Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

详细信息    查看全文

• 作者：Nicholas B Justice (112) (113)
  Anders Norman (112) (114)
  Christopher T Brown (112)
  Andrea Singh (112)
  Brian C Thomas (112)
  Jillian F Banfield (112)
  
  112. Department of Earth and Planetary Science ; University of California ; Berkeley ; CA ; 94720 ; USA
  113. Physical Biosciences Division ; Lawrence Berkeley National Lab ; Berkeley ; CA ; USA
  114. Section for Infection Microbiology ; Department of Systems Biology ; Technical University of Denmark ; Lyngby ; Denmark
  
• 刊名：BMC Genomics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：1,672 KB
• 参考文献：1. Norris, PR, Clark, DA, Owen, JP, Waterhouse, S (1996) Characteristics of Sulfobacillus acidophilus sp. nov. and other moderately thermophilic mineral-sulphide-oxidizing bacteria. Microbiol-Sgm 142: pp. 775-783
  2. Li, B, Chen, Y, Liu, Q, Hu, S, Chen, X (2011) Complete genome analysis of Sulfobacillus acidophilus strain TPY, isolated from a hydrothermal vent in the Pacific Ocean. J Bacteriol 193: pp. 5555-5556
  3. Johnson, DB, Okibe, N, Roberto, FF (2003) Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics. Arch Microbiol 180: pp. 60-68
  4. Baker, BJ, Banfield, JF (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44: pp. 139-152
  5. Watling, HR, Perrot, FA, Shiers, DW (2008) Comparison of selected characteristics of Sulfobacillus species and review of their occurrence in acidic and bioleaching environments. Hydrometallurgy 93: pp. 57-65
  6. Bond, PL, Druschel, GK, Banfield, JF (2000) Comparison of acid mine drainage microbial communities in physically and geochemically distinct ecosystems. Appl Environ Microbiol 66: pp. 4962-4971
  7. Justice, NB, Pan, C, Mueller, R, Spaulding, SE, Shah, V, Sun, CL, Yelton, AP, Miller, CS, Thomas, BC, Shah, M, VerBerkmoes, N, Hettich, R, Banfield, JF (2012) Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol 78: pp. 8321-8330
  8. Druschel, GK, Baker, BJ, Gihring, TM, Banfield, JF (2004) Acid mine drainage biogeochemistry at Iron Mountain, California. Geochem Trans 5: pp. 13-32
  9. Dick, GJ, Andersson, AF, Baker, BJ, Simmons, SL, Thomas, BC, Yelton, AP, Banfield, JF (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: pp. R85
  10. Melamud, VS, Pivovarova, TA, Tourova, TP, Kolganova, TV, Osipov, GA, Lysenko, AM, Kondrat鈥檈va, TF, Karavaiko, GI (2003) Sulfobacillus sibiricus sp. nov., a New Moderately Thermophilic Bacterium - Springer. Microbiology 72: pp. 605-612
  11. Bogdanova, TI, Tsaphna, IA, Kondrat鈥檈va, TF, Duda, VI, Suzina, NE, Melamud, VS, Tourova, TP, Karavaiko, GI (2006) Sulfobacillus thermotolerans sp. nov., a thermotolerant, chemolithotrophic bacterium. Int J Syst Evol Microbiol 56: pp. 1039-1042
  12. Golovacheva, RS, Karavaiko, GI (1978) Sulfobacillus, a new genus of thermophilic sporulating bacteria. Mikrobiologiia 47: pp. 815-822
  13. Johnson, DB, Joulian, C, d鈥橦ugues, P, Hallberg, KB (2008) Sulfobacillus benefaciens sp. nov., an acidophilic facultative anaerobic Firmicute isolated from mineral bioleaching operations. Extremophiles 12: pp. 789-798
  14. Bridge, T, Johnson, DB (1998) Reduction of soluble iron and reductive dissolution of ferric iron-containing minerals by moderately thermophilic iron-oxidizing bacteria. Appl Environ Microbiol 64: pp. 2181-2186
