of the largest unconventional natural gas resources. Although microbial activity may greatly contribute to coal-bed methane formation, it is unclear whether the complex aromatic organic compounds present in coal can be used for methanogenesis. We show that deep subsurface–derived Methermicoccus methanogens can produce methane from more than 30 types of methoxylated aromatic compounds (MACs) as well as from coals containing MACs. In contrast to known methanogenesis pathways involving one- and two-carbon compounds, this “methoxydotrophic” mode of methanogenesis couples O-demethylation, CO2 reduction, and possibly acetyl–coenzyme A metabolism. Because MACs derived from lignin may occur widely in subsurface sediments, methoxydotrophic methanogenesis would play an important role in the formation of natural gas not limited to coal-bed methane and in the global carbon cycle.
Coal-bed methane (CBM), a form of natural gas distributed in coal seams or adjacent sandstones, is a relatively untapped energy source with a large potential: The global reserves in 2014 were estimated at 50 trillion m3, equivalent to 11% of conventional natural gas resources (1). Large-scale CBM production has been implemented in the United States, Canada, Australia, and other countries worldwide. The contribution of biogenic methane to CBM is quite large (2, 3); geochemical studies have estimated that 40% of CBM produced in the United States is of microbial origin (4). Live microbial communities are present in coal seams and are associated with methanogenesis from coal in subsurface environments (5–10). Geomicrobiological studies have shown that enhanced CBM production in coal seams might be achieved by the stimulation of methanogenic activity (11). Although extensive efforts have been made to develop this technology, very little is known about what components of coal can be used for methanogenesis and which microorganisms possess the metabolic capabilities to do so.
Coal is an extremely complex and heterogeneous material whose structure consists of single and condensed aromatic rings (12, 13). Aromatic compounds in coal are derived from lignin monolignols and are often substituted with hydroxyl, methoxy, and carboxyl groups (14, 15). Methoxy groups are especially abundant and common in immature coal (14, 16). Because methanogenesis from coal tends to occur in immature coal rather than in mature coal (4, 17), coal-bed microorganisms may produce methane from methoxy groups. Methanogenic microorganisms in CBM fields are commonly dominated by methylotrophic methanogens belonging to the archaeal order Methanosarcinales (5, 18, 19). The methylotrophic methanogens are capable of using methyl compounds such as methanol, methylamines, and/or dimethylsulfide (20), but it is unclear whether they can directly use methoxylated aromatic compounds (MACs) as substrates.
To investigate the possibility of MACs as substrates for methylotrophic methanogens, we tested the methane production ability of one archaeal isolate (Methermicoccus shengliensis strain AmaM) obtained from a high-temperature deep subsurface oil reservoir in this study (fig. S1), and of 10 type strains belonging to the genera Methanosarcina, Methanolobus, Methanohalophilus, Methanosaeta, Methanomicrococcus, Methanococcoides, Methanohalobium, Methanosalsum, Methanomethylovorans, and Methermicoccus (i.e., M. shengliensis strain ZC-1) (21) in the order Methanosarcinales using seven types of MACs (2-methoxy-benzoate, 3-methoxy-benzoate, 4-methoxy-benzoate, 3,4,5-trimethoxy-benzoate, 3,4,5-trimethoxy-cinnamate, 1,2,3-trimethoxy-benzene, and 3,4,5-trimethoxy-benzylalcohol) as substrates. We only observed substantial methane production in the incubation of Methermicoccus shengliensis strains AmaM and ZC-1 with seven and six types of MACs, respectively (Fig. 1A). To investigate their substrate ranges, we incubated the strains AmaM and ZC-1 with 40 commercially available MACs. The results showed that the strains AmaM and ZC-1 used 35 and 34 types of MACs, respectively (Fig. 1B and table S1).
Fig. 1 Methoxydotrophic methanogenesis from various MACs.
