Advertisement

H2-Metabolizing Prokaryotes

  • Edward SchwartzEmail author
  • Johannes Fritsch
  • Bärbel Friedrich

Abstract

The reversible splitting of H2 into protons and electrons is a key process in the metabolism of many prokaryotes and has been studied extensively in a wide range of bacteria and archaea. Environmental H2 is an energy source for aerobic H2 oxidizers, methanogens, acetogens, and sulfate reducers and is a source of reducing power for anoxygenic phototrophs. H2 is released as a terminal metabolic product of both facultative and obligate fermenters. It is a byproduct of N2 fixation and phosphite oxidation. The H2-consuming and H2-evolving processes of microorganisms impact the global atmospheric H2 balance. N2 fixation in seas and lakes is a significant source of atmospheric H2. Soils are a major H2 sink. Entirely H2-based microbial ecosystems are widespread on the planet. The most important of them consists of the granitic layers of the planet’s crust, which on aggregate harbor a huge fraction of the total biomass on Earth. More spectacular are the submarine hydrothermal vents spewing H2-rich fluids. Current scenarios of pre- and protobiotic evolution envisage such sites as the cradle of terrestrial life. Based on their metal content, hydrogenases, the enzymes which catalyze the splitting of H2, can be divided into three groups of independent phylogenetic origin: [NiFe], [FeFe], and [Fe] hydrogenases. Three-dimensional structures available for representatives of all three groups reveal some remarkable features of these enzymes. The actual catalyst is a NiFe or Fe metallocomplex encased in a protein. Tunnels in the protein allow H2 to access or egress from the active site. A series of FeS clusters form an electrical circuit connecting the active site with binding sites (for cytochromes, pyridine nucleotides, and other redox partners) at the surface of the enzyme. The assembly and insertion of the active-site metallocomplex into the hydrogenase apoenzyme is an intricate, multistep process requiring several specialized accessory proteins. The genetic determinants for the hydrogenase catalytic components and for the accessory proteins are solitary or clustered. The mechanisms governing the expression of hydrogenase genes vary depending on physiological context. In obligate fermenters, for instance, expression of hydrogenase genes is typically constitutive. In facultative H2 oxidizers, on the other hand, hydrogenase gene expression is controlled by H2-sensing regulatory proteins. The diversity of metabolic processes involving H2 as an intermediate and the ubiquitous occurrence of hydrogenases in microbes testify to the importance of H2 metabolism in primeval cellular life forms.

Notes

Acknowledgments

The authors are indebted to their colleague O. Lenz for helpful comments on the manuscript.

References

  1. Abdel-Basset R, Bader KP (1998) Physiological analyses of the hydrogen gas exchange in cyanobacteria. J Photochem Photobiol B 43:146–151CrossRefGoogle Scholar
  2. Abram JW, Nedwell DB (1978) Hydrogen as a substrate for methanogenesis and sulphate reduction in anaerobic saltmarsh sediment. Arch Microbiol 117:93–97PubMedCrossRefGoogle Scholar
  3. Achtnich C, Bak F, Conrad R (1995a) Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers, and methanogens in anoxic paddy soil. Biol Fertil Soils 19:65–72CrossRefGoogle Scholar
  4. Achtnich C, Schuhmann A, Wind T, Conrad R (1995b) Role of interspecies H2 transfer to sulfate and ferric iron-reducing bacteria in acetate consumption in anoxic paddy soil. FEMS Microbiol Ecol 16:61–70CrossRefGoogle Scholar
  5. Adams MW (1990) The structure and mechanism of iron-hydrogenases. Biochim Biophys Acta 1020:115–145PubMedCrossRefGoogle Scholar
  6. Adams MW, Hall DO (1977) Isolation of the membrane-bound hydrogenase from Rhodospirillum rubrum. Biochem Biophys Res Commun 77:730–737PubMedCrossRefGoogle Scholar
  7. Adams MW, Hall DO (1979a) Properties of the solubilized membrane-bound hydrogenase from the photosynthetic bacterium Rhodospirillum rubrum. Arch Biochem Biophys 195:288–299PubMedCrossRefGoogle Scholar
  8. Adams MW, Hall DO (1979b) Purification of the membrane-bound hydrogenase of Escherichia coli. Biochem J 183:11–22PubMedGoogle Scholar
  9. Adams MW, Stiefel EI (1998) Biological hydrogen production: not so elementary. Science 282:1842–1843PubMedCrossRefGoogle Scholar
  10. Adams MW, Eccleston E, Howard JB (1989) Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum. Proc Natl Acad Sci USA 86:4932–4936PubMedCrossRefGoogle Scholar
  11. Adams MW, Holden JF, Menon AL, Schut GJ, Grunden AM, Hou C, Hutchins AM, Jenney FE Jr, Kim C, Ma K, Pan G, Roy R, Sapra R, Story SV, Verhagen MF (2001) Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 183:716–724PubMedCrossRefGoogle Scholar
  12. Afting C, Hochheimer A, Thauer RK (1998) Function of H2-forming methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum in coenzyme F420 reduction with H2. Arch Microbiol 169:206–210PubMedCrossRefGoogle Scholar
  13. Afting C, Kremmer E, Brucker C, Hochheimer A, Thauer RK (2000) Regulation of H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) and of HmdII and HmdIII in Methanothermobacter marburgensis. Arch Microbiol 174:225–232PubMedCrossRefGoogle Scholar
  14. Aggag M, Schlegel HG (1973) Studies on a gram-positive hydrogen bacterium, Nocardia opaca strain 1b.1. Description and physiological characterization. Arch Mikrobiol 88:299–318PubMedCrossRefGoogle Scholar
  15. Agron PG, Monson EK, Ditta GS, Helinski DR (1994) Oxygen regulation of expression of nitrogen-fixation genes in Rhizobium meliloti. Res Microbiol 145:454–459PubMedCrossRefGoogle Scholar
  16. Alain K, Pignet P, Zbinden M, Quillevere M, Duchiron F, Donval JP, Lesongeur F, Raguenes G, Crassous P, Querellou J, Cambon-Bonavita MA (2002) Caminicella sporogenes gen. nov., sp. nov., a novel thermophilic spore-forming bacterium isolated from an East-Pacific Rise hydrothermal vent. Int J Syst Evol Microbiol 52:1621–1628PubMedCrossRefGoogle Scholar
  17. Albracht SPJ (1994) Nickel hydrogenases: in search of the active site. Biochim Biophys Acta 1188:167–204PubMedCrossRefGoogle Scholar
  18. Albracht SPJ (2001) Spectroscopy—the functional puzzle. In: Cammack R, Frey M, Robson R (eds) Hydrogen as a fuel: learning from nature. Taylor & Francis, London, pp 110–158Google Scholar
  19. Albracht SPJ, Hedderich R (2000) Learning from hydrogenases: location of a proton pump and of a second FMN in bovine NADH–ubiquinone oxidoreductase (Complex I). FEBS Lett 485:1–6PubMedCrossRefGoogle Scholar
  20. Alex LA, Reeve JN, Orme-Johnson WH, Walsh CT (1990) Cloning, sequence determination, and expression of the genes encoding the subunits of the nickel-containing 8-hydroxy-5-deazaflavin reducing hydrogenase from Methanobacterium thermoautotrophicum delta H. Biochemistry 29:7237–7244PubMedCrossRefGoogle Scholar
  21. Anderson L, Fuller RC (1967) Photosynthesis in Rhodospirillum rubrum. I. Autotrophic carbon dioxide fixation. Plant Physiol 42:487–490PubMedCrossRefGoogle Scholar
  22. Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P, Guest JR (1997) A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system. Microbiology 143:3633–3647PubMedCrossRefGoogle Scholar
  23. Antal TK, Oliveira P, Lindblad P (2006) The bidirectional hydrogenase in the cyanobacterium Synechocystis sp. strain PCC 6803. Int J Hydrogen Energy 31:1439–1444CrossRefGoogle Scholar
  24. Appel J, Schulz R (1998) Hydrogen metabolism in organisms with oxygenic photosynthesis: hydrogenases as important regulatory devices for a proper redox poising? J Photochem Photobiol B 47:1–11CrossRefGoogle Scholar
  25. Appel J, Phunpruch S, Steinmüller K, Schulz R (2000) The bidirectional hydrogenase of Synechocystis sp. PCC 6803 works as an electron valve during photosynthesis. Arch Microbiol 173:333–338PubMedCrossRefGoogle Scholar
  26. Aragno M, Schlegel HG (1977) Alcaligenes ruhlandii (Packer and Vishniac) comb. nov., a peritrichous hydrogen bacterium previously assigned to pseudomonas. Int J Syst Bacteriol 27:279–281CrossRefGoogle Scholar
  27. Aragno M, Schlegel HG (1978) Aquaspirillum autotrophicum, a new species of hydrogen-oxidizing, facultatively autotrophic bacteria. Int J Syst Bacteriol 28:112–116CrossRefGoogle Scholar
  28. Aragno M, Schlegel HG (1992) The mesophilic hydrogen-oxidizing (knallgas) bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes. A handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, New York, pp 344–384Google Scholar
  29. Arp DJ (1992) Hydrogen recycling in symbiotic bacteria. In: Stacey GS, Burris RH, Evans HJ (eds) Biological nitrogen fixation. Chapman & Hall, New York, pp 432–460Google Scholar
  30. Aspen AJ, Wolin MJ (1966) Solubilization and reconstitution of a particulate hydrogenase from Vibrio succinogenes. J Biol Chem 241:4152–4156PubMedGoogle Scholar
  31. Atlung T, Knudsen K, Heerfordt L, Brondsted L (1997) Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation. J Bacteriol 179:2141–2146PubMedGoogle Scholar
  32. Atomi H, Fukui T, Kanai T, Morikawa M, Imanaka T (2004) Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archaea 1:263–267PubMedCrossRefGoogle Scholar
  33. Atta M, Meyer J (2000) Characterization of the gene encoding the [Fe]-hydrogenase from Megasphaera elsdenii. Biochim Biophys Acta 1476:368–371PubMedCrossRefGoogle Scholar
  34. Bader KP, Abdel-Basset R (1999) Mass spectrometric analysis of hydrogen photoevolution in the filamentous non-heterocystous cyanobacterium Oscillatoria chalybea. In: Peschek GA, Löffelhardt W, Schmetterer G (eds) The phototrophic prokaryotes. Kluwer/Plenum, New York, pp 603–609CrossRefGoogle Scholar
  35. Badziong W, Thauer RK, Zeikus JG (1978) Isolation and characterization of Desulfovibrio growing on hydrogen plus sulfate as the sole energy source. Arch Microbiol 116:41–49PubMedCrossRefGoogle Scholar
  36. Bagley KA, Van Garderen CJ, Chen M, Duin EC, Albracht SP, Woodruff WH (1994) Infrared studies on the interaction of carbon monoxide with divalent nickel in hydrogenase from Chromatium vinosum. Biochemistry 33:9229–9236PubMedCrossRefGoogle Scholar
  37. Bagley KA, Duin EC, Roseboom W, Albracht SP, Woodruff WH (1995) Infrared-detectable groups sense changes in charge density on the nickel center in hydrogenase from Chromatium vinosum. Biochemistry 34:5527–5535PubMedCrossRefGoogle Scholar
  38. Bagyinka C, Kovacs KL, Rak E (1982) Localization of hydrogenase in Thiocapsa roseopersicina photosynthetic membrane. Biochem J 202:255–258PubMedGoogle Scholar
  39. Balch WE, Schoberth S, Tanner RS, Wolfe RS (1977) Acetobacterium, a new genus of hydrogen-oxidizing, carbon dioxide-reducing, anaerobic bacteria. Int J Syst Bacteriol 27:355–361CrossRefGoogle Scholar
  40. Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol 47:515–521PubMedCrossRefGoogle Scholar
  41. Balk J, Pierik AJ, Netz DJ, Muhlenhoff U, Lill R (2004) The hydrogenase-like Nar1p is essential for maturation of cytosolic and nuclear iron-sulphur proteins. EMBO J 23:2105–2115PubMedCrossRefGoogle Scholar
  42. Ballantine SP, Boxer DH (1985) Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12. J Bacteriol 163:454–459PubMedGoogle Scholar
  43. Ballantine SP, Boxer DH (1986) Isolation and characterisation of a soluble active fragment of hydrogenase isoenzyme 2 from the membranes of anaerobically grown Escherichia coli. Eur J Biochem 156:277–284PubMedCrossRefGoogle Scholar
  44. Baltazar CSA, Marques MC, Soares CM, DeLacey AM, Pereira IAC, Matias PM (2011) Nickel–iron–selenium hydrogenases—an overview. Eur J Inorg Chem 2011:948–962CrossRefGoogle Scholar
  45. Baltazar CS, Teixeira VH, Soares CM (2012) Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach. J Biol Inorg Chem 17(4):543–555PubMedCrossRefGoogle Scholar
  46. Baron SF, Ferry JG (1989a) Purification and properties of the membrane-associated coenzyme F420-reducing hydrogenase from Methanobacterium formicicum. J Bacteriol 171:3846–3853PubMedGoogle Scholar
  47. Baron SF, Ferry JG (1989b) Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum. J Bacteriol 171:3854–3859PubMedGoogle Scholar
  48. Baron SF, Williams DS, May HD, Patel PS, Aldrich HC, Ferry JG (1989) Immunogold localization of coenzyme-F420-reducing formate dehydrogenase and coenzyme-F420-reducing hydrogenase in Methanobacterium formicicum. Arch Microbiol 151:307–313CrossRefGoogle Scholar
  49. Bartha R, Ordal EJ (1965) Nickel-dependent chemolithotrophic growth of two Hydrogenomonas strains. J Bacteriol 89:1015–1019PubMedGoogle Scholar
  50. Barton RM, Worman HJ (1999) Prenylated prelamin A interacts with Narf, a novel nuclear protein. J Biol Chem 274:30008–30018PubMedCrossRefGoogle Scholar
  51. Battaglia-Brunet F, Joulian C, Garrido F, Dictor MC, Morin D, Coupland K, Barrie Johnson D, Hallberg KB, Baranger P (2006) Oxidation of arsenite by Thiomonas strains and characterization of Thiomonas arsenivorans sp. nov. Antonie Van Leeuwenhoek 89:99–108PubMedCrossRefGoogle Scholar
  52. Baumgarten J, Reh M, Schlegel HG (1974) Taxonomic studies on some gram-positive coryneform hydrogen bacteria. Arch Microbiol 100:207–217CrossRefGoogle Scholar
  53. Belay N, Sparling R, Daniels L (1986) Relationship of formate to growth and methanogenesis by Methanococcus thermolithotrophicus. Appl Environ Microbiol 52:1080–1085PubMedGoogle Scholar
  54. Ben-Bassat A, Lamed R, Zeikus JG (1981) Ethanol production by thermophilic bacteria: metabolic control of end product formation in Thermoanaerobium brockii. J Bacteriol 146:192–199PubMedGoogle Scholar
  55. Berghöfer Y, Agha-Amiri K, Klein A (1994) Selenium is involved in the negative regulation of the expression of selenium-free [NiFe] hydrogenases in Methanococcus voltae. Mol Gen Genet 242:369–373PubMedCrossRefGoogle Scholar
  56. Bernalier A, Rochet V, Leclerc M, Dore J, Pochart P (1996a) Diversity of H2/CO2-utilizing acetogenic bacteria from feces of non-methane-producing humans. Curr Microbiol 33:94–99PubMedCrossRefGoogle Scholar
  57. Bernalier A, Willems A, Leclerc M, Rochet V, Collins MD (1996b) Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces. Arch Microbiol 166:176–183PubMedCrossRefGoogle Scholar
  58. Bernhard M, Schwartz E, Rietdorf J, Friedrich B (1996) The Alcaligenes eutrophus membrane-bound hydrogenase gene locus encodes functions involved in maturation and electron transport coupling. J Bacteriol 178:4522–4529PubMedGoogle Scholar
  59. Bernhard M, Benelli B, Hochkoeppler A, Zannoni D, Friedrich B (1997) Functional and structural role of the cytochrome b subunit of the membrane-bound hydrogenase complex of Alcaligenes eutrophus H16. Eur J Biochem 248:179–186PubMedCrossRefGoogle Scholar
  60. Bernhard M, Friedrich B, Siddiqui RA (2000) Ralstonia eutropha TF93 is blocked in tat-mediated protein export. J Bacteriol 182:581–588PubMedCrossRefGoogle Scholar
  61. Bernhard M, Buhrke T, Bleijlevens B, De Lacey AL, Fernandez VM, Albracht SP, Friedrich B (2001) The H2 sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine protein kinase. J Biol Chem 276:15592–15597PubMedCrossRefGoogle Scholar
  62. Bertram PA, Thauer RK (1994) Thermodynamics of the formylmethanofuran dehydrogenase reaction in Methanobacterium thermoautotrophicum. Eur J Biochem 226:811–818PubMedCrossRefGoogle Scholar
  63. Binder U, Maier T, Böck A (1996) Nickel incorporation into hydrogenase 3 from Escherichia coli requires the precursor form of the large subunit. Arch Microbiol 165:69–72PubMedCrossRefGoogle Scholar
  64. Bingemann R, Klein A (2000) Conversion of the central [4Fe-4S] cluster into a [3Fe-4S] cluster leads to reduced hydrogen-uptake activity of the F420-reducing hydrogenase of Methanococcus voltae. Eur J Biochem 267:6612–6618PubMedCrossRefGoogle Scholar
  65. Black LK, Fu C, Maier RJ (1994) Sequences and characterization of hupU and hupV genes of Bradyrhizobium japonicum encoding a possible nickel-sensing complex involved in hydrogenase expression. J Bacteriol 176:7102–7106PubMedGoogle Scholar
  66. Blamey JM, Mukund S, Adams MWW (1994) Properties of a thermostable 4Fe-ferredoxin from the hyperthermophilic bacterium Thermotoga maritima. FEMS Microbiol Lett 121:165–170PubMedCrossRefGoogle Scholar
  67. Blankenship RE (1992) Origin and early evolution of photosynthesis. Photosynth Res 33:91–111PubMedCrossRefGoogle Scholar
  68. Bleijlevens B, Buhrke T, van der Linden E, Friedrich B, Albracht SP (2004) The auxiliary protein HypX provides oxygen tolerance to the soluble [NiFe]-hydrogenase of ralstonia eutropha H16 by way of a cyanide ligand to nickel. J Biol Chem 279:46686–46691PubMedCrossRefGoogle Scholar
  69. Blöchl E, Rachel R, Burggraf S, Hafenbradl D, Jannasch HW, Stetter KO (1997) Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 °C. Extremophiles 1:14–21PubMedCrossRefGoogle Scholar
  70. Blokesch M, Paschos A, Theodoratou E, Bauer E, Hube M, Huth S, Bock A (2002) Metal insertion into NiFe-hydrogenases. Biochem Soc Trans 30:674–680PubMedCrossRefGoogle Scholar
  71. Blokesch M, Paschos A, Bauer A, Reissmann S, Drapal N, Böck A (2004) Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE. Eur J Biochem 271:3428–3436PubMedCrossRefGoogle Scholar
  72. Blotevogel KH, Fischer U, Mocha M, Jannsen S (1985) Methanobacterium thermoalcaliphilum spec. nov., a new moderately alkaliphilic and thermophilic autotrophic methanogen. Arch Microbiol 142:211–217CrossRefGoogle Scholar
  73. Blumentals II, Itoh M, Olson GJ, Kelly RM (1990) Role of polysulfides in reduction of elemental sulfur by the hyperthermophilic archaebacterium Pyrococcus furiosus. Appl Environ Microbiol 56:1255–1262PubMedGoogle Scholar
  74. Böck A, King PW, Blokesch M, Posewitz MC (2006) Maturation of hydrogenases. Adv Microb Physiol 51:1–71PubMedCrossRefGoogle Scholar
  75. Bogorov LV (1974) Properties of Thiocapsa roseopersicina strain BBS isolated from estuary of white sea. Mikrobiologiya 43:326–332Google Scholar
  76. Böhm R, Sauter M, Böck A (1990) Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components. Mol Microbiol 4:231–243PubMedCrossRefGoogle Scholar
  77. Boison G, Schmitz O, Mikheeva L, Shestakov S, Bothe H (1996) Cloning, molecular analysis and insertional mutagenesis of the bidirectional hydrogenase genes from the cyanobacterium Anacystis nidulans. FEBS Lett 394:153–158PubMedCrossRefGoogle Scholar
  78. Bomar M, Hippe H, Schink B (1991) Lithotrophic growth and hydrogen metabolism by Clostridium magnum. FEMS Microbiol Lett 67:347–349PubMedCrossRefGoogle Scholar
  79. Bone DH (1960) Localization of hydrogen activating enzymes in Pseudomonas saccharophila. Biochem Biophys Res Commun 3:211–214PubMedCrossRefGoogle Scholar
  80. Bone DH, Bernstein S, Vishniac W (1963) Purification and some properties of different forms of hydrogen dehydrogenase. Biochim Biophys Acta 67:581–588PubMedCrossRefGoogle Scholar
  81. Bonjour F, Aragno M (1984) Bacillus tusciae, a new species of thermoacidophilic, facultatively chemolithoautotrophic, hydrogen oxidizing sporeformer from a geothermal area. Arch Microbiol 139:397–401CrossRefGoogle Scholar
  82. Boone DR, Bryant MP (1980) Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from methanogenic ecosystems. Appl Environ Microbiol 40:626–632PubMedGoogle Scholar
  83. Bornstein BT, Barker HA (1948) The nutrition of Clostridium kluyveri. J Bacteriol 55:223–230PubMedGoogle Scholar
  84. Bothe H, Tennigkeit J, Eisbrenner G (1977) Utilization of molecular hydrogen by blue-green alga Anabaena cylindrica. Arch Microbiol 114:43–49PubMedCrossRefGoogle Scholar
  85. Bott M, Thauer RK (1987) Proton-motive-force-driven formation of CO from CO2 and H2 in methanogenic bacteria. Eur J Biochem 168:407–412PubMedCrossRefGoogle Scholar
  86. Brandis A, Thauer RK (1981) Growth of Desulfovibrio species on hydrogen and sulphate as sole energy source. J Gen Microbiol 126:249–252Google Scholar
  87. Braun K, Gottschalk G (1981) Effect of molecular hydrogen and carbon dioxide on chemo-organotrophic growth of Acetobacterium woodii and Clostridium aceticum. Arch Microbiol 128:294–298PubMedCrossRefGoogle Scholar
  88. Braun M, Mayer F, Gottschalk G (1981) Clostridium aceticum (Wieringa), a microorganism producing acetic acid from molecular hydrogen and carbon dioxide. Arch Microbiol 128:288–293PubMedCrossRefGoogle Scholar
