Discovering novel enzymes from marine ecosystems: a metagenomic approach

References

Alain, K. and J. Querellou. 2009. Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13: 583–594.10.1007/s00792-009-0261-3Search in Google Scholar PubMed

Alma’abadi, A.D., T. Gojobori and K. Mineta. 2015. Marine metagenome as a resource for novel enzymes. Gen. Prot. Bioinform. 3: 290–295.10.1016/j.gpb.2015.10.001Search in Google Scholar PubMed PubMed Central

Amann, R.I., W. Ludwig and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.10.1128/mr.59.1.143-169.1995Search in Google Scholar PubMed PubMed Central

August, P.R., T.H. Grossman, C. Minor, M.P. Draper, I.A. MacNeil, J.M. Pemberton, K.M. Call, D. Holt and M.S. Osburne. 2000. Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violaceum. J. Mol. Microbiol. Biotechnol. 2: 513–519.Search in Google Scholar

Barone, R., C. De Santi, F. Palma Esposito, P. Tedesco, F. Galati and M. Visone. 2014. Marine metagenomics, a valuable tool for enzymes and bioactive compounds discovery. Front. Mar. Sci. 4. https://doi.org/10.3389/fmars.2014.00038.10.3389/fmars.2014.00038Search in Google Scholar

Beja, O., L. Aravind, E.V. Koonin, M.T. Suzuki, A. Hadd, L.P. Nguyen, S.B. Jovanovich, C.M. Gates, R.A. Feldman, J.L. Spudich and E.F. DeLong. 2000a. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902–1906.10.1126/science.289.5486.1902Search in Google Scholar PubMed

Beja, O., M.T. Suzuki, E.V. Koonin, L. Aravind, A. Hadd, L.P. Nguyen, R. Villacorta, M. Amjadi, C. Garrigues, S.B. Jovanovich, R.A. Feldman and E.F. DeLong. 2000b. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2: 516–529.10.1046/j.1462-2920.2000.00133.xSearch in Google Scholar PubMed

Beja, O., E.N. Spudich, J.L. Spudich, M. Leclerc and E.F. DeLong. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411: 786–789.10.1038/35081051Search in Google Scholar PubMed

Beja, O., E.V. Koonin, L. Aravind, L.T. Taylor, H. Seitz, J.L. Stein, D.C. Bensen, R.A. Feldman, R.V. Swanson and E.F. DeLong. 2002a. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl. Environ. Microbiol. 68: 335–345.10.1128/AEM.68.1.335-345.2002Search in Google Scholar PubMed PubMed Central

Beja, O., M.T. Suzuki, J.F. Heidelberg, W.C. Nelson, C.M. Preston, T. Hamada, J.A. Eisen, C.M. Fraser and E.F. DeLong. 2002b. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415: 630–633.10.1038/415630aSearch in Google Scholar PubMed

Beja, O. 2004. To BAC or not to BAC: marine ecogenomics. Curr. Opin. Biotechnol.15: 187–190.10.1016/j.copbio.2004.03.005Search in Google Scholar PubMed

Beloqui, A., P.D. de María, P.N. Golyshin and M. Ferrer. 2008. Recent trends in industrial microbiology. Curr. Opin.Microbiol. 11: 240–248.10.1016/j.mib.2008.04.005Search in Google Scholar PubMed

Binga, E.K., R.S. Lasken and J.D. Neufeld. 2008. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J.2: 233–241.10.1038/ismej.2008.10Search in Google Scholar PubMed

Bonugli-Santos, C.R., R.M. dos Santos Vasconcelos, R.Z.M. Passarini, A.L.G. Vieira, C.P.V. Lopes, H.P. Mainardi, A.J. dos Santos, L. de Azevedo Duarte, V.R.I. Otero, M.A. da Silva Yoshida, A.V. Feitosa, A. Pessoa, Jr and D.L. Sette. 2015. Marine-derived fungi: diversity of enzymes and biotechnological applications. Front. Microbiol. 6: 269.10.3389/fmicb.2015.00269Search in Google Scholar PubMed PubMed Central

Borneman, J. 1999. Culture-independent identification of microorganisms that respond to specified stimuli. Appl. Environ. Microbiol. 65: 3398–3400.10.1128/AEM.65.8.3398-3400.1999Search in Google Scholar PubMed PubMed Central

Brady, S.F. and J. Clardy. 2000. Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J. Am. Chem. Soc. 122: 12903–12904.10.1021/ja002990uSearch in Google Scholar

Brady, S.F., C.J. Chao, J. Handelsman and J. Clardy. 2001. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org. Lett. 3: 1981–1984.10.1021/ol015949kSearch in Google Scholar PubMed

Brauer, W.N. and C. Loscher. 2010. Construction and screening of marine metagenomic libraries. Meth. Mol. Biol. 668: 51–65.10.1007/978-1-60761-823-2_3Search in Google Scholar PubMed

Breitbart, M., P. Salamon, B. Andresen, J.M. Mahaffy, A.M. Segall, D. Mead, F. Azam and F. Rohwer. 2002. Genomic analysis of uncultured marine viral communities. Proceed. Nat. Acad. Sci. USA 99: 14250–14255.10.1073/pnas.202488399Search in Google Scholar PubMed PubMed Central