(A) Methanogenesis from seven types of MACs by 10 type strains and one isolate belonging to the order Methanosarcinales. Each MAC was supplied with methoxy groups to a final concentration of 30 mM. Methane produced was measured after incubation for 9 months. Data are means of three individual incubations; error bars represent SD of these triplicates. (B) Substrate ranges of Methermicoccus shengliensis strains AmaM and ZC-1 for 40 types of MACs; an asterisk designates MACs analyzed for the media with coal samples. For each substrate, the average amount of methane produced (n = 3) is expressed by one of four ranges. Detailed methane production data are shown in table S1.
To confirm whether these “methoxydotrophic methanogens” could produce methane from coal, we incubated M. shengliensis AmaM with coals of different maturity levels: lignite (most immature) and subbituminous and bituminous (most mature) coals (fig. S2). A small but substantial amount of methane (7.5 to 10.8 μmol/g-coal) was produced in all of the three lignites (L-A, L-B, and L-C) and even in the subbituminous coal S-A and the bituminous coal B-A (Fig. 2A). M. shengliensis AmaM used MACs, methanol, and methylamines as substrates for methanogenesis (Fig. 1 and fig. S1), which suggests that coal may have provided some of these substrates. We analyzed growth media with coal before incubation for the 26 types of MACs usable for M. shengliensis AmaM (marked with asterisks in Fig. 1B) by gas chromatography–mass spectrometry (GC-MS). We detected either two or three types of methoxylated benzoates in each medium from which methane production was observed (Fig. 2B). The total concentrations of methanol and methylamines as well as of MACs detected in the media were too low to account for the concentrations of methane produced in the coal cultures alone (Fig. 2); for example, in bituminous coal culture B-A, 0.09 μmol/g-coal of MACs was detected but 9.39 μmol/g-coal of methane was produced. This result suggests that M. shengliensis AmaM produced methane from undetectable MACs dissolved in the media as well as those chemically or physically bound to the coal surface. This was supported by the ability of M. shengliensis AmaM to use a wide variety of MACs (>30 types of MACs) for methanogenesis (Fig. 1B).
Fig. 2 Methanogenesis from coal samples by Methermicoccus shengliensis AmaM.
(A) Methane production in a medium with lignite, subbituminous coal, or bituminous coal. Information for each coal sample is shown in fig. S2. A small amount of methane in the media without substrate was detected as a result of carryover from methanol-grown preculture. Data are means of three individual incubations; error bars represent SD of these triplicates. +, inoculated; –, not inoculated. (B) MACs, methanol, and methylamines detected in the media with coal samples before inoculation of M. shengliensis AmaM. The GC-MS analyses were performed in duplicate; average concentrations are shown. ND, not detected; TR, detected but below the range of concentration for which the calibration curve could be applied.
If methoxydotrophic methanogenesis proceeds in analogy to methylotrophic methanogenesis, it is expected from stoichiometry that ¾ mol of methane is produced from 1 mol of the methoxy group (4Ar-OCH3 + 2H2O → 4Ar-OH + 3CH4 + CO2, where Ar denotes any aromatic group). During incubation with 2-methoxy-benzoate, M. shengliensis AmaM produced methane and 2-hydroxy-benzoate with a decrease in 2-methoxy-benzoate (Fig. 3). The 2-hydroxy-benzoate produced was nearly equivalent to the 2-methoxy-benzoate consumed, which suggests that M. shengliensis AmaM produced methane via O-demethylation of the methoxy group.
Fig. 3 Methanogenesis from 2-methoxy-benzoate by Methermicoccus shengliensis AmaM.
All symbols represent means of three individual incubations; error bars represent SD of these triplicates.
We conducted stable isotope tracer experiments to elucidate the mode of metabolism in the methoxydotrophic methanogenesis. In the incubation of M. shengliensis AmaM with 2-[13C]methoxy-benzoate, the 13C contents of methane increased with increasing contents of 13C at the methoxy group (Fig. 4A), indicating that the methoxy carbon was incorporated into methane. However, the incorporation efficiency from the methoxy group to methane, estimated as the slope of the regression line between the 13C contents of methane and the methoxy group, was 63.6% (Fig. 4A). By contrast, in the incubation with [13C]methanol, we estimated that nearly all (96.4%) of the methane carbon came from the substrate methanol. This implies that additional carbon (other than methoxy carbon) is incorporated into methane during MACs-driven methanogenesis.