  89. Brazelton WJ, Schrenk MO, Kelley DS, Baross JA (2006) Methane- and sulfur-metabolizing microbial communities dominate the Lost City hydrothermal field ecosystem. Appl Environ Microbiol 72:6257–6270PubMedCrossRefGoogle Scholar
  90. Brazzolotto X, Rubach JK, Gaillard J, Gambarelli S, Atta M, Fontecave M (2006) The [Fe-Fe]-hydrogenase maturation protein HydF from Thermotoga maritima is a GTPase with an iron-sulfur cluster. J Biol Chem 281:769–774PubMedCrossRefGoogle Scholar
  91. Brecht M, van Gastel M, Buhrke T, Friedrich B, Lubitz W (2003) Direct detection of a hydrogen ligand in the [NiFe] center of the regulatory H2-sensing hydrogenase from Ralstonia eutropha in its reduced state by HYSCORE and ENDOR spectroscopy. J Am Chem Soc 125:13075–13083PubMedCrossRefGoogle Scholar
  92. Brewin NJ (1984) Hydrogenase and energy efficiency in nitrogen-fixing symbionts. In: Verma DPS, Hohn T (eds) Genes involved in plant-microbe interactions. Springer, New York, pp 179–203CrossRefGoogle Scholar
  93. Breznak JA (1982) Intestinal microbiota of termites and other xylophagous insects. Annu Rev Microbiol 36:323–343PubMedCrossRefGoogle Scholar
  94. Breznak JA, Switzer JM, Seitz HJ (1988) Sporomusa termitida sp. nov., an H2/CO2-utilizing acetogen isolated from termites. Arch Microbiol 150:282–288CrossRefGoogle Scholar
  95. Brisbarre N, Fardeau ML, Cueff V, Cayol JL, Barbier G, Cilia V, Ravot G, Thomas P, Garcia JL, Ollivier B (2003) Clostridium caminithermale sp. nov., a slightly halophilic and moderately thermophilic bacterium isolated from an Atlantic deep-sea hydrothermal chimney. Int J Syst Evol Microbiol 53:1043–1049PubMedCrossRefGoogle Scholar
  96. Brito B, Martinez M, Fernandez D, Rey L, Cabrera E, Palacios JM, Imperial J, Ruiz-Argueso T (1997) Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein NifA. Proc Natl Acad Sci USA 94:6019–6024PubMedCrossRefGoogle Scholar
  97. Brito B, Prieto RI, Cabrera E, Mandrand-Berthelot MA, Imperial J, Ruiz-Argueso T, Palacios JM (2010) Rhizobium leguminosarum hupE encodes a nickel transporter required for hydrogenase activity. J Bacteriol 192:925–935PubMedCrossRefGoogle Scholar
  98. Brock TD, Brock KM, Belly RT, Weiss RL (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84:54–68PubMedCrossRefGoogle Scholar
  99. Bronder M, Mell H, Stupperich E, Kroger A (1982) Biosynthetic pathways of Vibrio succinogenes growing with fumarate as terminal electron acceptor and sole carbon source. Arch Microbiol 131:216–223PubMedCrossRefGoogle Scholar
  100. Brøndsted L, Atlung T (1994) Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli. J Bacteriol 176:5423–5428PubMedGoogle Scholar
  101. Brøndsted L, Atlung T (1996) Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli. J Bacteriol 178:1556–1564PubMedGoogle Scholar
  102. Brugna M, Nitschke W, Toci R, Bruschi M, Giudici-Orticoni MT (1999) First evidence for the presence of a hydrogenase in the sulfur-reducing bacterium Desulfuromonas acetoxidans. J Bacteriol 181:5505–5508PubMedGoogle Scholar
  103. Bryant MP, Wolin EA, Wolin MJ, Wolfe RS (1967) Methanobacillus omelianskii, a symbiotic association of two species of bacteria. Arch Mikrobiol 59:20–31PubMedCrossRefGoogle Scholar
  104. Bryant FO, Adams MW (1989) Characterization of hydrogenase from the hyperthermophilic archaebacterium, Pyrococcus furiosus. J Biol Chem 264:5070–5079PubMedGoogle Scholar
  105. Bryant MP, Campbell LL, Reddy CA, Crabill MR (1977) Growth of Desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. Appl Environ Microbiol 33:1162–1169PubMedGoogle Scholar
  106. Brysch K, Schneider C, Fuchs G, Widdel F (1987) Lithoautotrophic growth of sulfate-reducing bacteria, and description of Desulfobacterium autotrophicum gen. nov., sp. nov. Arch Microbiol 148:264–274CrossRefGoogle Scholar
  107. Buckel W, Thauer RK (2012) Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation. Biochim Biophys Acta, in press, 10.1016/j.bbabio.2012.07.002Google Scholar
  108. Buhrke T, Bleijlevens B, Albracht SP, Friedrich B (2001) Involvement of hyp gene products in maturation of the H2-sensing [NiFe] hydrogenase of Ralstonia eutropha. J Bacteriol 183:7087–7093PubMedCrossRefGoogle Scholar
  109. Buhrke T (2002) Der H2-Sensor von Ralstonia eitropha: Struktur-Funktions- Beziehungen einer neuartigen [NiFe]-Hydrogenase. Ph D thesis. Humboldt-Universität zu Berlin, Berlin, GermanyGoogle Scholar
  110. Buhrke T, Lenz O, Porthun A, Friedrich B (2004) The H2-sensing complex of Ralstonia eutropha: interaction between a regulatory [NiFe] hydrogenase and a histidine protein kinase. Mol Microbiol 51:1677–1689PubMedCrossRefGoogle Scholar
  111. Buhrke T, Lenz O, Krauss N, Friedrich B (2005) Oxygen tolerance of the H2-sensing [NiFe] hydrogenase from Ralstonia eutropha H16 is based on limited access of oxygen to the active site. J Biol Chem 280:23791–23796PubMedCrossRefGoogle Scholar
  112. Bui ET, Johnson PJ (1996) Identification and characterization of [Fe]-hydrogenases in the hydrogenosome of Trichomonas vaginalis. Mol Biochem Parasitol 76:305–310PubMedCrossRefGoogle Scholar
  113. Bulen WA, Burns RC, Le Comte JR (1965a) Nitrogen fixation—hydrosulfite as electron donor with cell-free preparations of Azotobacter vinelandii and Rhodospirillum rubrum. Proc Natl Acad Sci USA 53:532–539PubMedCrossRefGoogle Scholar
  114. Bulen WA, Le Comte JR, Burns RC, Hinkson J (1965b) Nitrogen fixation studies with aerobic and photosynthetic bacteria. In: San Pietro A (ed) Non-heme iron proteins: role in energy conversion. Antioch, Yellow Springs, pp 261–274Google Scholar
  115. Bult CJ, White O, Olsen GJ, Zhou LX, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Roberts KM, Hurst MA, Kaine BP, Borodovsky M, Klenk HP, Fraser CM, Smith HO, Woese CR, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058–1073PubMedCrossRefGoogle Scholar
  116. Burgdorf T, De Lacey AL, Friedrich B (2002) Functional analysis by site-directed mutagenesis of the NAD(+)-reducing hydrogenase from Ralstonia eutropha. J Bacteriol 184:6280–6288PubMedCrossRefGoogle Scholar
  117. Burgdorf T, van der Linden E, Bernhard M, Yin QY, Back JW, Hartog AF, Muijsers AO, de Koster CG, Albracht SP, Friedrich B (2005) The soluble NAD+-Reducing [NiFe]-hydrogenase from Ralstonia eutropha H16 consists of six subunits and can be specifically activated by NADPH. J Bacteriol 187:3122–3132PubMedCrossRefGoogle Scholar
  118. Burggraf S, Fricke H, Neuner A, Kristjansson J, Rouvier P, Mandelco L, Woese CR, Stetter KO (1990a) Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system. Syst Appl Microbiol 13:263–269PubMedCrossRefGoogle Scholar
  119. Burggraf S, Jannasch HW, Nicolaus B, Stetter KO (1990b) Archaeoglobus profundus sp. nov., represents a new species within the sulfate-reducing archaebacteria. Syst Appl Microbiol 13:24–28CrossRefGoogle Scholar
  120. Bürstel I, Hummel P, Siebert E, Wisitruangsakul N, Zebger I, Friedrich B, Lenz O (2011) Probing the origin of the metabolic precursor of the CO ligand in the catalytic center of [NiFe] hydrogenase. J Biol Chem 286:44937–44944PubMedCrossRefGoogle Scholar
  121. Buurman G, Shima S, Thauer RK (2000) The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor. FEBS Lett 485:200–204PubMedCrossRefGoogle Scholar
  122. Caccavo F Jr, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ (1994) Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60:3752–3759PubMedGoogle Scholar
  123. Caffrey SM, Park HS, Voordouw JK, He Z, Zhou J, Voordouw G (2007) Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol 189:6159–6167PubMedCrossRefGoogle Scholar
  124. Cammack R (2001) The catalytic machinery. In: Cammack R, Frey M, Robson R (eds) Hydrogen as a fuel: learning from nature. Taylor & Francis, London, pp 159–180CrossRefGoogle Scholar
  125. Cammack R, Patil DS, Aguirre R, Hatchikian EC (1982) Redox properties of the ESR-detectable nickel in hydrogenase from Desulfovibrio gigas. FEBS Lett 142:289–292CrossRefGoogle Scholar
  126. Campbell BJ, Engel AS, Porter ML, Takai K (2006) The versatile epsilon-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 4:458–468PubMedCrossRefGoogle Scholar
  127. Carrasco CD, Buettner JA, Golden JW (1995) Programmed DNA rearrangement of a cyanobacterial hupL gene in heterocysts. Proc Natl Acad Sci USA 92:791–795PubMedCrossRefGoogle Scholar
  128. Carrasco CD, Holliday SD, Hansel A, Lindblad P, Golden JW (2005) Heterocyst-specific excision of the Anabaena sp. strain PCC 7120 hupL element requires xisC. J Bacteriol 187:6031–6038PubMedCrossRefGoogle Scholar
  129. Casalot L, Rousset M (2001) Maturation of the [NiFe] hydrogenases. Trends Microbiol 9:228–237PubMedCrossRefGoogle Scholar
  130. Casalot L, De Luca G, Dermoun Z, Rousset M, de Philip P (2002a) Evidence for a fourth hydrogenase in Desulfovibrio fructosovorans. J Bacteriol 184:853–856PubMedCrossRefGoogle Scholar
  131. Casalot L, Valette O, De Luca G, Dermoun Z, Rousset M, de Philip P (2002b) Construction and physiological studies of hydrogenase depleted mutants of Desulfovibrio fructosovorans. FEMS Microbiol Lett 214:107PubMedCrossRefGoogle Scholar
  132. Catling DC (2006) Comment on “A hydrogen-rich early Earth atmosphere”. Science 311:38PubMedCrossRefGoogle Scholar
  133. Cendron L, Berto P, D’Adamo S, Vallese F, Govoni C, Posewitz MC, Giacometti GM, Costantini P, Zanotti G (2011) Crystal structure of HydF scaffold protein provides insights into [FeFe]-hydrogenase maturation. J Biol Chem 286:43944–43950PubMedCrossRefGoogle Scholar
  134. Chan KH, Lee KM, Wong KB (2012) Interaction between hydrogenase maturation factors HypA and HypB is required for [NiFe]-hydrogenase maturation. PLoS One 7:e32592PubMedCrossRefGoogle Scholar
  135. Chapelle FH, O’Neill K, Bradley PM, Methe BA, Ciufo SA, Knobel LL, Lovley DR (2002) A hydrogen-based subsurface microbial community dominated by methanogens. Nature 415:312–315PubMedCrossRefGoogle Scholar
  136. Charlou JL, Donval JP, Douville E, Jean-Baptiste P, Radford-Knoery J, Fouquet Y, Dapoigny A, Stievenard M (2000) Compared geochemical signatures and the evolution of Menez Gwen (37°50′N) and Lucky Strike (37°17′N) hydrothermal fluids, south of the Azores Triple Junction on the Mid-Atlantic Ridge. Chem Geol 171:49–75CrossRefGoogle Scholar
  137. Charlou JL, Donval JP, Fouquet Y, Jean-Baptiste P, Holm N (2002) Geochemistry of high H2 and CH4 vent fluids issuing from ultramafic rocks at the rainbow hydrothermal field (36o 14' N, MAR). Chem Geol 191:345–359CrossRefGoogle Scholar
  138. Charlou JL, Donval JP, Konn C, Ondréas H, Fouquet Y, Jean-Baptiste P, Fourré E (2010) High production and fluxes of H2 and CH4 and evidence of abiotic hydrocarbon synthesis by serpentinization in ultramafic-hosted hydrothermal systems on the Mid-Atlantic Ridge. In: Rona PA, Devey CW, Dyment J, Murton BJ (eds) Diversity of hydrothermal systems on slow spreading ocean ridges, vol 188. AGU, Washington, DCCrossRefGoogle Scholar
  139. Chen JS, Blanchard DK (1978) Isolation and properties of a unidirectional H2-oxidizing hydrogenase from the strictly anaerobic N2-fixing bacterium Clostridium pasteurianum W5. Biochem Biophys Res Commun 84:1144–1150PubMedCrossRefGoogle Scholar
  140. Chen JS, Mortenson LE (1974) Purification and properties of hydrogenase from Clostridium pasteurianum W5. Biochim Biophys Acta 371:283–298PubMedCrossRefGoogle Scholar
  141. Chen YP, Yoch DC (1987) Regulation of two nickel-requiring (inducible and constitutive) hydrogenases and their coupling to nitrogenase in Methylosinus trichosporium OB3b. J Bacteriol 169:4778–4783PubMedGoogle Scholar
  142. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322:275–278PubMedCrossRefGoogle Scholar
  143. Clark JE, Ragsdale SW, Ljungdahl LG, Wiegel J (1982) Levels of enzymes involved in the synthesis of acetate from CO2 in Clostridium thermoautotrophicum. J Bacteriol 151:507–509PubMedGoogle Scholar
  144. Coates JD, Bhupathiraju VK, Achenbach LA, Mclnerney MJ, Lovley DR (2001) Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 51:581–588PubMedGoogle Scholar
  145. Cohen J, Kim K, King P, Seibert M, Schulten K (2005a) Finding gas diffusion pathways in proteins: application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects. Structure 13:1321–1329PubMedCrossRefGoogle Scholar
  146. Cohen J, Kim K, Posewitz M, Ghirardi ML, Schulten K, Seibert M, King P (2005b) Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase. Biochem Soc Trans 33:80–82PubMedCrossRefGoogle Scholar
  147. Colbeau A, Vignais PM (1992) Use of hupS::lacZ gene fusion to study regulation of hydrogenase expression in Rhodobacter capsulatus: stimulation by H2. J Bacteriol 174:4258–4264PubMedGoogle Scholar
  148. Colbeau A, Chabert J, Vignais PM (1983) Purification, molecular properties and localization in the membrane of the hydrogenase of Rhodopseudomonas capsulata. Biochim Biophys Acta 748:116–127CrossRefGoogle Scholar
  149. Colbeau A, Kovács KL, Chabert J, Vignais PM (1994) Cloning and sequence of the structural (hupSLC) and accessory (hupDHI) genes for hydrogenase biosynthesis in Thiocapsa roseopersicina. Gene 140:25–31PubMedCrossRefGoogle Scholar
  150. Colbeau A, Elsen S, Tomiyama M, Zorin NA, Dimon B, Vignais PM (1998) Rhodobacter capsulatus HypF is involved in regulation of hydrogenase synthesis through the HupUV proteins. Eur J Biochem 251:65–71PubMedCrossRefGoogle Scholar
  151. Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM (2006) Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 30:872–905PubMedCrossRefGoogle Scholar
  152. Conrad R (1984) Capacity of aerobic microorganisms to utilize and grow on atmospheric trace gases (H2, CO, CH4). In: Klug MG, Reddy, CA (eds) Current perspectives in microbial ecology. American Society for Microbiology, Washington DC, pp 461–467Google Scholar
  153. Conrad R (1988) Biogeochemistry and ecophysiology of atmospheric CO and H2. Adv Microb Ecol 10:231–283CrossRefGoogle Scholar
  154. Conrad R (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60:609–640PubMedGoogle Scholar
  155. Conrad R (1999) Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiol Ecol 28:193–202CrossRefGoogle Scholar
  156. Conrad R, Seiler W (1979) Role of hydrogen bacteria during the decomposition of hydrogen by soil. FEMS Microbiol Lett 6:143–145CrossRefGoogle Scholar
  157. Conrad R, Seiler W (1981) Decomposition of atmospheric hydrogen by soil-microorganisms and soil enzymes. Soil Biol Biochem 13:43–49CrossRefGoogle Scholar
  158. Conrad R, Seiler W (1985) Influence of temperature, moisture and organic carbon on the flux of H2 and CO between soil and atmosphere. Field studies in subtropical regions. J Geophys Res 90:5699–6709CrossRefGoogle Scholar
  159. Conrad R, Aragno M, Seiler W (1983a) Production and consumption of hydrogen in a eutrophic lake. Appl Environ Microbiol 45:502–510PubMedGoogle Scholar
  160. Conrad R, Aragno M, Seiler W (1983b) The inability of hydrogen bacteria to utilize atmospheric hydrogen is due to threshold and affinity for hydrogen. FEMS Microbiol Lett 18:207–210CrossRefGoogle Scholar
  161. Conrad R, Bonjour F, Aragno M (1985) Aerobic and anaerobic microbial consumption of hydrogen in geothermal spring water. FEMS Microbiol Lett 29:201–205CrossRefGoogle Scholar
  162. Conrad R, Schink B, Phelps TJ (1986) Thermodynamics of H2-consuming and H2-producing metabolic reactions in diverse methanogenic environments under in-situ conditions. FEMS Microbiol Ecol 38:353–360CrossRefGoogle Scholar
  163. Conrad R, Schütz H, Babbel M (1987) Temperature limitation of hydrogen turnover and methanogenesis in anoxic paddy soil. FEMS Microbiol Ecol 45:281–289CrossRefGoogle Scholar
  164. Constant P, Poissant L, Villemur R (2008) Isolation of Streptomyces sp. PCB7, the first microorganism demonstrating high-affinity uptake of tropospheric H2. ISME J 2:1066–1076PubMedCrossRefGoogle Scholar
  165. Constant P, Chowdhury SP, Hesse L, Pratscher J, Conrad R (2011) Genome data mining and soil survey for the novel group 5 [NiFe]-hydrogenase to explore the diversity and ecological importance of presumptive high-affinity H2-oxidizing bacteria. Appl Environ Microbiol 77:6027–6035PubMedCrossRefGoogle Scholar
  166. Coppi MV, O’Neil RA, Lovley DR (2004) Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens. J Bacteriol 186:3022–3028PubMedCrossRefGoogle Scholar
  167. Cornish AJ, Gartner K, Yang H, Peters JW, Hegg EL (2011) Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum. J Biol Chem 286:38341–38347PubMedCrossRefGoogle Scholar
  168. Corre E, Reysenbach AL, Prieur D (2001) Epsilon-proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol Lett 205:329–335PubMedGoogle Scholar
  169. Cracknell JA, Wait AF, Lenz O, Friedrich B, Armstrong FA (2009) A kinetic and thermodynamic understanding of O2 tolerance in [NiFe]-hydrogenases. Proc Natl Acad Sci USA 106:20681–20686PubMedCrossRefGoogle Scholar
  170. Csáki R, Hanczár T, Bodrossy L, Murrell JC, Kovács KL (2001) Molecular characterization of structural genes coding for a membrane bound hydrogenase in Methylococcus capsulatus (Bath). FEMS Microbiol Lett 205:203–207PubMedGoogle Scholar
  171. Cunningham SD, Kapulnik Y, Phillips DA (1986) Distribution of hydrogen-metabolizing bacteria in Alfalfa field soil. Appl Environ Microbiol 52:1091–1095PubMedGoogle Scholar
  172. Cypionka H, Dilling W (1986) Intracellular-localization of the hydrogenase in Desulfotomaculum orientis. FEMS Microbiol Lett 36:257–260CrossRefGoogle Scholar
  173. Daniel SL, Hsu T, Dean SI, Drake HL (1990) Characterization of the H2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui. J Bacteriol 172:4464–4471PubMedGoogle Scholar
  174. Daumas S, Cord-Ruwisch R, Garcia JL (1988) Desulfotomaculum geothermicum sp. nov., a thermophilic, fatty acid-degrading, sulfate-reducing bacterium isolated with H2 from geothermal ground water. Antonie Van Leeuwenhoek 54:165–178PubMedCrossRefGoogle Scholar
  175. Davis DH, Stanier RY, Doudoroff M, Mandel M (1970) Taxonomic studies on some gram negative polarly flagellated “hydrogen bacteria” and related species. Arch Mikrobiol 70:1–13PubMedCrossRefGoogle Scholar
  176. de Bok FA, Roze EH, Stams AJ (2002) Hydrogenases and formate dehydrogenases of Syntrophobacter fumaroxidans. Antonie Van Leeuwenhoek 81:283–291PubMedCrossRefGoogle Scholar
  177. De Lacey AL, Fernandez VM, Rousset M, Cammack R (2007) Activation and inactivation of hydrogenase function and the catalytic cycle: spectroelectrochemical studies. Chem Rev 107:4304–4330PubMedCrossRefGoogle Scholar
  178. Deckert G, Warren PV, Gaasterland T, Young WG, Lenox AL, Graham DE, Overbeek R, Snead MA, Keller M, Aujay M, Huber R, Feldman RA, Short JM, Olsen GJ, Swanson RV (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392:353–358PubMedCrossRefGoogle Scholar
  179. Dementin S, Burlat B, De Lacey AL, Pardo A, Adryanczyk-Perrier G, Guigliarelli B, Fernandez VM, Rousset M (2004) A glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase. J Biol Chem 279:10508–10513PubMedCrossRefGoogle Scholar
  180. Dementin S, Belle V, Bertrand P, Guigliarelli B, Adryanczyk-Perrier G, De Lacey AL, Fernandez VM, Rousset M, Leger C (2006) Changing the ligation of the distal [4Fe4S] cluster in NiFe hydrogenase impairs inter- and intramolecular electron transfers. J Am Chem Soc 128:5209–5218PubMedCrossRefGoogle Scholar
  181. Deppenmeier U (1995) Different structure and expression of the operons encoding the membrane-bound hydrogenases from Methanosarcina mazei Go1. Arch Microbiol 164:370–376PubMedCrossRefGoogle Scholar
  182. Deppenmeier U (2002) The unique biochemistry of methanogenesis. Prog Nucleic Acid Res Mol Biol 71:223–283PubMedCrossRefGoogle Scholar
  183. Deppenmeier U, Blaut M, Schmidt B, Gottschalk G (1992) Purification and properties of a F420-nonreactive, membrane-bound hydrogenase from Methanosarcina strain Go1. Arch Microbiol 157:505–511PubMedGoogle Scholar
  184. Deppenmeier U, Blaut M, Lentes S, Herzberg C, Gottschalk G (1995) Analysis of the vhoGAC and vhtGAC operons from Methanosarcina mazei strain Gö1, both encoding a membrane-bound hydrogenase and a cytochrome b. Eur J Biochem 227:261–269PubMedCrossRefGoogle Scholar
  185. Deppenmeier U, Lienard T, Gottschalk G (1999) Novel reactions involved in energy conservation by methanogenic archaea. FEBS Lett 457:291–297PubMedCrossRefGoogle Scholar