Brennerova, M.V., J. Josefiova, V. Brenner, D.H. Pieper and H. Junca. 2009. Metagenomics reveals diversity and abundance of meta cleavage pathways in microbial communities from soil highly contaminated with jet fuel under air-sparging bioremediation. Environ Microbiol. 11: 2216–2227.10.1111/j.1462-2920.2009.01943.xSearch in Google Scholar PubMed PubMed Central

Cane, D.E., C.T. Walsh and C. Khosla. 1998. Harnessing the biosynthetic code: combinations, permutations, and mutations. Science. 282: 63–68.10.1126/science.282.5386.63Search in Google Scholar PubMed

Cardenas, E. and J.M. Tiedje. 2008. New tools for discovering and characterizing microbial diversity. Curr. Opin. Biotechnol. 19: 544–549.10.1016/j.copbio.2008.10.010Search in Google Scholar PubMed

Chae, J.C., B. Song and G.J. Zylstra. 2008. Identification of genes coding for hydrolytic dehalogenation in the metagenome derived from a denitrifying 4-chlorobenzoate degrading consortium. FEMS. Microbiol.Lett. 281: 203–209.10.1111/j.1574-6968.2008.01106.xSearch in Google Scholar PubMed

Chen, Z.W., Y.Y. Liu, J.F. Wu, Q. She, C.Y. Jiang and S.J. Liu. 2007. Novel bacterial sulfur oxygenasereductases from bioreactors treating gold-bearing concentrates. Appl. Environ. Microbiol. 74: 688–698.10.1007/s00253-006-0691-0Search in Google Scholar PubMed

Chistoserdova, L. 2010. Recent progress and new challenges in metagenomics for. Biotechnol. Lett. 32: 1351–1359.10.1007/s10529-010-0306-9Search in Google Scholar PubMed

Cottrell, M.T., J.A. Moore and D.L. Kirchman. 1999. Chitinases from uncultured marine microorganisms. Appl. Environ. Microbiol. 65: 2553–2557.10.1128/AEM.65.6.2553-2557.1999Search in Google Scholar PubMed PubMed Central

Courtois, S., C.M. Cappellano, M. Ball, F.X. Francou, P. Normand, G. Helynck, A. Martinez, S.J. Kolvek, J. Hopke, M.S. Osburne, P.R. August, R. Nalin, M. Guérineau, P. Jeannin, P. Simonet and J.L. Pernodet. 2003. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl. Environ. Microbiol. 69: 49–55.10.1128/AEM.69.1.49-55.2003Search in Google Scholar PubMed PubMed Central

Cowan, D., Q. Meyer, W. Stafford, S. Muyanga, R. Cameron and P. Wittwer. 2005. Metagenomic gene discovery: past, present and future. Tren. Biotech. 23: 321–329.10.1016/j.tibtech.2005.04.001Search in Google Scholar PubMed

Craig, J.W., F.Y. Chang, J.H. Kim, S.C. Obiajulu and S.F. Brady. 2010. Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl. Environ. Microbiol. 76: 1633–1641.10.1128/AEM.02169-09Search in Google Scholar PubMed PubMed Central

Darling, A.E., G. Jospin, E. Lowe, F.A. Matsen, H.M. Bik and J.A. Eisen. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2: e243.10.7717/peerj.243Search in Google Scholar PubMed PubMed Central

Das, G., T.K. Dinesh Kumar, S. Thanedar and U. Varshney. 2005. Acquisition of a stable mutation in metYallows efficient initiation from an amber codon in Escherichia coli. Microbiol. 151: 1741–1750.10.1099/mic.0.27915-0Search in Google Scholar PubMed

Delmont, T.O., P. Robe, S. Cecillon, I.M. Clark, F. Constancias, P. Simonet, P.R. Hirsch and T.M. Vogel. 2011. Accessing the soil metagenome for studies of microbial diversity. Appl. Environ. Microbiol. 77: 1315–1324.10.1128/AEM.01526-10Search in Google Scholar PubMed PubMed Central

Demanèche, S., L. Philippot, M.M. David, E. Navarro, T.M. Vogel and P. Simonet. 2009. Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach. Appl. Environ. Microbiol. 75: 534–537.10.1128/AEM.01706-08Search in Google Scholar PubMed PubMed Central

Diaz-Torres, M.L., R. McNab, D.A. Spratt, A. Villedieu, N. Hunt, M. Wilson and P. Mullany. 2003. Novel tetracycline resistance determinant from the oral metagenome. Antimicrob. Agent. Chemother. 47: 1430–1432.10.1128/AAC.47.4.1430-1432.2003Search in Google Scholar PubMed PubMed Central

Dunford, E.A. and J.D. Neufeld. 2010. DNA stable-isotope probing (DNASIP). J. Visual. Experi. 42: 860–866.10.3791/2027Search in Google Scholar PubMed PubMed Central

