Emerging Fields in Functional Metagenomics and Its Industrial Relevance: Overcoming Limitations and Redirecting the Search for Novel Biocatalysts

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Volumn , Issue , 2011, Pages 481-498

  Perner, Mirjam ^a   Ilmberger, Nele ^a   Köhler, Hans Ulrich ^a   Chow, Jennifer ^a   Streit, Wolfgang R ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Metagenome bottleneck, novel biocatalysts; NC IUBMB, enzymes and reaction types; Novel biocatalysts from metagenomes

Indexed keywords

EID: 84877099041     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010549.ch47     Document Type: Chapter

References (153)

1. Afriat L, Roodveldt C, Manco G, Tawfik DS. 2006. The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry 45:13677-13686.
2. Aharoni A, Thieme K, Chiu CP, Buchini S, Lairson LL, et al. 2006. High-throughput screening methodology for the directed evolution of glycosyltransferases. Nat. Methods 3:609-614.
3. Alvarado B, Eduardo T. 2009. Recent patents in the use of peroxidases. Recent Pat. Biotechnol. 3:88-102.
4. Amann R, Ludwig W, Schleifer K-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Mol. Biol. Rev. 59:143-169.
5. Ando S, Ishida H, Kosugi Y, Ishikawa K. 2002. Hyperthermostable endoglucanase from Pyrococcus horikoshii. Appl. Environ. Microbiol. 68:430-433.
6. Aoshima M. 2007. Novel enzyme reactions related to the tricarboxylic acid cycle: Phylogenetic/functional implications and biotechnological applications. Appl. Microbiol. Biotechnol. 75:249-255.
7. Arai T, Matsuoka S, Cho H-Y, Yukawa H, Inui M, et al. 2007. Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation. Proc. Natl. Acad. Sci. USA 104:1456-1460.
8. Armstrong FA, Belsey NA, Cracknell JA, Goldet G, Parkin A, et al. 2009. Dynamic electrochemical investigations of hydrogen oxidation and production by enzymes and implications for future technology. Chem. Soc. Rev. 38:36-51.
9. Baneyx F. 1999. Recombinant protein expression in Escherichia coli. Curr. Opin. Biotechnol. 10:411-421.
10. Barri'ere F, Kavanagh P, Leech D. 2006. A laccase-glucose oxidase biofuel cell prototype operating in a physiological buffer. Electrochim. Acta 51:5187-5192.
11. B́ascones E, Imperial J, Ruiz-Arg ̈ ueso T, Palacios JM. 2000. Generation of new hydrogen-recycling Rhizobiaceae strains by introduction of a novel hup minitransposon. Appl. Environ. Microbiol. 66:4292-4299.
12. Beloqui A, Pita M, Polaina J, Martinez-Arias A, Golyshina OV, et al. 2006. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen-Biochemical properties, structural analysis, and phylogenetic relationships. J. Biol. Chem. 281:22933-22942.
13. Blokesch M, Magalon A, Bock A. 2001. Interplay between the specific chaperone-like proteins HybG and HypC in maturation of hydrogenases 1, 2, and 3 from Escherichia coli. J. Bacteriol. 183:2817-2822.
14. Böck AP, King PW, Blokesch M, Posewitz MC. 2006. Maturation of hydrogenases. Adv. Microb. Physiol. 51:1-71.
15. Boone JR, Ashby EC 1979 Reduction of cyclic and bicyclic ketones by complex metal hybrides. In Allinger NL, Eliel EL, eds. Topics in Stereochemistry. New York: John Wiley & Sons, pp. 53-95.
16. Brady SF, Chao CJ, Handelsman J, Clardy J. 2001. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org. Lett. 3:1981-1984.
17. Brennerova MV, Josefiova J, Brenner V, Pieper DH, Junca H. 2009. Metagenomics reveals diversity and abundance of metacleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ. Microbiol. 11:2216-2227.
18. Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, et al. 2009. Gene-centric metagenomics of the fiberadherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc. Natl. Acad. Sci. USA 106:1948-1953.
