Lessons from the genomes of extremely acidophilic bacteria and archaea with special emphasis on bioleaching microorganisms

Applied Microbiology and Biotechnology

Volumn 88, Issue 3, 2010, Pages 605-620

  Cárdenas, Juan Pablo ^a,b   Valdés, Jorge ^a,b,c   Quatrini, Raquel ^a   Duarte, Francisco ^a,b   Holmes, David S ^a,b  

^a Fundacion Ciencia para la Vida   (Chile)

^b UNIVERSIDAD ANDRÉS BELLO   (Chile)

^c UNIVERSIDAD DE TALCA   (Chile)

Author keywords

Acidophiles; Bioinformatics; Ecophysiology; Genomics; Metabolic reconstruction

Indexed keywords

ACIDIC ENVIRONMENT; ACIDOPHILES; ACIDOPHILIC BACTERIA; ARCHAEA; BIOLOGICAL PRINCIPLES; CURRENT STATUS; ECOPHYSIOLOGY; EVOLUTIONARY TREND; GENETIC INTERACTION; GENOME ARCHITECTURE; GENOME PROJECTS; GENOME SEQUENCING PROJECTS; GENOMIC INFORMATION; GENOMICS; INITIAL INFORMATION; INTELLECTUAL RESOURCES; METABOLIC RECONSTRUCTION; MICROBIAL COMMUNITIES; PRELIMINARY MODEL; SCIENTIFIC ADVANCES;

BACTERIOLOGY; BIOINFORMATICS; BIOLEACHING; DNA SEQUENCES; ECOLOGY; GENES; METABOLISM; PHYSIOLOGY; VIRUSES;

BACTERIA;

GENOMIC DNA; SULFUR DERIVATIVE;

BIOINFORMATICS; ECOPHYSIOLOGY; EVOLUTIONARY BIOLOGY; EXTREMOPHILE; GENOMICS; METABOLISM; MICROBIAL COMMUNITY; MICROBIOLOGY; PLASMID; PROKARYOTE; VIRUS;

ACIDITHIOBACILLUS; ACIDOPHILE; ARCHAEAL GENOME; ARCHAEBACTERIUM; AUTOTROPHY; BACTERIAL GENOME; BIOFILM; BIOINFORMATICS; BIOLEACHING; CARBON DIOXIDE FIXATION; CELL MOTILITY; CHEMICAL ENVIRONMENT; CHEMOTAXIS; CITRIC ACID CYCLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA FINGERPRINTING; DNA MICROARRAY; DNA SEQUENCE; GAMMAPROTEOBACTERIA; GENE CONTROL; GENE INTERACTION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOMICS; HOMEOSTASIS; METABOLIC ENGINEERING; METABOLIC REGULATION; METAGENOMICS; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROBIAL METABOLISM; MICROBIAL POPULATION DYNAMICS; MICROBIAL RESPIRATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; REGULATORY RNA SEQUENCE; SEQUENCE ANALYSIS; SHORT SURVEY; VIRUS;

ARCHAEA; BACTERIA; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; ENERGY METABOLISM; GENOME, BACTERIAL; SEQUENCE ANALYSIS, DNA; VIRUSES;

ACIDOPHILES; BACTERIA (MICROORGANISMS);

EID: 78149359126     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-010-2795-9     Document Type: Short Survey

References (113)

1. Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Micro 3:489-498
2. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF (2007) Genome dynamics in a natural archaeal population. Proc Natl Acad Sci 104:1883-1888
3. Amouric A, Appia-Ayme C, Yarzabal A, Bonnefoy V (2009) Regulation of the iron and sulfur oxidation pathways in the acidophilic Acidithiobacillus ferrooxidans. Adv Mater Res 71-73:163-166
4. Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320:1047-1050
5. Appia-Ayme C, Quatrini R, Denis Y, Denizot F, Silver S, Roberto F, Veloso F, Valdés J, Pablo Cárdenas J, Esparza M, Orellana O, Jedlicki E, Bonnefoy V, Holmes DS (2006) Microarray and bioinformatic analyses suggest models for carbon metabolism in the autotroph Acidithiobacillus ferrooxidans. Hydrometallurgy 83:273-280
6. Arsène-Ploetze F, Koechler S, Marchal M, Coppée J-Y, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN (2010) Structure, function, and evolution of the thiomonas spp. Genome. PLoS Genet 6: e1000859
7. Auernik KS, Maezato Y, Blum PH, Kelly RM (2008) The genome sequence of the metal-mobilizing, extremely thermoacidophilic archaeon Metallosphaera sedula provides insights into bioleaching-associated metabolism. Appl Environ Microbiol 74:682-692
8. Baker BJ, Banfield JF (2003) Microbial communities in acid mine drainage. FEMS Microbiol Ecol 44:139-152
9. Baker BJ, Tyson GW, Goosherst L, Banfield JF (2009) Insights into the diversity of eukaryotes in acid mine drainage biofilm communities. Appl Environ Microbiol 75:2192-2199
10. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Ver Berkmoes NC, Hettich RL, Banfield JF (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci 107:8806-8811
11. Baker-Austin C, Dopson M, Wexler M, Sawers RG, Bond PL (2005) Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1. Microbiology 151:2637-2646
12. Barreto M, Quatrini R, Bueno S, Arriagada C, Valdes J, Silver S, Jedlicki E, Holmes DS (2003) Aspects of the predicted physiology of Acidithiobacillus ferrooxidans deduced from an analysis of its partial genome sequence. Hydrometallurgy 71:97-105
13. Barreto M, Gehrke T, Harneit K, Sand W, Jedlicki E, Holmes D (2005a) Unexpected insights into biofilm formation by Acidithiobacillus ferrooxidans revealed by genome analysis and experimental approaches. In: Harrison S, Rawlings D, Peterson J (eds) 16th International Biohydrometallurgy Symposium. Cape Town, South Africa, pp 817-825
14. Barreto M, Jedlicki E, Holmes DS (2005b) Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans. Appl Environ Microbiol 71:2902-2909
15. Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, Alber BE, Fuchs G (2010a) Autotrophic carbon fixation in archaea. Nat Rev Micro 8:447-460
16. Berg IA, Ramos-Vera WH, Petri A, Huber H, Fuchs G (2010b) Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota. Microbiology 156:256-269
17. Bonnefoy V (2010) Bioinformatics and genomics of iron and sulfur oxidizing acidophiles. In: Barton L, Mandl M, Loy A (eds) Geomicrobiology: molecular and environmental perspective
18. Bouchal P, Zdráhal Z, Helánová S, Janiczek O, Hallberg KB, Mandl M (2006) Proteomic and bioinformatic analysis of iron-and sulfur-oxidizing Acidithiobacillus ferrooxidans using immobilized pH gradients and mass spectrometry. Proteomics 6:4278-4285
19. Brügger K, Torarinsson E, Redder P, Chen L, Garrett RA (2004) Shuffling of Sulfolobus genomes by autonomous and nonautonomous mobile elements. Biochem Soc Trans 32:179-183
20. Cabrejos M-E, Zhao H-L, Guacucano M, Bueno S, Levican G, Garcia E, Jedlicki E, Holmes DS (1999) IST1 insertional inactivation of the resB gene: implications for phenotypic switching in Thiobacillus ferrooxidans. FEMS Microbiol Lett 175:223-229
21. Castro M, Ruiz L, Díaz M, Mamani S, Jerez CA, Holmes DS, Guiliani N (2009) C-Di-GMP pathway in biomining bacteria. Adv Mater Res 71-73:223-226
22. Chen L, Brugger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk H-P, Garrett RA (2005) The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 187:4992-4999
23. Chi A, Valenzuela L, Beard S, Mackey AJ, Shabanowitz J, Hunt DF, Jerez CA (2007) Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans. Mol Cell Proteomics 6:2239-2251