Edwards, R.A. and E.A. Dinsdale. 2007. Marine environmental genomics: unlocking the ocean’s secrets. Oceanography20: 26–61.10.5670/oceanog.2007.48Search in Google Scholar

Entcheva, P., W. Liebl, A. Johann, T. Hartsch and W.R. Streit. 2001. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl. Environ. Microbiol. 67: 89–99.10.1128/AEM.67.1.89-99.2001Search in Google Scholar PubMed PubMed Central

Felczykowska, A., S.K. Bloch, B. Nejman-Faleńczyk and S. Barańska. 2012. Metagenomic approach in the investigation of new bioactive compounds in the marine environment. Acta. Biochim. Pol. 59: 501–505.10.18388/abp.2012_2084Search in Google Scholar

Feng, Y., C.J. Duan, H. Pang, X.C. Mo, C.F. Wu, Y. Yu, Y.L. Hu, J. Wei, J.L. Tang and J.X. Feng. 2007. Cloning and identification of novel cellulose genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Appl. Microbiol. Biotechnol. 75: 319–328.10.1007/s00253-006-0820-9Search in Google Scholar PubMed

Ferrer, M., O.V. Golyshina, T.N. Chernikova, A.N. Khachane, V.A.P.M. dos Santos, M.M. Yakimov, K.N. Timmis and P.N. Golyshin. 2005. Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem. Biol. 12: 895–904.10.1016/j.chembiol.2005.05.020Search in Google Scholar PubMed

Ferrer, M., A. Beloqui, O.V. Golyshina, F.J. Plou, A. Neef, T.N. Chernikova, L. Fernandez-Arrojo, I. Ghazi, A. Ballesteros, K. Elborough, K.N. Timmis and P.N. Golyshin. 2007. Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome. Biotechnol. J. 2: 207–213.10.1002/biot.200600183Search in Google Scholar PubMed

Ferrer, M., A. Beloqui, K.N. Timmis and P.N. Golyshin. 2009. Metagenomics for mining new genetic resources of microbial communities. J. Mol. Microbiol. Biotechnol. 16: 109–123.10.1159/000142898Search in Google Scholar PubMed

Fernández-Arrojo, L., M.E. Guazzaroni, N. López-Cortés, A. Beloqui and M. Ferrer. 2010. Metagenomic era for biocatalyst identification. Curr. Opin. Biotechnol. 21: 725–733.10.1016/j.copbio.2010.09.006Search in Google Scholar PubMed

Fieseler, L., U. Hentschel, L. Grozdanov, A. Schirmer, G. Wen, M. Platzer, S. Hrvatin, D. Butzke, K. Zimmermann and J. Piel. 2007. Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges. Appl. Environ. Microbiol. 73: 2144–2155.10.1128/AEM.02260-06Search in Google Scholar PubMed PubMed Central

Fisch, K.M., C. Gurgui, N. Heycke, S.A. van der Sar, S.A. Anderson, V.L. Webb, S. Taudien, M. Platzer, B.K. Rubio, S.J. Robinson, P. Crews and J. Piel. 2009. Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting. Nat. Chem. Biol. 5: 494–501.10.1038/nchembio.176Search in Google Scholar PubMed

Gabor, E.M., W.B.L. Alkema and D.B. Janssen. 2004. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ. Microbiol. 6: 879–886.10.1111/j.1462-2920.2004.00640.xSearch in Google Scholar PubMed

Gilbert, J.A. and L.C. Dupont. 2011. Microbial metagenomics: beyond the genome. Annu. Rev. Mar. Sci. 3: 347–371.10.1146/annurev-marine-120709-142811Search in Google Scholar PubMed

Gillespie, D.E., S.F. Brady, A.D. Bettermann, N.P. Cianciotto, M.R. Liles, M.R. Rondon, J. Clardy, R.M. Goodman and J. Handelsman. 2002. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68: 4301–4306.10.1128/AEM.68.9.4301-4306.2002Search in Google Scholar PubMed PubMed Central

Gloux, K., M. Leclerc, H. Iliozer, R. L’Haridon, C. Manichanh, G. Corthier, R. Nalin, H.M. Blottière. and J. Doré. 2007. Development of high throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl. Environ. Microbiol. 73: 3734–3737.10.1128/AEM.02204-06Search in Google Scholar PubMed PubMed Central

Green, B.D. and M. Keller. 2006. Capturing the uncultivated majority. Curr. Opin. Biotechnol. 17: 236–240.10.1016/j.copbio.2006.05.004Search in Google Scholar PubMed

Guan, C., J. Ju, B.R. Borlee, L.L. Williamson, B. Shen, K.F. Raffa and J. Handelsman. 2007. Signal mimics derived from a metagenomic analysis of the gypsy moth gut microbiota. Appl. Environ. Microbiol. 73: 3669–3676.10.1128/AEM.02617-06Search in Google Scholar PubMed PubMed Central

Handelsman, J., M.R. Rondon, S.F. Brady, J. Clardy and R.M. Goodman. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: 245–249.10.1016/S1074-5521(98)90108-9Search in Google Scholar

Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669–685.10.1128/MMBR.68.4.669-685.2004Search in Google Scholar PubMed PubMed Central

