Thermophiles in the genomic era: Biodiversity, science, and applications

Biotechnology Advances

Volumn 33, Issue 6, 2015, Pages 633-647

  Urbieta, M Sofía ^a   Donati, Edgardo R ^a   Chan, Kok Gan ^b   Shahar, Saleha ^c   Sin, Lee Li ^c   Goh, Kian Mau ^c  

^a Universidad Nacional de La Plata   (Argentina)

^b UNIVERSITY OF MALAYA   (Malaysia)

^c UNIVERSITI TEKNOLOGI MALAYSIA   (Malaysia)

Author keywords

Archaea; Biofuels; Biomining; Bioremediation; Extremophile; Hot spring; Metagenome; Microbiome; Thermophilic virus; Thermozyme

Indexed keywords

BIODIVERSITY; BIOFUELS; BIOREMEDIATION; COMPOSTING; GEOTHERMAL SPRINGS; HOT SPRINGS; VIRUSES;

ARCHAEA; BIOMINING; EXTREMOPHILES; METAGENOMES; MICROBIOME; THERMOZYMES;

GENES;

BIODIVERSITY; BIOFUEL; BIOME; BIOREMEDIATION; EXTREMOPHILE; GENOME; METABOLISM; SPATIAL DISTRIBUTION; THERMAL SPRING; THERMOPHILIC BACTERIUM; VIRUS;

AQUIFICAE; AQUIFICAE (CLASS); CRENARCHAEOTA; EURYARCHAEOTA; THERMOTOGAE; THERMOTOGAE (CLASS);

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; BIOFUEL; ENZYME;

ARCHAEON; BACTERIUM; BIOREMEDIATION; CHEMISTRY; ENZYMOLOGY; HEAT; METAGENOME; MICROBIOLOGY; SULFOLOBUS SOLFATARICUS;

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; BIOFUELS; ENZYMES; HOT TEMPERATURE; INDUSTRIAL MICROBIOLOGY; METAGENOME; SULFOLOBUS SOLFATARICUS;

EID: 84939267948     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2015.04.007     Document Type: Review

References (179)