24. Cid C, Garcia-Descalzo L, Casado-Lafuente V, Amils R, Aguilera A (2010) Proteomic analysis of the response of an acidophilic strain of Chlamydomonas sp. (Chlorophyta) to natural metal-rich water. Proteomics 10 (10):2026-2036
25. Clennel A, Johnston B, Rawlings D (1995) Structure and function of Tn5467, a Tn21-like transposon located on the Thiobacillus ferrooxidans broad-host-range plasmid pTF-FC2. Appl Environ Microbiol 61:4223-4229
26. Clum A, Nolan M, Lang E, Rio TGD, Tice H, Copeland A, Cheng J-F, Lucas S, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Göker M, Spring S, Land M, Hauser L, Chang Y-J, Jeffries CD, Chain P, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk H-P, Lapidus A (2009) Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT). Standards in Genomic Sciences
27. Demergasso CS, Galleguillos F, Soto P, Serón M, Iturriaga V (2010) Microbial succession during a heap bioleaching cycle of low grade copper sulfides. Does this knowledge mean a real input for industrial process design and control? Hydrometallurgy
28. Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, Ver Berkmoes NC, Hettich RL, Banfield JF (2010a) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci 107:2383-2390
29. Denef VJ, Mueller RS, Banfield JF (2010b) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4:599-610
30. Dick G, Andersson A, Baker B, Simmons S, Thomas B, Yelton AP, Banfield J (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85
31. Dopson M (2010) Ecology, adaptations, and applications of acidophiles. In: R A (ed) Extremophiles: microbiology and biotechnology. Horizon Press
32. Duarte F, Araya-Secchi R, González W, Perez-Acle T, González-Nilo D, Holmes DS (2009) Protein function in extremely acidic conditions: molecular simulation studies of a predicted aquaporin and a voltage gated potassium channel in Acidithiobacillus ferrooxidans. Adv Mater Res 71-73:211-214
33. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, de Winter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133-138
34. Esparza M, Bowien B, Jedlicki E, Holmes DS (2009) Gene organization and CO2-responsive expression of four Cbb operons in Acidithiobacillus ferrooxidans. Adv Mater Res 71-73:207-210
35. Esparza M, Cardenas JP, Bowien B, Jedlicki E, Holmes DS (2010) CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans. BMC Microbiology
36. Farah C, Vera M, Morin D, Haras D, Jerez CA, Guiliani N (2005) Evidence for a functional quorum-sensing type AI-1 system in the extremophilic bacterium Acidithiobacillus ferrooxidans. Appl Environ Microbiol 71:7033-7040
37. Filee J, Siguier P, Chandler M (2007) Insertion sequence diversity in archaea. Microbiol Mol Biol Rev 71:121-157
38. Fütterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci USA 101:9091-9096
39. Garrido P, González-Toril E, García-Moyano A, Moreno-Paz M, Amils R, Parro V (2008) An oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental RNA. Environ Microbiol 10:836-850
40. Goltsman DSA, Denef VJ, Singer SW, Ver Berkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF (2009) Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms. Appl Environ Microbiol 75:4599-4615
41. Gonzalez-Toril E, Llobet-Brossa E, Casamayor EO, Amann R, Amils R (2003) Microbial ecology of an extreme acidic environment, the Tinto River. Appl Environ Microbiol 69:4853-4865
42. González-Toril E, Aguilera A, Rodriguez N, Fernández- Remolar D, Gómez F, Diaz E, García-Moyano A, Sanz JL, Amils R (2010) Microbial ecology of Río Tinto, a natural extreme acidic environment of biohydrometallurgical interest. Hydrometallurgy (in press)
43. Hold C, Andrews BA, Asenjo JA (2009) A stoichiometric model of Acidithiobacillus ferrooxidans ATCC 23270 for metabolic flux analysis. Biotechnol Bioeng 102:1448-1459
44. Holmes DS, Bonnefoy V (2007) Genetic and bioinformatic insights into iron and sulfur oxidation mechanisms of bioleaching organisms. In: Rawlings DE, Johnson DB (eds) Biomining. Springer, Berlin, pp 281-307
45. Holmes DS, Barreto M, Valdes J, Dominguez C, Arriagada C, Silver S, Bueno S, Jedlicki E (2001) Genome sequence of Acidithiobacillus ferrooxidans: metabolic reconstruction, heavy metal resistance and other characteristics. In: Ciminelli V, Garcia O (eds) Biohydrometallurgy: fundamentals, technology and sustainable development. Elsevier, Amsterdam, pp 237-251