  186. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461PubMedGoogle Scholar
  187. Dernedde J, Eitinger M, Friedrich B (1993) Analysis of a pleiotropic gene region involved in formation of catalytically active hydrogenases in Alcaligenes eutrophus H16. Arch Microbiol 159:545–553PubMedCrossRefGoogle Scholar
  188. Dernedde J, Eitinger T, Patenge N, Friedrich B (1996) hyp gene products in Alcaligenes eutrophus are part of a hydrogenase-maturation system. Eur J Biochem 235:351–358PubMedCrossRefGoogle Scholar
  189. Dias AV, Mulvihill CM, Leach MR, Pickering IJ, George GN, Zamble DB (2008) Structural and biological analysis of the metal sites of Escherichia coli hydrogenase accessory protein HypB. Biochemistry 47:11981–11991PubMedCrossRefGoogle Scholar
  190. Diekert G, Wohlfarth G (1994) Metabolism of homocetogens. Antonie Van Leeuwenhoek 66:209–221PubMedCrossRefGoogle Scholar
  191. Dischert W, Vignais PM, Colbeau A (1999) The synthesis of Rhodobacter capsulatus HupSL hydrogenase is regulated by the two-component HupT/HupR system. Mol Microbiol 34:995–1006PubMedCrossRefGoogle Scholar
  192. Dixon RO (1968) Hydrogenase in pea root nodule bacteroids. Arch Mikrobiol 62:272–283PubMedCrossRefGoogle Scholar
  193. Dobrindt U, Blaut M (1996) Purification and characterization of a membrane-bound hydrogenase from Sporomusa sphaeroides involved in energy-transducing electron transport. Arch Microbiol 165:141–147PubMedCrossRefGoogle Scholar
  194. Dong Z, Wu L, Kettlewell B, Caldwell CD, Layzell DB (2003) Hydrogen fertilization of soils—is this a benefit of legumes in rotation? Plant Cell Environ 26:1875–1879CrossRefGoogle Scholar
  195. Drake HL (1982) Demonstration of hydrogenase in extracts of the homoacetate-fermenting bacterium Clostridium thermoaceticum. J Bacteriol 150:702–709PubMedGoogle Scholar
  196. Drake HL (1994) Acetogenesis, acetogenic bacteria and the acetyl-CoA “Wood/Ljungdahl” pathway: past and current perspectives. In: Drake HL (ed) Acetogenesis. Chapman & Hall, New York, pp 3–62CrossRefGoogle Scholar
  197. Drews J, Imhoff JF (1991) Phototrophic purple bacteria. In: Shively JM, Barton LL (eds) Variations in autotrophic life. Academic, London, pp 51–97Google Scholar
  198. Driesener RC, Challand MR, McGlynn SE, Shepard EM, Boyd ES, Broderick JB, Peters JW, Roach PL (2010) [FeFe]-hydrogenase cyanide ligands derived from S-adenosylmethionine-dependent cleavage of tyrosine. Angew Chem Int Ed Engl 49:1687–1690PubMedCrossRefGoogle Scholar
  199. Drobner E, Huber H, Stetter KO (1990) Thiobacillus ferrooxidans, a facultative hydrogen oxidizer. Appl Environ Microbiol 56:2922–2923PubMedGoogle Scholar
  200. Drobner E, Huber H, Rachel R, Stetter KO (1992) Thiobacillus plumbophilus spec. nov., a novel galena and hydrogen oxidizer. Arch Microbiol 157:213–217PubMedCrossRefGoogle Scholar
  201. Dross F, Geisler V, Lenger R, Theis F, Krafft T, Fahrenholz F, Kojro E, Duchêne A, Tripier D, Juvenal K, Kröger A (1992) The quinone-reactive Ni/Fe-hydrogenase of Wolinella succinogenes. Eur J Biochem 206:93–102PubMedCrossRefGoogle Scholar
  202. Dross F, Geisler V, Lenger R, Theis F, Krafft T, Fahrenholz F, Kojro E, Duchêne A, Tripier D, Juvenal K, Kröger A (1993) The quinone-reactive Ni/Fe-hydrogenase of Wolinella Succinogenes. Eur J Biochem 214:949–950PubMedGoogle Scholar
  203. Dubini A, Pye RL, Jack RL, Palmer T, Sargent F (2002) How bacteria get energy from hydrogen: a genetic analysis of periplasmic hydrogen oxidation in Escherichia coli. Int J Hydrogen Energy 27:1413–1420CrossRefGoogle Scholar
  204. Duché O, Elsen S, Cournac L, Colbeau A (2005) Enlarging the gas access channel to the active site renders the regulatory hydrogenase HupUV of Rhodobacter capsulatus O2 sensitive without affecting its transductory activity. FEBS J 272:3899–3908PubMedCrossRefGoogle Scholar
  205. Duchow A, Douglas HC (1949) Rhodomicrobium vannielii, a new photoheterotrophic bacterium. J Bacteriol 58:409–416PubMedGoogle Scholar
  206. Duffus BR, Hamilton TL, Shepard EM, Boyd ES, Peters JW, Broderick JB (2012) Radical AdoMet enzymes in complex metal cluster biosynthesis. Biochim Biophys Acta in press, 10.1016/j.bbapap.2012.01.002Google Scholar
  207. Durmowicz MC, Maier RJ (1997) Roles of HoxX and HoxA in biosynthesis of hydrogenase in Bradyrhizobium japonicum. J Bacteriol 179:3676–3682PubMedGoogle Scholar
  208. Eberhardt U (1966) On the hydrogen-activating system of Hydrogenomonas H 16. I. Distribution of the hydrogenase activity between two cellular fractions. Arch Mikrobiol 53:288–302PubMedCrossRefGoogle Scholar
  209. Eberhardt U (1969) On chemolithotrophy and hydrogenase of a gram-positive knallgas bacterium. Arch Mikrobiol 66:91–104PubMedCrossRefGoogle Scholar
  210. Eberz G, Friedrich B (1991) Three trans-acting regulatory functions control hydrogenase synthesis in Alcaligenes eutrophus. J Bacteriol 173:1845–1854PubMedGoogle Scholar
  211. Eberz G, Hogrefe C, Kortlüke C, Kamienski A, Friedrich B (1986) Molecular cloning of structural and regulatory hydrogenase (hox) genes of Alcaligenes eutrophus H16. J Bacteriol 168:636–641PubMedGoogle Scholar
  212. Edwards MR (1998) From a soup or a seed? Trends Ecol Evol 13:178–181PubMedCrossRefGoogle Scholar
  213. Efremov RG, Sazanov LA (2012) The coupling mechanism of respiratory complex I—A structural and evolutionary perspective. Biochim Biophys Acta 1817:1785–1795Google Scholar
  214. Eisenmann E, Beuerle J, Sulger K, Kroneck PMH, Schumacher W (1995) Lithotrophic growth of Sulfurospirillum deleyianum with sulfide as electron-donor coupled to respiratory reduction of nitrate to ammonia. Arch Microbiol 164:180–185CrossRefGoogle Scholar
  215. Eitinger T, Suhr J, Moore L, Smith JA (2005) Secondary transporters for nickel and cobalt ions: theme and variations. Biometals 18:399–405PubMedCrossRefGoogle Scholar
  216. Elsen S, Richaud P, Colbeau A, Vignais PM (1993) Sequence analysis and interposon mutagenesis of the hupT gene, which encodes a sensor protein involved in repression of hydrogenase synthesis in Rhodobacter capsulatus. J Bacteriol 175:7404–7412PubMedGoogle Scholar
  217. Elsen S, Colbeau A, Chabert J, Vignais PM (1996) The hupTUV operon is involved in negative control of hydrogenase synthesis in Rhodobacter capsulatus. J Bacteriol 178:5174–5181PubMedGoogle Scholar
  218. Elsen S, Dischert W, Colbeau A, Bauer CE (2000) Expression of uptake hydrogenase and molybdenum nitrogenase in Rhodobacter capsulatus is coregulated by the RegB-RegA two-component regulatory system. J Bacteriol 182:2831–2837PubMedCrossRefGoogle Scholar
  219. Elsen S, Duché O, Colbeau A (2003) Interaction between the H2 sensor HupUV and the histidine kinase HupT controls HupSL hydrogenase synthesis in Rhodobacter capsulatus. J Bacteriol 185:7111–7119PubMedCrossRefGoogle Scholar
  220. Emerich DW, Ruiz-Argueso T, Ching TM, Evans HJ (1979) Hydrogen-dependent nitrogenase activity and ATP formation in Rhizobium japonicum bacteroids. J Bacteriol 137:153–160PubMedGoogle Scholar
  221. Erauso G, Reysenbach AL, Godfroy A, Meunier JR, Crump B, Partensky F, Baross JA, Marteinsson V, Barbier G, Pace NR, Prieur D (1993) Pyrococcus abyssi sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Arch Microbiol 160:338–349CrossRefGoogle Scholar
  222. Evans HJ, Harker AR, Papen H, Russell SA, Hanus FJ, Zuber M (1987) Physiology, biochemistry, and genetics of the uptake hydrogenase in rhizobia. Annu Rev Microbiol 41:335–361PubMedCrossRefGoogle Scholar
  223. Ewart GD, Smith GD (1989) Purification and properties of soluble hydrogenase from the cyanobacterium Anabaena cylindrica. Arch Biochem Biophys 268:327–337PubMedCrossRefGoogle Scholar
  224. Fallon RD (1982) Influences of pH, temperature, and moisture on gaseous tritium uptake in surface soils. Appl Environ Microbiol 44:171–178PubMedGoogle Scholar
  225. Fauque G, Teixeira M, Moura I, Lespinat PA, Xavier AV, Dervartanian DV, Peck HD, Legall J, Moura JG (1984) Purification, characterization and redox properties of hydrogenase from Methanosarcina barkeri (DSM 800). Eur J Biochem 142:21–28PubMedCrossRefGoogle Scholar
  226. Fauque G, Peck HD Jr, Moura JJ, Huynh BH, Berlier Y, DerVartanian DV, Teixeira M, Przybyla AE, Lespinat PA, Moura I, Le Gall J (1988) The three classes of hydrogenases from sulfate-reducing bacteria of the genus Desulfovibrio. FEMS Microbiol Rev 4:299–344PubMedGoogle Scholar
  227. Fay P (1992) Oxygen relations of nitrogen fixation in cyanobacteria. Microbiol Rev 56:340–373PubMedGoogle Scholar
  228. Fdez Galvan I, Volbeda A, Fontecilla-Camps JC, Field MJ (2008) A QM/MM study of proton transport pathways in a [NiFe] hydrogenase. Proteins 73:195–203PubMedCrossRefGoogle Scholar
  229. Fernandez VM, Hatchikian EC, Cammack R (1985) Properties and reactivation of two different deactivated forms of Desulfovibrio gigas hydrogenase. Biochim Biophys Acta 832:69–79CrossRefGoogle Scholar
  230. Ferry JG, Lessner DJ (2008) Methanogenesis in marine sediments. Ann N Y Acad Sci 1125:147–157PubMedCrossRefGoogle Scholar
  231. Ferry JG, Smith PH, Wolfe RS (1974) Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungate. Int J Syst Bacteriol 24:465–469CrossRefGoogle Scholar
  232. Fiala G, Stetter KO (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100 °C. Arch Microbiol 145:56–61CrossRefGoogle Scholar
  233. Fichtner C, Laurich C, Bothe E, Lubitz W (2006) Spectroelectrochemical characterization of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F. Biochemistry 45:9706–9716PubMedCrossRefGoogle Scholar
  234. Fiebig K, Friedrich B (1989) Purification of the F420-reducing hydrogenase from Methanosarcina barkeri (strain Fusaro). Eur J Biochem 184:79–88PubMedCrossRefGoogle Scholar
  235. Filipiak M, Hagen WR, Veeger C (1989) Hydrodynamic, structural and magnetic properties of Megasphaera elsdenii Fe hydrogenase reinvestigated. Eur J Biochem 185:547–553PubMedCrossRefGoogle Scholar
  236. Finster K, Liesack W, Tindall BJ (1997) Sulfurospirillum arcachonense sp. nov., a new microaerophilic sulfur-reducing bacterium. Int J Syst Bacteriol 47:1212–1217PubMedCrossRefGoogle Scholar
  237. Fischer F, Zillig W, Stetter KO, Schreiber G (1983) Chemolithoautotrophic metabolism of anaerobic extremely thermophilic archaebacteria. Nature 301:511–513PubMedCrossRefGoogle Scholar
  238. Fischer J, Quentmeier A, Kostka S, Kraft R, Friedrich CG (1996) Purification and characterization of the hydrogenase from Thiobacillus ferrooxidans. Arch Microbiol 165:289–296PubMedCrossRefGoogle Scholar
  239. Flint HJ (1997) The rumen microbial ecosystem—some recent developments. Trends Microbiol 5:483–488PubMedCrossRefGoogle Scholar
  240. Flores GE, Campbell JH, Kirshtein JD, Meneghin J, Podar M, Steinberg JI, Seewald JS, Tivey MK, Voytek MA, Yang ZK, Reysenbach AL (2011) Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ Microbiol 13:2158–2171PubMedCrossRefGoogle Scholar
  241. Florin L, Tsokoglou A, Happe T (2001) A novel type of iron hydrogenase in the green alga Scenedesmus obliquus is linked to the photosynthetic electron transport chain. J Biol Chem 276:6125–6132PubMedCrossRefGoogle Scholar
  242. Fontaine FE, Peterson WH, McCoy E, Johnson MJ, Ritter GJ (1942) A new type of glucose fermentation by Clostridium thermoaceticum. J Bacteriol 43:701–715PubMedGoogle Scholar
  243. Fontecilla-Camps JC (1996) The active site of Ni-Fe hydrogenases: model chemistry and crystallographic results. J Biol Inorg Chem 1:91–98CrossRefGoogle Scholar
  244. Fontecilla-Camps JC, Frey M, Garcin E, Higuchi Y, Montet Y, Nicolet Y, Volbeda A (2001) Molecular architectures. In: Cammack R, Frey M, Robson R (eds) Hydrogen as a fuel: learning from nature. Taylor & Francis, London, pp 93–109Google Scholar
  245. Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y (2007) Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 107:4273–4303PubMedCrossRefGoogle Scholar
  246. Ford CM, Garg N, Garg RP, Tibelius KH, Yates MG, Arp DJ, Seefeldt LC (1990) The identification, characterization, sequencing and mutagenesis of the genes (hupSL) encoding the small and large subunits of the H2-uptake hydrogenase of Azotobacter chroococcum. Mol Microbiol 4:999–1008PubMedCrossRefGoogle Scholar
  247. Forzi L, Sawers RG (2007) Maturation of [NiFe]-hydrogenases in Escherichia coli. Biometals 20:565–578PubMedCrossRefGoogle Scholar
  248. Forzi L, Koch J, Guss AM, Radosevich CG, Metcalf WW, Hedderich R (2005) Assignment of the [4Fe-4S] clusters of Ech hydrogenase from Methanosarcina barkeri to individual subunits via the characterization of site-directed mutants. FEBS J 272:4741–4753PubMedCrossRefGoogle Scholar
  249. Forzi L, Hellwig P, Thauer RK, Sawers RG (2007) The CO and CN ligands to the active site Fe in [NiFe]-hydrogenase of Escherichia coli have different metabolic origins. FEBS Lett 581:3317–3321PubMedCrossRefGoogle Scholar
  250. Fournier M, Dermoun Z, Durand MC, Dolla A (2004) A new function of the Desulfovibrio vulgaris Hildenborough [Fe] hydrogenase in the protection against oxidative stress. J Biol Chem 279:1787–1793PubMedCrossRefGoogle Scholar
  251. Fox JA, Livingston DJ, Ormejohnson WH, Walsh CT (1987) 8-hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. 1. Purification and characterization. Biochemistry 26:4219–4227PubMedCrossRefGoogle Scholar
  252. Fox JD, He Y, Shelver D, Roberts GP, Ludden PW (1996a) Characterization of the region encoding the CO-induced hydrogenase of Rhodospirillum rubrum. J Bacteriol 178:6200–6208PubMedGoogle Scholar
  253. Fox JD, Kerby RL, Roberts GP, Ludden PW (1996b) Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme. J Bacteriol 178:1515–1524PubMedGoogle Scholar
  254. Franzmann PD, Liu Y, Balkwill DL, Aldrich HC, Conway de Macario E, Boone DR (1997) Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. Int J Syst Bacteriol 47:1068–1072PubMedCrossRefGoogle Scholar
  255. Frey M (1998) Nickel-iron hydrogenases: structural and functional properties. Struct Bond 90:97–126CrossRefGoogle Scholar
  256. Frey AD, Bailey JE, Kallio PT (2000) Expression of Alcaligenes eutrophus flavohemoprotein and engineered Vitreoscilla hemoglobin-reductase fusion protein for improved hypoxic growth of Escherichia coli. Appl Environ Microbiol 66:98–104PubMedCrossRefGoogle Scholar
  257. Frey M, Fontecilla-Camps JC, Volbeda A (2001) Nickel-iron hydrogenases. In: Messerschmidt A, Huber R, Poulos T, Wieghardt K (eds) Handbook of metalloproteins. Wiley, Chichester, pp 880–896Google Scholar
  258. Friedrich CG (1982) Depression of hydrogenase during limitation of electron donors and derepression of ribulosebisphosphate carboxylase during carbon limitation of Alcaligenes eutrophus. J Bacteriol 149:203–210PubMedGoogle Scholar
  259. Friedrich B, Schwartz E (1993) Molecular biology of hydrogen utilization in aerobic chemolithotrophs. Annu Rev Microbiol 47:351–383PubMedCrossRefGoogle Scholar
  260. Friedrich B, Heine E, Finck A, Friedrich CG (1981a) Nickel requirement for active hydrogenase formation in Alcaligenes eutrophus. J Bacteriol 145:1144–1149PubMedGoogle Scholar
  261. Friedrich B, Hogrefe C, Schlegel HG (1981b) Naturally occurring genetic transfer of hydrogen-oxidizing ability between strains of Alcaligenes eutrophus. J Bacteriol 147:198–205PubMedGoogle Scholar
  262. Friedrich B, Bernhard M, Dernedde J, Eitinger T, Lenz O, Massanz C, Schwartz E (1996) Hydrogen oxidation by Alcaligenes. In: Lidstrom ME, Tabita FR (eds) Microbial growth on C1 compounds. Kluwer, Dordrecht, pp 110–117CrossRefGoogle Scholar
  263. Friedrich T, Brors B, Hellwig P, Kintscher L, Rasmussen T, Scheide D, Schulte U, Mantele W, Weiss H (2000) Characterization of two novel redox groups in the respiratory NADH:ubiquinone oxidoreductase (complex I). Biochim Biophys Acta 1459:305–309PubMedCrossRefGoogle Scholar
  264. Friedrich B, Fritsch J, Lenz O (2011) Oxygen-tolerant hydrogenases in hydrogen-based technologies. Curr Opin Biotechnol 22:358–364PubMedCrossRefGoogle Scholar
  265. Frielingsdorf S, Schubert T, Pohlmann A, Lenz O, Friedrich B (2011) A trimeric supercomplex of the oxygen-tolerant membrane-bound [NiFe]-hydrogenase from Ralstonia eutropha H16. Biochemistry 50:10836–10843PubMedCrossRefGoogle Scholar
  266. Fritsch J, Lenz O, Friedrich B (2011a) The maturation factors HoxR and HoxT contribute to oxygen tolerance of membrane-bound [NiFe] hydrogenase in Ralstonia eutropha H16. J Bacteriol 193:2487–2497PubMedCrossRefGoogle Scholar
  267. Fritsch J, Scheerer P, Frielingsdorf S, Kroschinsky S, Friedrich B, Lenz O, Spahn CM (2011b) The crystal structure of an oxygen-tolerant hydrogenase uncovers a novel iron-sulphur centre. Nature 479:249–252PubMedCrossRefGoogle Scholar
  268. Fritsche E, Paschos A, Beisel HG, Bock A, Huber R (1999) Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli. J Mol Biol 288:989–998PubMedCrossRefGoogle Scholar
  269. Fröbel J, Rose P, Müller M (2012) Twin-arginine-dependent translocation of folded proteins. Philos Trans R Soc Lond B Biol Sci 367:1029–1046PubMedCrossRefGoogle Scholar
  270. Fu DJ, Broude NE, Koster H, Smith CL, Cantor CR (1995) A DNA sequencing strategy that requires only five bases of known terminal sequence for priming. Proc Natl Acad Sci USA 92:10162–10166PubMedCrossRefGoogle Scholar
  271. Fuchs G (1986) CO2 fixation in acetogenic bacteria: variations on a theme. FEMS Microbiol Rev 39:181–213CrossRefGoogle Scholar
  272. Fuchs G, Stupperich E (1985) Evolution of autotrophic CO2 fixation in: evolution of prokaryotes. In: Schleifer KH, Stackebrandt E (eds), FEMS symposium No. 29. Academic Press, London, pp 235–251Google Scholar
  273. Gadkari D, Schricker K, Acker G, Kroppenstedt RM, Meyer O (1990) Streptomyces thermoautotrophicus sp. nov., a thermophilic CO-oxidizing and H2-oxidizing obligate chemolithoautotroph. Appl Environ Microbiol 56:3727–3734PubMedGoogle Scholar
  274. Gaffron H (1935) On the metabolism of the purple bacteria II. Biochem Z 275:301–319Google Scholar
  275. Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC (1999) The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Struct Fold Des 7:557–566CrossRefGoogle Scholar
  276. Gasper R, Scrima A, Wittinghofer A (2006) Structural insights into HypB, a GTP-binding protein that regulates metal binding. J Biol Chem 281:27492–27502PubMedCrossRefGoogle Scholar
  277. Genthner BRS, Friedman SD, Devereux R (1997) Reclassification of Desulfovibrio desulfuricans Norway 4 as Desulfomicrobium norvegicum comb. nov. and confirmation of Desulfomicrobium escambiense (corrig, formerly “escambium”) as a new species in the genus Desulfomicrobium. Int J Syst Bacteriol 47:889–892CrossRefGoogle Scholar
  278. Gest H (1951) Enzymatic oxidation of molecular hydrogen by bacterial extracts. Fed Proc 10:188Google Scholar
  279. Gest H (1954) Oxidation and evolution of molecular hydrogen by microorganisms. Bacteriol Rev 18:43–73PubMedGoogle Scholar
  280. Gest H, Kamen MD (1949a) Photoproduction of molecular hydrogen by Rhodospirillum rubrum. Science 109:558–559PubMedCrossRefGoogle Scholar
  281. Gest H, Kamen MD (1949b) Photochemical production of molecular hydrogen by growing cultures of photosynthetic bacteria. J Bacteriol 58:239–245Google Scholar
  282. Ghirardi ML, Posewitz MC, Maness PC, Dubini A, Yu J, Seibert M (2007) Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms. Annu Rev Plant Biol 58:71–91PubMedCrossRefGoogle Scholar
  283. Gihring TM, Moser DP, Lin L-H, Davidson M, Onstott TC, Morgan L, Milleson M, Kieft TL, Trimarco E, Balkwill DL, Dollhopf ME (2006) The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa. Geomicrobiol J 23:415–430CrossRefGoogle Scholar
  284. Gitlitz PH, Krasna AI (1975) Structural and catalytic properties of hydrogenase from Chromatium. Biochemistry 14:2561–2568PubMedCrossRefGoogle Scholar
  285. Goenka A, Voordouw JK, Lubitz W, Gartner W, Voordouw G (2005) Construction of a [NiFe]-hydrogenase deletion mutant of Desulfovibrio vulgaris Hildenborough. Biochem Soc Trans 33:59–60PubMedCrossRefGoogle Scholar
  286. Gogotov IN (1968) Hydrogen excretion and carbon assimilation by purple bacteria in relation to light intensity. Dokl Akad Nauk SSSR 183:954–956PubMedGoogle Scholar
  287. Gogotov IN (1984) Hydrogenases of purple bacteria: properties and regulation of synthesis. Arch Microbiol 140:86–90CrossRefGoogle Scholar
