Role of Bacteria, Archaea and Fungi involved in Methane Release in Abandoned Coal Mines

REFERENCES

• Altschul , S F , Madden , T L , Schaffer , A A , Zhang , J H , Zhang , Z , Miller , W and Lipman , D J . 1997 . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs . Nucleic Acids Res , 25 : 3389 – 3402 .
   PubMed Web of Science ®Google Scholar
• Brodie , E , Edwards , S and Clipson , N . 2003 . Soil fungal community structure in a temperate upland grassland soil . FEMS Microbiol Ecolo , 45 : 105 – 114 .
   PubMed Web of Science ®Google Scholar
• Clausen , CA. 1995 . Dissociation of the multienzyme complex of the brown-rot fungus postia-placenta . FEMS Microbiol Lett , 127 : 73 – 78 .
   Web of Science ®Google Scholar
• Del Panno , M , Morelli , I , Engelen , B and Berthe-Corti , L . 2005 . Effect of petrochemical sludge concentration on microbial communities during a soil bioremediation process . FEMS Microbiol Ecol , 53 : 305 – 316 .
   PubMed Web of Science ®Google Scholar
• Denman , K , Brasseur , G , Chidthaisong , A , Ciais , P , Cox , P , Dickinson , R and Hauglustaine , D . 2007 . “ Couplings between changes in the climate system and biogeochemistry ” . In Climate Change 2007: The Physical Science Basis. Conribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change , Edited by: Solomon , S , Qin , D , Manning , M , Chen , Z , Marquis , M , Averyt , K B , Tignor , M and Miller , H L . Cambridge and New York : Cambridge University Press .
   Google Scholar
• Deobald , L A and Crawford , D L . 1987 . Activities of cellulase and other extracellular enzymes during lignin solubilization by Streptomyces-Viridosporus . Appl Microbiol Biotechnol , 26 : 158 – 163 .
   Web of Science ®Google Scholar
• Engelen , B , Ziegelmüller , K , Wolf , L , Köpke , B , Gittel , A , Cypionka , H , Treude , T , Nakagawa , S , Inagaki , F , Lever , M A and Steinsbu , B O . 2008 . Fluids from the oceanic crust support microbial activities within the deep biosphere . Geomicrobiol J , 25 : 56 – 66 .
   Web of Science ®Google Scholar
• Fakoussa , RM. 1990 . “ Microbiological treatment of German hard coal ” . In Bioprocessing and biotreatment of coal , Edited by: Wise , D L . 95 – 107 . New York : Marcel Dekker .
   Google Scholar
• Fakoussa , R M and Hofrichter , M . 1999 . Biotechnology and microbiology of coal degradation . Appl Microbiol Biotechnol , 52 : 25 – 40 .
   PubMed Web of Science ®Google Scholar
• Flores , RM. 2008 . Microbes, methanogenesis, and microbial gas in coal . Inter J Coal Geol , 76 : 1 – 2 .
   Web of Science ®Google Scholar
• Fry , C J , Horsfield , B , Sykes , R , Cragg , B A , Heywood , C , Kim , G T , Mangelsdorf , K , Mildenhall , D C , Rinna , J , Vieth , A , Zink , K-G , Sass , H , Weightman , A J and Parkes , R J . 2009 . Prokaryotic populations and activities in an interbedded coal deposit, including a previously deeply buried section (1.6-2.3 km) above 150 Ma basement rock . Geomicrobiol J , 26 : 163 – 178 .
   Web of Science ®Google Scholar
• Green , M S , Flanegan , K C and Gilcrease , P C . 2008 . Characterization of a methanogenic consortium enriched from a coalbed methane well in the Powder River Basin, USA . Inter J Coal Geol , 76 : 34 – 45 .
   Web of Science ®Google Scholar
• Head , I M , Jones , D M and Larter , S R . 2003 . Biological activity in the deep subsurface and the origin of heavy oil . Nature , 426 : 344 – 352 .
   PubMed Web of Science ®Google Scholar
• Hosgörmez , H , Yalcin , N M , Cramer , B , Gerling , P , Faber , E , Schäfer , R G and Mann , U . 2002 . Isotopic and molecular composition of coal-bed gas in the Amasra region (Zonguldak basin – western Black Sea) . Organ Geochem , 33 : 1429 – 1439 .