46. Hou S, Makarova K, Saw J, Senin P, Ly B, Zhou Z, Ren Y, Wang J, Galperin M, Omelchenko M, Wolf Y, Yutin N, Koonin E, Stott M, Mountain B, Crowe M, Smirnova A, Dunfield P, Feng L, Wang L, Alam M (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 3:26
47. Jerez CA (2008) The use of genomics, proteomics and other OMICS technologies for the global understanding of biomining microorganisms. Hydrometallurgy 94:162-169
48. Johnson DB (1998) Biodiversity and ecology of acidophilic microorganisms. FEMS Microbiol Ecol 27:307-317
49. Johnson DB (2008) Biodiversity and interactions of acidophiles: key to understanding and optimizing microbial processing of ores and concentrates. Trans Nonferrous Met Soc China 18:1367-1373
50. Kanao T, Matsumoto C, Shiraga K, Yoshida K, Takada J, Kamimura K (2010) Recombinant tetrathionate hydrolase from Acidithiobacillus ferrooxidans requires exposure to acidic conditions for proper folding. FEMS Microbiol Lett 309:43-47
51. Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Si B, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Otsuka R, Nakazawa H, Takamiya M, Kato Y, Yoshizawa T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, K-i A, Masuda S, Yanagii M, Nishimura M, Yamagishi A, Oshima T, Kikuchi H (2001) Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon, Sulfolobus tokodaii strain7. DNA Res 8:123-140
52. Kawashima T, Amano N, Koike H, Si M, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, Nunoshiba T, Yamamoto Y, Aramaki H, Makino K, Suzuki M (2000) Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci USA 97:14257-14262
53. Kondrat'eva T, Danilevich V, Ageeva S, Karavaiko G (2005) Identification of IS elements in Acidithiobacillus ferrooxidans strains grown in a medium with ferrous iron or adapted to elemental sulfur. Arch Microbiol 183:401-410
54. Kondrat'eva T, Danilevich V, Karavaiko G (2008) The primary structure and characteristics of the ISAfe600, an insertion sequence from Acidithiobacillus ferrooxidans strains. Mikrobiologiia 77:524-532
55. Kotze AA, Tuffin IM, Deane SM, Rawlings DE (2006) Cloning and characterization of the chromosomal arsenic resistance genes from Acidithiobacillus caldus and enhanced arsenic resistance on conjugal transfer of ars genes located on transposon TnAtcArs. Microbiology 152:3551-3560
56. Levican G, Ugalde JA, Ehrenfeld N, Maass A, Parada P (2008) Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9:581
57. Levicán G, Katz A, Valdés J, Quatrini R, Holmes DS, Orellana O (2009) A 300 Kb genome segment, including a complete set of tRNA genes, is dispensable for Acidithiobacillus ferrooxidans. Adv Mater Res 71-73:187-190
58. Lipps G (2006) Plasmids and viruses of the thermoacidophilic crenarchaeote Sulfolobus. Extremophiles 10:17-28
59. Lo I, Denef VJ, Ver Berkmoes NC, Shah MB, Goltsman D, Di Bartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature 446:537-541
60. Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Ver Berkmoes NC, Hettich RL, Banfield JF (2010) Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol Syst Biol 6
61. Navarro CA, Orellana LH, Mauriaca C, Jerez CA (2009) Transcriptional and functional studies of Acidithiobacillus ferrooxidans genes related to survival in the presence of copper. Appl Environ Microbiol 75:6102-6109
62. Oppon JC, Sarnovsky RJ, Craig NL, Rawlings DE (1998) A Tn7-like transposon is present in the glmUS region of the obligately chemoautolithotrophic bacterium Thiobacillus ferrooxidans. J Bacteriol 180:3007-3012
63. Osorio H, Martinez V, Nieto P, Holmes D, Quatrini R (2008a) Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility. BMC Microbiol 8:203
64. Osorio H, Martínez V, Veloso FA, Pedroso I, Valdés J, Jedlicki E, Holmes DS, Quatrini R (2008b) Iron homeostasis strategies in acidophilic iron oxidizers: studies in Acidithiobacillus and Leptospirillum. Hydrometallurgy 94:175-179
65. Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, Bowers J, Jarosz M, Milos PM (2009) Direct RNA sequencing. Nature 461:814-818