Hardeman, F. and S. Sjoling. 2007. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS. Microbiol. Ecol. 59: 524–534.10.1111/j.1574-6941.2006.00206.xSearch in Google Scholar PubMed

Healy, F.G., R.M. Ray, H.C. Aldrich, A.C. Wilkie, L.O. Ingram and K.T. Shanmugam. 1995. Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Appl. Microbiol. Biotechnol. 43: 667–674.10.1007/BF00164771Search in Google Scholar PubMed

Henne, A., R. Daniel, R.A. Schmitz and G. Gottschalk. 1999. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4- hydroxybutyrate. Appl. Environ. Microbiol. 65: 3901–3907.10.1128/AEM.65.9.3901-3907.1999Search in Google Scholar PubMed PubMed Central

Henne, A., R.A. Schmitz, M. Bomeke, G. Gottschalk and R. Daniel. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66: 3113–3116.10.1128/AEM.66.7.3113-3116.2000Search in Google Scholar PubMed PubMed Central

Hosokawa, M., Y. Hoshino, Y. Nishikawa, T. Hirose, D.H. Yoon and T. Mori. 2015. Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes. Biosens. Bioelectron. 67: 379–385.10.1016/j.bios.2014.08.059Search in Google Scholar PubMed

Ishoey, T., T. Woyke, R. Stepanauskas, M. Novotny and R.S. Lasken. 2008. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11: 198–204.10.1016/j.mib.2008.05.006Search in Google Scholar PubMed PubMed Central

Jiang, C., Z.Y. Hao, K.E. Jin, S.X. Li, Z.Q. Che, G.F. Ma and B. Wu. 2010. Identification of a metagenome-derived β-glucosidase from bioreactor contents. J. Mol. Catal. B Enzym. 63: 11–16.10.1016/j.molcatb.2009.11.009Search in Google Scholar

Karl, D.M. 2007. Microbial oceanography: paradigms, processes and promise. Nat. Rev. Microbiol. 5: 759–769.10.1038/nrmicro1749Search in Google Scholar PubMed

Kazimierczak, K.A., K.P. Scott, D. Kelly and R.I. Aminov. 2009. Tetracycline resistome of the organic pig gut. Appl. Environ. Microbiol. 75: 1717–1722.10.1128/AEM.02206-08Search in Google Scholar PubMed PubMed Central

Kennedy, J., J.R. Marchesi and A.D.W. Dobson. 2008. Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb. Cell Fact. 7: e27.10.1186/1475-2859-7-27Search in Google Scholar PubMed PubMed Central

Kennedy, J., B. Flemer, S.A. Jackson, D.P. Lejon, J.P. Morrissey, F. O’Gara and A.D. Dobson. 2010. Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Mar Drugs 8: 608–628.10.3390/md8030608Search in Google Scholar PubMed PubMed Central

Kennedy, J., N.D. O’Leary, G.S. Kiran, J.P. Morrissey, F. O’Gara, J. Selvin and A.D. Dobson. 2011. Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. J. Appl. Microbiol. 111: 787–799.10.1111/j.1365-2672.2011.05106.xSearch in Google Scholar PubMed

Kirk, O., T.V. Borchert and C.C. Fuglsang. 2002. Industrial enzyme applications. Curr. Opin. Biotechnol. 13: 345–351.10.1002/0471238961.0914042114090512.a01.pub2Search in Google Scholar

Knietsch, A., T. Waschkowitz, S. Bowien, A. Henne and R. Daniel. 2003. 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: 1408–1416.10.1128/AEM.69.3.1408-1416.2003Search in Google Scholar PubMed PubMed Central

Kodzius R. and T. Gojobori. 2015. Marine metagenomics as a source for bioprospecting. Mar. Genomics 1: 21–30.10.1016/j.margen.2015.07.001Search in Google Scholar PubMed

Langridge, G. 2009. Testing the water: marine metagenomics. Nat. Rev. Microbiol. 7: 552.10.1038/nrmicro2188Search in Google Scholar PubMed

Lasken, R.S. 2009. Genomic DNA, amplification by the multiple displacement amplification (MDA) method. Biochem. Soc. Trans. 37: 450–453.10.1042/BST0370450Search in Google Scholar PubMed

Lee, H.S., K.K. Kwon, S.G. Kang, S.S. Cha, S.J. Kim and J.H. Lee. 2010. Approaches for novel enzyme discovery from marine environments. Curr. Opin. Biotechnol. 21: 353–357.10.1016/j.copbio.2010.01.015Search in Google Scholar PubMed

Leis, B., A. Angelov and W. Liebl. 2013. Screening and expression of genes from metagenomes. Adv. Appl. Microbiol. 83: 1–68.10.1016/B978-0-12-407678-5.00001-5Search in Google Scholar PubMed

Liles, M.R., B.F. Manske, S.B. Bintrim, J. Handelsman and R.M. Goodman. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69: 2684–2691.10.1128/AEM.69.5.2684-2691.2003Search in Google Scholar PubMed PubMed Central