Fig. 4 Stable isotope tracer experiments to elucidate the mode of metabolism in methoxydotrophic methanogenesis.
(A) Carbon isotopic relationship between methane produced by M. shengliensis AmaM and either methanol or the methoxy group of 2-methoxy-benzoate added to the media. The slopes of the regression lines show the efficiency of carbon incorporation from each substrate into methane. (B) Carbon isotopic relationship between methane produced from either methanol or 2-methoxy-benzoate and carbon dioxide. The slopes of the regression lines show the efficiency of carbon incorporation from carbon dioxide into methane. Each symbol represents one of three individual incubations.
To identify this additional carbon, we evaluated whether CO2 was incorporated into methane via CO2 reduction. We incubated M. shengliensis AmaM with 2-methoxy-benzoate or methanol in the medium amended with [13C]bicarbonate. Although the 13C contents of methane increased only slightly in the presence of methanol, those of methane in the presence of 2-methoxy-benzoate increased far more substantially (Fig. 4B), indicating that CO2 is also incorporated into methane via CO2 reduction in methoxydotrophic methanogenesis. The incorporation efficiency from CO2 into methane, estimated as the slope of the regression line (Fig. 4B), was 29.6%. Considering that the incorporation efficiency from the methoxy group to methane is 63.6% (Fig. 4A), approximately one-third of methane carbon is derived from CO2 and two-thirds of methane carbon from the methoxy group. In the incubation of M. shengliensis AmaM with a variety of coals in the presence of [13C]bicarbonate, we observed the production of highly 13C-enriched methane, which indicates that methane produced from coal was mostly derived from MACs (fig. S3).
Further tracer experiments incubating M. shengliensis AmaM with 2-methoxy-benzoate in the medium amended with [2-13C]acetate revealed a small but substantial incorporation of the acetate methyl carbon into methane (fig. S4). The acetate concentration in the medium did not change during growth, implying no intentional uptake of extracellular acetate through acetoclastic methanogenesis. We therefore infer that acetyl–coenzyme A (CoA) could be a catabolic intermediate in the methoxydotrophic methanogenesis. M. shengliensis AmaM genes encode acetyl-CoA synthesis, acetyl-CoA oxidation, and CO2-reducing methanogenesis, but its genome lacks known acetogen-associated genes for O-demethylation of the methoxy group (e.g., Mtv system) (22, 23) and electron transport systems (e.g., Rnf, complete Fpo complex, etc.) (20) necessary for conventional methanogenesis (table S2). Although details of the metabolic pathway in the methoxydotrophic methanogenesis remain elusive, all the results indicate that the mode of metabolism is clearly different from the conventional methylotrophic methanogenesis.
Our finding that MACs serve as a direct substrate for methanogens may not be limited to coal-bed environments. In the deep subsurface, MACs are contained in sedimentary organic matter derived from lignin in higher plants, namely kerogen, with quantitative variation depending on the maturity (24). In fact, alkyl-methoxy-phenols with a short C1-C3 chain have been detected in the pyrolysates of immature kerogen extracted from a Cretaceous (Cenomanian) black shale (25). Kerogen is ubiquitous in sediments and accounts for most of the organic matter in subsurface environments (26). Microorganisms from the genus Methermicoccus and related clones have often been detected in deep subsurface environments worldwide (fig. S5). Methoxydotrophic methanogenesis may therefore play an important role in the biogeochemical carbon cycle in Earth as well as in the formation of biogenic gas, which accounts for more than 20% of natural gas resources, including CBM (27).