1. Abdollahi H., Shafaei S.Z., Noaparast M., Manafi Z., Niemelä S.I., Tuovinen O.H. Mesophilic and thermophilic bioleaching of copper from a chalcopyrite-containing molybdenite concentrate. Int J Miner Process 2014, 128:25-32.
2. Abraham J., Gea T., Sánchez A. Substitution of chemical dehairing by proteases from solid-state fermentation of hair wastes. J Clean Prod 2014, 74:191-198.
3. Alakangas E., Valtanen J., Levlin J.-E. CEN technical specification for solid biofuels - Fuel specification and classes. Biomass Bioenergy 2006, 30:908-914.
4. Al-Maghrabi I.M., Aqil A.B., Islam M., Chaalal O. Use of thermophilic bacteria for bioremediation of petroleum contaminants. Energy Sources 1999, 17-29. Taylor & Francis.
5. Baker G.C., Gaffar S., Cowan D.A., Suharto A.R. Bacterial community analysis of Indonesian hot springs. FEMS Microbiol Lett 2001, 200:103-109.
6. Barabote R.D., Parales J.V., Guo Y.-Y., Labavitch J.M., Parales R.E., Berry A.M. Xyn10A, a thermostable endoxylanase from Acidothermus cellulolyticus 11B. Appl Environ Microbiol 2010, 76:7363-7366.
7. Barns S.M., Fundyga R.E., Jeffries M.W., Pace N.R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci 1994, 91:1609-1613.
8. Basen M., Rhaesa A.M., Kataeva I., Prybol C.J., Scott I.M., Poole F.L., et al. Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii. Bioresour Technol 2014, 152:384-392.
9. Becher D., Bernhardt J., Fuchs S., Riedel K. Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics 2013, 2895-2909. Wiley Online Library.
10. Bergquist L.P., W.Morgan H., Saul D. Selected enzymes from extreme thermophiles with applications in biotechnology. Curr Biotechnol 2014, 3:45-59.
11. Bhalla A., Bansal N., Kumar S., Bischoff K.M., Sani R.K. Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. Bioresour Technol 2013, 128:751-759.
12. Bhandiwad A., Guseva A., Lynd L. Metabolic engineering of Thermoanaerobacterium thermosaccharolyticum for increased n-Butanol production. Adv Microbiol 2013, 3:46-51.
13. Bharali P., Das S., Konwar B., Thakur A. Crude biosurfactant from thermophilic Alcaligenes faecalis: feasibility in petro-spill bioremediation. Int Biodeter Biodegr 2011, 65:682-690.
14. Blainey P.C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 2013, 37:407-427.
15. Bolduc B., Shaughnessy D.P., Wolf Y.I., Koonin E.V., Roberto F.F., Young M. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J Virol 2012, 86:5562-5573.
16. Boonyaratanakornkit B.B., Simpson A.J., Whitehead T.A., Fraser C.M., El-Sayed N., Clark D.S. Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. Environ Microbiol 2005, 7:789-797.
17. Borges N., Matsumi R., Imanaka T., Atomi H., Santos H. Thermococcus kodakarensis mutants deficient in di-myo-inositol phosphate use aspartate to cope with heat stress. J Bacteriol 2010, 192:191-197.
18. Bowen De León K., Gerlach R., Peyton B.M., Fields M.W. Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park. Front Microbiol 2013, 4:330.
19. Bowman B., Shin M.Y., Lee J.-E., Cho Y.-J., Chun J. Analysis of full-length metagenomic 16S genes by SMRT sequencing. Chem 2013, 4:C2.
20. Cai L., Ye L., Tong A.H.Y., Lok S., Zhang T. Biased diversity metrics revealed by bacterial 16S pyrotags derived from different primer sets. PLoS One 2013, 8:e53649.
21. Canganella F., Wiegel J. Anaerobic thermophiles. Life 2014, 4:77-104.
22. Chai Y.Y., Rahman R.N., Illias R.M., Goh K.M. Cloning and characterization of two new thermostable and alkalitolerant α-amylases from the Anoxybacillus species that produce high levels of maltose. J Ind Microbiol Biotechnol 2012, 39:731-741.
23. Chatterjee S., Bhattacharjee I., Chandra G. Biosorption of heavy metals from industrial waste water by Geobacillus thermodenitrificans. J Hazard Mater 2010, 175:117-125.
24. Chernyh N.A., Gavrilov S.N., Sorokin V.V., German K.E., Sergeant C., Simonoff M., et al. Characterization of technetium (vII) reduction by cell suspensions of thermophilic bacteria and archaea. Appl Microbiol Biotechnol 2007, 76:467-472.
25. Chistoserdova L. Is metagenomics resolving identification of functions in microbial communities?. Microb Biotechnol 2014, 7:1-4.
26. Costas G., Amaya M., Liu Z., Tomsho L.P., Schuster S.C., Ward D.M., et al. Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum acidobacteria. Environ Microbiol 2012, 14:177-190.