Liu, J., H. Wang, H. Yang, Y. Zhang, J. Wang, F. Zhao and J. Qi. 2013. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acid Res. 41: e3.10.1093/nar/gks828Search in Google Scholar PubMed PubMed Central

Luo, W., L.L.P. Vrijmoed and E.B.G. Jones. 2005. Screening of marine fungi for lignocellulose-degrading enzyme activities. Bot. Mar. 48: 379–386.10.1515/bot.2005.051Search in Google Scholar

Maar, D., D. Liveris, J.K. Sussman, S. Ringquist, I. Moll, N. Heredia, A. Kil, U. Bläsi, I. Schwartz and R.W. Simons. 2008. A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels. J. Mol. Biol. 383: 937–944.10.1016/j.jmb.2008.09.012Search in Google Scholar PubMed

MacNeil, I.A., C.L. Tiong, C. Minor, P.R. August, T.H. Grossman, K.A. Loiacono, B.A. Lynch, T. Phillips, S. Narula, R. Sundaramoorthi, A. Tyler, T. Aldredge, H. Long, M. Gilman, D. Holt and M. S Osburne. 2001. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol. 3: 301–308.Search in Google Scholar

Majernik, A., G. Gottschalk and R. Daniel. 2001. Screening of environmental DNA libraries for the presence of genes conferring Naþ(Liþ)/Hþantiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J. Bacteriol. 183: 6645–6653.10.1128/JB.183.22.6645-6653.2001Search in Google Scholar PubMed PubMed Central

Manefield, M., A.S. Whiteley, R.I. Griffiths and M.J. Bailey. 2002a. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl. Environ. Microbiol. 68: 5367–5373.10.1128/AEM.68.11.5367-5373.2002Search in Google Scholar PubMed PubMed Central

Manefield, M., A.S. Whiteley, N. Ostle, P. Ineson and M.J. Bailey. 2002b. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun. Mass Spectrom. 16: 2179–2183.10.1002/rcm.782Search in Google Scholar PubMed

Marco, D. 2008. Metagenomics and the niche concept. Theory Biosci. 27: 241–247.10.1007/s12064-008-0028-xSearch in Google Scholar PubMed

Martinez, A., S.J. Kolvek, C.L.T. Yip, J. Hopke, K.A. Brown, I.A. MacNeil and M.S. Osburne. 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: 2452–2463.10.1128/AEM.70.4.2452-2463.2004Search in Google Scholar PubMed PubMed Central

Martinez, A., G.W. Tyson and E.F. Delong. 2010. Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environ. Microbiol. 12: 222–238.10.1111/j.1462-2920.2009.02062.xSearch in Google Scholar PubMed

Marzorati, M., F. de Ferra, H. Van Raemdonck, S. Borin, E. Allifranchini, G. Carpani, L. Serbolisca, W. Verstraete, N. Boon and D. Daffonchio. 2007. A novel reductive dehalogenase, identified in a contaminated groundwater enrichment culture and in Desulfitobacterium dichloroeliminans strain DCA1, is linked to dehalogenation of 1,2-dichloroethane. Appl. Environ. Microbiol. 73: 2990–2999.10.1128/AEM.02748-06Search in Google Scholar PubMed PubMed Central

McLeod, M.P., R.L. Warren, W.W. Hsiao, N. Araki, M. Myhre, C. Fernandes, D. Miyazawa, W. Wong, A.L. Lillquist, D. Wang, M. Dosanjh, H. Hara, A. Petrescu, R.D. Morin, G. Yang, J.M. Stott, J.E. Schein, H. Shin, D. Smailus, A.S. Siddiqui, M.A. Marra, S.J. Jones, R. Holt, F.S. Brinkman, K. Miyauchi, M. Fukuda, J.E. Davies, W.W. Mohn and L.D. Eltis. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc. Natl. Acad. Sci. USA 103: 15582–15587.10.1073/pnas.0607048103Search in Google Scholar PubMed PubMed Central

Mewis, K., M. Taupp and S.J. Hallam. 2011. A high throughput screen for biomining cellulase activity from metagenomic libraries. J. Vis. Exp. doi: 10.3791/2461.10.3791/2461Search in Google Scholar PubMed PubMed Central

Mirete, S., C.G. de Figueras and J.E. Gonzàlez-Pastor. 2007. Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl. Environ. Microbiol. 73: 6001–6011.10.1128/AEM.00048-07Search in Google Scholar PubMed PubMed Central

Miller, J.R., S. Koren and G. Sutton. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315–327.10.1016/j.ygeno.2010.03.001Search in Google Scholar PubMed PubMed Central

Mohn, W.W., J. Garmendia, T.C. Galvao and V. de Lorenzo. 2006. Surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane(gammahexachlorocyclohexane) into lacZ-based phenotypes. Environ. Microbiol. 8: 546–555.10.1111/j.1462-2920.2006.00983.xSearch in Google Scholar PubMed

Mori, T., S. Mizuta, H. Suenaga and K. Miyazaki. 2008. Metagenomic screening for bleomycin resistance genes. Appl. Environ. Microbiol. 74: 6803–6805.10.1128/AEM.00873-08Search in Google Scholar PubMed PubMed Central

