Abstract
In the present there is a great necessity of suitable biocatalysts with high process performance, as a “greener” complementary alternative to the chemical synthesis. It is expected that in the coming decade, up to 40% of bulk chemical synthesis processes could be substituted by enzymatic catalysis. The identification and optimization of an appropriate enzyme represent important requirements to obtain a successful and efficient enzymatic process. In this context, the establishment of enzymatic processes in the industry is mainly a problem of finding and optimizing new enzymes. In this sense, nature is the richest reservoir from which enzymes can be isolated because they are continuously changing and evolving as a consequence of natural processes of selection. We are now taking advantages of sequencing and extensive screening technologies to develop enzyme discovery strategies and to identify microbial enzymes with improved and unusual activities and specificities. These approaches, in combination with modern protein engineering methods and distinct combinatorial and rational methods, will increase our chances to generate new stabilized biocatalysts that fit industrial requirements. Here, we review the methodologies, obstacles, and solving problems around metagenomics investigations to screen for enzymes with activities of interest.
References
Adrio JL, Demain AL (2014) Microbial enzymes: tools for biotechnological processes. Biomolecules 4(1):117–139. doi:10.3390/biom4010117
Agresti JJ, Antipov E, Abate AR, Ahn K, Rowat AC, Baret J-C et al (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci 107(9):4004–4009. doi:10.1073/pnas.0910781107
Araújo R, Casal M, Cavaco-Paulo A (2008) Application of enzymes for textile fibres processing. Biocatal Biotransform 26(5):332–349. doi:10.1080/10242420802390457
Atomi H, Sato T, Kanai T (2011) Application of hyperthermophiles and their enzymes. Curr Opin Biotechnol 22(5):618–626. doi:10.1016/j.copbio.2011.06.010
Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D et al (2015) Degradation network reconstruction in uric acid and ammonium amendments in oil-degrading marine microcosms guided by metagenomic data. Front Microbiol 6:1270. doi:10.3389/fmicb.2015.01270
Béjà O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP et al (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (New York, NY) 289(5486):1902–1906. doi:10.1126/science.289.5486.1902
Bell PJL, Sunna A, Curach NC, Bergquist PL, Gibbs MD, Nevalainen H (2002) Prospecting for novel lipase genes using PCR a. Microbiology 148(8):2283–2291. doi:10.1099/00221287-148-8-2283
Bérdy J (2005) Bioactive microbial metabolites. J Antibiot 58(1):1–26. doi:10.1038/ja.2005.1
Bergquist PL, Hardiman EM, Ferrari BC, Winsley T (2009) Applications of flow cytometry in environmental microbiology and biotechnology. Extremophiles . doi:10.1007/s00792-009-0236-4 Springer Japan
Blanco L, Bernad A, Lázaro JM, Martín G, Garmendia C, Salas M (1989) Highly efficient DNA synthesis by the phage phi29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264(15):8935–8940
Bommarius AS, Paye MF, Bornscheuer UT, Pohl M, Lutz S, Ma SK et al (2013) Stabilizing biocatalysts. Chem Soc Rev 42(15):6534. doi:10.1039/c3cs60137d
Bornscheuer UT, Huisman GW, Kazlauskas RJ, Lutz S, Moore JC, Robins K (2012) Engineering the third wave of biocatalysis. Nature 485(7397):185–194. doi:10.1038/nature11117
Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, Hutchison JB et al (2009) Droplet microfluidic technology for single-cell high-throughput screening. Proc Natl Acad Sci 106(34):14195–14200. doi:10.1073/pnas.0903542106
Brzostowicz PC, Walters DM, Thomas SM, Nagarajan V, Rouvière PE (2003) mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species. Appl Environ Microbiol 69(1):334–342
Chen I-C, Thiruvengadam V, Lin W-D, Chang H-H, Hsu W-H (2010) Lysine racemase: a novel non-antibiotic selectable marker for plant transformation. Plant Mol Biol 72(1–2):153–169. doi:10.1007/s11103-009-9558-y
Cheng J, Pinnell L, Engel K, Neufeld JD, Charles TC (2014) Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. J Microbiol Methods 99:27–34. doi:10.1016/j.mimet.2014.01.015
Cherry JR, Fidantsef AL (2003) Directed evolution of industrial enzymes: an update. Curr Opin Biotechnol 14(4):438–443. doi:10.1016/S0958-1669(03)00099-5
Coll-Lladó M, Acinas SG, Pujades C, Pedrós-Alió C (2011) Transcriptome fingerprinting analysis: an approach to explore gene expression patterns in marine microbial communities. PLoS ONE 6(8):e22950. doi:10.1371/journal.pone.0022950
Craig JW, Chang F-Y, Kim JH, Obiajulu SC, Brady SF (2010) Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl Environ Microbiol 76(5):1633–1641. doi:10.1128/AEM.02169-09
Curtis TP, Sloan WT (2005) Microbiology. Exploring microbial diversity – a vast below. Science (New York, NY) 309(5739):1331–1333. doi:10.1126/science.1118176
Davis BG, Boyer V (2001) Biocatalysis and enzymes in organic synthesis. Nat Prod Rep 18(6): 618–640.