27. Davenport C.F., Tümmler B. Advances in computational analysis of metagenome sequences. Environ Microbiol 2013, 15:1-5.
28. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998, 392:353-358.
29. Deive F., Dominguez A., Barrio T., Moscoso F., Moran P., Longo M., et al. Decolorization of dye Reactive Black 5 by newly isolated thermophilic microorganisms from geothermal sites in Galicia (Spain). J Hazard Mater 2010, 182:735-742.
30. Dellas N., Lawrence C.M., Young M.J. A survey of protein structures from archaeal viruses. Life 2013, 3:118-130.
31. Deschavanne P., DuBow M.S., Regeard C. The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination. Virol J 2010, 7:163.
32. D'haeseleer P., Gladden J.M., Allgaier M., Chain P.S., Tringe S.G., Malfatti S.A., et al. Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PLoS One 2013, 8:e68465.
33. d'Hugues P., Foucher S., Galle-Cavalloni P., Morin D. Continuous bioleaching of chalcopyrite using a novel extremely thermophilic mixed culture. Int J Miner Process 2002, 66:107-119.
34. Dodsworth J.A., Blainey P.C., Murugapiran S.K., Swingley W.D., Ross C.A., Tringe S.G., et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 2013, 4:1854.
35. Donati E.R., Sand W. Microbial processing of metal sulfides 2007, Springer.
36. Eisenstein M. Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012, 30:295-296.
37. Elleuche S., Schröder C., Sahm K., Antranikian G. Extremozymes-biocatalysts with unique properties from extremophilic microorganisms. Curr Opin Biotechnol 2014, 29:116-123.
38. Empadinhas N., da Costa M.S. Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 2011, 13:2056-2077.
39. Falcicchio P., Wolterink-Van Loo S., Franssen M.C., van der Oost J. DHAP-dependent aldolases from (hyper) thermophiles: biochemistry and applications. Extremophiles 2014, 18:1-13.
40. Faria T.Q., Mingote A., Siopa F., Ventura R., Maycock C., Santos H. Design of new enzyme stabilizers inspired by glycosides of hyperthermophilic microorganisms. Carbohydr Res 2008, 343:3025-3033.
41. Fichot E.B., Norman R.S. Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome 2013, 1:10-14.
42. Fierer N., Leff J.W., Adams B.J., Nielsen U.N., Bates S.T., Lauber C.L., et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci 2012, 109:21390-21395.
43. Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 2005, 15:352-363.
44. Futterer O., Angelov A., Liesegang H., Gottschalk G., Schleper C., Schepers B., et al. Genome sequence of Picrophilus torridus and its implications for life around pH0. Proc Natl Acad Sci U S A 2004, 101:9091-9096.
45. Giaveno M.A., MSa Urbieta, Ulloa J.R., EGl Toril, Donati E.R. Physiologic versatility and growth flexibility as the main characteristics of a novel thermoacidophilic Acidianus strain isolated from Copahue geothermal area in Argentina. Microb Ecol 2013, 65:336-346.
46. Glass E.M., Wilkening J., Wilke A., Antonopoulos D., Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010, 5. [pdb.prot5368].
47. Glöckner J., Kube M., Shrestha P.M., Weber M., Glöckner F.O., Reinhardt R., et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ Microbiol 2010, 12:1218-1229.
48. Goh K.M., Chua Y.S., Abdul R.N.Z.R. A comparison of conventional and miniprimer PCR to elucidate bacteria diversity in Malaysia Ulu Slim hot spring using 16S rDNA clone library. Rom Biotechnol Lett 2011, 16:6247-6255.
49. Goh K.M., Kahar U.M., Chai Y.Y., Chong C.S., Chai K.P., Ranjani V., et al. Recent discoveries and applications of Anoxybacillus. Appl Microbiol Biotechnol 2013, 97:1475-1488.
50. Goh K.M., Gan H.M., Chan K.-G., Chan G.F., Shahar S., Chong C.S., et al. Analysis of Anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism. PLoS One 2014, 9:e90549.
51. Gorke B., Stulke J. Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 2008, 6:613-624.
52. Goulet A., Spinelli S., Blangy S., van Tilbeurgh H., Leulliot N., Basta T., et al. The thermo- and acido-stable ORF-99 from the archaeal virus AFV1. Protein Sci 2009, 18:1316-1320.
53. Gudiukait R., Gegeckas A., Kazlauskas D., Citavicius D. Influence of N-and/or C-terminal regions on activity, expression, characteristics and structure of lipase from Geobacillus sp. 95. Extremophiles 2014, 18:131-145.