  15. Tsaplina, IA, Zhuravleva, AE, Egorova, MA, Bogdanova, TI, Krasil鈥檔ikova, EN, Zakharchuk, LM, Kondrat鈥檈va, TF (2010) Response to oxygen limitation in bacteria of the genus sulfobacillus. Microbiology 79: pp. 13-22
  16. Travisany, D, Di Genova, A, Sepulveda, A, Bobadilla-Fazzini, RA, Parada, P, Maass, A (2012) Draft genome sequence of the Sulfobacillus thermosulfidooxidans Cutipay strain, an indigenous bacterium isolated from a naturally extreme mining environment in Northern Chile. J Bacteriol 194: pp. 6327-6328
  17. Anderson, I, Chertkov, O, Chen, A, Saunders, E, Lapidus, A, Nolan, M, Lucas, S, Hammon, N, Deshpande, S, Cheng, J-F, Han, C, Tapia, R, Goodwin, LA, Pitluck, S, Liolios, K, Pagani, I, Ivanova, N, Mikhailova, N, Pati, A, Palaniappan, K, Land, M, Pan, C, Rohde, M, Pukall, R, G枚ker, M, Detter, JC, Woyke, T, Bristow, J, Eisen, JA, Markowitz, V (2012) Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Stand Genomic Sci 6: pp. 1-13
  18. Guo, X, Yin, H, Liang, Y, Hu, Q, Zhou, X, Xiao, Y, Ma, L, Zhang, X, Qiu, G, Liu, X (2014) Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PLoS One 9: pp. e99417
  19. Markowitz, VM, Chen, I-MA, Palaniappan, K, Chu, K, Szeto, E, Pillay, M, Ratner, A, Huang, J, Woyke, T, Huntemann, M, Anderson, I, Billis, K, Varghese, N, Mavromatis, K, Pati, A, Ivanova, NN, Kyrpides, NC (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42: pp. D560-D567
  20. Denef, VJ, Denef, VJ, Kalnejais, LH, Kalnejais, LH, Mueller, RS, Mueller, RS, Wilmes, P, Wilmes, P, Baker, BJ, Baker, BJ, Thomas, BC, Thomas, BC, VerBerkmoes, NC, VerBerkmoes, NC, Hettich, RL, Hettich, RL, Banfield, JF, Banfield, JF (2010) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci 107: pp. 2383-2390
  21. Miller, CS, Baker, BJ, Thomas, BC, Singer, SW, Banfield, JF (2011) EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol 12: pp. R44
  22. JGI: Protocols in Production Sequencing. [http://jgi.doe.gov/collaborate-with-jgi/pmooverview/protocols-sample-preparation-information/]
  23. St John J: SeqPrep. [https://github.com/jstjohn/SeqPrep]
  24. Denef, VJ, Banfield, JF (2012) In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336: pp. 462-466
  25. Peng, Y, Leung, HCM, Yiu, SM, Chin, FYL (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: pp. 1420-1428
  26. Li, H, Durbin, R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: pp. 1754-1760
  27. Hyatt, D, Chen, G-L, LoCascio, PF, Land, ML, Larimer, FW, Hauser, LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: pp. 119
  28. Lowe, TM, Eddy, SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: pp. 955-964
  29. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215: pp. 403-410
  30. Suzek, BE, Huang, H, McGarvey, P, Mazumder, R, Wu, CH (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: pp. 1282-1288
  31. Ogata, H, Goto, S, Sato, K, Fujibuchi, W, Bono, H, Kanehisa, M (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: pp. 29-34
  32. Quevillon, E, Silventoinen, V, Pillai, S, Harte, N, Mulder, N, Apweiler, R, Lopez, R (2005) InterProScan: protein domains identifier. Nucleic Acids Res 33: pp. W116-W120
  33. Markowitz, VM, Chen, IMA, Palaniappan, K, Chu, K, Szeto, E, Grechkin, Y, Ratner, A, Jacob, B, Huang, J, Williams, P, Huntemann, M, Anderson, I, Mavromatis, K, Ivanova, NN, Kyrpides, NC (2011) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40: pp. D115-D122