de Carvalho CCCR (2011) Enzymatic and whole cell catalysis: finding new strategies for old processes. Biotechnol Adv 29(1):75–83. doi:10.1016/j.biotechadv.2010.09.001
de Carvalho CCCR (2016) Whole cell biocatalysts: essential workers from nature to the industry. Microb Biotechnol. doi:10.1111/1751-7915.12363
Demain AL, Adrio JL (2008) Contributions of microorganisms to industrial biology. Mol Biotechnol 38(1):41–55. doi:10.1007/s12033-007-0035-z
Fernández-Arrojo L, Guazzaroni M-E, López-Cortés N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21(6):725–733. doi:10.1016/j.copbio.2010.09.006
Ferrer M, Martínez-Abarca F, Golyshin PN (2005a) Mining genomes and “metagenomes” for novel catalysts. Curr Opin Biotechnol 16(6):588–593. doi:10.1016/j.copbio.2005.09.001
Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Martins dos Santos VAP, Yakimov MM et al (2005b) Microbial enzymes mined from the urania deep-sea hypersaline anoxic basin. Chem Biol 12(8):895–904. doi:10.1016/j.chembiol.2005.05.020
Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Dos Santos VAPM et al (2005c) Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol 7(12):1996–2010. doi:10.1111/j.1462-2920.2005.00920.x
Ferrer M, Golyshina O, Beloqui A, Golyshin PN (2007) Mining enzymes from extreme environments. Curr Opin Microbiol 10(3):207–214. doi:10.1016/j.mib.2007.05.004
Ferrer M, Beloqui A, Timmis KN, Golyshin PN (2009) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16(1–2):109–123. doi:10.1159/000142898
Ferrer M, Beloqui A, Golyshin PN (2010) Screening metagenomic libraries for laccase activities. Methods Mol Biol (Clifton, NJ) 668:189–202. doi:10.1007/978-1-60761-823-2_13
Ferrer M, Bargiela R, Martínez-Martínez M, Mir J, Koch R, Golyshina OV, Golyshin PN (2015) Biodiversity for biocatalysis: a review of the α/β-hydrolase fold superfamily of esterases-lipases discovered in metagenomes. Biocat Biotransform 33(5–6):235–249. doi:10.3109/10242422.2016.1151416
Ferrer M, Martínez-Martínez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 9(1):22–34. doi:10.1111/1751-7915.12309
Gabor EM, de Vries EJ, Janssen DB (2004) 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(9):948–958. doi:10.1111/j.1462-2920.2004.00643.x
Gabor E, Liebeton K, Niehaus F, Eck J, Lorenz P (2007) Updating the metagenomics toolbox. Biotechnol J 2(2):201–206. doi:10.1002/biot.200600250
Galvão TC, Mohn WW, de Lorenzo V (2005) Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol 23(10):497–506. doi:10.1016/j.tibtech.2005.08.002
Ge J, Lu D, Liu Z, Liu Z (2009) Recent advances in nanostructured biocatalysts. Biochem Eng J 44(1):53–59. doi:10.1016/j.bej.2009.01.002
Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S (2010) METAREP: JCVI metagenomics reports – an open source tool for high-performance comparative metagenomics. Bioinformatics (Oxford, England) 26(20):2631–2632. doi:10.1093/bioinformatics/btq455
Golyshina OV, Lünsdorf H, Kublanov IV, Goldenstein NI, Hinrichs KU, Golyshin PN (2016) The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. Nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales. Int J Syst Evol Microbiol 66(1):332–340. doi:10.1099/ijsem.0.000725
Gomes J, Steiner W (2004) The biocatalytic potential of extremophiles and extremozymes. Food Technol Biotechnol 42(4):223–225
Gomes I, Gomes J, Steiner W (2003) Highly thermostable amylase and pullulanase of the extreme thermophilic eubacterium Rhodothermus marinus: production and partial characterization. Bioresour Technol 90(2):207–214. doi:10.1016/S0960-8524(03)00110-X
Gong J-S, Lu Z-M, Li H, Zhou Z-M, Shi J-S, Xu Z-H (2013) Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases. Appl Microbiol Biotechnol 97(15):6603–6611. doi:10.1007/s00253-013-4932-8