19. Bühler B, Schmidt A. 2004. Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization. J. Biotechnol. 113:183-210.
20. Buhrke T, Lenz O, Krauss N, Friedrich B. 2005. Oxygen tolerance of the H2-sensing [NiFe] Hydrogenase from Ralstonia eutropha H16 Is based on limited access of oxygen to the active site. J. Biol. Chem. 280:23791-23796.
21. Campbell BJ, Stein JL, Cary SC. 2003. Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete. Appl. Environ. Microbiol. 69:5070-5078.
22. Casalot L, Rousset M. 2001. Maturation of [NiFe] hydrogenases. Trends Microbiol. 9:228-237.
23. Chen IC, Lin WD, Hsu SK, Thiruvengadam V, Hsu WH. 2009. Isolation and characterization of a novel lysine racemase from a soil metagenomic library. Appl. Environ. Microbiol. 75:5161-5166.
24. Chen ZW, Liu YY, Wu JF, She Q, Jiang CY, et al. 2007. Novel bacterial sulfur oxygenase reductases from bioreactors treating goldbearing concentrates. Appl. Microbiol. Biotechnol. 74:688-698.
25. Chung JW, Webster DA, Pagilla KR, Stark BC. 2001. Chromosomal integration of the Vitreoscilla hemoglobin gene in Burkholderia and Pseudomonas for the purpose of producing stable engineered strains with enhanced bioremediating ability. J. Ind. Microbiol. Biotechnol. 27:27-33.
26. Cieslinski H, Dlugolecka A, Kur J, Turkiewicz M. 2009. An MTA phosphorylase gene discovered in the metagenomic library derived from Antarctic top soil during screening for lipolytic active clones confers strong pink fluorescence in the presence of rhodamine B. FEMS Microbiol. Lett. 299:232-240.
27. Collier AC, Tingle MD, Keelan JA, Paxton JW, Mitchell MD. 2000. A highly sensitive fluorescent microplate method for the determination of UDP-glucuronosyl transferase activity in tissues and placental cell lines. Drug Metab. Dispos. 28:1184-1186.
28. Cottrell MT, Waidner LA, L. Y, Kirchman DL. 2005. Bacterial diversity of metagenomic and PCR libraries from the Delaware River. Environ. Microbiol. 7:1883.1895.
29. Courtois S, Cappellano C, Ball M, Francou F-X, Normand P, et al. 2003. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl. Environ. Microbiol. 69:49-55.
30. Couto SR, Herrera JLT. 2006. Industrial and biotechnological applications of laccases: A review. Biotechnol. Adv. 24:500-513.
31. Craig JW, Chang FY, Brady SF. 2009. Natural products from environmental DNA hosted in Ralstonia metallidurans. ACS Chem. Biol. 4:23-28.
32. Davies G, Henrissat B. 1995. Structures and mechanisms of glycosyl hydrolases. Structure 3:853.
33. de Lorenzo V. 2005. Problems with metagenomic screening. Nat. Biotechnol. 23:1045-1046.
34. Elam CC, Padro CEG, Sandrock G, Luzzi A, Lindblad P, et al. 2003. Realizing the hydrogen future: The International Energy Agency's efforts to advance hydrogen energy technologies. Int. J. Hydrogen Energy 28:601-607.
35. Entcheva P, Liebl W, Johann A, Hartsch T, Streit WR. 2001. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl. Environ. Microbiol. 67:89-99.
36. Fang JM, Lin CH, Bradshaw CW, Wong CH. 1995. Enzymes in organic-synthesis-Oxidoreductions. J. Chem. Soc. Perkin Trans. 1:967-978.
37. Feng Y, Duan CJ, Pang H, Mo XC, Wu CF, et al. 2007. Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Appl. Microbiol. Biotechnol. 75:319-328.
38. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, dos Santos VAPM, et al. 2005. Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem. Biol. 12:895-904.
39. Ferrer M, Beloqui A, Timmis KN, Golyshin PN. 2009. Metagenomics for mining new genetic resources of microbial communities. J. Mol. Microbiol. Biotechnol. 16:109-123.