  34. Edgar, RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: pp. 2460-2461
  35. Edgar, RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: pp. 1792-1797
  36. Castresana, J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: pp. 540-552
  37. Talavera, G, Castresana, J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: pp. 564-577
  38. Abascal, F, Zardoya, R, Posada, D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: pp. 2104-2105
  39. Stamatakis, A (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: pp. 2688-2690
  40. Letunic, I, Bork, P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: pp. 127-128
  41. Sorek, R, Zhu, Y, Creevey, CJ, Francino, MP, Bork, P, Rubin, EM (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: pp. 1449-1452
  42. Wu, M, Eisen, JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9: pp. R151
  43. Pruesse, E, Quast, C, Knittel, K, Fuchs, BM, Ludwig, W, Peplies, J, Glockner, FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: pp. 7188-7196
  44. Wright, ES, Yilmaz, LS, Noguera, DR (2012) DECIPHER, a search-based approach to Chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78: pp. 717-725
  45. Edgar, RC, Haas, BJ, Clemente, JC, Quince, C, Knight, R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: pp. 2194-2200
  46. DeSantis, TZ, Hugenholtz, P, Larsen, N, Rojas, M, Brodie, EL, Keller, K, Huber, T, Dalevi, D, Hu, P, Andersen, GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: pp. 5069-5072
  47. Caporaso, JG, Kuczynski, J, Stombaugh, J, Bittinger, K, Bushman, FD, Costello, EK, Fierer, N, Pe帽a, AG, Goodrich, JK, Gordon, JI, Huttley, GA, Kelley, ST, Knights, D, Koenig, JE, Ley, RE, Lozupone, CA, McDonald, D, Muegge, BD, Pirrung, M, Reeder, J, Sevinsky, JR, Turnbaugh, PJ, Walters, WA, Widmann, J, Yatsunenko, T, Zaneveld, J, Knight, R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: pp. 335-336
  48. Caporaso, JG, Bittinger, K, Bushman, FD, DeSantis, TZ, Andersen, GL, Knight, R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: pp. 266-267
  49. Bond, PL, Banfield, JF (2001) Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments. Microb Ecol 41: pp. 149-161
  50. Amann, R, Ludwig, W, Schleifer, KH (1995) Phylogenetic identification and in-situ detection of individual microbial-cells without cultivation. Microbiol Rev 59: pp. 143-169
  51. Saraste, M (1994) Structure and evolution of cytochrome oxidase. Antonie Van Leeuwenhoek 65: pp. 285-287
  52. Beinert, H (1997) Copper A of cytochrome c oxidase, a novel, long-embattled, biological electron-transfer site. Eur J Biochem 245: pp. 521-532
  53. Borisov, VB, Gennis, RB, Hemp, J, Verkhovsky, MI (1807) The cytochrome bd respiratory oxygen reductases. BBA - Bioenergetics 2011: pp. 1398-1413
  54. Moparthi, VK, H盲gerh盲ll, C (2011) The evolution of respiratory chain complex I from a smaller last common ancestor consisting of 11 protein subunits. J Mol Evol 72: pp. 484-497
  55. Kerscher, S, Dr枚se, S, Zickermann, V, Brandt, U (2008) The three families of respiratory NADH dehydrogenases. Results Probl Cell Differ 45: pp. 185-222
  56. Lancaster, CRD (2002) Succinate:quinone oxidoreductases: an overview. Biochim Biophys Acta 1553: pp. 1-6