Morimoto, S. and T. Fujii. 2009. A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl. Environ. Microbiol. 83: 389–396.10.1007/s00253-009-1992-xSearch in Google Scholar PubMed

Nagarajan, N. and M. Pop. 2013. Sequence assembly demystified. Nat. Rev. Genet.14: 157–167.10.1038/nrg3367Search in Google Scholar PubMed

Neelakanta, G. and H. Sultana. 2013. The use of metagenomic approaches to analyze changes in microbial communities. Microbiol. Insights 6: 37–48.10.4137/MBI.S10819Search in Google Scholar

Neufeld, J.D., M. Wagner and J.C. Murrell. 2007. Who eats what, where and when? Isotope-labelling experiments are coming of age. Int. Soc. Microb. Ecol. J. 1: 103–110.10.1038/ismej.2007.30Search in Google Scholar

Neufeld, J.D., Y. Chen, M.G. Dumont and J.C. Murrell. 2008. Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ. Microbiol. 10: 1526–1535.10.1111/j.1462-2920.2008.01568.xSearch in Google Scholar

O’Connor, M., S.T. Gregory and A.E. Dahlberg. 2004. Multiple defects in translation associated with altered ribosomal protein L4. Nucleic Acid Res. 32: 5750–5756.10.1093/nar/gkh913Search in Google Scholar

Ogawa, J. and S. Shimizu. 1999. Microbial enzymes: new industrial applications from traditional screening methods. Trends Biotechnol. 17: 13–21.10.1016/S0167-7799(98)01227-XSearch in Google Scholar

Ono, A., R. Miyazaki, M. Sota, Y. Ohtsubo, Y. Nagata and M. Tsuda. 2007. Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches. Appl. Environ. Microbiol. 74: 501–510.10.1007/s00253-006-0671-4Search in Google Scholar PubMed

Pace, N.R., D.A. Stahl, D.J. Lane and G.J. Olsen. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51: 4–12.Search in Google Scholar

Pennisi, E. 2011. Human genome 10th anniversary. Will computers crash genomics? Science 331: 666–668.10.1126/science.331.6018.666Search in Google Scholar PubMed

Piel, J. 2002. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc. Natl. Acad. Sci. USA 99: 14002–14007.10.1073/pnas.222481399Search in Google Scholar PubMed PubMed Central

Poli, A., I. Finore, I. Romano, A. Gioiello, L. Lama and B. Nicolaus. 2017. Microbial diversity in extreme marine habitats and their biomolecules. Microorganisms 5: 25.10.3390/microorganisms5020025Search in Google Scholar PubMed PubMed Central

Popovic, A., A. Tchigvintsev, H. Tran, T.N. Chernikova, O.V. Golyshina, M.M. Yakimov, P.N. Golyshin and A.F. Yakunin. 2015. Metagenomics as a tool for enzyme discovery: hydrolytic enzymes from marine-related metagenomes. Adv. Exp. Med. Biol. 883: 1–20.10.1007/978-3-319-23603-2_1Search in Google Scholar PubMed

Prifti, E. and J.D. Zucker. 2015. The new science of metagenomics and the challenges of its use in both developed and developing countries. In: (S. Morand, J.P. Dujardin, R. Lefait-Robin and C. Apiwathnasorn, eds) Socio-ecological dimensions of infectious diseases in Southeast Asia. Springer, Singapore.10.1007/978-981-287-527-3_12Search in Google Scholar

Quaiser, A., T. Ochsenreiter, H.P. Klenk, A. Kletzin, A.H. Treusch, G. Meurer, J. Eck, C.W. Sensen and C. Schleper. 2002. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4: 603–611.10.1046/j.1462-2920.2002.00345.xSearch in Google Scholar

Rhee, J.K., D.G. Ahn, Y.G. Kim and J.W. Oh. 2005. New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl. Environ. Microbiol. 71: 817–825.10.1128/AEM.71.2.817-825.2005Search in Google Scholar

Riesenfeld, C.S., P.D. Schloss and J. Handelsman. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525–552.10.1146/annurev.genet.38.072902.091216Search in Google Scholar

Rondon, M.R., P.R. August, A.D. Bettermann, S.F. Brady, T.H. Grossman, M.R. Liles, K.A. Loiacono, B.A. Lynch, I.A. MacNeil, C. Minor, C.L. Tiong, M. Gilman, M.S. Osburne, J. Clardy, J. Handelsman and R.M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541–2547.10.1128/AEM.66.6.2541-2547.2000Search in Google Scholar

Sandler, S.J., P. Hugenholtz, C. Schleper, E.F. DeLong, N.R. Pace and A.J. Clark. 1999. Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J. Bacteriol. 181: 907–915.10.1128/JB.181.3.907-915.1999Search in Google Scholar

Schipper, C., C. Hornung, P. Bijtenhoorn, M. Quitschau, S. Grond and W.R. Streit. 2009. Metagenome-derived clones encoding two novel lactonase family proteins involved in biofilm inhibition in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 75: 224–233.10.1128/AEM.01389-08Search in Google Scholar