  288. Gogotov IN, Zorin NA, Bogorov LV (1974) Metabolism of hydrogen and nitrogen fixation capacity of Thiocapsa roseopersicina. Mikrobiologiya 43:5–10Google Scholar
  289. Gogotov IN, Zorin NA, Kondrat’eva EN (1976) Purification and properties of hydrogenase from phototrophic bacterium Thiocapsa roseopersicina. Biokhimiia 41:836–842PubMedGoogle Scholar
  290. Gold T (1992) The deep, hot biosphere. Proc Natl Acad Sci USA 89:6045–6049PubMedCrossRefGoogle Scholar
  291. Goldet G, Brandmayr C, Stripp ST, Happe T, Cavazza C, Fontecilla-Camps JC, Armstrong FA (2009) Electrochemical kinetic investigations of the reactions of [FeFe]-hydrogenases with carbon monoxide and oxygen: comparing the importance of gas tunnels and active-site electronic/redox effects. J Am Chem Soc 131:14979–14989PubMedCrossRefGoogle Scholar
  292. Goodman TG, Hoffman PS (1983) Hydrogenase activity in catalase-positive strains of Campylobacter spp. J Clin Microbiol 18:825–829PubMedGoogle Scholar
  293. Goris T, Wait AF, Saggu M, Fritsch J, Heidary N, Stein M, Zebger I, Lendzian F, Armstrong FA, Friedrich B, Lenz O (2011) A unique iron-sulfur cluster is crucial for oxygen tolerance of a [NiFe]-hydrogenase. Nat Chem Biol 7:310–318PubMedCrossRefGoogle Scholar
  294. Gorrell TE, Uffen RL (1977) Fermentative metabolism of pyruvate by Rhodospirillum rubrum after anaerobic growth in darkness. J Bacteriol 131:533–543PubMedGoogle Scholar
  295. Gorrell TE, Uffen RL (1978) Reduction of nicotinamide adenine dinucleotide by pyruvate:lipoate oxidoreductase in anaerobic, dark-grown Rhodospirillum rubrum mutant C. J Bacteriol 134:830–836PubMedGoogle Scholar
  296. Gorwa MF, Croux C, Soucaille P (1996) Molecular characterization and transcriptional analysis of the putative hydrogenase gene of Clostridium acetobutylicum ATCC 824. J Bacteriol 178:2668–2675PubMedGoogle Scholar
  297. Gössner AS, Devereux R, Ohnemüller N, Acker G, Stackebrandt E, Drake HL (1999) Thermicanus aegyptius gen. nov., sp. nov., isolated from oxic soil, a fermentative microaerophile that grows commensally with the thermophilic acetogen Moorella thermoacetica. Appl Environ Microbiol 65:5124–5133PubMedGoogle Scholar
  298. Götz D, Banta A, Beveridge TJ, Rushdi AI, Simoneit BR, Reysenbach AL (2002) Persephonella marina gen. nov., sp. nov. and Persephonella guaymasensis sp. nov., two novel, thermophilic, hydrogen-oxidizing microaerophiles from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 52:1349–1359PubMedCrossRefGoogle Scholar
  299. Graber JR, Leadbetter JR, Breznak JA (2004) Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first spirochetes isolated from termite guts. Appl Environ Microbiol 70:1315–1320PubMedCrossRefGoogle Scholar
  300. Graf EG, Thauer RK (1981) Hydrogenase from Methanobacterium thermoautotrophicum. FEBS Lett 136:165–169CrossRefGoogle Scholar
  301. Gray CT, Gest H (1965) Biological formation of molecular hydrogen. Science 148:186–192PubMedCrossRefGoogle Scholar
  302. Gross R, Simon J, Lancaster CR, Kroger A (1998) Identification of histidine residues in Wolinella succinogenes hydrogenase that are essential for menaquinone reduction by H2. Mol Microbiol 30:639–646PubMedCrossRefGoogle Scholar
  303. Gross R, Simon J, Kroger A (1999) The role of the twin-arginine motif in the signal peptide encoded by the hydA gene of the hydrogenase from Wolinella succinogenes. Arch Microbiol 172:227–232PubMedCrossRefGoogle Scholar
  304. Grzeszik C, Lübbers M, Reh M, Schlegel HG (1997a) Genes encoding the NAD-reducing hydrogenase of Rhodococcus opacus MR11. Microbiology 143:1271–1286PubMedCrossRefGoogle Scholar
  305. Grzeszik C, Ross K, Schneider K, Reh M, Schlegel HG (1997b) Location, catalytic activity, and subunit composition of NAD-reducing hydrogenases of some Alcaligenes strains and Rhodococcus opacus MR22. Arch Microbiol 167:172–176CrossRefGoogle Scholar
  306. Guiral M, Aubert C, Giudici-Orticoni MT (2005a) Hydrogen metabolism in the hyperthermophilic bacterium Aquifex aeolicus. Biochem Soc Trans 33:22–24PubMedCrossRefGoogle Scholar
  307. Guiral M, Tron P, Aubert C, Gloter A, Iobbi-Nivol C, Giudici-Orticoni MT (2005b) A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J Biol Chem 280:42004–42015PubMedCrossRefGoogle Scholar
  308. Gutekunst K, Phunpruch S, Schwarz C, Schuchardt S, Schulz-Friedrich R, Appel J (2005) LexA regulates the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803 as a transcription activator. Mol Microbiol 58:810–823PubMedCrossRefGoogle Scholar
  309. Gutierrez D, Hernando Y, Palacios JM, Imperial J, Ruiz-Argueso T (1997) FnrN controls symbiotic nitrogen fixation and hydrogenase activities in Rhizobium leguminosarum biovar viciae UPM791. J Bacteriol 179:5264–5270PubMedGoogle Scholar
  310. Guyoneaud R, Matheron R, Liesack W, Imhoff JF, Caumette P (1997) Thiorhodococcus minus, gen. nov., sp. nov., A new purple sulfur bacterium isolated from coastal lagoon sediments. Arch Microbiol 168:16–23PubMedCrossRefGoogle Scholar
  311. Hafenbradl D, Keller M, Dirmeier R, Rachel R, Rossnagel P, Burggraf S, Huber H, Stetter KO (1996) Ferroglobus placidus gen. nov., sp. nov., A novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Microbiol 166:308–314PubMedCrossRefGoogle Scholar
  312. Halboth S, Klein A (1992) Methanococcus voltae harbors four gene clusters potentially encoding two [NiFe] and two [NiFeSe] hydrogenases, each of the cofactor F420-reducing or F420-non-reducing types. Mol Gen Genet 233:217–224PubMedCrossRefGoogle Scholar
  313. Hanczar T, Csaki R, Bodrossy L, Murrell JC, Kovacs KL (2002) Detection and localization of two hydrogenases in Methylococcus capsulatus (Bath) and their potential role in methane metabolism. Arch Microbiol 177:167–172PubMedCrossRefGoogle Scholar
  314. Hanus FJ, Maier RJ, Evans HJ (1979) Autotrophic growth of H2-uptake-positive strains of Rhizobium japonicum in an atmosphere supplied with hydrogen gas. Proc Natl Acad Sci USA 76:1788–1792PubMedCrossRefGoogle Scholar
  315. Happe T, Naber JD (1993) Isolation, characterization and N-terminal amino acid sequence of hydrogenase from the green alga Chlamydomonas reinhardtii. Eur J Biochem 214:475–481PubMedCrossRefGoogle Scholar
  316. Happe T, Mosler B, Naber JD (1994) Induction, localization and metal content of hydrogenase in the green alga Chlamydomonas reinhardtii. Eur J Biochem 222:769–774PubMedCrossRefGoogle Scholar
  317. Happe RP, Roseboom W, Pierik AJ, Albracht SP, Bagley KA (1997) Biological activation of hydrogen. Nature 385:126PubMedCrossRefGoogle Scholar
  318. Happe T, Schutz K, Bohme H (2000) Transcriptional and mutational analysis of the uptake hydrogenase of the filamentous cyanobacterium Anabaena variabilis ATCC 29413. J Bacteriol 182:1624–1631PubMedCrossRefGoogle Scholar
  319. Häring V, Klüber HD, Conrad R (1994) Localization of atmospheric H2-oxidizing soil hydrogenases in different particle fractions of soil. Biol Fertil Soils 18:109–114CrossRefGoogle Scholar
  320. Harker AR, Xu LS, Hanus FJ, Evans HJ (1984) Some properties of the nickel-containing hydrogenase of chemolithotrophically grown Rhizobium japonicum. J Bacteriol 159:850–856PubMedGoogle Scholar
  321. Harker AR, Lambert GR, Hanus FJ, Evans HJ (1985) Further evidence that two unique subunits are essential for expression of hydrogenase activity in Rhizobium japonicum. J Bacteriol 164:187–191PubMedGoogle Scholar
  322. Harmsen HJ, Kengen KM, Akkermans AD, Stams AJ (1995) Phylogenetic analysis of two syntrophic propionate-oxidizing bacteria in enrichment cultures. Syst Appl Microbiol 18:67–73CrossRefGoogle Scholar
  323. Haselkorn R, Buikema WJ (1992) Nitrogen fixation in cyanobacteria. In: Stacey G, Burris RH, Evans HJ (eds) Biological nitrogen fixation. Chapman and Hall, London, pp 166–190Google Scholar
  324. Hatchikian EC, Zeikus JG (1983) Characterization of a new type of dissimilatory sulfite reductase present in Thermodesulfobacterium commune. J Bacteriol 153:1211–1220PubMedGoogle Scholar
  325. Hatchikian EC, Chaigneau M, Le Gall J (1976) Analysis of gas production by growing cultures of three species of sulfate-reducing bacteria. In: Schlegel HG, Gottschalk G, Pfennig N (eds) Microbial production and utilization of gases. E. Goltze, Gottingen, pp 109–118Google Scholar
  326. Hatchikian EC, Bruschi M, Le Gall J (1978) Characterization of the periplasmic hydrogenase from Desulfovibrio gigas. Biochem Biophys Res Commun 82:451–461PubMedCrossRefGoogle Scholar
  327. Hatchikian EC, Magro V, Forget N, Nicolet Y, Fontecilla-Camps JC (1999) Carboxy-terminal processing of the large subunit of [Fe] hydrogenase from Desulfovibrio desulfuricans ATCC 7757. J Bacteriol 181:2947–2952PubMedGoogle Scholar
  328. Hattori S, Kamagata Y, Hanada S, Shoun H (2000) Thermoacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int J Syst Evol Microbiol 50:1601–1609PubMedCrossRefGoogle Scholar
  329. Hayashi NR, Ishida T, Yokota A, Kodama T, Igarashi Y (1999) Hydrogenophilus thermoluteolus gen. nov., sp. nov., a thermophilic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol 49:783–786PubMedCrossRefGoogle Scholar
  330. Hayes JM (1983) Geochemical evidence bearing on the origin of aerobiosis, a speculative hypothesis. In: Schopf JW (ed) Earth’s earliest biosphere: its origin and evolution. Princeton University Press, Princeton, pp 291–301Google Scholar
  331. He SH, Teixeira M, LeGall J, Patil DS, Moura I, Moura JJ, DerVartanian DV, Huynh BH, Peck HD Jr (1989) EPR studies with 77Se-enriched (NiFeSe) hydrogenase of Desulfovibrio baculatus. Evidence for a selenium ligand to the active site nickel. J Biol Chem 264:2678–2682PubMedGoogle Scholar
  332. Hedderich R, Forzi L (2005) Energy-converting [NiFe] hydrogenases: more than just H2 activation. J Mol Microbiol Biotechnol 10:92–104PubMedCrossRefGoogle Scholar
  333. Hedderich R, Klimmek O, Kröger A, Dirmeier R, Keller M, Stetter KO (1999) Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiol Rev 22:353–381CrossRefGoogle Scholar
  334. Heidelberg JF, Seshadri R, Haveman SA, Hemme CL, Paulsen IT, Kolonay JF, Eisen JA, Ward N, Methe B, Brinkac LM, Daugherty SC, Deboy RT, Dodson RJ, Durkin AS, Madupu R, Nelson WC, Sullivan SA, Fouts D, Haft DH, Selengut J, Peterson JD, Davidsen TM, Zafar N, Zhou L, Radune D, Dimitrov G, Hance M, Tran K, Khouri H, Gill J, Utterback TR, Feldblyum TV, Wall JD, Voordouw G, Fraser CM (2004) The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Nat Biotechnol 22:554–559PubMedCrossRefGoogle Scholar
  335. Hennecke H (1990) Nitrogen fixation genes involved in the Bradyrhizobium japonicum-soybean symbiosis. FEBS Lett 268:422–426PubMedCrossRefGoogle Scholar
  336. Hernando Y, Palacios JM, Imperial J, Ruiz-Argueso T (1995) The hypBFCDE operon from Rhizobium leguminosarum biovar viciae is expressed from an Fnr-type promoter that escapes mutagenesis of the fnrN gene. J Bacteriol 177:5661–5669PubMedGoogle Scholar
  337. Herrero A, Muro-Pastor AM, Valladares A, Flores E (2004) Cellular differentiation and the NtcA transcription factor in filamentous cyanobacteria. FEMS Microbiol Rev 28:469–487PubMedCrossRefGoogle Scholar
  338. Heyer H, Stal L, Krumbein WE (1989) Simultaneous heterolactic and acetate fermentation in the marine cyanobacterium oscillatoria-limosa incubated anaerobically in the dark. Arch Microbiol 151:558–564CrossRefGoogle Scholar
  339. Hidalgo E, Palacios JM, Murillo J, Ruiz-Argueso T (1992) Nucleotide sequence and characterization of four additional genes of the hydrogenase structural operon from Rhizobium leguminosarum bv. viciae. J Bacteriol 174:4130–4139PubMedGoogle Scholar
  340. Higuchi Y, Yagi T, Yasuoka N (1997) Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis. Structure 5:1671–1680PubMedCrossRefGoogle Scholar
  341. Hiromoto T, Ataka K, Pilak O, Vogt S, Stagni MS, Meyer-Klaucke W, Warkentin E, Thauer RK, Shima S, Ermler U (2009a) The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. FEBS Lett 583:585–590PubMedCrossRefGoogle Scholar
  342. Hiromoto T, Warkentin E, Moll J, Ermler U, Shima S (2009b) The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H2 activation. Angew Chem Int Ed Engl 48:6457–6460PubMedCrossRefGoogle Scholar
  343. Hoehler TM, Bebout BM, Des Marais DJ (2001) The role of microbial mats in the production of reduced gases on the early Earth. Nature 412:324–327PubMedCrossRefGoogle Scholar
  344. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJ (1998) Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol 169:313–321PubMedCrossRefGoogle Scholar
  345. Holo H, Sirevag R (1986) Autotrophic growth and CO2 fixation of Chloroflexus aurantiacus. Arch Microbiol 145:173–180CrossRefGoogle Scholar
  346. Horch M, Lauterbach L, Saggu M, Hildebrandt P, Lendzian F, Bittl R, Lenz O, Zebger I (2010) Probing the active site of an O2-tolerant NAD+-reducing [NiFe]-hydrogenase from Ralstonia eutropha H16 by in situ EPR and FTIR spectroscopy. Angew Chem Int Ed Engl 49:8026–8029PubMedCrossRefGoogle Scholar
  347. Horch M, Lauterbach L, Lenz O, Hildebrandt P, Zebger I (2012) NAD(H)-coupled hydrogen cycling – structure-function relationships of bidirectional [NiFe] hydrogenases. FEBS Lett 586:545–556PubMedCrossRefGoogle Scholar
  348. Horner DS, Foster PG, Embley TM (2000) Iron hydrogenases and the evolution of anaerobic eukaryotes. Mol Biol Evol 17:1695–1709PubMedCrossRefGoogle Scholar
  349. Horner DS, Heil B, Happe T, Embley TM (2002) Iron hydrogenases—ancient enzymes in modern eukaryotes. Trends Biochem Sci 27:148–153PubMedCrossRefGoogle Scholar
  350. Houchins JP, Burris RH (1981a) Comparative characterization of two distinct hydrogenases from Anabaena sp. strain 7120. J Bacteriol 146:215–221PubMedGoogle Scholar
  351. Houchins JP, Burris RH (1981b) Occurrence and localization of two distinct hydrogenases in the heterocystous cyanobacterium Anabaena sp. strain 7120. J Bacteriol 146:209–214PubMedGoogle Scholar
  352. Howarth DC, Codd GA (1985) The uptake and production of molecular-hydrogen by unicellular cyanobacteria. J Gen Microbiol 131:1561–1569Google Scholar
  353. Hube M, Blokesch M, Böck A (2002) Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF. J Bacteriol 184:3879–3885PubMedCrossRefGoogle Scholar
  354. Huber H, Thomm M, Konig H, Thies G, Stetter KO (1982) Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch Microbiol 132:47–50CrossRefGoogle Scholar
  355. Huber R, Langworthy TA, Konig H, Thomm M, Woese CR, Sleytr UB, Stetter KO (1986) Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90 °C. Arch Microbiol 144:324–333CrossRefGoogle Scholar
  356. Huber R, Kristjansson JK, Stetter KO (1987) Pyrobaculum gen. nov., a new genus of neutrophilic, rod-shaped archaebacteria from continental solfataras growing optimally at 100°C. Arch Microbiol 149:95–101CrossRefGoogle Scholar
  357. Huber G, Spinnler C, Gambacorta A, Stetter KO (1989) Metallosphaera sedula gen. nov. and sp. nov. represents a new genus of aerobic, metal-mobilizing, thermoacidophilic archaebacteria. Syst Appl Microbiol 12:38–47CrossRefGoogle Scholar
  358. Huber R, Woese CR, Langworthy TA, Kristjansson JK, Stetter KO (1990) Fervidobacterium islandicum sp. nov., a new extremely thermophilic eubacterium belonging to the “Thermotogales”. Arch Microbiol 154:105–111CrossRefGoogle Scholar
  359. Huber R, Wilharm T, Huber D, Trincone A, Burggraf S, König H, Rachel R, Rockinger I, Fricke H, Stetter KO (1992) Aquifex pyrophilus gen. nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacterium. Syst Appl Microbiol 15:340–351CrossRefGoogle Scholar
  360. Huber R, Eder W, Heldwein S, Wanner G, Huber H, Rachel R, Stetter KO (1998) Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl Environ Microbiol 64:3576–3583PubMedGoogle Scholar
  361. Huber H, Burggraf S, Mayer T, Wyschkony I, Rachel R, Stetter KO (2000a) Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp. nov. and Ignicoccus pacificus sp. nov. Int J Syst Evol Microbiol 50:2093–2100PubMedCrossRefGoogle Scholar
  362. Huber R, Huber H, Stetter KO (2000b) Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties. FEMS Microbiol Rev 24:615–623PubMedCrossRefGoogle Scholar
  363. Huber H, Diller S, Horn C, Rachel R (2002) Thermovibrio ruber gen. nov., sp. nov., an extremely thermophilic, chemolithoautotrophic, nitrate-reducing bacterium that forms a deep branch within the phylum Aquificae. Int J Syst Evol Microbiol 52:1859–1865PubMedCrossRefGoogle Scholar
  364. Hügler M, Petersen JM, Dubilier N, Imhoff JF, Sievert SM (2011) Pathways of carbon and energy metabolism of the epibiotic community associated with the deep-sea hydrothermal vent shrimp Rimicaris exoculata. PLoS One 6:e16018PubMedCrossRefGoogle Scholar
  365. Hungate RE (1966) The rumen and its microbes. Academic, New YorkGoogle Scholar
  366. Huynh BH, Patil DS, Moura I, Teixeira M, Moura JJ, DerVartanian DV, Czechowski MH, Prickril BC, Peck HD Jr, LeGall J (1987) On the active sites of the [NiFe] hydrogenase from Desulfovibrio gigas. Mössbauer and redox-titration studies. J Biol Chem 262:795–800PubMedGoogle Scholar
  367. Hyndman LA, Burris RH, Wilson PW (1953) Properties of hydrogenase from Azotobacter vinelandii. J Bacteriol 65:522–531PubMedGoogle Scholar
  368. Ide T, Baumer S, Deppenmeier U (1999) Energy conservation by the H2:heterodisulfide oxidoreductase from Methanosarcina mazei Gö1: identification of two proton-translocating segments. J Bacteriol 181:4076–4080PubMedGoogle Scholar
  369. Igarashi Y, Kodama T, Minoda Y (1980) Identification and characterization of a new amylolytic hydrogen bacterium, Pseudomonas hydrogenovora. Agric Biol Chem 44:1277–1281CrossRefGoogle Scholar
  370. Jack RL, Buchanan G, Dubini A, Hatzixanthis K, Palmer T, Sargent F (2004) Coordinating assembly and export of complex bacterial proteins. EMBO J 23:3962–3972PubMedCrossRefGoogle Scholar
  371. Jackson BE, Bhupathiraju VK, Tanner RS, Woese CR, McInerney MJ (1999) Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch Microbiol 171:107–114PubMedCrossRefGoogle Scholar
  372. Jacobs NJ, Wolin MJ (1963) Electron-transport system of Vibrio succinogenes.1. Enzymes and cytochromes of electron-transport system. Biochim Biophys Acta 69:18–28PubMedCrossRefGoogle Scholar
  373. Jacobson FS, Daniels L, Fox JA, Walsh CT, Orme-Johnson WH (1982) Purification and properties of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. J Biol Chem 257:3385–3388PubMedGoogle Scholar
  374. Jankielewicz A, Klimmek O, Kroger A (1995) The electron transfer from hydrogenase and formate dehydrogenase to polysulfide reductase in the membrane of Wolinella succinogenes. Biochim Biophys Acta 1231:157–162CrossRefGoogle Scholar
  375. Jannasch HW, Mottl MJ (1985) Geomicrobiology of deep-sea hydrothermal vents. Science 229:717–725PubMedCrossRefGoogle Scholar
  376. Jannasch HW, Huber R, Belkins S, Stetter KO (1988) Thermotoga neapolitana sp. nov. of the extremely thermophilic, eubacterial genus Thermotoga. Arch Microbiol 150:103–104CrossRefGoogle Scholar
  377. Jansen K, Thauer RK, Widdel F, Fuchs G (1984) Carbon assimilation pathways in sulfate-reducing bacteria: formate, carbon dioxide, carbon monoxide, and acetate assimilation by Desulfovibrio baarsii. Arch Microbiol 138:257–262CrossRefGoogle Scholar
  378. Jayasinghearachchi HS, Lal B (2011) Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells. Int J Syst Evol Microbiol 61:554–560PubMedCrossRefGoogle Scholar
  379. Jeanthon C, L’Haridon S, Reysenbach AL, Vernet M, Messner P, Sleytr UB, Prieur D (1998) Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 48:913–919PubMedCrossRefGoogle Scholar
  380. Jeanthon C, L’Haridon S, Reysenbach AL, Corre E, Vernet M, Messner P, Sleytr UB, Prieur D (1999) Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213 T as Methanococcus fervens sp. nov. Int J Syst Bacteriol 49:583–589PubMedCrossRefGoogle Scholar
  381. Jenney FE Jr, Adams MW (2008) Hydrogenases of the model hyperthermophiles. Ann N Y Acad Sci 1125:252–266PubMedCrossRefGoogle Scholar
  382. Jin SLC, Blanchard DK, Chen JS (1983) 2 hydrogenases with distinct electron-carrier specificity and subunit composition in Methanobacterium formicicum. Biochim Biophys Acta 748:8–20CrossRefGoogle Scholar
  383. Jochimsen B, Peinemann-Simon S, Völker H, Stüben D, Botz R, Stoffers P, Dando PR, Thomm M (1997) Stetteria hydrogenophila, gen. nov. and sp. nov., a novel mixotrophic sulfur-dependent crenarchaeote isolated from Milos, Greece. Extremophiles 1:67–73PubMedCrossRefGoogle Scholar