  57. Schafer, G, Anemuller, S, Moll, R (2002) Archaeal complex II: 鈥榗lassical鈥?and 鈥渘on-classical鈥?succinate : quinone reductases with unusual features. BBA - Bioenergetics 1553: pp. 57-73
  58. Schippers, A, Jozsa, P, Sand, W (1996) Sulfur chemistry in bacterial leaching of pyrite. Appl Environ Microbiol 62: pp. 3424-3431
  59. Dopson, M, Johnson, DB (2012) Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms. Environ Microbiol 14: pp. 2620-2631
  60. Luther, GW (1987) Pyrite oxidation and reduction: molecular orbital theory considerations. Geochim Cosmochim Acta 51: pp. 3193-3199
  61. Urich, T, Gomes, CM, Kletzin, A, Fraz茫o, C (2006) X-ray structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science 311: pp. 996-1000
  62. Chen, L, Ren, Y, Lin, J, Liu, X, Pang, X, Lin, J (2012) Acidithiobacillus caldus sulfur oxidation model based on transcriptome analysis between the wild type and sulfur oxygenase reductase defective mutant. PLoS One 7: pp. e39470
  63. Zhang, H, Guo, W, Xu, C, Zhou, H, Chen, X (2013) Site-specific mutagenesis and functional analysis of active sites of sulfur oxygenase reductase from Gram-positive moderate thermophile Sulfobacillus acidophilus TPY. Microbiol Res 168: pp. 654-660
  64. Hedderich, R, Forzi, L (2005) Energy-converting [NiFe] hydrogenases: more than just H2 activation. J Mol Microbiol Biotechnol 10: pp. 92-104
  65. Grein, F, Ramos, AR, Venceslau, SS, Pereira, IAC (1827) Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. Biochim Biophys Acta 2013: pp. 145-160
  66. Hedderich, R, Klimmek, O, Kr枚ger, A, Dirmeier, R, Keller, M, Stetter, KO (1999) Anaerobic respiration with elemental sulfur and with disulfides. FEMS Microbiol Rev 22: pp. 353-381
  67. Quatrini, R, Appia-Ayme, C, Denis, Y, Jedlicki, E, Holmes, DS, Bonnefoy, V (2009) Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans. BMC Genomics 10: pp. 394
  68. Rohwerder, T (2003) The sulfane sulfur of persulfides is the actual substrate of the sulfur-oxidizing enzymes from Acidithiobacillus and Acidiphilium spp. Microbiology 149: pp. 1699-1710
  69. Rohwerder, T, Sand, W (2007) Oxidation of inorganic sulfur compounds in acidophilic prokaryotes. Eng Life Sci 7: pp. 301-309
  70. Hamann, N, Mander, GJ, Shokes, JE, Scott, RA, Bennati, M, Hedderich, R (2007) A cysteine-rich CCG domain contains a novel [4Fe-4S] cluster binding motif as deduced from studies with subunit B of heterodisulfide reductase from Methanothermobacter marburgensis. Biochemistry 46: pp. 12875-12885
  71. Stockdreher, Y, Sturm, M, Josten, M, Sahl, H-G, Dobler, N, Zigann, R, Dahl, C (2014) New proteins involved in sulfur trafficking in the cytoplasm of allochromatium vinosum. J Biol Chem 289: pp. 12390-12403
  72. Stockdreher, Y, Venceslau, SS, Josten, M, Sahl, H-G, Pereira, IAC, Dahl, C (2012) Cytoplasmic sulfurtransferases in the purple sulfur bacterium allochromatium vinosum: evidence for sulfur transfer from DsrEFH to DsrC. PLoS One 7: pp. e40785
  73. Morris, TW, Reed, KE, Cronan, JE (1994) Identification of the gene encoding lipoate-protein ligase-a of escherichia-coli - molecular-cloning and characterization of the Lpla gene and gene-product. J Biol Chem 269: pp. 16091-16100
  74. Perham, RN (2000) Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions. Annu Rev Biochem 69: pp. 961-1004