   Web of Science ®Google Scholar
• Hurek , T and Reinholdhurek , B . 1995 . Identification of grass-associated and toluene-degrading diazotrophs, Azoarcus spp, by analyses of partial 16S ribosomal DNA-sequences . Appl EnvironMicrobiol , 61 : 2257 – 2261 .
   PubMed Web of Science ®Google Scholar
• Jurgensen , MF. 1973 . Relationship between nonsymbiotic and nitrogen fixation and soil nutrient status – A review . J Soil Sci , 24 : 512 – 522 .
   Web of Science ®Google Scholar
• Jurgensen , M F , Larsen , M J , Spano , S D , Harvey , A E and Gale , M R . 1984 . Nitrogen fixation associated with increased wood decay in Douglas-Fir Residue . Forest Sci , 30 : 1038 – 1044 .
   Web of Science ®Google Scholar
• Krüger , M , Frenzel , P and Conrad , R . 2001 . Microbial processes influencing methane emission from rice fields . Global Change Biol , 7 : 49 – 63 .
   Web of Science ®Google Scholar
• Krüger , M , Beckmann , S , Engelen , B , Thielemann , T , Cramer , B , Schippers , A and Cypionka , H . 2008 . Microbial methane formation from hard coal and timber in an abandoned coal mine . Geomicrobiol J , 25 : 315 – 321 .
   Web of Science ®Google Scholar
• Küsel , K , Dorsch , T , Acker , G , Stackebrandt , E and Drake , H L . 2000 . Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments . Inter J Syst Evol Microbiol , 50 : 537 – 546 .
   PubMed Web of Science ®Google Scholar
• Lane , D. 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic acid techniques in bacterial systematica , Edited by: Stackebrandt , E and Goodfellow , M . 205 – 248 . Chichester, UK : Wiley .
   Google Scholar
• Larena , I , Salazar , O , Gonzalez , V , Julian , M C and Rubio , V . 1999 . Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes . J Biotechnol , 75 : 187 – 194 .
   PubMed Web of Science ®Google Scholar
• Larsen , M J , Jurgensen , M F and Harvey , A E . 1978 . N2 fixation associated with wood decayed by some common fungi in Western Montana . Canadian Journal of Forest Research-Revue Canadienne De Recherche Forestiere , 8 : 341 – 345 .
   Web of Science ®Google Scholar
• Martini , A M , Lynn , M W and McIntosh , J C . 2008 . Identification of microbial and thermogenic gas components from Upper Devonian black shale cores, Illinois and Michigan basins . American Association of Petroleum Geologists Bulletin , 3 : 327 – 339 .
   Web of Science ®Google Scholar
• Muyzer , G , Dewaal , E C and Uitterlinden , A G . 1993 . Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA . Appl Environ Microbiol , 59 : 695 – 700 .
   PubMed Web of Science ®Google Scholar
• Muyzer , G , Teske , A , Wirsen , C O and Jannasch , H W . 1995 . Phylogenetic-relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel-electrophoresis of 16S rDNA fragments . Arch Microbiol , 164 : 165 – 172 .
   PubMed Web of Science ®Google Scholar
• Rogers , G M and Baecker , A AW . 1991 . Clostridium-Xylanolyticum sp-nov, an anaerobic xylanolytic bacterium from decayed Pinus-Patula wood chips . Inter J System Bacteriol , 41 : 140 – 143 .
   Google Scholar
• Schleper , C , Holben , W and Klenk , H P . 1997 . Recovery of crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments . Appl Environ Microbiol , 63 : 321 – 323 .
   PubMed Web of Science ®Google Scholar
• Scott , A C and Fleet , A J . 1994 . Coal and coal-bearing strata as oil-prone source rocks: current problems and future directions . Geological Society of London, Special Publications , 77 : 201 – 205 .
   Google Scholar
• Shimizu , S , Akiyama , M , Naganuma , T , Fujioka , M , Nako , M and Ishijima , Y . 2007 . Molecular characterization of microbial communities in deep coal seam groundwater of northern Japan . Geobiology , 5 : 423 – 433 .