54. Guerrero-Barajas C., Ordaz A., Garibay-Orijel C., García-Solares S.M., Bastida-González F., Zárate-Segura P.B. Enhanced sulfate reduction and trichloroethylene (TCE) biodegradation in a UASB reactor operated with a sludge developed from hydrothermal vents sediments: process and microbial ecology. Int Biodeterior Biodegradation 2014, 94:182-191.
55. Guo F., Ju F., Cai L., Zhang T. Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PLoS One 2013, 8:e76185.
56. Han Y., Agarwal V., Dodd D., Kim J., Bae B., Mackie R.I., et al. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus. J Biol Chem 2012, 287:34946-34960.
57. Hanreich A., Heyer R., Benndorf D., Rapp E., Pioch M., Reichl U., et al. Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass. Can J Microbiol 2012, 58:917-922.
58. Hawkes F.R., Hussy I., Kyazze G., Dinsdale R., Hawkes D.L. Continuous dark fermentative hydrogen production by mesophilic microflora: principles and progress. Int J Hydrog Energy 2007, 32:172-184.
59. Heine M., Chandra S.B. The linkage between reverse gyrase and hyperthermophiles: a review of their invariable association. J Microbiol 2009, 47:229-234.
60. Hickey D.A., Singer G. Genomic and proteomic adaptations to growth at high temperature. Genome Biol 2004, 5:117.
61. Hongoh Y., Yuzawa H., Ohkuma M., Kudo T. Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment. FEMS Microbiol Lett 2003, 221:299-304.
62. Hou W., Wang S., Dong H., Jiang H., Briggs B.R., Peacock J.P., et al. A comprehensive census of microbial diversity in hot springs of Tengchong, Yunnan Province China using 16S rRNA gene pyrosequencing. PLoS One 2013, 8:e53350.
63. Hreggvidsson O.G., Fridjonsson H.O., Petursdóttir K.S., Aevarsson A., Altenbuchner J., Fotheringham I., et al. Amyloenzymes captured by targetedmetagenomics. Carbohydr Bioeng 2011.
64. Hugenholtz P., Pitulle C., Hershberger K.L., Pace N.R. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998, 180:366-376.
65. Huson D.H., Auch A.F., Qi J., Schuster S.C. MEGAN analysis of metagenomic data. Genome Res 2007, 17:377-386.
66. Ilyas S. Lee J-c, Kim B-s. Bioremoval of heavy metals from recycling industry electronic waste by a consortium of moderate thermophiles: process development and optimization. J Clean Prod 2014, 70:194-202.
67. Inskeep W.P., Rusch D.B., Jay Z.J., Herrgard M.J., Kozubal M.A., Richardson T.H., et al. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 2010, 5:e9773.
68. Inskeep W.P., Jay Z.J., Tringe S.G., Herrgård M.J., Rusch D.B., Committee Y.M.P.S., et al. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front Microbiol 2013, 4:67-81.
69. Isenbarger T.A., Finney M., Ríos-Velázquez C., Handelsman J., Ruvkun G. Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol 2008, 74:840-849.
70. Jabbour D., Sorger A., Sahm K., Antranikian G. A highly thermoactive and salt-tolerant α-amylase isolated from a pilot-plant biogas reactor. Appl Microbiol Biotechnol 2013, 97:2971-2978.
71. Jiang B., Liang X., Chen Y., Ma T., Liu L., Li J., et al. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep 2012, 2:936.
72. Jiménez D.J., Andreote F.D., Chaves D., Montaña J.S., Osorio-Forero C., Junca H., et al. Structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the Colombian Andes. PLoS One 2012, 7:e52069.
73. Johnson D.B., Okibe N., Wakeman K., Yajie L. Effect of temperature on the bioleaching of chalcopyrite concentrates containing different concentrations of silver. Hydrometallurgy 2008, 94:42-47.
74. Jones E.J., Voytek M.A., Warwick P.D., Corum M.D., Cohn A., Bunnell J.E., et al. Bioassay for estimating the biogenic methane-generating potential of coal samples. Int J Coal Geol 2008, 76:138-150.
75. Joshi S., Bharucha C., Jha S., Yadav S., Nerurkar A., Desai A.J. Biosurfactant production using molasses and whey under thermophilic conditions. Bioresour Technol 2008, 99:195-199.
76. Kahar U.M., Chan K.-G., Salleh M.M., Hii S.M., Goh K.M. A high molecular-mass Anoxybacillus sp. SK3-4 amylopullulanase: characterization and its relationship in carbohydrate utilization. Int J Mol Sci 2013, 14:11302-11318.