  75. Liu, L-J, Stockdreher, Y, Koch, T, Sun, S-T, Fan, Z, Josten, M, Sahl, H-G, Wang, Q, Luo, Y-M, Liu, S-J, Dahl, C, Jiang, C-Y (2014) Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon metallosphaera cuprina. J Biol Chem 289: pp. 26949-26959
  76. Strittmatter, AW, Liesegang, H, Rabus, R, Decker, I, Amann, J, Andres, S, Henne, A, Fricke, WF, Martinez-Arias, R, Bartels, D, Goesmann, A, Krause, L, Puehler, A, Klenk, H-P, Richter, M, Schueler, M, Gloeckner, FO, Meyerdierks, A, Gottschalk, G, Amann, R (2009) Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ Microbiol 11: pp. 1038-1055
  77. Marcia, M, Ermler, U, Peng, G, Michel, H (2009) A new structure-based classification of sulfide:quinone oxidoreductases. Proteins: Struct Funct Bioinformatics 78: pp. 1073-1083
  78. Wakai, S, Tsujita, M, Kikumoto, M, Manchur, MA, Kanao, T, Kamimura, K (2007) Purification and characterization of sulfide: quinone oxidoreductase from an acidophilic iron-oxidizing bacterium, Acidithiobacillus ferrooxidans. Biosci Biotechnol Biochem 71: pp. 2735-2742
  79. Cherney, MM, Zhang, Y, Solomonson, M, Weiner, JH, James, MNG (2010) Crystal structure of sulfide: quinone oxidoreductase from acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J Mol Biol 398: pp. 292-305
  80. Lencina, AM, Ding, Z, Schurig-Briccio, LA, Gennis, RB (1827) Characterization of the type III sulfide:quinone oxidoreductase from Caldivirga maquilingensis and its membrane binding. Biochim Biophys Acta 2013: pp. 266-275
  81. De Jong, GA, Hazeu, W, Bos, P, Kuenen, JG (1997) Isolation of the tetrathionate hydrolase from Thiobacillus acidophilus. Eur J Biochem 243: pp. 678-683
  82. Kanao, T, Kamimura, K, Sugio, T (2007) Identification of a gene encoding a tetrathionate hydrolase in Acidithiobacillus ferrooxidans. J Biotechnol 132: pp. 16-22
  83. Bugaytsova, Z, Lindstr枚m, EB (2004) Localization, purification and properties of a tetrathionate hydrolase from Acidithiobacillus caldus. Eur J Biochem 271: pp. 272-280
  84. Egorova, MA, Tsaplina, IA, Zakharchuk, LM, Bogdanova, TI, Krasil鈥檔ikova, EN (2004) Effect of cultivation conditions on the growth and activities of sulfur metabolism enzymes and carboxylases of Sulfobacillus thermosulfidooxidans subsp asporogenes strain 41. Appl Biochem Microbiol 40: pp. 381-387
  85. Shiers, DW, Ralph, DE, Watling, HR (2010) A comparative study of substrate utilisation by Sulfobacillus species in mixed ferrous ion and tetrathionate growth medium. Hydrometallurgy 104: pp. 363-369
  86. Protze, J, M眉ller, F, Lauber, K, Na脽, B, Mentele, R, Lottspeich, F, Kletzin, A (2011) An extracellular tetrathionate hydrolase from the thermoacidophilic archaeon acidianus ambivalens with an activity optimum at pH聽1. Front Microbiol 2: pp. 68
  87. M眉ller, FH, Bandeiras, TM, Urich, T, Teixeira, M, Gomes, CM, Kletzin, A (2004) Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase. Mol Microbiol 53: pp. 1147-1160
  88. Rothery, RA, Workun, GJ, Weiner, JH (2008) The prokaryotic complex iron-sulfur molybdoenzyme family. Biochim Biophys Acta 1778: pp. 1897-1929
  89. Hinsley, AP, Berks, BC (2002) Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica. Microbiol-Sgm 148: pp. 3631-3638
  90. Guiral, M, Tron, P, Aubert, C, Gloter, A, Iobbi-Nivol, C, Giudici-Orticoni, M-T (2005) A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J Biol Chem 280: pp. 42004-42015