40. Fishman A, Tao Y, Rui LY, Wood TK. 2005. Controlling the regiospecific oxidation of aromatics via active site engineering of toluene para-monooxygenase of Ralstonia pickettii PKO1. J. Biol. Chem. 280:506-514.
41. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. 2005. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA 102:14683-14688.
42. Friedrich B, Friedrich CG, Meyer M, Schlegel HG. 1984. Expression of hydrogenase in Alcaligenes spp. is altered by interspecific plasmid exchange. J. Bacteriol. 158:331-333.
43. Gabor EM, Alkema WB, Janssen DB. 2004a. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ. Microbiol. 6:879-886.
44. Gabor EM, de Vries EJ, Janssen DB. 2004b. Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ. Microbiol. 6:948-958.
45. Gilbert HJ. 2007. Cellulosomes: Microbial nanomachines that display plasticity in quaternary structure. Mol. Microbiol. 63:1568-1576.
46. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359.
47. Grant S, Sorokin DY, Grant WD, Jones BE, Heaphy S. 2004. A phylogenetic analysis of Wadi el Natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. Extremophiles 8:421-429.
48. Guiral M, Aubert C, Guidici-Orticoni M-T. 2005. Hydrogen metabolism in the hyperthermophilic bacterium Aquifex aeolicus. Biochem. Soc. Trans. 33:22-24.
49. Guiral M, Trona P, Bellea V, Auberta C, Ĺegera C, et al. 2006. Hyperthermostable and oxygen resistant hydrogenases from a hyperthermophilic bacterium Aquifex aeolicus: Physicochemical properties. Int. J. Hydrogen Energy 31:1424-1431.
50. Gustafsson C, Govindarajan S, Minshull J. 2004. Codon bias and heterologous protein expression. Trends Biotechnol. 22:346-353.
51. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem. Biol. 5:245-249.
52. Healy FG, Ray RM, Aldrich HC, Wilkie AC, Ingram LO, et al. 1995. Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl. Microbiol. Biotechnol. 43:667-674.
53. Heath C, Hu XP, Cary SC, Cowan D. 2009. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil. Appl. Environ. Microbiol. 75:4657-4659.
54. Heinze T, Schwikal K, Barthel S. 2005. Ionic liquids as reaction medium in cellulose functionalization. Macromol. Biosci. 5:520-525.
55. Henning H, Leggewie C, Pohl M, Muller M, Eggert T, et al. 2006. Identification of novel benzoylformate decarboxylases by growth selection. Appl. Environ. Microbiol. 72:7510-7517.
56. Heuermann D, Haas R. 1998. A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation. Mol. Gen. Genet. 257:519-528.
57. Holmes AJ, Coleman NV. 2008. Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts. Antorie van Leeuwenhoek Int. J. Gen. Mol. Microbiol. 94:75-84.
58. Hu Y, Zhang G, Li A, Chen J, Ma L. 2008. Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach. Appl. Microbiol. Biotechnol. 80:823-830.
59. Hube M, Blokesch M, Bock A. 2002. Network of hydrogenase maturation in Escherichia coli: Role of accessory proteins HypA and HybF. J. Bacteriol. 184:3879-3885.
60. Hummel W. 1997. New alcohol dehydrogenases for the synthesis of chiral compounds. Adv. Biochem. Eng./Biotechnol. 58:145-184.
61. Hummel W. 1999. Large-scale applications of NAD(P)-dependent oxidoreductases: Recent developments. Trends Biotechnol. 17:487-492.
62. Inoue K, Makino Y, Itoh N. 2005. Purification and characterization of a novel alcohol dehydrogenase from Leifsonia sp. Strain S749: A promising biocatalyst for an asymmetric hydrogen transfer bioreduction. Appl. Environ. Microbiol. 71:3633-3641.
63. Jaeger KE, Eggert T. 2002. Lipases for biotechnology. Curr. Opin. Biotechnol. 13:390-397.
64. Jiang CJ, Shen PH, Yan B, Wu B. 2009. Biochemical characterization of a metagenome-derived decarboxylase. Enzyme Microb. Technol. 45:58-63.