  384. Jones WJ, Leigh JA, Mayer F, Woese CR, Wolfe RS (1983a) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136:254–261CrossRefGoogle Scholar
  385. Jones WJ, Paynter MJB, Gupta R (1983b) Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt-marsh sediment. Arch Microbiol 135:91–97CrossRefGoogle Scholar
  386. Jones AK, Lenz O, Strack A, Buhrke T, Friedrich B (2004) NiFe hydrogenase active site biosynthesis: identification of Hyp protein complexes in Ralstonia eutropha. Biochemistry 43:13467–13477PubMedCrossRefGoogle Scholar
  387. Jorgensen BB (1989) Biogeochemistry of chemoautotrophic bacteria. In: Schlegel HG, Bowien B (eds) Autotrophic bacteria. Science Tech/Springer, Madison, pp 117–146Google Scholar
  388. Jorgensen BB (2001) Biogeochemistry. Space for hydrogen. Nature 412:286–287 and 289PubMedCrossRefGoogle Scholar
  389. Joyner AE, Winter WT, Godbout DM (1977) Studies on some characteristics of hydrogen production by cell-free extracts of rumen anaerobic bacteria. Can J Microbiol 23:346–353PubMedCrossRefGoogle Scholar
  390. Jungermann K, Schön G (1974) Pyruvate formate lyase in Rhodospirillum rubrum Ha adapted to anaerobic dark conditions. Arch Microbiol 99:109–116PubMedCrossRefGoogle Scholar
  391. Juszczak A, Aono S, Adams MW (1991) The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten. J Biol Chem 266:13834–13841PubMedGoogle Scholar
  392. Kaesler B, Schönheit P (1989) The role of sodium ions in methanogenesis. Formaldehyde oxidation to CO2 and 2H2 in methanogenic bacteria is coupled with primary electrogenic Na+ translocation at a stoichiometry of 2–3 Na+/CO2. Eur J Biochem 184:223–232PubMedCrossRefGoogle Scholar
  393. Kaksonen AH, Spring S, Schumann P, Kroppenstedt RM, Puhakka JA (2006) Desulfotomaculum thermosubterraneum sp. nov., a thermophilic sulfate-reducer isolated from an underground mine located in a geothermally active area. Int J Syst Evol Microbiol 56:2603–2608PubMedCrossRefGoogle Scholar
  394. Kämpf C, Pfennig N (1980) Capacity of chromatiaceae for chemotropic growth—specific respiration rates of Thiocystis violacea and Chromatium vinosum. Arch Microbiol 127:125–135CrossRefGoogle Scholar
  395. Kämpf C, Pfennig N (1986) Isolation and characterization of some chemoautotrophic chromatiaceae. J Basic Microbiol 26:507–515CrossRefGoogle Scholar
  396. Kane MD, Brauman A, Breznak JA (1991) Clostridium mayombei sp. nov., an H2/CO2 acetogenic bacterium from the gut of the African soil-feeding termite, Cubitermes speciosus. Arch Microbiol 156:99–104CrossRefGoogle Scholar
  397. Kane MD, Breznak JA (1991) Acetonema longum gen. nov. sp. nov., an H2/CO2 acetogenic bacterium from the termite, Pterotermes occidentis. Arch Microbiol 156:91–98PubMedCrossRefGoogle Scholar
  398. Kärst U, Suetin S, Friedrich CG (1987) Purification and properties of a protein linked to the soluble hydrogenase of hydrogen-oxidizing bacteria. J Bacteriol 169:2079–2085PubMedGoogle Scholar
  399. Kaserer H (1906) Die Oxydation des Wasserstoffes durch Mikroorganismen. Centr Bakteriol Parasitenk 16:681–696Google Scholar
  400. Kashefi K, Lovley DR (2000) Reduction of Fe(III), Mn(IV), and toxic metals at 100 degrees C by Pyrobaculum islandicum. Appl Environ Microbiol 66:1050–1056PubMedCrossRefGoogle Scholar
  401. Kashefi K, Holmes DE, Reysenbach AL, Lovley DR (2002a) Use of Fe(III) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of Geothermobacterium ferrireducens gen. nov., sp. nov. Appl Environ Microbiol 68:1735–1742PubMedCrossRefGoogle Scholar
  402. Kashefi K, Tor JM, Holmes DE, Gaw Van Praagh CV, Reysenbach AL, Lovley DR (2002b) Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor. Int J Syst Evol Microbiol 52:719–728PubMedCrossRefGoogle Scholar
  403. Kasting JF (1993) Earth’s early atmosphere. Science 259:920–926PubMedCrossRefGoogle Scholar
  404. Kasting JF, Holland HD, Kump LR (1992) Atmospheric evolution: the rise of oxygen. In: Schopf JW, Klein C (eds) The proterozoic biosphere: a multidisciplinary study. Cambridge University Press, Cambridge, pp 159–163Google Scholar
  405. Kawasumi T, Igarashi Y, Kodama T, Minoda Y (1984) Hydrogenobacter thermophilus gen. nov., sp. nov., an extremely thermophilic, aerobic, hydrogen-oxidizing bacterium. Int J Syst Bacteriol 34:5–10CrossRefGoogle Scholar
  406. Kelley DS, Karson JA, Fruh-Green GL, Yoerger DR, Shank TM, Butterfield DA, Hayes JM, Schrenk MO, Olson EJ, Proskurowski G, Jakuba M, Bradley A, Larson B, Ludwig K, Glickson D, Buckman K, Bradley AS, Brazelton WJ, Roe K, Elend MJ, Delacour A, Bernasconi SM, Lilley MD, Baross JA, Summons RE, Sylva SP (2005) A serpentinite-hosted ecosystem: the Lost City hydrothermal field. Science 307:1428–1434PubMedCrossRefGoogle Scholar
  407. Keltjens JT, Vogels GD (1993) Conversion of methanol and methylamines to methane and carbon dioxide. In: Ferry JG (ed) Methanogenesis. Chapman & Hall, New York, pp 253–303CrossRefGoogle Scholar
  408. Kentemich T, Bahnweg M, Mayer F, Bothe H (1989) Localization of the reversible hydrogenase in cyanobacteria. Z Naturforsch C 44:384–391Google Scholar
  409. Kerby R, Zeikus JG (1983) Growth of Clostridium thermoaceticum on H2/CO2 or CO as energy source. Curr Microbiol 8:27–30CrossRefGoogle Scholar
  410. Kiessling M, Meyer O (1982) Profitable oxidation of carbon monoxide or hydrogen during heterotrophic growth of Pseudomonas carboxydoflava. FEMS Microbiol Lett 13:333–338CrossRefGoogle Scholar
  411. King PW, Posewitz MC, Ghirardi ML, Seibert M (2006) Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system. J Bacteriol 188:2163–2172PubMedCrossRefGoogle Scholar
  412. Kiss E, Kos PB, Vass I (2009) Transcriptional regulation of the bidirectional hydrogenase in the cyanobacterium Synechocystis 6803. J Biotechnol 142:31–37PubMedCrossRefGoogle Scholar
  413. Kleihues L, Lenz O, Bernhard M, Buhrke T, Friedrich B (2000) The H2 sensor of Ralstonia eutropha is a member of the subclass of regulatory [NiFe] hydrogenases. J Bacteriol 182:2716–2724PubMedCrossRefGoogle Scholar
  414. Klemme J-H, Schlegel HG (1967) Light-dependent pyridine nucleotide reduction with molecarhydrogen by subcellular photopigment particles from Rhodopseudomonas capsulata. Z Naturforsch B 22:899–900PubMedGoogle Scholar
  415. Klemps R, Cypionka H, Widdel F, Pfennig N (1985) Growth with hydrogen, and further physiological-characteristics of Desulfotomaculum species. Arch Microbiol 143:203–208CrossRefGoogle Scholar
  416. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Venter JC et al (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364–370PubMedCrossRefGoogle Scholar
  417. Knüttel K, Schneider K, Schlegel HG, Müller A (1989) The membrane-bound hydrogenase from Paracoccus denitrificans. Purification and molecular characterization. Eur J Biochem 179:101–108PubMedCrossRefGoogle Scholar
  418. Knüttel K, Schneider K, Erkens A, Plass W, Müller A, Bill E, Trautwein AX (1994) Redox properties of the metal centres in the membrane-bound hydrogenase from Alcaligenes eutrophus CH34. Bull Pol Acad Sci Chem 42:495–511Google Scholar
  419. Kodama T, Igarashi Y, Minoda Y (1975) Isolation and culture conditions of a bacterium grown on hydrogen and carbon dioxide. Agric Biol Chem 39:77–82CrossRefGoogle Scholar
  420. Kohlmiller EF Jr, Gest H (1951) A comparative study of the light and dark fermentations of organic acids by Rhodospirillum rubrum. J Bacteriol 61:269–282PubMedGoogle Scholar
  421. Kojima N, Fox JA, Hausinger RP, Daniels L, Orme-Johnson WH, Walsh C (1983) Paramagnetic centers in the nickel-containing, deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum. Proc Natl Acad Sci USA 80:378–382PubMedCrossRefGoogle Scholar
  422. Kondratieva EN, Gogotov IN (1983) Production of molecular hydrogen in microorganisms. Adv Biochem Eng Biotechnol 28:139–190Google Scholar
  423. Kortlüke C, Horstmann K, Schwartz E, Rohde M, Binsack R, Friedrich B (1992) A gene complex coding for the membrane-bound hydrogenase of Alcaligenes eutrophus H16. J Bacteriol 174:6277–6289PubMedGoogle Scholar
  424. Kotelnikova S, Pedersen K (1998) Distribution and activity of methanogens and homoacetogens in deep granitic aquifers at Äspö Hard Rock Laboratory, Sweden. FEMS Microbiol Ecol 26:121–134Google Scholar
  425. Kotelnikova S, Macario AJ, Pedersen K (1998) Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. Int J Syst Bacteriol 48:357–367PubMedCrossRefGoogle Scholar
  426. Kotsyurbenko OR, Simankova MV, Nozhevnikova AN, Zhilina TN, Bolotina NP, Lysenko AM, Osipov GA (1995) New species of psychrophilic acetogens—Acetobacterium bakii sp. nov., A. paludosum sp. nov., A. fimetarium sp. nov. Arch Microbiol 163:29–34CrossRefGoogle Scholar
  427. Kovacs KL, Bagyinka C, Serebriakova LT (1983) Distribution and orientation of hydrogenase in various photosynthetic bacteria. Curr Microbiol 9:215–218CrossRefGoogle Scholar
  428. Kovács KL, Fodor B, Kovács ÁT, Csanádi G, Maróti G, Balogh J, Arvani S, Rákhely G (2002) Hydrogenases, accessory genes and the regulation of [NiFe] hydrogenase biosynthesis in Thiocapsa roseopersicina. Int J Hydrogen Energy 27:1463–1469CrossRefGoogle Scholar
  429. Kovács AT, Rákhely G, Balogh J, Maróti G, Cournac L, Carrier P, Mészáros LS, Peltier G, Kovács KL (2005a) Hydrogen independent expression of hupSL genes in Thiocapsa roseopersicina BBS. FEBS J 272:4807–4816PubMedCrossRefGoogle Scholar
  430. Kovács AT, Rákhely G, Browning DF, Fülöp A, Maróti G, Busby SJ, Kovács KL (2005b) An FNR-type regulator controls the anaerobic expression of hyn hydrogenase in Thiocapsa roseopersicina. J Bacteriol 187:2618–2627PubMedCrossRefGoogle Scholar
  431. Kovács KL, Kovács AT, Maróti G, Mészáros LS, Balogh J, Latinovics D, Fülöp A, David R, Doroghazi E, Rákhely G (2005c) The hydrogenases of Thiocapsa roseopersicina. Biochem Soc Trans 33:61–63PubMedCrossRefGoogle Scholar
  432. Krasna AI (1979) Hydrogenase—properties and applications. Enzyme Microb Technol 1:165–172CrossRefGoogle Scholar
  433. Krasna AI (1980) Regulation of hydrogenase activity in enterobacteria. J Bacteriol 144:1094–1097PubMedGoogle Scholar
  434. Krasna AI (1984) Mutants of Escherichia coli with altered hydrogenase activity. J Gen Microbiol 130:779–787PubMedGoogle Scholar
  435. Kristjansson JK, Schonheit P, Thauer RK (1982) Different ks-values for hydrogen of methanogenic bacteria and sulfate reducing bacteria—an explanation for the apparent inhibition of methanogenesis by sulfate. Arch Microbiol 131:278–282CrossRefGoogle Scholar
  436. Kroger A, Innerhofer A (1976) Function of b cytochromes in electron-transport from formate to fumarate of Vibrio succinogenes. Eur J Biochem 69:497–506CrossRefGoogle Scholar
  437. Krylova NI, Janssen PH, Conrad R (1997) Turnover of propionate in methanogenic paddy soil. FEMS Microbiol Ecol 23:107–117CrossRefGoogle Scholar
  438. Kryukov VR, Savelyeva ND, Pusheva MA (1983) Calderobacterium hydrogenophilum nov. gen., nov. sp., an extremely thermophilic hydrogen bacterium and its hydrogenase activity. Mikrobiologiya 52:781–788Google Scholar
  439. Kubas GJ (2007) Fundamentals of H2 binding and reactivity on transition metals underlying hydrogenase function and H2 production and storage. Chem Rev 107:4152–4205PubMedCrossRefGoogle Scholar
  440. Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M, Ishiura M (2005) Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 187:2190–2199PubMedCrossRefGoogle Scholar
  441. Kühnemund H (1971) Zur Verwertung von molekularem Wasserstoff durch Micrococcus denitrificans. PhD thesis. Universität Göttingen. Göttingen, GermanyGoogle Scholar
  442. Kuhner CH, Frank C, Griesshammer A, Schmittroth M, Acker G, Gössner A, Drake HL (1997) Sporomusa silvacetica sp, nov., an acetogenic bacterium isolated from aggregated forest soil. Int J Syst Bacteriol 47:352–358PubMedCrossRefGoogle Scholar
  443. Künkel A, Vorholt JA, Thauer RK, Hedderich R (1998) An Escherichia coli hydrogenase-3-type hydrogenase in methanogenic archaea. Eur J Biochem 252:467–476PubMedCrossRefGoogle Scholar
  444. Kurr M, Huber R, König H, Jannasch HW, Fricke H, Trincone A, Kristjansson JK, Stetter KO (1991) Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110 °C. Arch Microbiol 156:239–247CrossRefGoogle Scholar
  445. Küsel K, Dorsch T, Acker G, Stackebrandt E, Drake HL (2000) Clostridium scatologenes strain SL1 isolated as an acetogenic bacterium from acidic sediments. Int J Syst Evol Microbiol 50:537–546PubMedCrossRefGoogle Scholar
  446. L’Haridon SL, Miroshnichenko ML, Hippe H, Fardeau ML, Bonch-Osmolovskaya E, Stackebrandt E, Jeanthon C (2001) Thermosipho geolei sp. nov., a thermophilic bacterium isolated from a continental petroleum reservoir in western Siberia. Int J Syst Evol Microbiol 51:1327–1334Google Scholar
  447. L’Haridon S, Reysenbach AL, Banta A, Messner P, Schumann P, Stackebrandt E, Jeanthon C (2003) Methanocaldococcus indicus sp. nov., a novel hyperthermophilic methanogen isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 53:1931–1935PubMedCrossRefGoogle Scholar
  448. L’Haridon S, Reysenbach AL, Tindall BJ, Schönheit P, Banta A, Johnsen U, Schumann P, Gambacorta A, Stackebrandt E, Jeanthon C (2006) Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria. Int J Syst Evol Microbiol 56:2843–2852PubMedCrossRefGoogle Scholar
  449. La Favre JS, Focht DD (1983) Conservation in soil of H2 liberated from N2 fixation by Hup nodules. Appl Environ Microbiol 46:304–311PubMedGoogle Scholar
  450. Laanbroek HJ, Abee T, Voogd IL (1982) Alcohol conversions by Desulfobulbus propionicus Lindhorst in the presence and absence of sulfate and hydrogen. Arch Microbiol 133:178–184CrossRefGoogle Scholar
  451. Lalucat J, Pares R, Schlegel HG (1982) Pseudomonas taeniospiralis sp. nov., an R-body-containing hydrogen bacterium. Int J Syst Bacteriol 32:332–338CrossRefGoogle Scholar
  452. Lambert GR, Smith GD (1980) Hydrogen metabolism by filamentous cyanobacteria. Arch Biochem Biophys 205:36–50PubMedCrossRefGoogle Scholar
  453. Lampreia J, Fauque G, Speich N, Dahl C, Moura I, Truper HG, Moura JJ (1991) Spectroscopic studies on APS reductase isolated from the hyperthermophilic sulfate-reducing archaebacterium Archaeoglobus fulgidus. Biochem Biophys Res Commun 181:342–347PubMedCrossRefGoogle Scholar
  454. Lancaster CR (2001) Succinate:quinone oxidoreductases—what can we learn from Wolinella succinogenes quinol:fumarate reductase? FEBS Lett 504:133–141PubMedCrossRefGoogle Scholar
  455. Laska S, Lottspeich F, Kletzin A (2003) Membrane-bound hydrogenase and sulfur reductase of the hyperthermophilic and acidophilic archaeon Acidianus ambivalens. Microbiology 149:2357–2371PubMedCrossRefGoogle Scholar
  456. Lauerer G, Kristjansson JK, Langworthy TA, König H, Stetter KO (1986) Methanothermus sociabilis sp. nov., a second species within the Methanothermaceae growing at 97 °C. Syst Appl Microbiol 8:100–105CrossRefGoogle Scholar
  457. Lauterbach L, Idris Z, Vincent KA, Lenz O (2011a) Catalytic properties of the isolated diaphorase fragment of the NAD-reducing [NiFe]-hydrogenase from Ralstonia eutropha. PLoS One 6:e25939PubMedCrossRefGoogle Scholar
  458. Lauterbach L, Liu JA, Horch M, Hummel P, Schwarze A, Haumann M, Vincent KA, Lenz O, Zebger I (2011b) The hydrogenase subcomplex of the NAD+-Reducing [NiFe] hydrogenase from Ralstonia eutropha—insights into catalysis and redox interconversions. Eur J Inorg Chem 2011(7):1067–1079CrossRefGoogle Scholar
  459. Leach MR, Zamble DB (2007) Metallocenter assembly of the hydrogenase enzymes. Curr Opin Chem Biol 11:159–165PubMedCrossRefGoogle Scholar
  460. Leclerc M, Colbeau A, Cauvin B, Vignais PM (1988) Cloning and sequencing of the genes encoding the large and the small subunits of the H2 uptake hydrogenase (hup) of Rhodobacter capsulatus. Mol Gen Genet 214:97–107PubMedCrossRefGoogle Scholar
  461. Lee SB, Wilson PW (1943) Hydrogenase and nitrogenase in Azotobacter. J Biol Chem 151:377–385Google Scholar
  462. Lehman RM, Roberto FF, Earley D, Bruhn DF, Brink SE, O’Connell SP, Delwiche ME, Colwell FS (2001) Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer. Appl Environ Microbiol 67:2095–2106PubMedCrossRefGoogle Scholar
  463. Leigh JA, Mayer F, Wolfe RS (1981) Acetogenium kivui, a new thermophilic, hydrogen-oxidizing, acetogenic bacterium. Arch Microbiol 129:275–280CrossRefGoogle Scholar
  464. Leitao E, Oxelfelt F, Oliveira P, Moradas-Ferreira P, Tamagnini P (2005) Analysis of the hupSL operon of the nonheterocystous cyanobacterium Lyngbya majuscula CCAP 1446/4: regulation of transcription and expression under a light–dark regimen. Appl Environ Microbiol 71:4567–4576PubMedCrossRefGoogle Scholar
  465. Lelieveld J, Crutzen PJ, Dentener FJ (1998) Changing concentration, lifetime and climate forcing of atmospheric methane. Tellus B Chem Phys Meteorol 50:128–150CrossRefGoogle Scholar
  466. Lemon BJ, Peters JW (1999) Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. Biochemistry 38:12969–12973PubMedCrossRefGoogle Scholar
  467. Lenz O, Friedrich B (1998) A novel multicomponent regulatory system mediates H2 sensing in Alcaligenes eutrophus. Proc Natl Acad Sci USA 95:12474–12479PubMedCrossRefGoogle Scholar
  468. Lenz O, Schwartz E, Dernedde J, Eitinger M, Friedrich B (1994) The Alcaligenes eutrophus H16 hoxX gene participates in hydrogenase regulation. J Bacteriol 176:4385–4393PubMedGoogle Scholar
  469. Lenz O, Strack A, Tran-Betcke A, Friedrich B (1997) A hydrogen-sensing system in transcriptional regulation of hydrogenase gene expression in Alcaligenes species. J Bacteriol 179:1655–1663PubMedGoogle Scholar
  470. Lenz O, Bernhard M, Buhrke T, Schwartz E, Friedrich B (2002) The hydrogen-sensing apparatus in Ralstonia eutropha. J Mol Microbiol Biotechnol 4:255–562PubMedGoogle Scholar
  471. Lenz O, Zebger I, Hamann J, Hildebrandt P, Friedrich B (2007) Carbamoylphosphate serves as the source of CN, but not of the intrinsic CO in the active site of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha. FEBS Lett 581:3322–3326PubMedCrossRefGoogle Scholar
  472. Lenz O, Ludwig M, Schubert T, Bürstel I, Ganskow S, Goris T, Schwarze A, Friedrich B (2010) H2 conversion in the presence of O2 as performed by the membrane-bound [NiFe]-hydrogenase of Ralstonia eutropha. Chemphyschem 11:1107–1119PubMedCrossRefGoogle Scholar
  473. Leschine SB (1995) Cellulose degradation in anaerobic environments. Annu Rev Microbiol 49:399–426PubMedCrossRefGoogle Scholar
  474. Lill SO, Siegbahn PE (2009) An autocatalytic mechanism for NiFe-hydrogenase: reduction to Ni(I) followed by oxidative addition. Biochemistry 48:1056–1066PubMedCrossRefGoogle Scholar
  475. Lindblad P, Sellstedt A (1990) Occurrence and localization of an uptake hydrogenase in the filamentous heterocystous cyanobacterium Nostoc PCC 73102. Protoplasma 159:9–15CrossRefGoogle Scholar
  476. Lipscomb GL, Keese AM, Cowart DM, Schut GJ, Thomm M, Adams MW, Scott RA (2009) SurR: a transcriptional activator and repressor controlling hydrogen and elemental sulphur metabolism in Pyrococcus furiosus. Mol Microbiol 71:332–349PubMedCrossRefGoogle Scholar
  477. Liu Y, Balkwill DL, Aldrich HC, Drake GR, Boone DR (1999) Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. Int J Syst Bacteriol 49:545–556PubMedCrossRefGoogle Scholar
  478. Ljungdahl L, Wood HG (1982) Acetate biosynthesis. In: Dolphin D (ed) B12. Wiley, New York, pp 166–202Google Scholar
  479. Longnecker K, Reysenbach A (2001) Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the southern East Pacific Rise. FEMS Microbiol Ecol 35:287–293PubMedGoogle Scholar
  480. Lorowitz WH, Bryant MP (1984) Peptostreptococcus productus strain that grows rapidly with CO as the energy source. Appl Environ Microbiol 47:961–964PubMedGoogle Scholar
  481. Lovley DR, Chapelle FH (1996) Hydrogen-based microbial ecosystems in the Earth. Science 272:896bPubMedCrossRefGoogle Scholar
  482. Lovley DR, Klug MJ (1982) Intermediary metabolism of organic-matter in the sediments of a eutrophic lake. Appl Environ Microbiol 43:552–560PubMedGoogle Scholar
  483. Lovley DR, Klug MJ (1983) Sulfate reducers can out-compete methanogens at fresh-water sulfate concentrations. Appl Environ Microbiol 45:187–192PubMedGoogle Scholar