Acknowledgments
We thank Japan Petroleum Exploration Co., Ltd. (JAPEX) for providing samples from an oil reservoir; F. Nozawa, K. Shuin, Y. Shinotsuka, T. Ujiie, and X. Meng for technical support; and M. Nobu for valuable comments. Supported by JSPS KAKENHI grants JP26709070, JP25289333, JP26710012, and JP26106004. M. shengliensis strain AmaM has been deposited as accession number NBRC 112467 in the Biological Resource Center, National Institute of Technology and Evaluation (NBRC). Genomic data of M. shengliensis strain AmaM are available in the Integrated Microbial Genomes system of the U.S. Department of Energy Joint Genome Institute with ID no. 2516653088 (Gold Project ID: Gp0021722).
Supplementary Material
Summary
Materials and Methods
Figs. S1 to S5
Tables S1 and S2
Resources
File (mayumi.sm.pdf)
- Download
- 11.86 MB
References and Notes
1
World Energy Outlook 2015 (International Energy Agency, 2015).
2
Strąpoć D., Mastalerz M., Eble C., Schimmelmann A., Characterization of the origin of coalbed gases in southeastern Illinois Basin by compound-specific carbon and hydrogen stable isotope ratios. Org. Geochem. 38, 267–287 (2007).
3
Thielemann T., Cramer B., Schippers A., Coalbed methane in the Ruhr Basin, Germany: A renewable energy resource? Org. Geochem. 35, 1537–1549 (2004).
4
Strąpoć D., Mastalerz M., Dawson K., Macalady J., Callaghan A. V., Wawrik B., Turich C., Ashby M., Biogeochemistry of microbial coal-bed methane. Annu. Rev. Earth Planet. Sci. 39, 617–656 (2011).
5
Shimizu S., Akiyama M., Naganuma T., Fujioka M., Nako M., Ishijima Y., Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan. Geobiology 5, 423–433 (2007).
6
Green M. S., Flanegan K. C., Gilcrease P. C., Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, USA. Int. J. Coal Geol. 76, 34–45 (2008).
7
Harris S. H., Smith R. L., Barker C. E., Microbial and chemical factors influencing methane production in laboratory incubations of low-rank subsurface coals. Int. J. Coal Geol. 76, 46–51 (2008).
8
Krüger M., Beckmann S., Engelen B., Thielemann T., Cramer B., Schippers A., Cypionka H., Microbial methane formation from hard coal and timber in an abandoned coal mine. Geomicrobiol. J. 25, 315–321 (2008).
9
Penner T. J., Foght J. M., Budwill K., Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures. Int. J. Coal Geol. 82, 81–93 (2010).
10
Inagaki F., Hinrichs K.-U., Kubo Y., Bowles M. W., Heuer V. B., Hong W.-L., Hoshino T., Ijiri A., Imachi H., Ito M., Kaneko M., Lever M. A., Lin Y.-S., Methé B. A., Morita S., Morono Y., Tanikawa W., Bihan M., Bowden S. A., Elvert M., Glombitza C., Gross D., Harrington G. J., Hori T., Li K., Limmer D., Liu C.-H., Murayama M., Ohkouchi N., Ono S., Park Y.-S., Phillips S. C., Prieto-Mollar X., Purkey M., Riedinger N., Sanada Y., Sauvage J., Snyder G., Susilawati R., Takano Y., Tasumi E., Terada T., Tomaru H., Trembath-Reichert E., Wang D. T., Yamada Y., Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor. Science 349, 420–424 (2015).
Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10(4) cells cm(-3). Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.
11
Ritter D., Vinson D., Barnhart E., Akob D. M., Fields M. W., Cunningham A. B., Orem W., McIntosh J. C., Enhanced microbial coalbed methane generation: A review of research, commercial activity, and remaining challenges. Int. J. Coal Geol. 146, 28–41 (2015).
12
D. W. van Krevelen, Coal: Typology, Chemistry, Physics, Constitution (Elsevier, 1993).
13
Vandenbroucke M., Largeau C., Kerogen origin, evolution and structure. Org. Geochem. 38, 719–833 (2007).
14
Stout S. A., Boon J. J., Spackman W., Molecular aspects of the peatification and early coalification of angiosperm and gymnosperm woods. Geochim. Cosmochim. Acta 52, 405–414 (1988).
15
Stafford H. A., Proanthocyanidins and the lignin connection. Phytochemistry 27, 1–6 (1988).