Guo Z, Xu X (2005) New opportunity for enzymatic modification of fats and oils with industrial potentials. Org Biomol Chem 3(14):2615–2619. doi:10.1039/b506763d
Gupta R, Beg Q, Lorenz P (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbiol Biotechnol 59(1):15–32. doi:10.1007/s00253-002-0975-y
Gupta R, Gupta N, Rathi P (2004) Bacterial lipases: an overview of production, purification and biochemical properties. Appl Microbiol Biotechnol . doi:10.1007/s00253-004-1568-8Springer-Verlag
Gurung N, Ray S, Bose S, Rai V (2013) A broader view: microbial enzymes and their relevance in industries, medicine, and beyond. Biomed Res Int . doi:10.1155/2013/329121Hindawi Publishing Corporation
Gustafsson H, Küchler A, Holmberg K, Walde P, Mateo C, Palomo JM et al (2015) Co-immobilization of enzymes with the help of a dendronized polymer and mesoporous silica nanoparticles. J Mater Chem B 3(30):6174–6184. doi:10.1039/C5TB00543D
Hallin PF, Binnewies TT, Ussery DW, Fleischmann RD, Adams MD, White O et al (2008) The genome BLASTatlas – a GeneWiz extension for visualization of whole-genome homology. Mol BioSyst 4(5):363. doi:10.1039/b717118h
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev: MMBR 68(4):669–685. doi:10.1128/MMBR.68.4.669-685.2004
Harrington ED, Singh AH, Doerks T, Letunic I, von Mering C, Jensen LJ et al (2007) Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci U S A 104(35):13913–13918. doi:10.1073/pnas.0702636104
He Z, Deng Y (2012) Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 23(1):49–55. doi:10.1016/j.copbio.2011.11.001
Herbert RA (1992) A perspective on the biotechnological potential of extremophiles. Trends Biotechnol 10:395–402. doi:10.1016/0167-7799(92)90282-Z
Hess M (2008) Thermoacidophilic proteins for biofuel production. Trends Microbiol 16(9):414–419. doi:10.1016/j.tim.2008.06.001
Hjort K, Bergström M, Adesina MF, Jansson JK, Smalla K, Sjöling S (2010) Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil. FEMS Microbiol Ecol 71(2):197–207. doi:10.1111/j.1574-6941.2009.00801.x
Hosokawa M, Hoshino Y, Nishikawa Y, Hirose T, Yoon DH, Mori T et al (2015) Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes. Biosens Bioelectron 67:379–385. doi:10.1016/j.bios.2014.08.059
Hough DW, Danson MJ (1999) Extremozymes. Curr Opin Chem Biol 3(1):39–46. doi:10.1016/S1367-5931(99)80008-8
Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E et al (2008) High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol 26(9):1029–1034. doi:10.1038/nbt.1488
Kazimierczak KA, Scott KP, Kelly D, Aminov RI (2009) Tetracycline resistome of the organic pig gut. Appl Environ Microbiol 75(6):1717–1722. doi:10.1128/AEM.02206-08
Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD (2010) Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics 10(4):687–699. doi:10.1002/pmic.200900519
Klibanov AM (2001) Improving enzymes by using them in organic solvents. Nature 409(6817):241–246. doi:10.1038/35051719
Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) 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 5(1):46–56 doi:68724
Kodzius R (2016) Single-cell technologies in environmental omics. Gene 576(2):701–707. doi:10.1016/j.gene.2015.10.031
Koeller KM, Wong C-H (2001) Enzymes for chemical synthesis. Nature 409(6817):232–240. doi:10.1038/35051706
Kumar L, Awasthi G, Singh B (2011) Extremophiles: a novel source of industrially important enzymes. Biotechnology 10(2):121–135. doi:10.3923/biotech.2011.121.135
Kumar V, Marín-Navarro J, Shukla P (2016) Thermostable microbial xylanases for pulp and paper industries: trends, applications and further perspectives. World J Microbiol Biotechnol . doi:10.1007/s11274-015-2005-0Springer Netherlands
Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT et al (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 12(8):e1001920. doi:10.1371/journal.pbio.1001920
Lam KN, Charles TC (2015) Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries. Microbiome 3:22. doi:10.1186/s40168-015-0086-5
Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC (2015) Current and future resources for functional metagenomics. Front Microbiol 6:1196. doi:10.3389/fmicb.2015.01196
Lei C, Shin Y, Liu J, Ackerman EJ (2002) Entrapping enzyme in a functionalized nanoporous support. J Am Chem Soc 124(38):11242–11243. doi:10.1021/ja026855o
Liang P, Averboukh L, Pardee AB (1993) Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization. Nucleic Acids Res 21(14):3269–3275
Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T et al (2014) Alternative hosts for functional (meta)genome analysis. Appl Microbiol Biotechnol . doi:10.1007/s00253-014-5961-7Springer Berlin Heidelberg
Liu M, Dai X, Guan R, Xu X (2014) Immobilization of Aspergillus niger xylanase A on Fe3O4-coated chitosan magnetic nanoparticles for xylooligosaccharide preparation. Catal Commun 55:6. doi:10.1016/j.catcom.2014.06.002
Loeschcke A, Markert A, Wilhelm S, Wirtz A, Rosenau F, Jaeger K-E, Drepper T (2013) TREX: a universal tool for the transfer and expression of biosynthetic pathways in bacteria. ACS Synth Biol 2(1):22–33. doi:10.1021/sb3000657
Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nature 3:510–516. doi:10.1038/nrmicro1161
Madern D, Ebel C, Zaccai G (2000) Halophilic adaptation of enzymes. Extremophiles Life Under Extreme Cond 4(2):91–98
Méndez-García C, Peláez AI, Mesa V, Sánchez J, Golyshina OV, Ferrer M (2015) Microbial diversity and metabolic networks in acid mine drainage habitats. Front Microbiol 6:475. doi:10.3389/fmicb.2015.00475
Meyer F, Paarmann D, D’Souza M, Olson R, Glass E, Kubal M et al (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinforma 9(1):386. doi:10.1186/1471-2105-9-386
Mirete S, de Figueras CG, Gonzalez-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73(19):6001–6011. doi:10.1128/AEM.00048-07
Mitidieri S, Souza Martinelli AH, Schrank A, Vainstein MH (2006) Enzymatic detergent formulation containing amylase from Aspergillus niger: a comparative study with commercial detergent formulations. Bioresour Technol 97(10):1217–1224. doi:10.1016/j.biortech.2005.05.022
Monsan P, O’Donohue MJ (2010) In: Soetaert W, Vandamme EJ (eds) Industrial biotechnology in the food and feed sector. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. doi:10.1002/9783527630233
Mori T, Kamei I, Hirai H, Kondo R (2014) Identification of novel glycosyl hydrolases with cellulolytic activity against crystalline cellulose from metagenomic libraries constructed from bacterial enrichment cultures. Springer Plus 3:365. doi:10.1186/2193-1801-3-365
Neufeld JD, Chen Y, Dumont MG, Murrell JC (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10(6):1526–1535. doi:10.1111/j.1462-2920.2008.01568.x
Nguyen D, Zhang X, Jiang Z-H, Audet A, Paice MG, Renaud S, Tsang A (2008) Bleaching of kraft pulp by a commercial lipase: accessory enzymes degrade hexenuronic acids. Enzym Microb Technol 43(2):130–136. doi:10.1016/j.enzmictec.2007.11.012
Park S-J, Kang C-H, Chae J-C, Rhee S-K, Allgaier M, Uphoff H et al (2008) Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol Lett 284(1):28–34. doi:10.1111/j.1574-6968.2008.01180.x
Phale PS, Basu A, Majhi PD, Deveryshetty J, Vamsee-Krishna C, Shrivastava R (2007) Metabolic diversity in bacterial degradation of aromatic compounds. OMICS: J Integr Biol 11(3):252–279. doi:10.1089/omi.2007.0004