  484. Lovley DR, Dwyer DF, Klug MJ (1982) Kinetic-analysis of competition between sulfate reducers and methanogens for hydrogen in sediments. Appl Environ Microbiol 43:1373–1379PubMedGoogle Scholar
  485. Lovley DR, Phillips EJ, Lonergan DJ (1989) Hydrogen and formate oxidation coupled to dissimilatory reduction of iron or manganese by Alteromonas putrefaciens. Appl Environ Microbiol 55:700–706PubMedGoogle Scholar
  486. Lubitz W, Reijerse E, van Gastel M (2007) [NiFe] and [FeFe] hydrogenases studied by advanced magnetic resonance techniques. Chem Rev 107:4331–4365PubMedCrossRefGoogle Scholar
  487. Ludwig M, Schubert T, Zebger I, Wisitruangsakul N, Saggu M, Strack A, Lenz O, Hildebrandt P, Friedrich B (2009) Concerted action of two novel auxiliary proteins in assembly of the active site in a membrane-bound [NiFe] hydrogenase. J Biol Chem 284:2159–2168PubMedCrossRefGoogle Scholar
  488. Lukey MJ, Roessler MM, Parkin A, Evans RM, Davies RA, Lenz O, Friedrich B, Sargent F, Armstrong FA (2011) Oxygen-tolerant [NiFe]-hydrogenases: the individual and collective importance of supernumerary cysteines at the proximal Fe-S cluster. J Am Chem Soc 133:16881–16892PubMedCrossRefGoogle Scholar
  489. Lupton FS, Conrad R, Zeikus JG (1984) Physiological function of hydrogen metabolism during growth of sulfidogenic bacteria on organic substrates. J Bacteriol 159:843–849PubMedGoogle Scholar
  490. Lutz S, Bohm R, Beier A, Bock A (1990) Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli. Mol Microbiol 4:13–20PubMedCrossRefGoogle Scholar
  491. Lutz S, Jacobi A, Schlensog V, Böhm R, Sawers G, Böck A (1991) Molecular characterization of an operon (hyp) necessary for the activity of the three hydrogenase isoenzymes in Escherichia coli. Mol Microbiol 5:123–135PubMedCrossRefGoogle Scholar
  492. Lyon EJ, Shima S, Boecher R, Thauer RK, Grevels FW, Bill E, Roseboom W, Albracht SP (2004a) Carbon monoxide as an intrinsic ligand to iron in the active site of the iron-sulfur-cluster-free hydrogenase H2-forming methylenetetrahydromethanopterin dehydrogenase as revealed by infrared spectroscopy. J Am Chem Soc 126:14239–14248PubMedCrossRefGoogle Scholar
  493. Lyon EJ, Shima S, Buurman G, Chowdhuri S, Batschauer A, Steinbach K, Thauer RK (2004b) UV-A/blue-light inactivation of the ‘metal-free’ hydrogenase (Hmd) from methanogenic archaea. Eur J Biochem 271:195–204PubMedCrossRefGoogle Scholar
  494. Ma K, Schicho RN, Kelly RM, Adams MW (1993) Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor. Proc Natl Acad Sci USA 90:5341–5344PubMedCrossRefGoogle Scholar
  495. Ma K, Adams MW (1994) Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J Bacteriol 176:6509–6517PubMedGoogle Scholar
  496. Ma K, Weiss R, Adams MW (2000) Characterization of hydrogenase II from the hyperthermophilic archaeon Pyrococcus furiosus and assessment of its role in sulfur reduction. J Bacteriol 182:1864–1871PubMedCrossRefGoogle Scholar
  497. Maden BEH (1995) No soup for starters—autotrophy and the origins of metabolism. Trends Biochem Sci 20:337–341PubMedCrossRefGoogle Scholar
  498. Madigan MT, Gest H (1978) Growth of a photosynthetic bacterium anaerobically in darkness, supported by “oxidant-dependent” sugar fermentation. Arch Microbiol 117:119–122PubMedCrossRefGoogle Scholar
  499. Madigan MT, Gest H (1979) Growth of the photosynthetic bacterium Rhodopseudomonas capsulata chemoautotrophically in darkness with H2 as the energy source. J Bacteriol 137:524–530PubMedGoogle Scholar
  500. Magalon A, Böck A (2000) Analysis of the HypC-hycE complex, a key intermediate in the assembly of the metal center of the Escherichia coli hydrogenase 3. J Biol Chem 275:21114–21120PubMedCrossRefGoogle Scholar
  501. Magalon A, Blokesch M, Zehelein E, Böck A (2001) Fidelity of metal insertion into hydrogenases. FEBS Lett 499:73–76PubMedCrossRefGoogle Scholar
  502. Mah RA (1980) Isolation and characterization of Methanococcus mazei. Curr Microbiol 3:321–326CrossRefGoogle Scholar
  503. Maier T, Böck A (1996a). Nickel incorporation into hydrogenases. In: Hausinger RP, Eichhorn GL, Marzilli LG (eds) Mechanisms of Metallocenter Assembly. VCH Publishers. New York, NY. 173–192Google Scholar
  504. Maier T, Böck A (1996) Generation of active [NiFe] hydrogenase in vitro from a nickel-free precursor form. Biochemistry 35:10089–10093PubMedCrossRefGoogle Scholar
  505. Maier T, Lottspeich F, Bock A (1995) GTP hydrolysis by HypB is essential for nickel insertion into hydrogenases of Escherichia coli. Eur J Biochem 230:133–138PubMedCrossRefGoogle Scholar
  506. Maier RJ, Fu C, Gilbert J, Moshiri F, Olson J, Plaut AG (1996a) Hydrogen uptake hydrogenase in Helicobacter pylori. FEMS Microbiol Lett 141:71–76PubMedCrossRefGoogle Scholar
  507. Maier T, Binder U, Böck A (1996b) Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism. Arch Microbiol 165:333–341PubMedCrossRefGoogle Scholar
  508. Maimaiti J, Zhang Y, Yang J, Cen YP, Layzell DB, Peoples M, Dong Z (2007) Isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. Environ Microbiol 9:435–444PubMedCrossRefGoogle Scholar
  509. Major TA, Liu Y, Whitman WB (2010) Characterization of energy-conserving hydrogenase B in Methanococcus maripaludis. J Bacteriol 192:4022–4030PubMedCrossRefGoogle Scholar
  510. Malik KA, Claus D (1979) Xanthobacter flavus, a new species of nitrogen-fixing hydrogen bacteria. Int J Syst Bacteriol 29:283–287CrossRefGoogle Scholar
  511. Malik KA, Schlegel HG (1981) Chemolithoautotrophic growth of bacteria able to grow under N2-fixing conditions. FEMS Microbiol Lett 11:63–67CrossRefGoogle Scholar
  512. Malik B, Su WW, Wald HL, Blumentals II, Kelly RM (1989) Growth and gas-production for hyperthermophilic archaebacterium, Pyrococcus furiosus. Biotechnol Bioeng 34:1050–1057PubMedCrossRefGoogle Scholar
  513. Malki S, Saimmaime I, De Luca G, Rousset M, Dermoun Z, Belaich JP (1995) Characterization of an operon encoding an NADP-reducing hydrogenase in Desulfovibrio fructosovorans. J Bacteriol 177:2628–2636PubMedGoogle Scholar
  514. Malki S, De Luca G, Fardeau ML, Rousset M, Belaich JP, Dermoun Z (1997) Physiological characteristics and growth behavior of single and double hydrogenase mutants of Desulfovibrio fructosovorans. Arch Microbiol 167:38–45PubMedCrossRefGoogle Scholar
  515. Maness PC, Huang J, Smolinski S, Tek V, Vanzin G (2005) Energy generation from the CO oxidation-hydrogen production pathway in Rubrivivax gelatinosus. Appl Environ Microbiol 71:2870–2874PubMedCrossRefGoogle Scholar
  516. Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New HavenGoogle Scholar
  517. Maróti G, Fodor BD, Rákhely G, Kovács AT, Arvani S, Kovács KL (2003) Accessory proteins functioning selectively and pleiotropically in the biosynthesis of [NiFe] hydrogenases in Thiocapsa roseopersicina. Eur J Biochem 270:2218–2227PubMedCrossRefGoogle Scholar
  518. Maróti J, Farkas A, Nagy IK, Maróti G, Kondorosi E, Rákhely G, Kovács KL (2010) A second soluble Hox-type NiFe enzyme completes the hydrogenase set in Thiocapsa roseopersicina BBS. Appl Environ Microbiol 76:5113–5123PubMedCrossRefGoogle Scholar
  519. Marques MC, Coelho R, De Lacey AL, Pereira IA, Matias PM (2010) The three-dimensional structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough: a hydrogenase without a bridging ligand in the active site in its oxidised, “as-isolated” state. J Mol Biol 396:893–907PubMedCrossRefGoogle Scholar
  520. Martin WF (2012) Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation. FEBS Lett 586:485–493PubMedCrossRefGoogle Scholar
  521. Martin W, Muller M (1998) The hydrogen hypothesis for the first eukaryote. Nature 392:37–41PubMedCrossRefGoogle Scholar
  522. Martin DR, Lundie LL, Kellum R, Drake HL (1983) Carbon monoxide-dependent evolution of hydrogen by the homoacetate-fermenting bacterium Clostridium thermoaceticum. Curr Microbiol 8:337–340CrossRefGoogle Scholar
  523. Martin W, Russell MJ (2007) On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc Lond B Biol Sci 362:1887–1925PubMedCrossRefGoogle Scholar
  524. Martin W, Baross J, Kelley D, Russell MJ (2008) Hydrothermal vents and the origin of life. Nat Rev Microbiol 6:805–814PubMedGoogle Scholar
  525. Martinez M, Brito B, Imperial J, Ruiz-Argueso T (2004) Characterization of a new internal promoter (P3) for Rhizobium leguminosarum hydrogenase accessory genes hupGHIJ. Microbiology 150:665–675PubMedCrossRefGoogle Scholar
  526. Massanz C, Friedrich B (1999) Amino acid replacements at the H2-activating site of the NAD-reducing hydrogenase from Alcaligenes eutrophus. Biochemistry 38:14330–14337PubMedCrossRefGoogle Scholar
  527. Massanz C, Fernandez VM, Friedrich B (1997) C-terminal extension of the H2-activating subunit, HoxH, directs maturation of the NAD-reducing hydrogenase in Alcaligenes eutrophus. Eur J Biochem 245:441–448PubMedCrossRefGoogle Scholar
  528. Massanz C, Schmidt S, Friedrich B (1998) Subforms and in vitro reconstitution of the NAD-reducing hydrogenase of Alcaligenes eutrophus. J Bacteriol 180:1023–1029PubMedGoogle Scholar
  529. Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA (2001) [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3. J Biol Inorg Chem 6:63–81PubMedCrossRefGoogle Scholar
  530. Matias PM, Coelho AV, Valente FM, Placido D, LeGall J, Xavier AV, Pereira IA, Carrondo MA (2002) Sulfate respiration in Desulfovibrio vulgaris Hildenborough. Structure of the 16-heme cytochrome c HmcA AT 2.5-A resolution and a view of its role in transmembrane electron transfer. J Biol Chem 277:47907–47916PubMedCrossRefGoogle Scholar
  531. Matias PM, Pereira IA, Soares CM, Carrondo MA (2005) Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview. Prog Biophys Mol Biol 89:292–329PubMedCrossRefGoogle Scholar
  532. McCrae RE, Hanus J, Evans HJ (1978) Properties of the hydrogenase system in Rhizobium japonicum bacteroids. Biochem Biophys Res Commun 80:384–390PubMedCrossRefGoogle Scholar
  533. McGlynn SE, Ruebush SS, Naumov A, Nagy LE, Dubini A, King PW, Broderick JB, Posewitz MC, Peters JW (2007) In vitro activation of [FeFe] hydrogenase: new insights into hydrogenase maturation. J Biol Inorg Chem 12:443–447PubMedCrossRefGoogle Scholar
  534. McGlynn SE, Shepard EM, Winslow MA, Naumov AV, Duschene KS, Posewitz MC, Broderick WE, Broderick JB, Peters JW (2008) HydF as a scaffold protein in [FeFe] hydrogenase H-cluster biosynthesis. FEBS Lett 582:2183–2187PubMedCrossRefGoogle Scholar
  535. McGlynn SE, Mulder DW, Shepard EM, Broderick JB, Peters JW (2009) Hydrogenase cluster biosynthesis: organometallic chemistry nature’s way. Dalton Trans 2009(22):4274–4285CrossRefGoogle Scholar
  536. McGlynn SE, Boyd ES, Shepard EM, Lange RK, Gerlach R, Broderick JB, Peters JW (2010) Identification and characterization of a novel member of the radical AdoMet enzyme superfamily and implications for the biosynthesis of the Hmd hydrogenase active site cofactor. J Bacteriol 192:595–598PubMedCrossRefGoogle Scholar
  537. McInerney MJ, Bryant MP, Pfennig N (1979) Anaerobic bacterium that degrades fatty-acids in syntrophic association with methanogens. Arch Microbiol 122:129–135CrossRefGoogle Scholar
  538. McInerney MJ, Bryant MP, Hespell RB, Costerton JW (1981a) Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl Environ Microbiol 41:1029–1039PubMedGoogle Scholar
  539. McInerney MJ, Mackie RI, Bryant MP (1981b) Syntrophic association of a butyrate-degrading bacterium and methanosarcina enriched from bovine rumen fluid. Appl Environ Microbiol 41:826–828PubMedGoogle Scholar
  540. McIntosh CL, Germer F, Schulz R, Appel J, Jones AK (2011) The [NiFe]-hydrogenase of the cyanobacterium Synechocystis sp. PCC 6803 works bidirectionally with a bias to H2 production. J Am Chem Soc 133:11308–11319PubMedCrossRefGoogle Scholar
  541. Melis A, Zhang L, Forestier M, Ghirardi ML, Seibert M (2000) Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii. Plant Physiol 122:127–136PubMedCrossRefGoogle Scholar
  542. Menon AL, Robson RL (1994) In vivo and in vitro nickel-dependent processing of the [NiFe] hydrogenase in Azotobacter vinelandii. J Bacteriol 176:291–295PubMedGoogle Scholar
  543. Menon NK, Robbins J, Peck HD, Chatelus CY, Choi ES, Przybyla AE (1990) Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames. J Bacteriol 172:1969–1977PubMedGoogle Scholar
  544. Menon NK, Robbins J, Wendt JC, Shanmugam KT, Przybyla AE (1991) Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1. J Bacteriol 173:4851–4861PubMedGoogle Scholar
  545. Menon NK, Chatelus CY, Dervartanian M, Wendt JC, Shanmugam KT, Peck HD, Przybyla AE (1994) Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2. J Bacteriol 176:4416–4423PubMedGoogle Scholar
  546. Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Vangijsegem F (1985) Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol 162:328–334PubMedGoogle Scholar
  547. Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, Wattiez R (2003) Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27:385–410PubMedCrossRefGoogle Scholar
  548. Meuer J, Bartoschek S, Koch J, Kunkel A, Hedderich R (1999) Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri. Eur J Biochem 265:325–335PubMedCrossRefGoogle Scholar
  549. Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc Natl Acad Sci USA 99:5632–5637PubMedCrossRefGoogle Scholar
  550. Meyer O (1989) Aerobic, carbon monoxide-oxidizing bacteria. In: Schlegel HG, Bowien B (eds) Autotrophic bacteria. Science Tech/Springer, Madison, pp 331–350Google Scholar
  551. Meyer J, Gagnon J (1991) Primary structure of hydrogenase I from Clostridium pasteurianum. Biochemistry 30:9697–9704PubMedCrossRefGoogle Scholar
  552. Meyer O, Schlegel HG (1978) Reisolation of carbon-monoxide utilizing hydrogen bacterium Pseudomonas carboxydovorans (kistner) comb. nov. Arch Microbiol 118:35–43PubMedCrossRefGoogle Scholar
  553. Mikheeva LE, Schmitz O, Shestakov SV, Bothe H (1995) Mutants of the cyanobacterium Anabaena variabilis altered in hydrogenase activities. Z Naturforsch C 50:505–510Google Scholar
  554. Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science 117:528–529PubMedCrossRefGoogle Scholar
  555. Miller SL, Orgel LE (1974) The origins of life on earth. Prentice Hall, Englewood CliffsGoogle Scholar
  556. Miller TL, Wolin MJ (1973) Formation of hydrogen and formate by Ruminococcus albus. J Bacteriol 116:836–846PubMedGoogle Scholar
  557. Miller TL, Wolin MJ (1979) Fermentations by saccharolytic intestinal bacteria. Am J Clin Nutr 32:164–172PubMedGoogle Scholar
  558. Miller TL, Wolin MJ (1985) Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch Microbiol 141:116–122PubMedCrossRefGoogle Scholar
  559. Miller TL, Wolin MJ, Zhao HX, Bryant MP (1986) Characteristics of methanogens isolated from bovine rumen. Appl Environ Microbiol 51:201–202PubMedGoogle Scholar
  560. Miroshnichenko ML, Bonch-Osmolovskaya EA (2006) Recent developments in the thermophilic microbiology of deep-sea hydrothermal vents. Extremophiles 10:85–96PubMedCrossRefGoogle Scholar
  561. Miroshnichenko ML, Bonch-Osmolovskaya EA, Neuner A, Kostrikina NA, Chernych NA, Alekseev VA (1989) Thermococcus stetteri sp. nov., a new extremely thermophilic marine sulfur-metabolizing archaebacterium. Syst Appl Microbiol 12:257–262CrossRefGoogle Scholar
  562. Miroshnichenko ML, Gongadze GA, Lysenko AM, Bonch-Osmolovskaya EA (1994) Desulfurella multipotens sp. nov., a new sulfur-respiring thermophilic eubacterium from Raoul Island (Kermadec archipelago, New Zealand). Arch Microbiol 161:88–93Google Scholar
  563. Miroshnichenko ML, Rainey FA, Hippe H, Chernyh NA, Kostrikina NA, Bonch-Osmolovskaya EA (1998) Desulfurella kamchatkensis sp. nov. and Desulfurella propionica sp. nov., new sulfur-respiring thermophilic bacteria from Kamchatka thermal environments. Int J Syst Bacteriol 48:475–479PubMedCrossRefGoogle Scholar
  564. Miroshnichenko ML, Rainey FA, Rhode M, Bonch-Osmolovskaya EA (1999) Hippea maritima gen. nov., sp. nov., a new genus of thermophilic, sulfur-reducing bacterium from submarine hot vents. Int J Syst Bacteriol 49:1033–1038PubMedCrossRefGoogle Scholar
  565. Miroshnichenko ML, Kostrikina NA, L’Haridon S, Jeanthon C, Hippe H, Stackebrandt E, Bonch-Osmolovskaya EA (2002) Nautilia lithotrophica gen. nov., sp. nov., a thermophilic sulfur-reducing epsilon-proteobacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 52:1299–1304PubMedCrossRefGoogle Scholar
  566. Miroshnichenko ML, Kostrikina NA, Chernyh NA, Pimenov NV, Tourova TP, Antipov AN, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA (2003a) Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage. Int J Syst Evol Microbiol 53:323–329PubMedCrossRefGoogle Scholar
  567. Miroshnichenko ML, L’Haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA (2003b) Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 53:747–752PubMedCrossRefGoogle Scholar
  568. Miroshnichenko ML, L’Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C (2003c) Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 53:1143–1148PubMedCrossRefGoogle Scholar
  569. Miroshnichenko ML, Slobodkin AI, Kostrikina NA, L’Haridon S, Nercessian O, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C (2003d) Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 53:1637–1641PubMedCrossRefGoogle Scholar
  570. Miroshnichenko ML, L’Haridon S, Schumann P, Spring S, Bonch-Osmolovskaya EA, Jeanthon C, Stackebrandt E (2004) Caminibacter profundus sp. nov., a novel thermophile of Nautiliales ord. nov. within the class ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 54:41–45PubMedCrossRefGoogle Scholar
  571. Moezelaar R, Stal LJ (1994) Fermentation in the unicellular cyanobacterium Microcystis PCC7806. Arch Microbiol 162:63–69CrossRefGoogle Scholar
  572. Moezelaar R, Bijvank SM, Stal LJ (1996) Fermentation and sulfur reduction in the mat-building cyanobacterium Microcoleus chthonoplastes. Appl Environ Microbiol 62:1752–1758PubMedGoogle Scholar
  573. Moller D, Schauder R, Fuchs G, Thauer RK (1987) Acetate oxidation to CO2 via a citric-acid cycle involving an atp-citrate lyase—a mechanism for the synthesis of atp via substrate level phosphorylation in Desulfobacter postgatei growing on acetate and sulfate. Arch Microbiol 148:202–207CrossRefGoogle Scholar
  574. Montet Y, Amara P, Volbeda A, Vernede X, Hatchikian EC, Field MJ, Frey M, Fontecilla-Camps JC (1997) Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics. Nat Struct Biol 4:523–526PubMedCrossRefGoogle Scholar
  575. Moreira D, Lopez-Garcia P (1998) Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J Mol Evol 47:517–530PubMedCrossRefGoogle Scholar
  576. Mountfort DO, Brulla WJ, Krumholz LR, Bryant MP (1984) Syntrophus buswellii gen. nov., sp. nov.: a benzoate catabolizer from methanogenic ecosystems. Int J Syst Bacteriol 34:216–217CrossRefGoogle Scholar
  577. Moussard H, L’Haridon S, Tindall BJ, Banta A, Schumann P, Stackebrandt E, Reysenbach AL, Jeanthon C (2004) Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 54:227–233PubMedCrossRefGoogle Scholar
  578. Moyer CL, Dobbs FC, Karl DM (1995) Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 61:1555–1562PubMedGoogle Scholar
  579. Mulder DW, Boyd ES, Sarma R, Lange RK, Endrizzi JA, Broderick JB, Peters JW (2010) Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG). Nature 465:248–251PubMedCrossRefGoogle Scholar
  580. Mulder DW, Shepard EM, Meuser JE, Joshi N, King PW, Posewitz MC, Broderick JB, Peters JW (2011) Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. Structure 19:1038–1052PubMedCrossRefGoogle Scholar
  581. Müller M (1993) The hydrogenosome. J Gen Microbiol 139:2879–2889PubMedCrossRefGoogle Scholar
  582. Muller S, Klein A (2001) Coordinate positive regulation of genes encoding [NiFe] hydrogenases in Methanococcus voltae. Mol Genet Genomics 265:1069–1075PubMedCrossRefGoogle Scholar
  583. Mura GM, Pedroni P, Pratesi C, Galli G, Serbolisca L, Grandi G (1996) The [Ni-Fe] hydrogenase from the thermophilic bacterium Acetomicrobium flavidum. Microbiology 142:829–836PubMedCrossRefGoogle Scholar
  584. Murry MA, Lopez MF (1989) Interaction between hydrogenase, nitrogenase, and respiratory activities in a Frankia isolate from Alnus rubra. Can J Microbiol 35:636–641PubMedCrossRefGoogle Scholar
  585. Muth E, Morschel E, Klein A (1987) Purification and characterization of an 8-hydroxy-5-deazaflavin-reducing hydrogenase from the archaebacterium Methanococcus voltae. Eur J Biochem 169:571–577PubMedCrossRefGoogle Scholar