77. Kang J., Park K.-M., Choi K.-H., Park C.-S., Kim G.-E., Kim D., et al. Molecular cloning and biochemical characterization of a heat-stable type I pullulanase from Thermotoga neapolitana. Enzyme Microb Technol 2011, 48:260-266.
78. Kataoka M., Yamaoka A., Kawasaki K., Shigeri Y., Watanabe K. Extraordinary denaturant tolerance of keratinolytic protease complex assemblies produced by Meiothermus ruber H328. Appl Microbiol Biotechnol 2014, 98:2973-2980.
79. Kembel S.W., Wu M., Eisen J.A., Green J.L. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol 2012, 8:e1002743.
80. Klindworth A., Pruesse E., Schweer T. Peplies Jr, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2012, 41:e1.
81. Kongjan P., Kotay M., Min B., Angelidaki I. Biohydrogen production from wheat straw hydrolysate by dark fermentation using extreme thermophilic mixed culture. Biotechnol Bioeng 2010, 105:899-908.
82. Kotelnikova S. Microbial production and oxidation of methane in deep subsurface. Earth Sci Rev 2002, 58:367-395.
83. Lasken R.S. Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 2012, 10:631-640.
84. Lavania M., Cheema S., Sarma P.M., Ganapathi R., Lal B. Methanogenic potential of a thermophilic consortium enriched from coal mine. Int Biodeter Biodegr 2014, 93:177-185.
85. Lee J., Lee C., Hugunin K., Maute C., Dysko R. Bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study. Water Res 2010, 44:5050-5058.
86. Lewin A., Wentzel A., Valla S. Metagenomics of microbial life in extreme temperature environments. Curr Opin Biotechnol 2013, 24:516-525.
87. Li C., Fang H.H. Fermentative hydrogen production from wastewater and solid wastes by mixed cultures. Crit Rev Environ Sci Technol 2007, 37:1-39.
88. Li S., Zhong H., Hu Y., Zhao J., He Z., Gu G. Bioleaching of a low-grade nickel-copper sulfide by mixture of four thermophiles. Bioresour Technol 2014, 153:300-306.
89. Lin L., Xu J. Dissecting and engineering metabolic and regulatory networks of thermophilic bacteria for biofuel production. Biotechnol Adv 2013, 31:827-837.
90. Lindahl B.D., Kuske C.R. Metagenomics for study of fungal ecology. The Ecological Genomics of Fungi 2013, 279-303. Wiley Online Library.
91. Liu Z., Klatt C.G., Wood J.M., Rusch D.B., Ludwig M., Wittekindt N., et al. Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat. ISME J 2011, 5:1279-1290.
92. Lü F., Bize A., Guillot A., Monnet V., Madigou C., Chapleur O., et al. Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME J 2014, 8:88-102.
93. Margesin R., Schinner F. Biodegradation and bioremediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol 2001, 56:650-663.
94. Marshall I.P., Blainey P.C., Spormann A.M., Quake S.R. A single-cell genome for Thiovulum sp. Appl Environ Microbiol 2012, 78:8555-8563.
95. McClendon S.D., Batth T., Petzold C.J., Adams P.D., Simmons B.A., Singer S.W. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels 2012, 5:1-10.
96. McLean J.S., Lombardo M.-J., Badger J.H., Edlund A., Novotny M., Yee-Greenbaum J., et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc Natl Acad Sci 2013, 110:E2390-E2399.
97. Millard A.D., Hands-Portman I., Zwirglmaier K. Morphotypes of virus-like particles in two hydrothermal vent fields on the East Scotia Ridge. Antarctia. Bacteriophage 2014, 4:e28732.
98. Meyer-Dombard D., Shock E., Amend J. Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology 2005, 3:211-227.
99. Mnif S., Chamkha M., Labat M., Sayadi S. Simultaneous hydrocarbon biodegradation and biosurfactant production by oilfield-selected bacteria. J Appl Microbiol 2011, 111:525-536.
100. Mnif S., Sayadi S., Chamkha M. Biodegradative potential and characterization of a novel aromatic-degrading bacterium isolated from a geothermal oil field under saline and thermophilic conditions. Int Biodeter Biodegr 2014, 86:258-264.
101. Mori H., Maruyama F., Kurokawa K. VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics 2010, 11:332-340.
102. Murakami S., Fujishima K., Tomita M., Kanai A. Metatranscriptomic analysis of microbes in an oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Appl Environ Microbiol 2012, 78:1015-1022.
103. Namiki T., Hachiya T., Tanaka H., Sakakibara Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 2012, 40:e155.
104. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H., et al. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399:323-329.