   Web of Science ®Google Scholar
• Shin , S G , Lee , C S , Hwang , K , Ahn , J H and Hwang , S . 2008 . Use of order-specific primers to investigate the methanogenic diversity in acetate enrichment system . J Indust Microbiol Biotechnol , 35 : 1345 – 1352 .
   PubMed Web of Science ®Google Scholar
• Smit , E , Leeflang , P , Glandorf , B , van Elsas , J D and Wernars , K . 1999 . Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis . Appl Environ Microbiol , 65 : 2614 – 2621 .
   PubMed Web of Science ®Google Scholar
• Spano , S D , Jurgensen , M F , Larsen , M J and Harvey , A E . 1982 . Nitrogen-fixing bacteria in Douglas-Fir Residue decayed by Fomitopsis-Pinicola . Plant Soil , 68 : 117 – 123 .
   Web of Science ®Google Scholar
• Strapoc , D , Picardal , F W , Turich , C , Schaperdoth , I , Macalady , J L , Lipp , J S , Lin , Y S , Ertefai , T F , Schubotz , F , Hinrichs , K U , Mastalerz , M and Schimmelmann , A . 2008a . Methane-producing microbial community in a coal bed of the Illinois basin . Appl Environ Microbiol , 74 : 3918 – 3918 .
   Web of Science ®Google Scholar
• Strapoc , D , Mastalerz , M , Schimmelmann , A , Drobniak , A and Hedges , S . 2008b . Variability of geochemical properties in a microbially dominated coalbed gas system from the eastern margin of the Illinois Basin, USA . Inter J Coal Geol , 76 : 98 – 110 .
   Web of Science ®Google Scholar
• Sü , J , Schubert , K , Sass , H , Cypionka , H , Overmann , J and Engelen , B . 2006 . Widespread distribution and high abundance of Rhizobium radiobacter within Mediterranean subsurface sediments . Environ Microbiol , 8 : 1753 – 1763 .
   PubMed Web of Science ®Google Scholar
• Tao , M X , Shi , B G , Li , J Y , Wang , W C , Li , X B and Gao , B . 2007 . Secondary biological coalbed gas in the Xinji area, Anhui province, China: Evidence from the geochemical features and secondary changes . Inter J Coal Geol , 71 : 358 – 370 .
   Web of Science ®Google Scholar
• Thielemann , T , Cramer , B and Schippers , A . 2004 . Coalbed methane in the Ruhr Basin, Germany: a renewable energy resource? . Organ Geochem , 35 : 1537 – 1549 .
   Web of Science ®Google Scholar
• Ulrich , G and Bower , S . 2008 . Active methanogenesis and acetate utilization in Powder River Basin coals, United States . Inter J Coal Geol , 76 : 25 – 33 .
   Web of Science ®Google Scholar
• Vetriani , C , Jannasch , H W , MacGregor , B J , Stahl , D A and Reysenbach , A L . 1999 . Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments . Appl Environ Microbiol , 65 : 4375 – 4384 .
   PubMed Web of Science ®Google Scholar
• Warwick , P D , Breland , F C and Hackley , P C . 2008 . Biogenic origin of coalbed gas in the northern Gulf of Mexico Coastal Plain, USA . Inter J Coal Geol , 76 : 119 – 137 .
   Web of Science ®Google Scholar
• Widdel , F and Bak , F . 1992 . “ Gram-negative mesophilic sulfate-reducing bacteria ” . In The Prokaryotes , Edited by: Balows , A , Dworkin , M , Harder , W and Schleifer , K H . 3352 – 3378 . New York : Springer-Verlag .
   Google Scholar
• Wilms , R , Sass , H , Köpke , B , Cypionka , H and Engelen , B . 2007 . Methane and sulfate profiles within the subsurface of a tidal flat are reflected by the distribution of sulfate-reducing bacteria and methanogenic archaea . FEMS Microbiol Ecol , 59 : 611 – 621 .
   PubMed Web of Science ®Google Scholar
• Zinder , SH. 1993 . “ Physiological ecology of methanogens ” . In Methanogenesis: ecology, physiology, biochemistry and genetics , Edited by: Ferry , J C . New York : Chapman & Hall .
   Google Scholar