  91. Dahl, C, Franz, B, Hensen, D, Kesselheim, A, Zigann, R (2013) Sulfite oxidation in the purple sulfur bacterium Allochromatium vinosum: identification of SoeABC as a major player and relevance of SoxYZ in the process. Microbiol-Sgm 159: pp. 2626-2638
  92. Kopriva, S, Buchert, T, Fritz, G, Suter, M, Benda, RD, Schunemann, V, Koprivova, A, Schurmann, P, Trautwein, AX, Kroneck, P, Brunold, C (2002) The presence of an iron-sulfur cluster in adenosine 5 鈥?phosphosulfate reductase separates organisms utilizing adenosine 5 鈥?phosphosulfate and phosphoadenosine 5鈥?phosphosulfate for sulfate assimilation. J Biol Chem 277: pp. 21786-21791
  93. Bick, JA, Dennis, JJ, Zylstra, GJ, Nowack, J, Leustek, T (2000) Identification of a new class of 5鈥?adenylylsulfate (APS) reductases from sulfate-assimilating bacteria. J Bacteriol 182: pp. 135-142
  94. Bonnefoy, V, Holmes, DS (2011) Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol 14: pp. 1597-1611
  95. Coupland, K, Johnson, DB (2008) Evidence that the potential for dissimilatory ferric iron reduction is widespread among acidophilic heterotrophic bacteria. FEMS Microbiol Lett 279: pp. 30-35
  96. Johnson, DB, Kanao, T, Hedrich, S (2012) Redox transformations of iron at extremely low pH: fundamental and applied aspects. Front Microbiol 3: pp. 1-13
  97. Ohmura, N, Sasaki, K, Matsumoto, N, Saiki, H (2002) Anaerobic respiration using Fe3+, S0, and H2 in the chemolithoautotrophic bacterium acidithiobacillus ferrooxidans. J Bacteriol 184: pp. 2081-2087
  98. Kucera, J, Bouchal, P, Cerna, H, Potesil, D, Janiczek, O, Zdrahal, Z, Mandl, M (2011) Kinetics of anaerobic elemental sulfur oxidation by ferric iron in Acidithiobacillus ferrooxidans and protein identification by comparative 2-DE-MS/MS. Antonie Van Leeuwenhoek 101: pp. 561-573
  99. Osorio, H, Mangold, S, Denis, Y, Nancucheo, I, Esparza, M, Johnson, DB, Bonnefoy, V, Dopson, M, Holmes, DS (2013) Anaerobic sulfur metabolism coupled to dissimilatory iron reduction in the extremophile acidithiobacillus ferrooxidans. Appl Environ Microbiol 79: pp. 2172-2181
  100. Thamdrup, B, Finster, K, Hansen, JW, Bak, F (1993) Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese. Appl Environ Microbiol 59: pp. 101-108
  101. Hardisty, DS, Olyphant, GA, Bell, JB, Johnson, AP, Pratt, LM (2013) Acidophilic sulfur disproportionation. Geochim Cosmochim Acta 113: pp. 136-151
  102. Karavaiko, GI, Krasil鈥檔ikova, EN, Tsaplina, IA, Bogdanova, TI, Zakharchuk, LM (2001) Growth and carbohydrate metabolism of sulfobacilli. Microbiology 70: pp. 245-250
  103. Vignais, PM, Billoud, B (2007) Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 107: pp. 4206-4272
  104. Constant, P, Chowdhury, SP, Pratscher, J, Conrad, R (2010) Streptomycetes contributing to atmospheric molecular hydrogen soil uptake are widespread and encode a putative high-affinity [NiFe]-hydrogenase. Environ Microbiol 12: pp. 821-829
  105. 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 H-2-oxidizing bacteria. Appl Environ Microbiol 77: pp. 6027-6035
  106. Thauer, RK, Kaster, A-K, Goenrich, M, Schick, M, Hiromoto, T, Shima, S (2010) Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H 2Storage. Annu Rev Biochem 79: pp. 507-536
  107. Coppi, MV (2005) The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiol-Sgm 151: pp. 1239-1254