105. Novakova J., Farkasovsky M. Bioprospecting microbial metagenome for natural products. Biologia 2013, 68:1079-1086.
106. Nunoura T., Takaki Y., Kakuta J., Nishi S., Sugahara J., Kazama H., et al. Insights into the evolution of archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 2010, 39:3204-3223.
107. Ondov B.D., Bergman N.H., Phillippy A.M. Interactive metagenomic visualization in a web browser. BMC Bioinformatics 2011, 12:385-393.
108. Parisutham V., Kim T.H., Lee S.K. Feasibilities of consolidated bioprocessing microbes: from pretreatment to biofuel production. Bioresour Technol 2014, 161:431-440.
109. Parmar A., Singh N.K., Pandey A., Gnansounou E., Madamwar D. Cyanobacteria and microalgae: a positive prospect for biofuels. Bioresour Technol 2011, 102:10163-10172.
110. Peng Y., Leung H.C., Yiu S.-M., Chin F.Y. Meta-IDBA: a de novo assembler for metagenomic data. Bioinformatics 2011, 27:i94-i101.
111. Peng Y., Leung H.C., Yiu S.-M., Chin F.Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012, 28:1420-1428.
112. Pham V.H., Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol 2012, 30:475-484.
113. Plumb J.J., Haddad C.M., Gibson J.A., Franzmann P.D. Acidianus sulfidivorans sp. nov., an extremely acidophilic, thermophilic archaeon isolated from a solfatara on Lihir Island, Papua New Guinea, and emendation of the genus description. Int J Syst Evol Microbiol 2007, 57:1418-1423.
114. Podar M., Anderson I., Makarova K.S., Elkins J.G., Ivanova N., Wall M.A., et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 2008, 9:R158.
115. Pride D.T., Schoenfeld T. Genome signature analysis of thermal virus metagenomes reveals archaea and thermophilic signatures. BMC Genomics 2008, 9:420.
116. Purcell D., Sompong U., Yim L.C., Barraclough T.G., Peerapornpisal Y., Pointing S.B. The effects of temperature, pH and sulphide on the community structure of hyperthermophilic streamers in hot springs of northern Thailand. FEMS Microbiol Ecol 2007, 60:456-466.
117. Qin W., Yang C., Lai S., Wang J., Liu K., Zhang B. Bioleaching of chalcopyrite by moderately thermophilic microorganisms. Bioresour Technol 2013, 129:200-208.
118. Rastogi G., Muppidi G.L., Gurram R.N., Adhikari A., Bischoff K.M., Hughes S.R., et al. Isolation and characterization of cellulose-degrading bacteria from the deep subsurface of the Homestake gold mine, Lead, South Dakota, USA. J Ind Microbiol Biotechnol 2009, 36:585-598.
119. Rastogi G., Bhalla A., Adhikari A., Bischoff K.M., Hughes S.R., Christopher L.P., et al. Characterization of thermostable cellulases produced by Bacillus and Geobacillus strains. Bioresour Technol 2010, 101:8798-8806.
120. Raven N., Ladwa N., Cossar D., Sharp R. Continuous culture of the hyperthermophilic archaeum Pyrococcus furiosus. Appl Microbiol Biotechnol 1992, 38:263-267.
121. Roberts R.J., Carneiro M.O., Schatz M.C. The advantages of SMRT sequencing. Genome Biol 2013, 14:405.
122. Ruepp A., Graml W., Santos-Martinez M.-L., Koretke K.K., Volker C., Mewes H.W., et al. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 2000, 407:508-513.
123. Ryu H.-W., Yoo S.-K., Choi J.M., Cho K.-S., Cha D.K. Thermophilic biofiltration of H2S and isolation of a thermophilic and heterotrophic H2S-degrading bacterium, Bacillus sp. TSO3. J Hazard Mater 2009, 168:501-506.
124. Sabath N., Ferrada E., Barve A., Wagner A. Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biol Evol 2013, 5:966-977.
125. Santos H., Da Costa M.S. Compatible solutes of organisms that live in hot saline environments. Environ Microbiol 2002, 4:501-509.
126. Sar P., Kazy S.K., Paul D., Sarkar A. Metal bioremediation by thermophilic microorganisms. Thermophilic Microbes in Environmental and Industrial Biotechnology 2013, 171-201. Springer. 2nd ed.
127. Saranya P., Kumari H.S., Rao B.P., Sekaran G. Lipase production from a novel thermo-tolerant and extreme acidophile Bacillus pumilus using palm oil as the substrate and treatment of palm oil-containing wastewater. Environ Sci Pollut Res Int 2014, 21:3907-3919.
128. Satoh T., Watanabe K., Yamamoto H., Yamamoto S., Kurosawa N. Archaeal community structures in the Solfataric acidic hot springs with different temperatures and elemental compositions. Archaea 2013 2013.