16
Hatcher P. G., Clifford D. J., The organic geochemistry of coal: From plant materials to coal. Org. Geochem. 27, 251–274 (1997).
17
Jones E. J. P., Voytek M. A., Warwick P. D., Corum M. D., Cohn A., Bunnell J. E., Clark A. C., Orem W. H., Bioassay for estimating the biogenic methane-generating potential of coal samples Int. J. Coal Geol. 76, 138–150 (2008).
18
Guo H., Yu Z., Liu R., Zhang H., Zhong Q., Xiong Z., Methylotrophic methanogenesis governs the biogenic coal bed methane formation in Eastern Ordos Basin, China. Appl. Microbiol. Biotechnol. 96, 1587–1597 (2012).
To identify themethanogenic pathways present in a deep coal bed methane (CBM) reservoir associated with Eastern Ordos Basin in China, a series of geochemical and microbiological studies was performed using gas and water samples produced from the Liulin CBM reservoir. The composition and stable isotopic ratios of CBM implied a mixed biogenic and thermogenic origin of the methane. Archaeal 16S rRNA gene analysis revealed the dominance of the methylotrophic methanogen Methanolobus in the water produced. The high potential of methane production by methylotrophic methanogens was found in the enrichments using the water samples amended with methanol and incubated at 25 and 35 °C. Methylotrophic methanogens were the dominant archaea in both enrichments as shown by polymerase chain reaction (PCR)–denaturing gradient gel electrophoresis (DGGE). Bacterial 16S rRNA gene analysis revealed that fermentative, sulfate-reducing, and nitrate-reducing bacteria inhabiting the water produced were a factor in coal biodegradation to fuel methanogens. These results suggested that past and ongoing biodegradation of coal by methylotrophic methanogens and syntrophic bacteria, as well as thermogenic CBM production, contributed to the Liulin CBM reserves associated with the Eastern Ordos Basin.
19
D. Strąpoć, M. Ashby, L. Wood, R. Levinson, B. Huizinga, in Applied Microbiology and Molecular Biology in Oilfield Systems, C. Whitby, T. Skovhus, Eds. (Springer, 2010), chap. 25.
20
Thauer R. K., Kaster A.-K., Seedorf H., Buckel W., Hedderich R., Methanogenic archaea: Ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6, 579–591 (2008).
Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.
21
Cheng L., Qiu T.-L., Yin X.-B., Wu X.-L., Hu G.-Q., Deng Y., Zhang H., Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int. J. Syst. Evol. Microbiol. 57, 2964–2969 (2007).
A thermophilic, methylotrophic methanogen, strain ZC-1(T), was isolated from the Shengli oilfield, China. Cells of strain ZC-1(T) were motile cocci, 0.7-1.0 microm in diameter and always occurred in clusters of two to four cells. Lysis-susceptibility experiments and analysis of transmission electron micrographs of strain ZC-1(T) suggested the presence of a proteinaceous cell wall. Strain ZC-1(T) used methanol, methylamine and trimethylamine as substrates for methanogenesis. Optimal growth, with a doubling time of around 5 h, occurred at pH 6.0-6.5, 65 degrees C, 0.3-0.5 M NaCl and 0.05-0.20 M MgCl(2). The DNA G+C content of this organism was 56 mol%. Analysis of 16S rRNA gene sequence and the inferred amino acid sequence of the mcrA gene of strain ZC-1(T) indicated that it is related specifically to members of the family Methanosaetaceae (90.6 and 76.6 % sequence similarity, respectively). However, strain ZC-1(T) failed to grow with acetate as substrate for methanogenesis, which is a special characteristic of the family Methanosaetaceae. Based on these phenotypic and phylogenic characteristics, strain ZC-1(T) is proposed to represent a novel genus and species, for which the name Methermicoccus shengliensis gen. nov., sp. nov. is proposed. The type strain is ZC-1(T) (=CGMCC 1.5056(T)=DSM 18856(T)). Methermicoccaceae fam. nov. is also proposed.