Placido A, Hai T, Ferrer M, Chernikova TN, Distaso M, Armstrong D et al (2015) Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase. Appl Microbiol Biotechnol 99:10031–10046. doi:10.1007/s00253–015-6873-x
Popovic A, Tchigvintsev A, Tran H, Chernikova TN, Golyshina OV, Yakimov MM et al (2015) Metagenomics as a tool for enzyme discovery: hydrolytic enzymes from marine-related metagenomes. Adv Exp Med Biol 883:1–20. doi:10.1007/978-3-319-23603-2_1
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403(6770):646–649. doi:10.1038/35001054
Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC et al (2005) Community proteomics of a natural microbial biofilm. Science (New York, NY) 308(5730):1915–1920. doi:10.1126/science. 1109070
Riesenfeld CS, Goodman RM, Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6(9):981–989. doi:10.1111/j.1462-2920.2004.00664.x
Rinke C, Lee J, Nath N, Goudeau D, Thompson B, Poulton N et al (2014) Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics. Nat Protoc 9(5):1038–1048. doi:10.1038/nprot.2014.067
Sabree ZL, Rondon MR., Handelsman J (2009) Metagenomics. In: Schaechter M (ed), Encyclopedia of microbiology, 3rd ed. Amsterdam, the Netherlands, Elsevier Academic Press. p 622–633.
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science (New York, NY) 239(4839):487–491. doi:10.1126/science.2448875
Scanlon TC, Dostal SM, Griswold KE (2014) A high-throughput screen for antibiotic drug discovery. Biotechnol Bioeng 111(2):232–243. doi:10.1002/bit.25019
Schiraldi C, De Rosa M (2002) The production of biocatalysts and biomolecules from extremophiles. Trends Biotechnol 20(12):515–521. doi:10.1016/S0167-7799(02)02073-5
Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2(7):e92. doi:10.1371/journal.pcbi.0020092
Schnoes AM, Brown SD, Dodevski I, Babbitt PC (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5(12):e1000605. doi:10.1371/journal.pcbi.1000605
Sheikh Abdul Hamid N, Zen HB, Tein OB, Halifah YM, Saari N, Bakar FA (2003) Screening and identification of extracellular lipase-producing thermophilic bacteria from a Malaysian hot spring. World J Microbiol Biotechnol 19(9):961–968. doi:10.1023/B:WIBI.0000007330.84569.39
Shukoor MI, Natalio F, Therese HA, Tahir MN, Ksenofontov V, Panthöfer M et al (2008) Fabrication of a silica coating on magnetic γ-Fe2O3 nanoparticles by an immobilized enzyme. Chem Mater 20(11):3567–3573. doi:10.1021/cm7029954
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(9):2964–2968. doi:10.1128/AEM.02644-08
Singh BK (2010) Exploring microbial diversity for biotechnology: the way forward. Trends Biotechnol 28(3):111–116. doi:10.1016/j.tibtech.2009.11.006
Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, Liebaers I, Sermon K (2006) Whole-genome multiple displacement amplification from single cells. Nat Protoc 1(4):1965–1970. doi:10.1038/nprot.2006.326
Sul WJ, Park J, Quensen JF, Rodrigues JLM, Seliger L, Tsoi TV et al (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501–5506. doi:10.1128/AEM.00121-09
Tchigvintsev A, Tran H, Popovic A, Kovacic F, Brown G, Flick R et al (2015) The environment shapes microbial enzymes: five cold-active and salt-resistant carboxylesterases from marine metagenomes. Appl Microbiol Biotechnol 99(5):2165–2178. doi:10.1007/s00253-014-6038-3
Tran DN, Balkus KJ (2011) Perspective of recent progress in immobilization of enzymes. ACS Catal 1(8):956–968. doi:10.1021/cs200124a
Turnbaugh PJ, Turnbaugh PJ, Ley RE, Ley RE, Hamady M, Hamady M et al (2007) The human microbiome project. Nature 449(7164):804–810. doi:10.1038/nature06244
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428(6978):37–43. doi:10.1038/nature02340