129. Satyanarayana T., Littlechild J., Kawarabayasi Y. Thermophilic microbes in environmental and industrial biotechnology. biotechnology of thermophiles. 2013, Springer. 2nd ed.
130. Schoenfeld T., Patterson M., Richardson P.M., Wommack K.E., Young M., Mead D. Assembly of viral metagenomes from yellowstone hot springs. Appl Environ Microbiol 2008, 74:4164-4174.
131. Schoenfeld T., Liles M., Wommack K.E., Polson S.W., Godiska R., Mead D. Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol 2010, 18:20-29.
132. Schroder C., Elleuche S., Blank S., Antranikian G. Characterization of a heat-active archaeal β-glucosidase from a hydrothermal spring metagenome. Enzyme Microb Technol 2014, 57:48-54.
133. Sen S.K., Raut S., Dora T.K., Mohapatra P.K.D. Contribution of hot spring bacterial consortium in cadmium and lead bioremediation through quadratic programming model. J Hazard Mater 2014, 265:47-60.
134. Seshadri R., Kravitz S.A., Smarr L., Gilna P., Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol 2007, 5:e75.
135. Sharafi H., Abdoli M., Hajfarajollah H., Samie N., Alidoust L., Abbasi H., et al. First report of a lipopeptide biosurfactant from thermophilic bacterium Aneurinibacillus thermoaerophilus MK01 newly isolated from municipal landfill site. Appl Biochem Biotechnol 2014, 173:1236-1249.
136. Sharma V.K., Kumar N., Prakash T., Taylor T.D. MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets. Nucleic Acids Res 2009, 38:D468-D472.
137. Simon C., Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol 2011, 77:1153-1161.
138. Singer G.A., Hickey D.A. Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 2003, 317:39-47.
139. Sizova M., Izquierdo J., Panikov N., Lynd L. Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost. Appl Environ Microbiol 2011, 77:2282-2291.
140. Soliman N., Abdel-Fattah Y., Mostafa H.E., Gaballa A. Heterologous expression of thermostable esterase gene from Geobacillus thermoleovorans YN under different expression promoters. Int J Environ Sci Technol 2014, 11:119-126.
141. Somboonna N., Assawamakin A., Wilantho A., Tangphatsornruang S., Tongsima S. Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand. BMC Genomics 2012, 13:S29.
142. Staufenberger T., Imhoff J.F., Labes A. First crenarchaeal chitinase found in Sulfolobus tokodaii. Microbiol Res 2012, 167:262-269.
143. Stewart E.J. Growing unculturable bacteria. J Bacteriol 2012, 194:4151-4160.
144. Su X., Han Y., Dodd D., Moon Y.H., Yoshida S., Mackie R.I., et al. Reconstitution of a thermostable xylan-degrading enzyme mixture from the bacterium Caldicellulosiruptor bescii. Appl Environ Microbiol 2013, 79:1481-1490.
145. Swingley W.D., Meyer-Dombard D.R., Shock E.L., Alsop E.B., Falenski H.D., Havig J.R., et al. Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS One 2012, 7:e38108.
146. Tabak H.H., Lens P., van Hullebusch E.D., Dejonghe W. Developments in bioremediation of soils and sediments polluted with metals and radionuclides-1. Microbial processes and mechanisms affecting bioremediation of metal contamination and influencing metal toxicity and transport. Rev Environ Sci Biotechnol 2005, 4:115-156.
147. Takami H., Noguchi H., Takaki Y., Uchiyama I., Toyoda A., Nishi S., et al. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS One 2012, 7:e30559.
148. Talluri S., Raj S.M., Christopher L.P. Consolidated bioprocessing of untreated switchgrass to hydrogen by the extreme thermophile Caldicellulosiruptor saccharolyticus DSM 8903. Bioresour Technol 2013, 139:272-279.
149. Techtmann S.M., Colman A.S., Robb F.T. 'That which does not kill us only makes us stronger': the role of carbon monoxide in thermophilic microbial consortia. Environ Microbiol 2009, 11:1027-1037.
150. Thielemann T., Cramer B., Schippers A. Coalbed methane in the Ruhr Basin, Germany: a renewable energy resource?. Org Geochem 2004, 35:1537-1549.
151. Thomas T., Gilbert J., Meyer F. Metagenomics-a guide from sampling to data analysis. Microb Inform Exp 2012, 2:3.
152. Tirawongsaroj P., Sriprang R., Harnpicharnchai P., Thongaram T., Champreda V., Tanapongpipat S., et al. Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library. J Biotechnol 2008, 133:42-49.