66. Parro V, Moreno-Paz M, González-Toril E (2007) Analysis of environmental transcriptomes by DNA microarrays. Environ Microbiol 9:453-464
67. Prangishvili D, Albers S-V, Holz I, Arnold HP, Stedman K, Klein T, Singh H, Hiort J, Schweier A, Kristjansson JK, Zillig W (1998) Conjugation in archaea: frequent occurrence of conjugative plasmids in sulfolobus. Plasmid 40:190-202
68. Prangishvili D, Stedman K, Zillig W (2001) Viruses of the extremely thermophilic archaeon Sulfolobus. Trends Microbiol 9:39-43
69. Prangishvili D, Forterre P, Garrett RA (2006) Viruses of the archaea: a unifying view. Nat Rev Micro 4:837-848
70. Quatrini R, Veloso F, Jedlicki E, Holmes DS (2004) Bioinformatic analysis of iron uptake in Acidithiobacillus ferrooxidans. In: Tsezos M, Hatzikioseyian A, Remoudaki E (eds) BioHydrometallurgy: a sustainable technology in evolution. National Technical University of Athens, Athens, pp 989-996
71. Quatrini R, Jedlicki E, Holmes DS (2005a) Genomic insights into the iron uptake mechanisms of the biomining microorganism Acidithiobacillus ferrooxidans. J Ind Microbiol Biotechnol 32:606-614
72. Quatrini R, Lefimil C, Holmes DS, Jedlicki E (2005b) The ferric iron uptake regulator (Fur) from the extreme acidophile Acidithiobacillus ferrooxidans. Microbiology 151:2005-2015 (Pubitemid 40909042)
73. Quatrini R, Lefimil C, Veloso F, Pedroso I (2007a) Bioinformatic prediction and experimental verification of Fur-regulated genes in the extreme acidophile Acidithiobacillus ferrooxidans. Nucleic Acids Res 35:2153-2166
74. Quatrini R, Martinez V, Osorio H, Veloso F, Pedroso I, Valdes J, Jedlicki E, Holmes DS (2007b) Iron homeostasis strategies in acidophilic iron oxidizers: comparative genome analysis. Adv Mater Res 20-21:439-442
75. Quatrini R, Valdes J, Jedlicki E, Holmes D (2007c) The use of bioinformatics and genome biology to advance our understanding of bioleaching microorganisms. In: Donati E, Sand W (eds) Microbial processing of metal sulfides. Springer, Netherlands, pp 221-239
76. Ram RJ, Ver Berkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC II, Shah M, Hettich RL, Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308:1915-1920
77. Rawlings DE (2005) The evolution of pTF-FC2 and pTC-F14, two related plasmids of the IncQ-family. Plasmid 53:137-147
78. Rawlings DE, Johnson DB (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology 153:315-324
79. Rawlings DE, Kusano T (1994) Molecular genetics of Thiobacillus ferrooxidans. Microbiol Mol Biol Rev 58:39-55
80. Redder P, Garrett RA (2006) Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol 188:4198-4206
81. Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci 106:8605-8610
82. Reysenbach A-L, Hamamura N, Podar M, Griffiths E, Ferreira S, Hochstein R, Heidelberg J, Johnson J, Mead D, Pohorille A, Sarmiento M, Schweighofer K, Seshadri R, Voytek MA (2009) Complete and draft genome sequences of six members of the aquificales. J Bacteriol 191:1992-1993
83. Rivas M, Seeger M, Holmes DS, Jedlicki E (2005) A Lux-like quorum sensing system in the extreme acidophile Acidithiobacillus ferrooxidans. Biological Res 38:283-297 (Pubitemid 41535629)
84. Rivas M, Seeger M, Jedlicki E, Holmes DS (2007) Second acyl homoserine lactone production system in the extreme acidophile Acidithiobacillus ferrooxidans. Appl Environ Microbiol 73:3225-3231
85. Ruepp A, Graml W, Santos-Martinez M-L, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN, Baumeister W (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407:508-513
86. Schippers A, Breuker A, Blazejak A, Bosecker K, Kock D, Wright TL (2010) The biogeochemistry and microbiology of sulfidic mine waste and bioleaching dumps and heaps, and novel Fe (II) - oxidizing bacteria. Hydrometallurgy (in press)
87. Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M (2000) Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. Proc Natl Acad Sci USA 97:3509-3514
88. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC-Y, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PMK, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835-7840 (Pubitemid 32642647)
89. Shmaryahu A, Holmes DS (2007) Discovery of small regulatory RNAs in the extremophile acidithiobacillus genus suggests novel genetic regulation. Adv Mater Res 20-21:535-538