Uchiyama T, Miyazaki K (2010) Substrate-induced gene expression screening: a method for high-throughput screening of metagenome libraries. Methods Mol Biol (Clifton, NJ) 668:153–168. doi:10.1007/978-1-60761-823-2_10
Uchiyama T, Miyazaki K (2013) Metagenomic screening for aromatic compound-responsive transcriptional regulators. PLoS ONE 8(9):e75795. doi:10.1371/journal.pone.0075795
Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23(1):88–93. doi:10.1038/nbt1048
Valdés-Solís T, Rebolledo AF, Sevilla M, Valle-Vigón P, Bomatí-Miguel O, Fuertes AB, Tartaj P (2009) Preparation, characterization, and enzyme immobilization capacities of superparamagnetic silica/iron oxide nanocomposites with mesostructured porosity. Chem Mater 21(9):1806–1814. doi:10.1021/cm8005937
Van den Burg B (2003) Extremophiles as a source for novel enzymes. Curr Opin Microbiol. doi:10.1016/S1369-5274(03)00060-2
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science (New York, NY) 304(5667):66–74. doi:10.1126/science.1093857
Vieille C, Zeikus GJ (2001) Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev: MMBR 65(1):1–43. doi:10.1128/MMBR.65.1.1-43.2001
Walters DM, Russ R, Knackmuss H-J, Rouvière PE (2001) High-density sampling of a bacterial operon using mRNA differential display. Gene 273(2):305–315. doi:10.1016/S0378-1119(01)00597-2
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(12):1917–1926. doi:10.1111/j.1462-2920.2005.00854.x
Wild J, Hradecna Z, Szybalski W (2002) Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome Res 12(9):1434–1444. doi:10.1101/gr.130502
Wilson ZE, Brimble MA, Pikuta EV, Hoover RB, Tang J, MacElroy RD et al (2009) Molecules derived from the extremes of life. Nat Prod Rep 26(1):44–71. doi:10.1039/B800164M
Wooley JC, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol 6(2):e1000667. doi:10.1371/journal.pcbi.1000667
Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H et al (2009) Assembling the marine metagenome, one cell at a time. PLoS ONE 4(4):e5299. doi:10.1371/journal.pone.0005299
Yakimov MM, Denaro R, Genovese M, Cappello S, D’Auria G, Chernikova TN et al (2005) Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 7(9):1426–1441. doi:10.1111/j.1462-5822.2005.00829.x
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K-H et al (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12(9):635–645. doi:10.1038/nrmicro3330
Yin H, Cao L, Qiu G, Wang D, Kellogg L, Zhou J et al (2007) Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in acid mine drainages and bioleaching systems. J Microbiol Methods 70(1):165–178. doi:10.1016/j.mimet.2007.04.011
Acknowledgments
The authors gratefully acknowledge the financial support provided by the European Community project KILL-SPILL (FP7-KBBE-2012-312139) European Union’s Horizon 2020 Project INMARE (grant agreement No 634486. This work was further funded by grants BIO2011-25012, PCIN-2014-107, and BIO2014-54494-R from the Spanish Ministry of Economy and Competitiveness. The present investigation was funded by the Spanish Ministry of Economy and Competitiveness, the UK Biotechnology and Biological Sciences Research Council (BBSRC) (Grant Nr BB/MO29085/1) within the ERA NET-IB2 program, grant number ERA-IB-14-030. MF gratefully acknowledges the financial support provided by the European Regional Development Fund (ERDF).
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Distaso, M.A., Tran, H., Ferrer, M., Golyshin, P.N. (2016). Metagenomic Mining of Enzyme Diversity. In: Lee, S. (eds) Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Production of Fuels and Chemicals. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-31421-1_216-1
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DOI: https://doi.org/10.1007/978-3-319-31421-1_216-1
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