153. Treangen T.J., Koren S., Sommer D.D., Liu B., Astrovskaya I., Ondov B., et al. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biol 2013, 14:R2.
154. Trivedi S., Rao S.R., Gehlot H.S. Nucleic acid stability in thermophilic prokaryotes: a review. J Mol Cell Biol 2005, 4:61-69.
155. Tsudome M., Deguchi S., Tsujii K., Ito S., Horikoshi K. Versatile solidified nanofibrous cellulose-containing media for growth of extremophiles. Appl Environ Microbiol 2009, 75:4616-4619.
156. Tu Q., Yu H., He Z., Deng Y., Wu L., Nostrand J.D., et al. GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 2014, 14:914-928.
157. Turnbaugh P.J., Gordon J.I. An invitation to the marriage of metagenomics and metabolomics. Cell 2008, 134:708-713.
158. Urbieta M.S., Rascovan N., Castro C., Revale S., Giaveno M.A., Vazquez M., et al. Draft genome sequence of the novel thermoacidophilic archaeon Acidianus copahuensis strain ALE1, isolated from the Copahue volcanic area in Neuquén, Argentina. Genome Announc 2014, 2:e00259-14.
159. Urbieta M.S., Toril E.G., Giaveno M.A., Bazan A.A., Donati E.R. Archaeal and bacterial diversity in five different hydrothermal ponds in the Copahue region in Argentina. Syst Appl Microbiol 2014, 37:429-441.
160. van Heel A.J., de Jong A., Montalbán-López M., Kok J., Kuipers O.P. BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic Acids Res 2013, 41:W448-W453.
161. Vartoukian S.R., Palmer R.M., Wade W.G. Strategies for culture of 'unculturable' bacteria. FEMS Microbiol Lett 2010, 309:1-7.
162. Vick T., Dodsworth J.A., Costa K., Shock E., Hedlund B.P. Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera. Geobiology 2010, 8:140-154.
163. Walther J., Sierocinski P., van der Oost J. Hot transcriptomics. Archaea 2011, 2010.
164. Wang S. Copper leaching from chalcopyrite concentrates. JOM 2005, 57:48-51.
165. Wang Q., Qian C., Zhang X.-Z., Liu N., Yan X., Zhou Z. Characterization of a novel thermostable β-glucosidase from a metagenomic library of termite gut. Enzyme Microb Technol 2012, 51:319-324.
166. Wang Y., Leung H.C., Yiu S.-M., Chin F.Y. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Bioinformatics 2012, 28:i356-i362.
167. Wang Z., Tong W., Wang Q., Bai X., Chen Z., Zhao J., et al. The temperature dependent proteomic analysis of Thermotoga maritima. PLoS One 2012, 7:e46463.
168. Wemheuer B., Taube R., Akyol P., Wemheuer F., Daniel R. Microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the Kamchatka Peninsula. Archaea 2013 2013, 136714.
169. Wilson M.S., Siering P.L., White C.L., Hauser M.E., Bartles A.N. Novel archaea and bacteria dominate stable microbial communities in North America's largest hot spring. Microb Ecol 2008, 56:292-305.
170. Woodward J., Orr M., Cordray K., Greenbaum E. Biotechnology: enzymatic production of biohydrogen. Nature 2000, 405:1014-1015.
171. Woyke T., Tighe D., Mavromatis K., Clum A., Copeland A., Schackwitz W., et al. One bacterial cell, one complete genome. PLoS One 2010, 5:e10314.
172. Wu D., Raymond J., Wu M., Chatterji S., Ren Q., Graham J.E., et al. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One 2009, 4:e4207.
173. Xia Y., Wang Y., Fang H.H., Jin T., Zhong H., Zhang T. Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis. Scientific reports 2014, 4. Nature Publishing Group.
174. Xie Y., Wu G., Tang J., Luo R., Patterson J., Liu S., et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 2014, 30:1660-1666.
175. Youssef N.H., Blainey P.C., Quake S.R., Elshahed M.S. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol 2011, 77:7804-7814.
176. Zeldovich K.B., Berezovsky I.N., Shakhnovich E.I. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 2007, 3:e5.
177. Zhaxybayeva O., Swithers K.S., Lapierre P., Fournier G.P., Bickhart D.M., DeBoy R.T., et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci 2009, 106:5865-5870.
178. Zhu Z., Tam T.K., Sun F., You C., Zhang Y.-H.P. A high-energy-density sugar biobattery based on a synthetic enzymatic pathway. Nat Commun 2014, 5:3026.
179. Zucko J., Fridjonsson H.O., Petursdottir K.S., Gacesa R., Diminic J., Long F.P., et al. Browsing metagenomes for novel starch and carbohydrate industry enzymes-AMYLOMICS case study. Curr Opin Biotechnol 2013, 245:521-527.