22
Pierce E., Xie G., Barabote R. D., Saunders E., Han C. S., Detter J. C., Richardson P., Brettin T. S., Das A., Ljungdahl L. G., Ragsdale S. W., The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ. Microbiol. 10, 2550–2573 (2008).
This paper describes the genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood-Ljungdahl pathway of CO and CO(2) fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into 3 mol of acetate and to grow autotrophically using H(2) and CO as electron donors and CO(2) as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO(2). Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols and aromatic compounds) and electron acceptors (CO(2), nitrate, nitrite, thiosulfate, dimethylsulfoxide and aromatic carboxyl groups). The genome consists of a single circular 2 628 784 bp chromosome encoding 2615 open reading frames (ORFs), which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. A total of 2384 (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in orthologue clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.
23
Ragsdale S. W., Pierce E., Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim. Biophys. Acta 1784, 1873–1898 (2008).
Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO(2) fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO(2) fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered.
24
J. W. De Leeuw, C. Largeau, in Organic Geochemistry, M. H. Engel, S. A. Macko, Eds. (Plenum, 1993), chap. 2.
25
Salmon V., Derenne S., Largeau C., Beaudoin B., Bardoux G., Mariotti A., Kerogen chemical structure and source organisms in a Cenomanian organic-rich black shale (Central Italy) - Indications for an important role of the “sorptive protection” pathway. Org. Geochem. 27, 423–438 (1997).
26
B. Durand, Kerogen, Insoluble Organic Matter from Sedimentary Rocks (Editions Technip, 1980), chap. 1.
27
Katz B. J., Microbial processes and natural gas accumulations. Open Geol. J. 5, 75–83 (2011).
28
Sekiguchi Y., Kamagata Y., Nakamura K., Ohashi A., Harada H., Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int. J. Syst. Evol. Microbiol. 50, 771–779 (2000).
A new anaerobic, thermophilic, syntrophic, fatty-acid-oxidizing bacterium designated strain TGB-C1T was isolated from granular sludge in a thermophilic upflow anaerobic sludge blanket (UASB) reactor. The cells were slightly curved rods and were weakly motile. Spore formation was not observed. The optimal temperature for growth was around 55 degrees C and growth occurred in the range 45 to 60 degrees C. The pH range for growth was 5.8-7.5, and the optimum pH was 6.5-7.0. Crotonate was the only substrate that allowed the strain to grow in pure culture. However, in co-culture with the thermophilic, hydrogenotrophic Methanobacterium thermoautotrophicum strain delta H, the isolate could syntrophically oxidize saturated fatty acids with 4-10 carbon atoms, including isobutyrate. During the degradation of isobutyrate by the co-culture, isobutyrate was isomerized to butyrate, which was then oxidized. The strain was not able to utilize sulfate, sulfite, thiosulfate, nitrate, fumarate or Fe(III) as electron acceptor. The DNA base composition was 51.0 mol%. 16S rDNA sequence analysis revealed that the strain belongs to the family Syntrophomonadaceae, but it was only distantly related to other known species of beta-oxidizing syntrophs. Hence, the name Syntrophothermus lipocalidus is proposed for TGB-C1T as a new species of a new genus.
29
Pati A., Ivanova N. N., Mikhailova N., Ovchinnikova G., Hooper S. D., Lykidis A., Kyrpides N. C., GenePRIMP: A gene prediction improvement pipeline for prokaryotic genomes. Nat. Methods 7, 455–457 (2010).
We present ‘gene prediction improvement pipeline’ (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.
30
Markowitz V. M., Mavromatis K., Ivanova N. N., Chen I. M., Chu K., Kyrpides N. C., IMG ER: A system for microbial genome annotation expert review and curation. Bioinformatics 25, 2271–2278 (2009).
Motivation: A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct.
Results: We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG’s rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER’s annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG’s comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.
31
Markowitz V. M., Chen I. M., Palaniappan K., Chu K., Szeto E., Pillay M., Ratner A., Huang J., Woyke T., Huntemann M., Anderson I., Billis K., Varghese N., Mavromatis K., Pati A., Ivanova N. N., Kyrpides N. C., IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 42, D560–D567 (2014).