90. Shmaryahu A, Lefimil C, Jedlicki E, Holmes DS (2009) Small regulatory RNA genes in Acidithiobacillus ferrooxidans: case studies of 6 S RNA and frr. Adv Mater Res 71-73:191-194
91. Siezen RJ, Wilson G (2009) Bioleaching genomics. Microb Biotechnol 2:297-303
92. Simmons SL, Di Bartolo G, Denef VJ, Goltsman DSA, Thelen MP, Banfield JF (2008) Population genomic analysis of strain variation in leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol 6: e177
93. Soulère L, Guiliani N, Queneau Y, Jerez C, Doutheau A (2008) Molecular insights into quorum sensing in Acidithiobacillus ferrooxidans bacteria via molecular modelling of the transcriptional regulator AfeR and of the binding mode of long-chain acyl homoserine lactones. J Mol Model 14:599-606
94. Tuffin IM, de Groot P, Deane SM, Rawlings DE (2005) An unusual Tn21-like transposon containing an ars operon is present in highly arsenic-resistant strains of the biomining bacterium Acidithiobacillus caldus. Microbiology 151:3027-3039
95. Tuffin IM, Hector SB, Deane SM, Rawlings DE (2006) Resistance determinants of a highly arsenic-resistant strain of Leptospirillum ferriphilum isolated from a commercial biooxidation tank. Appl Environ Microbiol 72:2247-2253
96. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43
97. Valdés JH, Holmes DS (2009) Genomic lessons from biomining organisms: case study of the acidithiobacillus genus. Adv Mater Res 71-73:215-218
98. Valdés J, Veloso F, Jedlicki E, Holmes D (2003) Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis. BMC Genomics 4:51
99. Valdés J, Pedroso I, Quatrini R, Dodson R, Tettelin H, Blake R, Eisen J, Holmes D (2008a) Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9:597
100. Valdés J, Pedroso I, Quatrini R, Holmes DS (2008b) Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: insights into their metabolism and ecophysiology. Hydrometallurgy 94:180-184
101. Valdés J, Quatrini R, Hallberg K, Mangold S, Dopson M, Valenzuela PTD, Holmes DS (2009) Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus. J Bacteriol 191:5877-5878
102. Valdés J, Osorio H, Lefimil C, Duarte F, Jedlicki E, Quatrini R, Holmes DS (2010) Comparative genomics begins to unravel the ecophysiology of bioleaching. Hydrometallurgy (in press)
103. Valenzuela L, Chi A, Beard S, Orell A, Guiliani N, Shabanowitz J, Hunt DF, Jerez CA (2006) Genomics, metagenomics and proteomics in biomining microorganisms. Biotechnol Adv 24:197-211
104. van Zyl LJ, Deane SM, Louw L-A, Rawlings DE (2008) Presence of a family of plasmids (29 to 65 Kilobases) with a 26-Kilobase common region in different strains of the sulfur-oxidizing bacterium Acidithiobacillus caldus. Appl Environ Microbiol 74:4300-4308
105. Ver Berkmoes NC, Denef VJ, Hettich RL, Banfield JF (2009) Systems biology: functional analysis of natural microbial consortia using community proteomics. Nat Rev Micro 7:196-205
106. Wächtershäuser G (1988) Before enzymes and templates: theory of surface metabolism. Microbiol Rev 52:452-484
107. Wächtershäuser G (2007) On the chemistry and evolution of the pioneer organism. Chem Biodivers 4:584-602
108. Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, De Boy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR (2009) Three genomes from the phylum acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046-2056
109. Whitaker RJ, Banfield JF (2006) Population genomics in natural microbial communities. Trends Ecol Evol 21:508-516
110. Wood AP, Aurikko JP, Kelly DP (2004) A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy? FEMS Microbiol Rev 28:335-352
111. Yamada T, Hiraoka Y, Das Gupta TK, Chakrabarty AM (2004) Rusticyanin, a bacterial electron transfer protein, causes G1 arrest in J774 and apoptosis in human cancer cells. Cell Cycle 3:1182-1187
112. Yates JR, Holmes DS (1987) Two families of repeated DNA sequences in Thiobacillus ferrooxidans. J Bacteriol 169:1861-1870
113. Zhao HL, Holmes DS (1993) Insertion sequence IST1 and associated phenotypic switching in Thiobacillus ferrooxidans. In: A. E. Torma, M. L. Apel, and C. L. Brierley (eds) Biohydrometallurgical technologies, TMS Press, Warrendale, PA, 2:667-671