65. Jiang CJ, Wu B. 2007. Molecular cloning and functional characterization of a novel decarboxylase from uncultured microorganisms. Biochem. Biophys. Res. Commun. 357:421-426.
66. Kazuoka T, Oikawa T, Muraoka I, Kuroda S, Soda K. 2007. A cold-active and thermostable alcohol dehydrogenase of a psychrotorelant from Antarctic seawater, Flavobacterium frigidimaris KUC-1. Extremophiles 11:257-267.
67. Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R. 2003a. Construction and screening of metagenomic libraries derived from enrichment cultures: Generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl. Environ. Microbiol. 69:1408-1416.
68. Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R. 2003b. Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J. Mol. Microbiol. Biotechnol. 39:1-16.
69. Kobayashi M, Shimizu S. 1994. Versatile nitrilases: Nitrilehydrolysing enzymes. FEMS Microbiol. Lett. 120:217-223.
70. Köhler U, Streit WR. Unpublished data.
71. Komori H, Miyazaki K, Higuchi Y. 2009a. Crystallization and preliminary X-ray diffraction analysis of a putative two-domain-type laccase from a metagenome. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65:264-266.
72. Komori H, Miyazaki K, Higuchi Y. 2009b. X-ray structure of a twodomain type laccase: A missing link in the evolution of multi-copper proteins. FEBS Lett. 583:1189-1195.
73. Kotlova EK, Chestukhina GG, Astaurova OB, Leonova TE, Yanenko AS, et al. 1999. Isolation and primary characterization of an amidase from Rhodococcus rhodochrous. Biochemistry (Moscow). 64:384-389.
74. Kourist R, Bartsch S, Fransson L, Hult K, Bornscheuer U. 2008. Understanding promiscuous amidase activity of an esterase from Bacillus subtilis. ChemBioChem 9:67-69.
75. Kunamneni A, Plou F, Ballesteros A, Alcalde M. 2008. Laccases and their applications: a patent review. Recent Pat. Biotechnol. 2:10-24.
76. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14:169-181.
77. Lenz O, Geliche A, Strack A, Freidrich B. 2005. Requirements for heterolgous production of a complex metalloenzyme: The membranebound [NiFe] hydrogenase. J. Bacteriol. 187:6590-6595.
78. Li Y, Wexler M, Richardson DJ, Bond PL, Johnston AW. 2005. Screening a wide host-range, waste-water metagenomic library in tryptophan auxotrophs of Rhizobium leguminosarum and of Escherichia coli reveals different classes of cloned trp genes. Environ. Microbiol. 7:1927-1936.
79. Lim HK, Chung EJ, Kim JC, Choi GJ, Jang KS, et al. 2005. Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli. Appl. Environ. Microbiol. 71:7768-7777.
80. Ludwig M, Cracknell JA, Vincent KA, Armstrong FA, Lenz O. 2009. Oxygen-tolerant H2 oxidation by membrane-bound [NiFe] hydrogenases of Ralstonia Species: Coping with low level H2 in air. J. Biol. Chem. 284:465-477.
81. Luzhetskyy A, Bechthold A. 2008. Features and applications of bacterial glycosyltransferases: Current state and prospects. Appl. Microbiol. Biotechnol. 80:945-952.
82. Lynd LR, Zhang Y. 2002. Quantitative determination of cellulase concentration as distinct from cell concentration in studies of microbial cellulose utilization: Analytical framework and methodological approach. Biotechnol. Bioeng. 77:467-475.
83. Maroti G, Tong Y, Yooseph S, Baden-Tillson H, Smith HO, et al. 2009. Discovery of [NiFe] hydrogenase genes in metagenomic DNA: Cloning and heterologous expression in Thiocapsa roseopersicina. Appl. Environ. Microbiol. 75:5821-5830.
84. Martinez A, Kolvek SJ, Yip CL, Hopke J, Brown KA, et al. 2004. Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl. Environ. Microbiol. 70:2452-2463.
85. May SW, Padgette SR. 1983. Oxidoreductase enzymes in biotechnology: Current status and future potential. Nat. Biotechnol. 1:677-686.