  586. Nakagawa S, Takai K (2008) Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 65:1–14PubMedCrossRefGoogle Scholar
  587. Nakagawa S, Takai K, Horikoshi K, Sako Y (2003) Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 53:863–869PubMedCrossRefGoogle Scholar
  588. Nakagawa S, Inagaki F, Takai K, Horikoshi K, Sako Y (2005a) Thioreductor micantisoli gen. nov., sp. nov., a novel mesophilic, sulfur-reducing chemolithoautotroph within the epsilon-Proteobacteria isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 55:599–605PubMedCrossRefGoogle Scholar
  589. Nakagawa S, Takai K, Inagaki F, Horikoshi K, Sako Y (2005b) Nitratiruptor tergarcus gen. nov., sp. nov. and Nitratifractor salsuginis gen. nov., sp. nov., nitrate-reducing chemolithoautotrophs of the epsilon-Proteobacteria isolated from a deep-sea hydrothermal system in the Mid-Okinawa Trough. Int J Syst Evol Microbiol 55:925–933PubMedCrossRefGoogle Scholar
  590. Nakamura H (1939) Further studies on hydrogen metabolism in purple bacteria and a comment on the mutual relationship between Thio- and Athirhodacea. Acta Phochim 11:109–125Google Scholar
  591. Nakamura H (1941) Further studies on bacterial photosynthesis. Acta Phochim 12:43–64Google Scholar
  592. Nakos G, Mortenson LE (1971) Structural properties of hydrogenase from Clostridium pasteurianum W5. Biochemistry 10:2442–2449PubMedCrossRefGoogle Scholar
  593. Nandi R, Sengupta S (1998) Microbial production of hydrogen: an overview. CRC Crit Rev Microbiol 24:61–84CrossRefGoogle Scholar
  594. Nealson KH, Inagaki F, Takai K (2005) Hydrogen-driven subsurface lithoautotrophic microbial ecosystems (SLiMEs): do they exist and why should we care? Trends Microbiol 13:405–410PubMedCrossRefGoogle Scholar
  595. Nelson LM, Salminen SO (1982) Uptake hydrogenase activity and ATP formation in Rhizobium leguminosarum bacteroids. J Bacteriol 151:989–995PubMedGoogle Scholar
  596. Nercessian O, Bienvenu N, Moreira D, Prieur D, Jeanthon C (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environ Microbiol 7:118–132PubMedCrossRefGoogle Scholar
  597. Nesbit AD, Giel JL, Rose JC, Kiley PJ (2009) Sequence-specific binding to a subset of IscR-regulated promoters does not require IscR Fe-S cluster ligation. J Mol Biol. 387:28–41PubMedCrossRefGoogle Scholar
  598. Neuner A, Jannasch HW, Belkin S, Stetter KO (1990) Thermococcus litoralis sp. nov.: a new species of extremely thermophilic marine archaebacteria. Arch Microbiol 153:205–207CrossRefGoogle Scholar
  599. Nicolet Y, Fontecilla-Camps JC (2012) Structure-function relationships in [FeFe]-hydrogenase active site maturation. J Biol Chem 287:13532–13540PubMedCrossRefGoogle Scholar
  600. Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC (1999) Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Structure 7:13–23PubMedCrossRefGoogle Scholar
  601. Nicolet Y, Lemon BJ, Fontecilla-Camps JC, Peters JW (2000) A novel FeS cluster in Fe-only hydrogenases. Trends Biochem Sci 25:138–143PubMedCrossRefGoogle Scholar
  602. Nicolet Y, Rubach JK, Posewitz MC, Amara P, Mathevon C, Atta M, Fontecave M, Fontecilla-Camps JC (2008) X-ray structure of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima. J Biol Chem 283:18861–18872PubMedCrossRefGoogle Scholar
  603. Niklewski W (1910) On the oxidation of hydrogen by microorganisms. Jahrb Wiss Bot 48:113–142Google Scholar
  604. Nilsen RK, Beeder J, Thorstenson T, Torsvik T (1996) Distribution of thermophilic marine sulfate reducers in north sea oil field waters and oil reservoirs. Appl Environ Microbiol 62:1793–1798PubMedGoogle Scholar
  605. Nisbet EG, Fowler CMR (1999) Archaean metabolic evolution of microbial mats. Proc R Soc Lond B 266:2375–2382CrossRefGoogle Scholar
  606. Nishihara H, Igarashi Y, Kodama T (1989) Isolation of an obligately chemolithoautotrophic, halophilic and aerobic hydrogen-oxidizing bacterium from marine environment. Arch Microbiol 152:39–43CrossRefGoogle Scholar
  607. Nishihara H, Igarashi Y, Kodama T (1990) A new isolate of Hydrogenobacter, an obligately chemolithoautotrophic, thermophilic, halophilic and aerobic hydrogen-oxidizing bacterium from seaside saline hot-spring. Arch Microbiol 153:294–298CrossRefGoogle Scholar
  608. Nishihara H, Igarashi Y, Kodama T (1991) Hydrogenovibrio marinus gen. nov., sp. nov., a marine obligately chemolithoautotrophic hydrogen-oxidizing bacterium. Int J Syst Bacteriol 41:130–133CrossRefGoogle Scholar
  609. Nishihara H, Miyashita Y, Aoyama K, Kodama T, Igarashi Y, Takamura Y (1997) Characterization of an extremely thermophilic and oxygen-stable membrane-bound hydrogenase from a marine hydrogen-oxidizing bacterium Hydrogenovibrio marinus. Biochem Biophys Res Commun 232:766–770PubMedCrossRefGoogle Scholar
  610. Nivière V, Wong SL, Voordouw G (1992) Site-directed mutagenesis of the hydrogenase signal peptide consensus box prevents export of a beta-lactamase fusion protein. J Gen Microbiol 138:2173–2183PubMedCrossRefGoogle Scholar
  611. Noll I, Muller S, Klein A (1999) Transcriptional regulation of genes encoding the selenium-free [NiFe]-hydrogenases in the archaeon Methanococcus voltae involves positive and negative control elements. Genetics 152:1335–1341PubMedGoogle Scholar
  612. Nouailler M, Morelli X, Bornet O, Chetrit B, Dermoun Z, Guerlesquin F (2006) Solution structure of HndAc: a thioredoxin-like domain involved in the NADP-reducing hydrogenase complex. Protein Sci 15:1369–1378PubMedCrossRefGoogle Scholar
  613. Odom JM, Peck HD (1981) Localization of dehydrogenases, reductases, and electron transfer components in the sulfate-reducing bacterium Desulfovibrio gigas. J Bacteriol 147:161–169PubMedGoogle Scholar
  614. Oelgeschläger E, Rother M (2008) Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Arch Microbiol 190:257–269PubMedCrossRefGoogle Scholar
  615. Oelmüller U, Schlegel HG, Friedrich CG (1990) Differential stability of mRNA species of Alcaligenes eutrophus soluble and particulate hydrogenases. J Bacteriol 172:7057–7064PubMedGoogle Scholar
  616. Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi SI, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y (2002) Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen. J Am Chem Soc 124:11628–11635PubMedCrossRefGoogle Scholar
  617. Ogata H, Lubitz W, Higuchi Y (2009) [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism. Dalton Trans 2009(37):7577–7587CrossRefGoogle Scholar
  618. Ohi K, Takada N, Komemushi S, Okazaki M, Miura Y (1979) A new species of hydrogen-utilizing bacterium. J Gen Appl Microbiol 25:53–58CrossRefGoogle Scholar
  619. Oliveira P, Lindblad P (2005) LexA, a transcription regulator binding in the promoter region of the bidirectional hydrogenase in the cyanobacterium Synechocystis sp. PCC 6803. FEMS Microbiol Lett 251:59–66PubMedCrossRefGoogle Scholar
  620. Oliveira P, Lindblad P (2008) An AbrB-Like protein regulates the expression of the bidirectional hydrogenase in Synechocystis sp. strain PCC 6803. J Bacteriol 190:1011–1019PubMedCrossRefGoogle Scholar
  621. Oliveira P, Lindblad P (2009) Transcriptional regulation of the cyanobacterial bidirectional Hox-hydrogenase. Dalton Trans 2009(45):9990–9996CrossRefGoogle Scholar
  622. Oliveira P, Leitao E, Tamagnini P, Moradas-Ferreira P, Oxelfelt F (2004) Characterization and transcriptional analysis of hupSLW in Gloeothece sp. ATCC 27152: an uptake hydrogenase from a unicellular cyanobacterium. Microbiology 150:3647–3655PubMedCrossRefGoogle Scholar
  623. Ollivier B, Fardeau ML, Cayol JL, Magot M, Patel BK, Prensier G, Garcia JL (1998) Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well. Int J Syst Bacteriol 48:821–828PubMedCrossRefGoogle Scholar
  624. Olson JW, Maier RJ (2002) Molecular hydrogen as an energy source for Helicobacter pylori. Science 298:1788–1790PubMedCrossRefGoogle Scholar
  625. Olson JW, Fu C, Maier RJ (1997) The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase. Mol Microbiol 24:119–128PubMedCrossRefGoogle Scholar
  626. Olson JW, Mehta NS, Maier RJ (2001) Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in Helicobacter pylori. Mol Microbiol 39:176–182PubMedCrossRefGoogle Scholar
  627. Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M (2001) Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci USA 98:12215–12220PubMedCrossRefGoogle Scholar
  628. Oremland RS, Polcin S (1982) Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in an estuarine environment. Appl Environ Microbiol 44:1270–1276PubMedGoogle Scholar
  629. Ormerod JG, Gest H (1962) Hydrogen photosynthesis and alternative metabolic pathways in photosynthetic bacteria. Bacteriol Rev 26:51–66PubMedGoogle Scholar
  630. Ovtsyna AO, Schultze M, Tikhonovich IA, Spaink HP, Kondorosi E, Kondorosi A, Staehelin C (2000) Nod factors of Rhizobium leguminosarum bv. viciae and their fucosylated derivatives stimulate a nod factor cleaving activity in pea roots and are hydrolyzed in vitro by plant chitinases at different rates. Mol Plant Microbe Interact 13:799–807PubMedCrossRefGoogle Scholar
  631. Packer L, Vishniac W (1955) Chemosynthetic fixation of carbon dioxide and characteristics of hydrogenase in resting cell suspensions of Hydrogenomonas ruhlandii nov. spec. J Bacteriol 70:216–223PubMedGoogle Scholar
  632. Palacios JM, Murillo J, Leyva A, Ditta G, Ruiz-Argueso T (1990) Differential expression of hydrogen uptake (hup) genes in vegetative and symbiotic cells of Rhizobium leguminosarum. Mol Gen Genet 221:363–370PubMedCrossRefGoogle Scholar
  633. Palacios JM, Manyani H, Martinez M, Ureta AC, Brito B, Bascones E, Rey L, Imperial J, Ruiz-Argueso T (2005) Genetics and biotechnology of the H2-uptake [NiFe] hydrogenase from Rhizobium leguminosarum bv. viciae, a legume endosymbiotic bacterium. Biochem Soc Trans 33:94–96PubMedCrossRefGoogle Scholar
  634. Palleroni NJ, Palleroni AV (1978) Alcaligenes latus, a new species of hydrogen-utilizing bacteria. Int J Syst Bacteriol 28:416–424CrossRefGoogle Scholar
  635. Pandelia ME, Fourmond V, Tron-Infossi P, Lojou E, Bertrand P, Leger C, Giudici-Orticoni MT, Lubitz W (2010) Membrane-bound hydrogenase I from the hyperthermophilic bacterium Aquifex aeolicus: enzyme activation, redox intermediates and oxygen tolerance. J Am Chem Soc 132:6991–7004PubMedCrossRefGoogle Scholar
  636. Pandelia ME, Nitschke W, Infossi P, Giudici-Orticoni MT, Bill E, Lubitz W (2011) Characterization of a unique [FeS] cluster in the electron transfer chain of the oxygen tolerant [NiFe] hydrogenase from Aquifex aeolicus. Proc Natl Acad Sci USA 108:6097–6102PubMedCrossRefGoogle Scholar
  637. Pandelia ME, Infossi P, Stein M, Giudici-Orticoni MT, Lubitz W (2012) Spectroscopic characterization of the key catalytic intermediate Ni-C in the O2-tolerant [NiFe] hydrogenase I from Aquifex aeolicus: evidence of a weakly bound hydride. Chem Commun (Camb) 48:823–825CrossRefGoogle Scholar
  638. Pandey AS, Harris TV, Giles LJ, Peters JW, Szilagyi RK (2008) Dithiomethylether as a ligand in the hydrogenase H-cluster. J Am Chem Soc 130:4533–4540PubMedCrossRefGoogle Scholar
  639. Paper W, Jahn U, Hohn MJ, Kronner M, Nather DJ, Burghardt T, Rachel R, Stetter KO, Huber H (2007) Ignicoccus hospitalis sp. nov., the host of ‘Nanoarchaeum equitans’. Int J Syst Evol Microbiol 57:803–808PubMedCrossRefGoogle Scholar
  640. Park SS, DeCicco BT (1974) Autotrophic growth with hydrogen of Mycobacterium gordonae and another scotochromogenic Mycobacterium. Int J Syst Bacteriol 24:338–345CrossRefGoogle Scholar
  641. Parkin A, Goldet G, Cavazza C, Fontecilla-Camps JC, Armstrong FA (2008) The difference a Se makes? Oxygen-tolerant hydrogen production by the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum. J Am Chem Soc 130:13410–13416PubMedCrossRefGoogle Scholar
  642. Paschos A, Glass RS, Böck A (2001) Carbamoylphosphate requirement for synthesis of the active center of [NiFe]-hydrogenases. FEBS Lett 488:9–12PubMedCrossRefGoogle Scholar
  643. Paynter MJ, Hungate RE (1968) Characterization of Methanobacterium mobilis, sp. n., isolated from the bovine rumen. J Bacteriol 95:1943–1951PubMedGoogle Scholar
  644. Peck HD, Gest H (1957) Formic dehydrogenase and the hydrogenlyase enzyme complex in coli-aerogenes bacteria. J Bacteriol 73:706–721PubMedGoogle Scholar
  645. Pedersen K (1997) Microbial life in deep granitic rock. FEMS Microbiol Rev 20:399–414CrossRefGoogle Scholar
  646. Pedersen K, Arlinger J, Ekendahl S, Hallbeck L (1996) 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Äspö Hard Rock Laboratory, Sweden. FEMS Microbiol Ecol 19:249–262Google Scholar
  647. Pedroni P, Della Volpe A, Galli G, Mura GM, Pratesi C, Grandi G (1995) Characterization of the locus encoding the [Ni-Fe] sulfhydrogenase from the archaeon Pyrococcus furiosus: evidence for a relationship to bacterial sulfite reductases. Microbiology 141:449–458PubMedCrossRefGoogle Scholar
  648. Pedrosa FO, Döbereiner J, Yates MG (1980) Hydrogen-dependent growth and autotrophic carbon dioxide fixation in Derxia. J Gen Microbiol 119:547–551Google Scholar
  649. Perez-Rodriguez I, Ricci J, Voordeckers JW, Starovoytov V, Vetriani C (2010) Nautilia nitratireducens sp. nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 60:1182–1186PubMedCrossRefGoogle Scholar
  650. Pérez-Rodríguez I, Grosche A, Massenburg L, Starovoytov V, Lutz RA, Vetriani C (2011) Phorcysia thermohydrogeniphila gen. nov., sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent on the East Pacific Rise. Int J Syst Evol Microbiol doi:10.1099/ijs.0.035642-0Google Scholar
  651. Peschek GA (1979) Anaerobic hydrogenase activity in Anacystis nidulans. H2-dependent photoreduction and related reactions. Biochim Biophys Acta 548:187–202PubMedCrossRefGoogle Scholar
  652. Peters JW (1999) Structure and mechanism of iron-only hydrogenases. Curr Opin Struct Biol 9:670–676PubMedCrossRefGoogle Scholar
  653. Peters JW, Fisher K, Dean DR (1995) Nitrogenase structure and function: a biochemical-genetic perspective. Annu Rev Microbiol 49:335–366PubMedCrossRefGoogle Scholar
  654. Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC (1998) X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science 282:1853–1858PubMedCrossRefGoogle Scholar
  655. Petkun S, Shi R, Li Y, Asinas A, Munger C, Zhang L, Waclawek M, Soboh B, Sawers RG, Cygler M (2011) Structure of hydrogenase maturation protein HypF with reaction intermediates shows two active sites. Structure 19:1773–1783PubMedCrossRefGoogle Scholar
  656. Pezacka E, Wood HG (1984) The synthesis of acetyl-CoA by Clostridium thermoaceticum from carbon dioxide, hydrogen, coenzyme A and methyltetrahydrofolate. Arch Microbiol 137:63–69PubMedCrossRefGoogle Scholar
  657. Phelps TJ, Zeikus JG (1984) Influence of pH on terminal carbon metabolism in anoxic sediments from a mildly acidic lake. Appl Environ Microbiol 48:1088–1095PubMedGoogle Scholar
  658. Pierik AJ, Hulstein M, Hagen WR, Albracht SP (1998) A low-spin iron with CN and CO as intrinsic ligands forms the core of the active site in [Fe]-hydrogenases. Eur J Biochem 258:572–578PubMedCrossRefGoogle Scholar
  659. Pierik AJ, Roseboom W, Happe RP, Bagley KA, Albracht SP (1999) Carbon monoxide and cyanide as intrinsic ligands to iron in the active site of [NiFe]-hydrogenases. NiFe(CN)2CO, biology’s way to activate H2. J Biol Chem 274:3331–3337PubMedCrossRefGoogle Scholar
  660. Pihl TD, Maier RJ (1991) Purification and characterization of the hydrogen uptake hydrogenase from the hyperthermophilic archaebacterium Pyrodictium brockii. J Bacteriol 173:1839–1844PubMedGoogle Scholar
  661. Pihl TD, Schicho RN, Kelly RM, Maier RJ (1989) Characterization of hydrogen-uptake activity in the hyperthermophile Pyrodictium brockii. Proc Natl Acad Sci USA 86:138–141PubMedCrossRefGoogle Scholar
  662. Pikuta EV, Zhilina TN, Zavarzin GA, Kostrikina NA, Osipov GA, Rainey FA (1998) Desulfonatronum lacustre gen. nov., sp. nov.: a new alkaliphilic sulfate-reducing bacterium utilizing ethanol. Mikrobiologiya 67:123–131Google Scholar
  663. Pikuta EV, Marsic D, Itoh T, Bej AK, Tang J, Whitman WB, Ng JD, Garriott OK, Hoover RB (2007) Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 57:1612–1618PubMedCrossRefGoogle Scholar
  664. Pilkington SJ, Skehel JM, Gennis RB, Walker JE (1991) Relationship between mitochondrial NADH-ubiquinone reductase and a bacterial NAD-reducing hydrogenase. Biochemistry 30:2166–2175PubMedCrossRefGoogle Scholar
  665. Pinkwart M, Schneider K, Schlegel HG (1983) Purification and properties of the membrane-bound hydrogenase from N2-fixing Alcaligenes latus. Biochim Biophys Acta 745:267–278PubMedCrossRefGoogle Scholar
  666. Pinske C, Sawers G (2011) Iron restriction induces preferential down-regulation of H2-consuming over H2-evolving reactions during fermentative growth of Escherichia coli. BMC Microbiol 11:196PubMedCrossRefGoogle Scholar
  667. Pinske C, Kruger S, Soboh B, Ihling C, Kuhns M, Braussemann M, Jaroschinsky M, Sauer C, Sargent F, Sinz A, Sawers RG (2011) Efficient electron transfer from hydrogen to benzyl viologen by the [NiFe]-hydrogenases of Escherichia coli is dependent on the coexpression of the iron-sulfur cluster-containing small subunit. Arch Microbiol 193:893–903PubMedCrossRefGoogle Scholar
  668. Pinske C, McDowall JS, Sargent F, Sawers RG (2012) Analysis of hydrogenase 1 levels reveals an intimate link between carbon and hydrogen metabolism in Escherichia coli K-12. Microbiology 158:856–868PubMedCrossRefGoogle Scholar
  669. Pley U, Schipka J, Gambacorta A, Jannasch HW, Fricke H, Rachel R, Stetter KO (1991) Pyrodictium abyssi sp. nov. represents a novel heterotrophic marine archaeal hyperthermophile growing at 110 °C. Syst Appl Microbiol 14:245–253CrossRefGoogle Scholar
  670. Podzuweit HG, Schneider K, Schlegel HG (1983) Autotrophic growth and hydrogenase activity of Pseudomonas saccharophila strains. FEMS Microbiol Lett 19:169–173CrossRefGoogle Scholar
  671. Pohorelic BK, Voordouw JK, Lojou E, Dolla A, Harder J, Voordouw G (2002) Effects of deletion of genes encoding Fe-only hydrogenase of Desulfovibrio vulgaris Hildenborough on hydrogen and lactate metabolism. J Bacteriol 184:679–686PubMedCrossRefGoogle Scholar
  672. Posewitz MC, King PW, Smolinski SL, Zhang L, Seibert M, Ghirardi ML (2004a) Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase. J Biol Chem 279:25711–25720PubMedCrossRefGoogle Scholar
  673. Posewitz MC, Smolinski SL, Kanakagiri S, Melis A, Seibert M, Ghirardi ML (2004b) Hydrogen photoproduction is attenuated by disruption of an isoamylase gene in Chlamydomonas reinhardtii. Plant Cell 16:2151–2163PubMedCrossRefGoogle Scholar
  674. Posewitz MC, King PW, Smolinski SL, Smith RD, Ginley AR, Ghirardi ML, Seibert M (2005) Identification of genes required for hydrogenase activity in Chlamydomonas reinhardtii. Biochem Soc Trans 33:102–104PubMedCrossRefGoogle Scholar
  675. Postgate JR (1952) Competitive and non-competitive inhibitors of bacterial sulphate reduction. J Gen Microbiol 6:128–142PubMedCrossRefGoogle Scholar
  676. Przybyla AE, Robbins J, Menon N, Peck HD (1992) Structure-function relationships among the nickel-containing hydrogenases. FEMS Microbiol Rev 8:109–135PubMedGoogle Scholar
  677. Pusheva MA, Rainina EI, Borodulina NP, Ryabokon AM, Makhlis TA, Kotsyurbenko OR (1991) Acetate formation from hydrogen and carbon-dioxide by a thermophilic homoacetic bacterium Acetogenium kivui. Microbiology 60:422–426Google Scholar
  678. Qadri SM, Hoare DS (1968) Formic hydrogenlyase and photoassimilation of formate by a strain of Rhodopseudomonas palustris. J Bacteriol 95:2344–2357PubMedGoogle Scholar
  679. Ragsdale SW, Ljungdahl LG (1984) Hydrogenase from Acetobacterium woodii. Arch Microbiol 139:361–365PubMedCrossRefGoogle Scholar
  680. Ragsdale SW, Pierce E (2008) Acetogenesis and the Wood-Ljungdahl pathway of CO2 fixation. Biochim Biophys Acta 1784:1873–1898PubMedCrossRefGoogle Scholar
  681. Rákhely G, Colbeau A, Garin J, Vignais PM, Kovács KL (1998) Unusual organization of the genes coding for HydSL, the stable [NiFe]hydrogenase in the photosynthetic bacterium Thiocapsa roseopersicina BBS. J Bacteriol 180:1460–1465PubMedGoogle Scholar