The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).
32
G. D. Stricker, R. M. Flores, M. H. Trippi, M. S. Ellis, C. M. Olson, J. E. Sullivan, K. I. Takahashi, Coal Quality and Major, Minor, and Trace Elements in the Power River, Green River, and Williston Basins, Wyoming and North Dakota (U.S. Geological Survey Open-File Report 2007-1116, 2007).
(0)eLetters
eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.
Log In to Submit a ResponseNo eLetters have been published for this article yet.
Information & Authors
Information
Published In
Science
Volume 354 | Issue 6309
14 October 2016
14 October 2016
Copyright
Copyright © 2016, American Association for the Advancement of Science.
Submission history
Received: 12 May 2016
Accepted: 29 August 2016
Published in print: 14 October 2016
Acknowledgments
We thank Japan Petroleum Exploration Co., Ltd. (JAPEX) for providing samples from an oil reservoir; F. Nozawa, K. Shuin, Y. Shinotsuka, T. Ujiie, and X. Meng for technical support; and M. Nobu for valuable comments. Supported by JSPS KAKENHI grants JP26709070, JP25289333, JP26710012, and JP26106004. M. shengliensis strain AmaM has been deposited as accession number NBRC 112467 in the Biological Resource Center, National Institute of Technology and Evaluation (NBRC). Genomic data of M. shengliensis strain AmaM are available in the Integrated Microbial Genomes system of the U.S. Department of Energy Joint Genome Institute with ID no. 2516653088 (Gold Project ID: Gp0021722).
Authors
Metrics & Citations
Metrics
Article Usage
Altmetrics
Citations
Cite as
- Daisuke Mayumi et al.
Export citation
Select the format you want to export the citation of this publication.
Cited by
- Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China, Frontiers in Microbiology, 14, (2023).https://doi.org/10.3389/fmicb.2023.1114201
- Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles, Microbiology Spectrum, 11, 2, (2023).https://doi.org/10.1128/spectrum.04145-22
- Coalbed Methane Hydrate Separation: An Experimental Study Using Ordered Mesoporous Materials, Industrial & Engineering Chemistry Research, 62, 12, (4864-4874), (2023).https://doi.org/10.1021/acs.iecr.2c03994
- Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens, Environmental Science & Technology, 57, 12, (5089-5101), (2023).https://doi.org/10.1021/acs.est.2c07461
- Proteomic profiling of robust acetoclastic methanogen in chrysene-altered anaerobic digestion: Global dissection of enzymes, Water Research, 233, (119817), (2023).https://doi.org/10.1016/j.watres.2023.119817
- Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri, Water Research, 232, (119664), (2023).https://doi.org/10.1016/j.watres.2023.119664
- Feasibility analysis of clean utilization of kitchen waste oil and lignite by co-fermentation treatment, Journal of Cleaner Production, 397, (136267), (2023).https://doi.org/10.1016/j.jclepro.2023.136267
- Field experiment of stress sensitivity effect in the Mabidong CBM block, southern Qinshui Basin, China, Geoenergy Science and Engineering, 222, (211441), (2023).https://doi.org/10.1016/j.geoen.2023.211441
- Effect of fat, oil and grease (FOG) on the conversion of lignite to biogenic methane, Fuel, 331, (125367), (2023).https://doi.org/10.1016/j.fuel.2022.125367
- Biogenic methane in coastal unconsolidated sediment systems: A review, Environmental Research, 227, (115803), (2023).https://doi.org/10.1016/j.envres.2023.115803
- See more
Loading...
View Options
View options
PDF format
Download this article as a PDF file
Download PDFCheck Access
Log in to view the full text
AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.
- Become a AAAS Member
- Activate your AAAS ID
- Purchase Access to Other Journals in the Science Family
- Account Help
Log in via OpenAthens.
Log in via Shibboleth.
More options
Register for free to read this article
As a service to the community, this article is available for free. Login or register for free to read this article.
Buy a single issue of Science for just $15 USD.