86. Mileni M, MacMillan F, Tziatzios C, Zwicker K, Haas A, et al. 2006. Heterologous production in Wolinella succinogenes and characterization of the quinol:fumarate reductase enzymes from Helicobacter pylori and Campylobacter jejuni. Biochem. J. 395:191-201.
87. Mingardon F, Perret S, Belaich A, Tardif C, Belaich J-P, et al. 2005. Heterologous Production, Assembly, and Secretion of a Minicellulosome by Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 71:1215-1222.
88. Murashima K, Chen CL, Kosugi A, Tamaru Y, Doi RH, et al. 2002. Heterologous production of Clostridium cellulovorans engB, using protease-deficient Bacillus subtilis, and preparation of active recombinant cellulosomes. J. Bacteriol. 184:76-81.
89. Nakagawa S, Takai K. 2008. Deep-sea vent chemoautotrophs: Diversity, biochemistry and ecological significance. FEMS Microbiol. Ecol. 65:1-14.
90. Northen TR, Lee JC, Hoang L, Raymond J, Hwang DR, et al. 2008. A nanostructure-initiator mass spectrometry-based enzyme activity assay. Proc. Nat. Acad. Sci. USA 105:3678-3683.
91. Novo C, Farnaud S, Tata Re, Clemente A, Brown PR. 2002. Support for a three-dimensional structure predicting a Cys-Glu-Lys catalytic triad for Pseudomonas aeruginosa amidase comes from site-directed mutagenesis and mutations altering substrate specificity. Biochem. J. 365:731-738.
92. Ogawa J, Shimizu S. 1999. Microbial enzymes: New industrial applications from traditional screening methods. Trends Biotechnol. 17:13-21.
93. Ouverney CC, Fuhrman JA. 2000. Marine planktonic archaea take up amino acids. Appl. Environ. Microbiol. 66:4829-4833.
94. Park S, Hanna L, Taylor RT, Droege MW. 2004. Batch cultivation of Methylosinus trichosporium OB3b. I: Production of soluble methane monooxygenase. Biotechnol. Bioeng. 38:423-433.
95. Park S-J, Kang C-H, Chae J-C, Rhee S-K. 2008. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol. Lett. 284:28-34.
96. Pathak G, Ehrenreich A, Losi A, Streit WR, G̈artner W. 2009. Novel blue light-sensitive proteins from a metagenomic approach. Environ. Microbiol. 11:2388-2399.
97. Pilone MS, Pollegioni L. 2002. D-Amino acid oxidase as an industrial biocatalyst. Biocatal. Biotransform. 20:145-159.
98. Polizeli ML, Rizzatti AC, Monti R, Terenzi HF, Jorge JA, et al. 2005. Xylanases from fungi: Properties and industrial applications. Appl. Microbiol. Biotechnol. 67:577-591.
99. Pollard DJ, Woodley JM. 2007. Biocatalysis for pharmaceutical intermediates: The future is now. Trends Biotechnol. 25:66-73.
100. Porthun A, Bernhard M, Friedrich B. 2002. Expression of a functional NAD-reducing [NiFe] hydrogenase from the gram-positive Rhodococcus opacus in the gram-negative Ralstonia eutropha. Arch. Microbiol. 177:159-166.
101. Pottk̈amper J, Barthen P, Ilmberger N, Schwaneberg U, Schenk A, et al. 2009. Applying metagenomics for the identification of bacterial cellulases that are stable in ionic liquids. Green Chem. 11:957-965.
102. Purdy D, Park S. 2006. Heterologous gene expression in Campylobacter coli: The use of bacterial luciferase in a promoter probe vector. FEMS Microbiol. Lett. 111:233-237.
103. Rajan SS, Yang X, Collart F, Yip VLY, Withers SG, et al. 2004. Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+-dependent phospho-±-glucosidase from Bacillus subtilis. Structure 12:1619.
104. Rashamuse K, Magomani V, Ronneburg T, Brady D. 2009. A novel family VIII carboxylesterase derived from a leachate metagenome library exhibits promiscuous beta-lactamase activity on nitrocefin. Appl. Microbiol. Biotechnol. 83:491-500.