  108. Marreiros, BC, Batista, AP, Duarte, AMS, Pereira, MM (1827) A missing link between complex I and group 4 membrane-bound [NiFe] hydrogenases. BBA - Bioenergetics 2013: pp. 198-209
  109. King, GM, Weber, CF (2007) Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat Rev Microbiol 5: pp. 107-118
  110. Lin, JT, Lin, JT, Stewart, V, Stewart, V (1998) Nitrate assimilation by bacteria. Adv Microb Physiol 39: pp. 1-30
  111. Richardson, DJ, Berks, BC, Russell, DA, Spiro, S, Taylor, CJ (2001) Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 58: pp. 165-178
  112. Gardner, PR (2005) Nitric oxide dioxygenase function and mechanism of flavohemoglobin, hemoglobin, myoglobin and their associated reductases. J Inorg Biochem 99: pp. 247-266
  113. Poole, RK, Hughes, MN (2000) New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress. Mol Microbiol 36: pp. 775-783
  114. Caldwell, PE, MacLean, MR, Norris, PR (2007) Ribulose bisphosphate carboxylase activity and a Calvin cycle gene cluster in Sulfobacillus species. Microbiol-Sgm 153: pp. 2231-2240
  115. Tabita, FR, Hanson, TE, Li, HY, Satagopan, S, Singh, J, Chan, S (2007) Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev 71: pp. 576-599
  116. Barrie Johnson, D, Hallberg, KB Carbon, Iron and Sulfur Metabolism in Acidophilic Micro-Organisms. In: Poole, RK eds. (2008) Advances in Microbial Physiology, volume 54. pp. 201-255
  117. Sugiyama, M, Suzuki, S-I, Tonouchi, N, Yokozeki, K (2003) Transaldolase/glucose-6-phosphate isomerase bifunctional enzyme and ribulokinase as factors to increase xylitol production from D-arabitol in Gluconobacter oxydans. Biosci Biotechnol Biochem 67: pp. 2524-2532
  118. Kim, S, Lee, SB (2008) Identification and characterization of the bacterial d-gluconate dehydratase in Achromobacter xylosoxidans. Biotechnol Bioprocess Eng 13: pp. 436-444
  119. Krasil鈥檔ikova, EN, Zakharchuk, LM, Egorova, MA, Bogdanova, TI, Zhuravleva, AE, Tsaplina, IA (2010) Regulation of metabolic pathways in sulfobacilli under different aeration regimes. Microbiology 79: pp. 147-152
  120. Nancucheo, I, Johnson, DB (2010) Production of glycolic acid by chemolithotrophic iron- and sulfur-oxidizing bacteria and its role in delineating and sustaining acidophilic sulfide mineral-oxidizing consortia. Appl Environ Microbiol 76: pp. 461-467
  121. Chai, Y, Kolter, R, Losick, R (2009) A widely conserved gene cluster required for lactate utilization in bacillus subtilis and its involvement in biofilm formation. J Bacteriol 191: pp. 2423-2430
  122. Tholozan, JL, Touzel, JP, Samain, E, Grivet, JP, Prensier, G, Albagnac, G (1992) Clostridium neopropionicum sp. nov., a strict anaerobic bacterium fermenting ethanol to propionate through acrylate pathway. Arch Microbiol 157: pp. 249-257
  123. Schink, B, Kremer, DR, Hansen, TA (1987) Pathway of propionate formation from ethanol in Pelobacter propionicus. Arch Microbiol 147: pp. 321-327
  124. Tsaplina, IA, Osipov, GA, Bogdanova, TI, NEDOREZOVA, TP, Karavaiko, GI (1994) Fatty-acid composition of lipids in thermoacidophilic bacteria of the genus sulfobacillus. Microbiology 63: pp. 459-464
  125. Kaneda, T (1991) Iso-and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiol Rev 55: pp. 288-302
  126. Oshima, M, Ariga, T (1975) Omega-cyclohexyl fatty-acids in acidophilic thermophilic bacteria - studies on their presence, structure, and biosynthesis using precursors labeled with stable isotopes and radioisotopes. J Biol Chem 250: pp. 6963-6968