Schleper, C., E.F. DeLong, C.M. Preston, R.A. Feldman, K.Y. Wu and R.V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180: 5003–5009.10.1128/JB.180.19.5003-5009.1998Search in Google Scholar

Schloss, P.D. and J. Handelsman. 2003. Biotechnological prospects from metagenomics. Curr. Opin. Biotechnol. 14: 303–310.10.1016/S0958-1669(03)00067-3Search in Google Scholar

Schloss, P.D. and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501–1506.10.1128/AEM.71.3.1501-1506.2005Search in Google Scholar PubMed PubMed Central

Schmid, A., J.S. Dordick, B. Hauer, A. Kiener, M. Wubbolts and B. Witholt. 2001. Industrial biocatalysis today and tomorrow. Nature 409: 258–268.10.1038/35051736Search in Google Scholar

Schmeisser, C., H. Steele and W.R. Streit. 2007. Metagenomics, biotechnology with non culturable microbes. Appl. Microbiol. Biotechnol. 75: 955–962.10.1007/s00253-007-0945-5Search in Google Scholar

Schmitz, J.E., A. Daniel, M. Collin, R. Schuch and V.A. Fischetti. 2008. Rapid DNA library construction for functional genomic and metagenomic screening. Appl. Environ. Microbiol. 74: 1649–1652.10.1128/AEM.01864-07Search in Google Scholar

Schulz, B., S. Draeger, T.E. Dela Cruz, J. Rheinheimer, K. Siems, S. Loesgen, J. Bitzer, O. Schloerke, A. Zeeck, I. Kock and H. Hussain. 2008. Screening strategies for obtaining novel, biologically active, fungal secondary metabolites from marine habitats. Bot. Mar. 51: 219–234.10.1515/BOT.2008.029Search in Google Scholar

Simon, C. and R. Daniel. 2011. Metagenomic analyses: past and future trends. Appl. Environ. Microbiol. 77: 1153–1161.10.1128/AEM.02345-10Search in Google Scholar

Singh, J., A. Behal, N. Singla, A. Joshi, N. Birbian, S. Singh, V. Bali and N. Batra. 2009. Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol. J. 4: 480–494.10.1002/biot.200800201Search in Google Scholar

Sleator, R.D., C. Shortall and C. Hill. 2008. Metagenomics. Lett. Appl. Microbiol. 47: 361–366.10.1111/j.1472-765X.2008.02444.xSearch in Google Scholar

Smyth, G.K. and T. Speed. 2003. Normalization of cDNA microarray data. Methods31: 265–273.10.1016/S1046-2023(03)00155-5Search in Google Scholar

Sorensen, H.P. and K.K. Mortensen. 2005. Advanced genetic strategies for recombinant protein expression in Escherichia coli. J. Biotechnol. 115: 113–128.10.1016/j.jbiotec.2004.08.004Search in Google Scholar PubMed

Sorek, R., Y.W. Zhu, C.J. Creevey, M.P. Francino, P. Bork and E.M. Rubin. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 1449–1452.10.1126/science.1147112Search in Google Scholar PubMed

Steele, H.L. and W.R. Streit. 2005. Metagenomics: advances in ecology and biotechnology. FEMS Microbiol. Lett. 247: 105–111.10.1016/j.femsle.2005.05.011Search in Google Scholar PubMed

Steele, H.L., K.E. Jaeger, R. Daniel and W.R. Streit. 2009. Advances in recovery of novel biocatalysts from metagenomes. J. Mol. Microbiol. Biotechnol. 16: 25–37.10.1159/000142892Search in Google Scholar PubMed

Stein, J.L., T.L. Marsh, K.Y. Wu, H. Shizuya and E.F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178: 591–599.10.1128/jb.178.3.591-599.1996Search in Google Scholar PubMed PubMed Central

Streit, W.R. and R.A. Schmitz. 2004. Metagenomics–the key to the uncultured microbes. Curr. Opin. Microbiol. 7: 492–498.10.1016/j.mib.2004.08.002Search in Google Scholar PubMed

Suenaga, H., T. Ohnuki and K. Miyazaki. 2007. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ. Microbiol. 9: 2289–2297.10.1111/j.1462-2920.2007.01342.xSearch in Google Scholar PubMed

Suzuki, M.T., O. Beja, L.T. Taylor and E.F. Delong. 2001. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ. Microbiol. 3: 323–331.10.1046/j.1462-2920.2001.00198.xSearch in Google Scholar PubMed

Tang, K., R.S. Kobayashi, V. Champreda, L. Eurwilaichitr and S. Tanapongpipat. 2008. Isolation and characterization of a novel thermostable neopullulanase-like enzyme from a hot spring in Thailand. Biosci. Biotechnol. Biochem. 72: 1448–1456.10.1271/bbb.70754Search in Google Scholar PubMed

Taupp, M., S. Lee, A. Hawley, J. Yang and S.J. Hallman. 2009. Large insert environmental genomic library production. J. Vis. Exp. 23. doi: 10.3791/1387.10.3791/1387Search in Google Scholar PubMed PubMed Central