105. Rees HC, Grant S, Jones B, Grant WD, Heaphy S. 2003. Detecting cellulase and esterase enzyme activities encoded by novel genes present in environmental DNA libraries. Extremophiles 7:415-421.
106. Reetz MT. 2002. Lipases as practical biocatalysts. Curr. Opin. Chem. Biol. 6:145-150.
107. Riaz K, Elmerich C, Moreira D, Raffoux A, Dessaux Y, et al. 2008. A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases. Environ. Microbiol. 10:560-570.
108. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, et al. 2008. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environ. Microbiol. 10:727-737.
109. Rondon MR, SR, Goodman R, Handelsman J. 1999. Toward functional genomics in bacteria: Analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc. Natl. Acad. Sci. USA 96:6451-6455.
110. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, et al. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
111. Rousset M, Magro V, Forget N, Guigliarelli B, Belaich J-P, et al. 1998. Heterologous expression of the Desulfovibrio gigas [NiFe] hydrogenase in Desulfovibrio fructosovorans MR400. J. Bacteriol. 180:4982-4986.
112. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5:398-431.
113. Schipper C, Hornung C, Bijtenhoorn P, Quitschau M, Grond S, et al. 2009. Metagenome-derived clones encoding two novel lactonase family proteins involved in biofilm inhibition in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 75:224-233.
114. Schmeisser C, Steele H, Streit WR. 2007. Metagenomics, biotechnology with non-culturable microbes. Appl. Microbiol. Biotechnol. 75:955-962.
115. Schwarz WH. 2001. The cellulosome and cellulose degradation by anaerobic bacteria. Appl. Microbiol. Biotechnol. 56:634-649.
116. Schwecke T, Aparicio JF, Molnar I, Konig A, Khaw LE, et al. 1995. The biosynthetic gene-cluster for the polyketide immunosuppressant Rapamycin. Proc. Natl. Acad. Sci. USA 92:7839-7843.
117. Sebat JL, Colwell F, Crawford R. 2003. Metagenomic profiling: microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 69:4927-4934.
118. Sharma S, Khan F, Qazi G. 2010. Molecular cloning and characterization of amylase from soil metagenomic library derived from Northwestern Himalayas. Appl. Microbiol. Biotechnol. 86(6):1821-1828.
119. Simon C, Daniel R. 2009. Achievements and new knowledge unraveled by metagenomic approaches. Appl. Microbiol. Biotechnol. 85:265-276.
120. Simon C, Herath J, Rockstroh S, Daniel R. 2009. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl. Environ. Microbiol. 75:2964-2968.
121. Singh J, Behal A, Singla N, Joshi A, Birbian N, et al. 2009. Metagenomics: Concept, methodology, ecological inference and recent advances. Biotechnol. J. 4:480-494.
122. Solbak AI, Richardson TH, McCann RT, Kline KA, Bartnek F, et al. 2005. Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric. J. Biol. Chem. 280:9431-9438.
123. Steele HL, Jaeger K-E, Daniel R, Streit WR. 2009. Advances in recovery of novel biocatalysts from metagenomes. J. Mol. Microbiol. Biotechnol. 16:25-37.
124. Suenaga H, Mizuta S, Miyazaki K. 2009a. The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome. FEMS Microbiol. Ecol. 69:472-480.
125. Suenaga H, Yoshinori K, Masatoshi M, Ryo M, Hirokazu Y, et al. 2009b. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 3:1335-1348.
126. Swatloski RP, Spear SK, Holbrey JD, Rogers RD. 2002. Dissolution of cellulose [correction of cellose] with ionic liquids. J. Am. Chem. Soc. 124:4974-4975.
127. Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, et al. 2005. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl. Environ. Microbiol. 71:7310-7320.
128. Tee KL, Schwaneberg U. 2007. Directed evolution of oxygenases: Screening systems, success stories and challenges. Comb. Chem. High Throughput Screening 10:197-217.