  127. Duda, VI, Suzina, NE, Severina, LO, Dmitriev, VV, Karavaiko, GI (2001) Formation of flat lamellar intramembrane lipid structures in microorganisms. J Membr Biol 180: pp. 33-48
  128. Kannenberg, EL, Poralla, K (1999) Hopanoid biosynthesis and function in bacteria. Naturwissenschaften 86: pp. 168-176
  129. Spanova, M, Daum, G (2011) Squalene - biochemistry, molecular biology, process biotechnology, and applications. Eur J Lipid Sci Technol 113: pp. 1299-1320
  130. Jones, DS, Jones, DS, Albrecht, HL, Albrecht, HL, Dawson, KS, Dawson, KS, Schaperdoth, I, Schaperdoth, I, Freeman, KH, Freeman, KH, Pi, Y, Pi, Y, Pearson, A, Pearson, A, Macalady, JL, Macalady, JL (2011) Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME J 6: pp. 158-170
  131. Welander, PV, Doughty, DM, Wu, C-H, Mehay, S, Summons, RE, Newman, DK (2012) Identification and characterization of Rhodopseudomonas palustris TIE-1 hopanoid biosynthesis mutants. Geobiology 10: pp. 163-177
  132. C谩rdenas, JP, Moya, F, Covarrubias, P, Shmaryahu, A, Levic谩n, G, Holmes, DS, Quatrini, R (2012) Comparative genomics of the oxidative stress response in bioleaching microorganisms. Hydrometallurgy 127-128: pp. 162-167
  133. Norambuena, J, Flores, R, C谩rdenas, JP, Quatrini, R, Ch谩vez, R, Levic谩n, G (2012) Thiol/disulfide system plays a crucial role in redox protection in the acidophilic iron-oxidizing bacterium leptospirillum ferriphilum. PLoS One 7: pp. e44576
  134. Empadinhas, N, da Costa, MS (2006) Diversity and biosynthesis of compatible solutes in hyper/thermophiles. Int Microbiol 9: pp. 199-206
  135. Mosier, AC, Justice, NB, Bowen, BP, Baran, R, Thomas, BC, Northen, TR, Banfield, JF (2013) Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics. MBio 4: pp. e00484鈥?2
  136. Bren, A, Eisenbach, M (2000) How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. J Bacteriol 182: pp. 6865-6873
  137. Ghauri, MA, Johnson, DB (1991) Physiological diversity amongst some moderately thermophilic iron-oxidizing bacteria. FEMS Microbiol Ecol 85: pp. 327-334
  138. Wood, AP, Kelly, DP (1983) Autotrophic and mixotrophic growth of three thermoacidophilic iron-oxidizing bacteria. FEMS Microbiol Lett 20: pp. 107-112
  139. Wood, AP, Kelly, DP (1984) Growth and sugar metabolism of a thermoaddophilic iron-oxidizing mixotrophic bacterium. Microbiology 130: pp. 1337-1349
  140. Tsaplina, IA, Krasil鈥檔ikova, EN, Zhuravleva, AE, Egorova, MA, Zakharchuk, LM, Suzina, NE, Duda, VI, Bogdanova, TI, Stadnichuk, IN, Kondrat鈥檈va, TF (2008) The dependence of intracellular ATP level on the nutrition mode of the acidophilic bacteria Sulfobacillus thermotolerans and Alicyclobacillus tolerans. Microbiology 77: pp. 654-664
  141. Ma, S, Banfield, JF (2011) Micron-scale Fe2+/Fe3+, intermediate sulfur species and O2 gradients across the biofilm-solution-sediment interface control biofilm organization. Geochim Cosmochim Acta 75: pp. 3568-3580
  142. Druschel, GK, Hamers, RJ, Banfield, JF (2003) Kinetics and mechanism of polythionate oxidation to sulfate at low pH by O2 and Fe3. Geochim Cosmochim Acta 67: pp. 4457-4469
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. Results Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. Conclusions Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.