  682. Rákhely G, Zhou ZH, Adams MW, Kovács KL (1999) Biochemical and molecular characterization of the [NiFe] hydrogenase from the hyperthermophilic archaeon, Thermococcus litoralis. Eur J Biochem 266:1158–1165PubMedCrossRefGoogle Scholar
  683. Rákhely G, Kovács AT, Maróti G, Fodor BD, Csanadi G, Latinovics D, Kovács KL (2004) Cyanobacterial-type, heteropentameric, NAD+-reducing NiFe hydrogenase in the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina. Appl Environ Microbiol 70:722–728PubMedCrossRefGoogle Scholar
  684. Rákhely G, Laurinavichene TV, Tsygankov AA, Kovács KL (2007) The role of Hox hydrogenase in the H2 metabolism of Thiocapsa roseopersicina. Biochim Biophys Acta 1767:671–676PubMedCrossRefGoogle Scholar
  685. Rangarajan ES, Asinas A, Proteau A, Munger C, Baardsnes J, Iannuzzi P, Matte A, Cygler M (2008) Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF. J Bacteriol 190:1447–1458PubMedCrossRefGoogle Scholar
  686. Ravot G, Magot M, Fardeau ML, Patel BK, Prensier G, Egan A, Garcia JL, Ollivier B (1995) Thermotoga elfii sp. nov., a novel thermophilic bacterium from an African oil-producing well. Int J Syst Bacteriol 45:308–314PubMedCrossRefGoogle Scholar
  687. Reeve JN, Beckler GS, Cram DS, Hamilton PT, Brown JW, Krzycki JA, Kolodziej AF, Alex L, Orme-Johnson WH, Walsh CT (1989) A hydrogenase-linked gene in Methanobacterium thermoautotrophicum strain delta H encodes a polyferredoxin. Proc Natl Acad Sci USA 86:3031–3035PubMedCrossRefGoogle Scholar
  688. Reissmann S, Hochleitner E, Wang H, Paschos A, Lottspeich F, Glass RS, Böck A (2003) Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands. Science 299:1067–1070PubMedCrossRefGoogle Scholar
  689. Rey L, Fernandez D, Brito B, Hernando Y, Palacios JM, Imperial J, Ruiz-Argueso T (1996) The hydrogenase gene cluster of Rhizobium leguminosarum bv. viciae contains an additional gene (hypX), which encodes a protein with sequence similarity to the N10-formyltetrahydrofolate-dependent enzyme family and is required for nickel-dependent hydrogenase processing and activity. Mol Gen Genet 252:237–248PubMedGoogle Scholar
  690. Reysenbach AL, Longnecker K, Kirshtein J (2000) Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl Environ Microbiol 66:3798–3806PubMedCrossRefGoogle Scholar
  691. Rhee TS, Brenninkmeijer CAM, Röckmann T (2006) The overwhelming role of soils in the global atmospheric hydrogen cycle. Atmos Chem Phys Disscuss 6:1611–1625CrossRefGoogle Scholar
  692. Richard DJ, Sawers G, Sargent F, McWalter L, Boxer DH (1999) Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli. Microbiology 145:2903–2912PubMedGoogle Scholar
  693. Ricke SC, Martin SA, Nisbet DJ (1996) Ecology, metabolism, and genetics of ruminal selenomonads. Crit Rev Microbiol 22:27–65PubMedCrossRefGoogle Scholar
  694. Rieder R, Cammack R, Hall DO (1984) Purification and properties of the soluble hydrogenase from Desulfovibrio desulfuricans (strain Norway 4). Eur J Biochem 145:637–643PubMedCrossRefGoogle Scholar
  695. Rieu-Lesme F, Morvan B, Collins MD, Fonty G, Willems A (1996) A new H2/CO2-using acetogenic bacterium from the rumen: description of Ruminococcus schinkii sp. nov. FEMS Microbiol Lett 140:281–286PubMedGoogle Scholar
  696. Robinson JA, Tiedje JM (1982) Kinetics of hydrogen consumption by rumen fluid, anaerobic digestor sludge, and sediment. Appl Environ Microbiol 44:1374–1384PubMedGoogle Scholar
  697. Robinson JA, Tiedje JM (1984) Competition between sulfate-reducing and methanogenic bacteria for H2 under resting and growing conditions. Arch Microbiol 137:26–32CrossRefGoogle Scholar
  698. Rodrigue A, Chanal A, Beck K, Muller M, Wu LF (1999) Co-translocation of a periplasmic enzyme complex by a hitchhiker mechanism through the bacterial tat pathway. J Biol Chem 274:13223–13228PubMedCrossRefGoogle Scholar
  699. Roelofsen PA (1934) On the metabolism of the purple sulphur bacteria. Proc K Ned Akad Wet 37:660–669Google Scholar
  700. Romesser JA, Wolfe RS, Mayer F, Spiess E, Walter-Mauruschat A (1979) Methanogenium, a novel genus of marine methanogenic bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. Arch Microbiol 121:147–153CrossRefGoogle Scholar
  701. Rossi M, Pollock WB, Reij MW, Keon RG, Fu R, Voordouw G (1993) The hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough encodes a potential transmembrane redox protein complex. J Bacteriol 175:4699–4711PubMedGoogle Scholar
  702. Rossmann R, Sauter M, Lottspeich F, Böck A (1994) Maturation of the large subunit (HYCE) of Escherichia coli hydrogenase 3 requires nickel incorporation followed by C-terminal processing at Arg537. Eur J Biochem 220:377–384PubMedCrossRefGoogle Scholar
  703. Roussel EG, Konn C, Charlou JL, Donval JP, Fouquet Y, Querellou J, Prieur D, Bonavita MA (2011) Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems. FEMS Microbiol Ecol 77:647–665PubMedCrossRefGoogle Scholar
  704. Rousset M, Dermoun Z, Hatchikian CE, Belaich JP (1990) Cloning and sequencing of the locus encoding the large and small subunit genes of the periplasmic [NiFe]hydrogenase from Desulfovibrio fructosovorans. Gene 94:95–101PubMedCrossRefGoogle Scholar
  705. Rousset M, Magro V, Forget N, Guigliarelli B, Belaich JP, Hatchikian EC (1998a) Heterologous expression of the Desulfovibrio gigas [NiFe] hydrogenase in Desulfovibrio fructosovorans MR400. J Bacteriol 180:4982–4986PubMedGoogle Scholar
  706. Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC (1998b) [3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis. Proc Natl Acad Sci USA 95:11625–11630PubMedCrossRefGoogle Scholar
  707. Rozanova EP, Nazina TN, Galushko AS (1988) Isolation of a new genus of sulfate-reducing bacteria and description of a new species of this genus, Desulfomicrobium apsheronum gen. nov., sp. nov. Mikrobiologiya (Moskva) 57:634–641Google Scholar
  708. Rubach JK, Brazzolotto X, Gaillard J, Fontecave M (2005) Biochemical characterization of the HydE and HydG iron-only hydrogenase maturation enzymes from Thermatoga maritima. FEBS Lett 579:5055–5060PubMedCrossRefGoogle Scholar
  709. Russell MJ, Martin W (2004) The rocky roots of the acetyl-CoA pathway. Trends Biochem Sci 29:358–363PubMedCrossRefGoogle Scholar
  710. Ryde U, Greco C, De Gioia L (2010) Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand. J Am Chem Soc 132:4512–4513PubMedCrossRefGoogle Scholar
  711. Saggu M, Zebger I, Ludwig M, Lenz O, Friedrich B, Hildebrandt P, Lendzian F (2009) Spectroscopic insights into the oxygen-tolerant membrane-associated [NiFe] hydrogenase of Ralstonia eutropha H16. J Biol Chem 284:16264–16276PubMedCrossRefGoogle Scholar
  712. Sahl JW, Schmidt R, Swanner ED, Mandernack KW, Templeton AS, Kieft TL, Smith RL, Sanford WE, Callaghan RL, Mitton JB, Spear JR (2008) Subsurface microbial diversity in deep-granitic-fracture water in Colorado. Appl Environ Microbiol 74:143–152PubMedCrossRefGoogle Scholar
  713. Sakai S, Imachi H, Hanada S, Ohashi A, Harada H, Kamagata Y (2008) Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 58:929–936PubMedCrossRefGoogle Scholar
  714. Sakai S, Takaki Y, Shimamura S, Sekine M, Tajima T, Kosugi H, Ichikawa N, Tasumi E, Hiraki AT, Shimizu A, Kato Y, Nishiko R, Mori K, Fujita N, Imachi H, Takai K (2011) Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PLoS One 6:e22898PubMedCrossRefGoogle Scholar
  715. Santiago B, Meyer O (1997) Purification and molecular characterization of the H2 uptake membrane-bound NiFe-hydrogenase from the carboxidotrophic bacterium Oligotropha carboxidovorans. J Bacteriol 179:6053–6060PubMedGoogle Scholar
  716. Sapra R, Verhagen MFJM, Adams MWW (2000) Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 182:3423–3428PubMedCrossRefGoogle Scholar
  717. Sapra R, Bagramyan K, Adams MW (2003) A simple energy-conserving system: proton reduction coupled to proton translocation. Proc Natl Acad Sci USA 100:7545–7550PubMedCrossRefGoogle Scholar
  718. Sasikala K, Ramana CV, Rao PR, Kovács KL (1993) Anoxygenic photosynthetic bacteria: physiology and advances in hydrogen production technology. Adv Appl Microbiol 68:211–295CrossRefGoogle Scholar
  719. Sass H, Cypionka H (2004) Isolation of sulfate-reducing bacteria from the terrestrial deep subsurface and description of Desulfovibrio cavernae sp. nov. Syst Appl Microbiol 27:541–548PubMedCrossRefGoogle Scholar
  720. Sattley WM, Madigan MT (2010) Temperature and nutrient induced responses of Lake Fryxell sulfate-reducing prokaryotes and description of Desulfovibrio lacusfryxellense, sp. nov., a pervasive, cold-active, sulfate-reducing bacterium from Lake Fryxell, Antarctica. Extremophiles 14:357–366PubMedCrossRefGoogle Scholar
  721. Sauter M, Bohm R, Bock A (1992) Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli. Mol Microbiol 6:1523–1532PubMedCrossRefGoogle Scholar
  722. Savant DV, Shouche YS, Prakash S, Ranade DR (2002) Methanobrevibacter acididurans sp. nov., a novel methanogen from a sour anaerobic digester. Int J Syst Evol Microbiol 52:1081–1087PubMedCrossRefGoogle Scholar
  723. Sawers G (1994) The hydrogenases and formate dehydrogenases of Escherichia coli. Antonie Van Leeuwenhoek 66:57–88PubMedCrossRefGoogle Scholar
  724. Sawers G, Boxer DH (1986) Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12. Eur J Biochem 156:265–275PubMedCrossRefGoogle Scholar
  725. Sawers G, Ballantine SP, Boxer DH (1985) Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: evidence for a third isoenzyme. J Bacteriol 164:1324–1331PubMedGoogle Scholar
  726. Sayavedra-Soto LA, Powell GK, Evans HJ, Morris RO (1988) Nucleotide sequence of the genetic loci encoding subunits of Bradyrhizobium japonicum uptake hydrogenase. Proc Natl Acad Sci USA 85:8395–8399PubMedCrossRefGoogle Scholar
  727. Schäfer T, Schönheit P (1991) Pyruvate metabolism of the hyperthermophilic archaebacterium Pyrococcus furiosus. Acetate formation from acetyl-CoA and ATP synthesis are catalyzed by an acetyl-CoA synthetase (ADP-forming). Arch Microbiol 155:366–377CrossRefGoogle Scholar
  728. Schauder R, Preuss A, Jetten M, Fuchs G (1989) Oxidative and reductive acetyl coa carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum. 2. Demonstration of the enzymes of the pathway and comparison of CO dehydrogenase. Arch Microbiol 151:84–89CrossRefGoogle Scholar
  729. Scheifinger CC, Linehan B, Wolin MJ (1975) H2 production by Selenomonas ruminantium in the absence and presence of methanogenic bacteria. Appl Microbiol 29:480–483PubMedGoogle Scholar
  730. Schenk A, Aragno M (1979) Bacillus schlegelii, a new species of thermophilic, facultatively chemolithoautotrophic bacterium oxidizing molecular-hydrogen. J Gen Microbiol 115:333–341CrossRefGoogle Scholar
  731. Schick M, Xie X, Ataka K, Kahnt J, Linne U, Shima S (2012) Biosynthesis of the iron-guanylylpyridinol cofactor of [Fe]-hydrogenase in methanogenic archaea as elucidated by stable-isotope labeling. J Am Chem Soc 134:3271–3280PubMedCrossRefGoogle Scholar
  732. Schink B (1982) Isolation of a hydrogenase-cytochrome b complex from cytoplasmic membranes of Xanthobacter autotrophicus GZ29. FEMS Microbiol Lett 13:289–293CrossRefGoogle Scholar
  733. Schink B, Schlegel HG (1979) The membrane-bound hydrogenase of Alcaligenes eutrophus. I. Solubilization, purification, and biochemical properties. Biochim Biophys Acta 567:315–324PubMedCrossRefGoogle Scholar
  734. Schink B, Stieb M (1983) Fermentative degradation of polyethylene glycol by a strictly anaerobic, gram-negative, nonsporeforming bacterium, Pelobacter venetianus sp. nov. Appl Environ Microbiol 45:1905–1913PubMedGoogle Scholar
  735. Schlensog V, Bock A (1990) Identification and sequence analysis of the gene encoding the transcriptional activator of the formate hydrogenlyase system of Escherichia coli. Mol Microbiol 4:1319–1327PubMedCrossRefGoogle Scholar
  736. Schlensog V, Lutz S, Bock A (1994) Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli. J Biol Chem 269:19590–19596PubMedGoogle Scholar
  737. Schmidt U, Conrad R (1993) Hydrogen, carbon monoxide, and methane dynamics in Lake Constance. Limnol Oceanogr 38:1214–1226CrossRefGoogle Scholar
  738. Schmitz O, Bothe H (1996) NAD(P)+-dependent hydrogenase activity in extracts from the cyanobacterium Anacystis nidulans. FEMS Microbiol Lett 135:97–101Google Scholar
  739. Schmitz O, Boison G, Hilscher R, Hundeshagen B, Zimmer W, Lottspeich F, Bothe H (1995) Molecular biological analysis of a bidirectional hydrogenase from cyanobacteria. Eur J Biochem 233:266–276PubMedCrossRefGoogle Scholar
  740. Schmitz O, Katayama M, Williams SB, Kondo T, Golden SS (2000) CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock. Science 289:765–768PubMedCrossRefGoogle Scholar
  741. Schmitz O, Boison G, Bothe H (2001) Quantitative analysis of expression of two circadian clock-controlled gene clusters coding for the bidirectional hydrogenase in the cyanobacterium Synechococcus sp. PCC7942. Mol Microbiol 41:1409–1417PubMedCrossRefGoogle Scholar
  742. Schmitz O, Boison G, Salzmann H, Bothe H, Schutz K, Wang SH, Happe T (2002) HoxE—a subunit specific for the pentameric bidirectional hydrogenase complex (HoxEFUYH) of cyanobacteria. Biochim Biophys Acta 1554:66–74PubMedCrossRefGoogle Scholar
  743. Schneider K, Schlegel HG (1976) Purification and properties of soluble hydrogenase from Alcaligenes eutrophus H16. Biochim Biophys Acta 452:66–80PubMedCrossRefGoogle Scholar
  744. Schneider K, Schlegel HG (1977) Localization and stability of hydrogenases from aerobic hydrogen bacteria. Arch Microbiol 112:229–238PubMedCrossRefGoogle Scholar
  745. Schneider K, Rudolph V, Schlegel HG (1973) Description and physiological characterization of a coryneform hydrogen bacterium, strain-14 g. Arch Mikrobiol 93:179–193PubMedCrossRefGoogle Scholar
  746. Schneider K, Cammack R, Schlegel HG (1984a) Content and localization of FMN, Fe-S clusters and nickel in the NAD-linked hydrogenase of Nocardia opaca 1b. Eur J Biochem 142:75–84PubMedCrossRefGoogle Scholar
  747. Schneider K, Schlegel HG, Jochim K (1984b) Effect of nickel on activity and subunit composition of purified hydrogenase from Nocardia opaca 1 b. Eur J Biochem 138:533–541PubMedCrossRefGoogle Scholar
  748. Scholz-Muramatsu H, Neumann A, Messmer M, Moore E, Diekert G (1995) Isolation and characterization of Dehalospirillum multivorans gen. nov., sp. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch Microbiol 63:48–56CrossRefGoogle Scholar
  749. Schön G (1968) Function of reserve-material for adaptive utilization of fructose and synthesis of bacteriochlorophyll in anaerobic dark and light cultures of Rhodospirillum rubrum. Arch Mikrobiol 63:362–375PubMedCrossRefGoogle Scholar
  750. Schön G, Biedermann M (1973) Growth and adaptive hydrogen production of Rhodospirillum rubrum (f1) in anaerobic dark cultures. Biochim Biophys Acta 304:65–75PubMedCrossRefGoogle Scholar
  751. Schönheit P, Kristjansson JK, Thauer RK (1982) Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Arch Microbiol 132:285–288CrossRefGoogle Scholar
  752. Schrenk MO, Kelley DS, Bolton SA, Baross JA (2004) Low archaeal diversity linked to subseafloor geochemical processes at the Lost City hydrothermal field, Mid-Atlantic Ridge. Environ Microbiol 6:1086–1095PubMedCrossRefGoogle Scholar
  753. Schropp SJ, Scranton MI, Schwarz JR (1987) Dissolved hydrogen, facultatively anaerobic, hydrogen-producing bacteria, and potential production rates in the western North Atlantic Ocean and Gulf of Mexico. Limnol Oceanogr 32:386–402CrossRefGoogle Scholar
  754. Schubert KR, Evans HJ (1976) Hydrogen evolution; a major factor affecting the efficiency of nitrogen fixation in nodulated symbionts. Proc Natl Acad Sci USA 73:1207–1211PubMedCrossRefGoogle Scholar
  755. Schubert T, Lenz O, Krause E, Volkmer R, Friedrich B (2007) Chaperones specific for the membrane-bound [NiFe]-hydrogenase interact with the Tat signal peptide of the small subunit precursor in Ralstonia eutropha H16. Mol Microbiol 66:453–467PubMedCrossRefGoogle Scholar
  756. Schuler S, Conrad R (1990) Soils contain 2 different activities for oxidation of hydrogen. FEMS Microbiol Ecol 73:77–83CrossRefGoogle Scholar
  757. Schuler S, Conrad R (1991a) Hydrogen oxidation activities in soil as influenced by pH, temperature, moisture, and season. Biol Fertil Soils 12:127–130CrossRefGoogle Scholar
  758. Schuler S, Conrad R (1991b) Hydrogen oxidation in soil following rhizobial H2 production due to N2 fixation by a Vicia faba-Rhizobium leguminosarum symbiosis. Biol Fertil Soils 11:190–195CrossRefGoogle Scholar
  759. Schultz JE, Weaver PF (1982) Fermentation and anaerobic respiration by Rhodospirillum rubrum and Rhodopseudomonas capsulata. J Bacteriol 149:181–190PubMedGoogle Scholar
  760. Schumacher W, Kroneck PMH, Pfennig N (1992) Comparative systematic study on Spirillum 5175, campylobacter and Wolinella species—description of Spirillum 5175 as Sulfurospirillum deleyianum gen. nov., spec. nov. Arch Microbiol 158:287–293CrossRefGoogle Scholar
  761. Schut GJ, Adams MW (2009) The iron-hydrogenase of Thermotoga maritima utilizes ferredoxin and NADH synergistically: a new perspective on anaerobic hydrogen production. J Bacteriol 191:4451–4457PubMedCrossRefGoogle Scholar
  762. Schut GJ, Bridger SL, Adams MW (2007) Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A-dependent NAD(P)H sulfur oxidoreductase. J Bacteriol 189:4431–4441PubMedCrossRefGoogle Scholar
  763. Schut GJ, Nixon WJ, Lipscomb GL, Scott RA, Adams MW (2012) Mutational analyses of the enzymes involved in the metabolism of hydrogen by the hyperthermophilic archaeon Pyrococcus furiosus. Front Microbiol 3:163PubMedCrossRefGoogle Scholar
  764. Schütz H, Conrad R, Goodwin S, Seiler W (1988) Emission of hydrogen from deep and shallow freshwater environments. Biogeochemistry 5:295–311CrossRefGoogle Scholar
  765. Schwartz E, Gerischer U, Friedrich B (1998) Transcriptional regulation of Alcaligenes eutrophus hydrogenase genes. J Bacteriol 180:3197–3204PubMedGoogle Scholar
  766. Schwartz E, Buhrke T, Gerischer U, Friedrich B (1999) Positive transcriptional feedback controls hydrogenase expression in Alcaligenes eutrophus H16. J Bacteriol 181:5684–5692PubMedGoogle Scholar
  767. Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G (2003) Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H2-based lithoautotrophy and anaerobiosis. J Mol Biol 332:369–383PubMedCrossRefGoogle Scholar
  768. Seefeldt LC, Arp DJ (1986) Purification to homogeneity of Azotobacter vinelandii hydrogenase: a nickel and iron containing alpha beta dimer. Biochimie 68:25–34PubMedCrossRefGoogle Scholar
  769. Seefeldt LC, Hoffman BM, Dean DR (2012) Electron transfer in nitrogenase catalysis. Curr Opin Chem Biol 16:19–25PubMedCrossRefGoogle Scholar
  770. Segerer A, Neuner A, Kristjansson JK, Stetter KO (1986) Acidianus infernus gen. nov., sp. nov., and Acidianus brierleyi comb. nov.—facultatively aerobic, extremely acidophilic thermophilic sulfur-metabolizing archaebacteria. Int J Syst Bacteriol 36:559–564CrossRefGoogle Scholar
  771. Segerer AH, Trincone A, Gahrtz M, Stetter KO (1991) Stygiolobus azoricus gen. nov., sp. nov. represents a novel genus of anaerobic, extremely thermoacidophilic archaebacteria of the order sulfolobales. Int J Syst Bacteriol 41:495–501CrossRefGoogle Scholar
  772. Seiler W (1978) The influence of the biosphere on the atmospheric CO and H2 cycles. In: Krumbein W (ed) Environmental biogeochemistry and geomicrobiology. Ann Arbor Science Publishing, Ann Arbor, pp 773–810Google Scholar
  773. Self WT, Hasona A, Shanmugam KT (2004) Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli. J Bacteriol 186:580–587PubMedCrossRefGoogle Scholar
  774. Sellstedt A (1989) Occurrence and activity of hydrogenase in symbiotic Frankia from field-collected Alnus incana. Physiol Plant 75:304–308CrossRefGoogle Scholar
  775. Serebryakova LT, Zorin NA, Lindblad P (1994) Reversible hydrogenase in Anabaena variabilis ATCC 29413. Arch Microbiol 161:140–144Google Scholar
  776. Serebryakova LT, Medina M, Zorin NA, Gogotov IN, Cammack R (1996) Reversible hydrogenase of Anabaena variabilis ATCC 29413: catalytic properties and characterization of redox centres. FEBS Lett 383:79–82PubMedCrossRefGoogle Scholar
  777. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF (2005) Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307:105–108PubMedCrossRef