129. Terwisscha van Scheltinga AC, Armand S, Kalk KH, Isogai A, Henrissat B, et al. 1995. Stereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and x-ray structure of a complex with allosamidin evidence for substrate assisted catalysis. Biochemistry 34:15619.
130. Turner MB, Spear SK, Huddleston JG, Holbrey JD, Rogers RD. 2003. Ionic liquid salt-induced inactivation and unfolding of cellulase from Trichoderma reesei. Green Chem. 5:443-447.
131. Uchiyama T, Abe T, Ikemura T, Watanabe K. 2005. Substrateinduced gene expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 23:88-93.
132. Ullrich R, Nuske J, Scheibner K, Spantzel J, Hofrichter M. 2004. Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Appl. Environ. Microbiol. 70:4575-4581.
133. Umeda F, Min H, Urushihara M, Okazaki M, Miura Y. 1986. Conjugal transfer of hydrogen-oxidizing ability of Alcaligenes hydrogenophilus to Pseudomonas oxalaticus. Biochem. Biophys. Res. Commun. 137:108-113.
134. Urlacher VB, Eiben S. 2006. Cytochrome P450 monooxygenases: perspectives for synthetic application. Trends Biotechnol. 24:324-330.
135. Urlacher VB, Schmid RD. 2006. Recent advances in oxygenasecatalyzed biotransformations. Curr. Opin. Chem. Biol. 10:156-161.
136. van Beilen JB, Duetz WA, Schmid A, Witholt B. 2003. Practical issues in the application of oxygenases. Trends Biotechnol. 21:170-177.
137. van Elsas J, Costa R, Jansson J, Sjöling S, Bailey M, et al. 2008. The metagenomics of disease-suppressive soils-experiences from the METACONTROL project. Trends Biotechnol. 26:591-601.
138. van Hellemond EW, Janssen DB, Fraaije MW. 2007. Discovery of a novel styrene monooxygenase originating from the metagenome. Appl. Environ. Microbiol. 73:5832-5839.
139. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
140. Vignais PM, Billoud B. 2007. Occurrence, classification, and biological function of hydrogenases: An overview. Chem. Rev. 107:4206-4272.
141. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger K-E, et al. 2003. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69:6235-6242.
142. Voget S, Steele HL, Streit WR. 2006. Characterization of a metagenome-derived halotolerant cellulase. J. Biotechnol. 126:26-36.
143. Wang F, Zhoub H, Mengc J, Pengb X, Jianga L, et al. 2009. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl. Acad. Sci. USA 106:4840-4845.
144. Wang GY, Graziani E, Waters B, Pan W, Li X, et al. 2000. Novel natural products from soil DNA libraries in a Streptomycete host. Org. Lett. 2:2401-2404.
145. Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, et al. 2007. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:560-565.
146. Wexler M, Bond PL, Richardson DJ, Johnston AWB. 2005. A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase. Environ. Microbiol. 7:1917-1926.
147. Williamson L, Borlee B, Schloss P, Guan C, Allen H, et al. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl. Environ. Microbiol. 71:6335-6344.
148. Wu J, Zhang J, Zhang H, He J, Ren Q, et al. 2004. Homogeneous acetylation of cellulose in a new ionic liquid. Biomacromolecules 5:266-268.
149. Yang M, Brazier M, Edwards R, Davis BG. 2005. High-throughput mass-spectrometry monitoring for multisubstrate enzymes: Determining the kinetic parameters and catalytic activities of glycosyltransferases. ChemBioChem. 6:346-357.
150. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. 2007. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 5:e16.
151. Yun J, Kang S, Park S, Yoon H, Kim MJ, et al. 2004. Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl. Environ. Microbiol. 70:7229-7235.
152. Zaballos M, Lopez-Lopez A, Ovreas L, Bartual SG, D'Auria G, et al. 2006. Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbiol. Ecol. 56:389-405.
153. Zhang YH, Lynd LR. 2004. Toward an aggregated understanding of enzymatic hydrolysis of cellulose: Noncomplexed cellulase systems. Biotechnol. Bioeng. 88:797-824.