Taupp, M., K. Mewis and S.J. Hallam. 2011. The art and design of functional metagenomic screens. Curr. Opin. Biotechnol. 22: 465–472.10.1016/j.copbio.2011.02.010Search in Google Scholar PubMed

Tracy, B.P., S.M. Gaida and E.T. Papoutsakis. 2010. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr. Opin. Biotechnol. 21: 85–99.10.1016/j.copbio.2010.02.006Search in Google Scholar PubMed

Troeschel, S.C., T. Drepper, C. Leggewie, W.R. Streit and K.E. Jaeger. 2010. Novel tools for the functional expression of metagenomic DNA. In: (W.R. Streit and R. Daniel, eds) Metagenomics: methods and protocols methods in molecular biology. Humana Press, New York, NY. pp. 117–139.10.1007/978-1-60761-823-2_8Search in Google Scholar PubMed

Tsai, Y.L. and B.H. Olson. 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol. 58: 2292–2295.10.1128/aem.58.7.2292-2295.1992Search in Google Scholar PubMed PubMed Central

Uchiyama, T. and K. Miyazaki. 2009. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr. Opin. Biotechnol. 20: 616–622.10.1016/j.copbio.2009.09.010Search in Google Scholar PubMed

Uchiyama, T. and K. Watanabe. 2006. Improved inverse PCR scheme for metagenome walking. BioTechniques 41: 183–188.10.2144/000112210Search in Google Scholar PubMed

Uchiyama, T. and K. Watanabe. 2007. The SIGEX scheme: high throughput screening of environmental metagenomes for the isolation of novel catabolic genes. Biotechnol. Genet. Eng. Rev. 24: 107–116.10.1080/02648725.2007.10648094Search in Google Scholar PubMed

Uchiyama, T. and K. Watanabe. 2008. Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat. Protoc. 3: 1202–1212.10.1038/nprot.2008.96Search in Google Scholar PubMed

Uchiyama, T., T. Abe, T. Ikemura and K. Watanabe. 2005. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 23: 88–93.10.1038/nbt1048Search in Google Scholar PubMed

Urbach, E., K.L. Vergin and S.J. Giovannoni. 1999. Immunochemical detection and isolation of DNA from metabolically active bacteria. Appl. Environ. Microbiol. 65: 1207–1213.10.1128/AEM.65.3.1207-1213.1999Search in Google Scholar PubMed PubMed Central

Uria, A.R. and D.S. Zilda. 2016. Metagenomics-guided mining of commercially useful biocatalysts from marine microorganisms. Adv. Food. Nutr. Res. 78: 1–26.10.1016/bs.afnr.2016.05.001Search in Google Scholar PubMed

Van SintFiet, S., J.B. van Beilen and B. Witholt. 2006. Selection of biocatalysts for chemical synthesis. Proc. Natl. Acad. Sci. USA 103: 1693–1698.10.1073/pnas.0504733102Search in Google Scholar PubMed PubMed Central

Velmurugan, N., D. Kalpana, J.H. Han, H.J. Cha and Y.S. Lee. 2011. A novel low temperature chitinase from the marine fungus Plectosphaerella sp strain MF-1. Bot. Mar. 54: 75–81.10.1515/bot.2010.068Search in Google Scholar

Vergin, K.L., E. Urbach, J.L. Stein, E.F. DeLong, B.D. Lanoil and S.J. Giovannoni. 1998. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl. Environ. Microbiol. 64: 3075–3078.10.1128/AEM.64.8.3075-3078.1998Search in Google Scholar PubMed PubMed Central

Voget, S., C. Leggewie, A. Uesbeck, C. Raasch, K.E. Jaeger and W.R. Streit. 2003. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69: 6235–6242.10.1128/AEM.69.10.6235-6242.2003Search in Google Scholar PubMed PubMed Central

Waksman, S.A. and R.E. Curtis. 1916. The actinomyces of the soil. Soil. Sci. 1: 99–134.10.1097/00010694-191602000-00001Search in Google Scholar

Waksman, S.A. and J.W. Foster. 1937. Associative and antagonistic effects of microorganisms: II. Antagonistic effects of microorganisms grown on artificial substrates. Soil Sci. 43: 69–76.10.1097/00010694-193701000-00008Search in Google Scholar

Wang, G.Y., E. Graziani, B. Waters, W. Pan, X. Li, J. McDermott, G. Meurer, G. Saxena, R.J. Andersen and J. Davies. 2000. Novel natural products from soil DNA libraries in a streptomycete host. Org. Lett. 2: 2401–2404.10.1021/ol005860zSearch in Google Scholar PubMed

Ward, N. 2006. New directions and interactions in metagenomics research. FEMS. Microbiol. Ecol. 55: 331–338.10.1111/j.1574-6941.2005.00055.xSearch in Google Scholar PubMed

Warnecke, F. and P. Hugenholtz. 2007. Building on basic metagenomics with complementary technologies. Genome Biol.8: 231.10.1186/gb-2007-8-12-231Search in Google Scholar PubMed PubMed Central

Warren, R.L., J.D. Freeman, R.C. Levesque, D.E. Smailus, S. Flibotte and R.A. Holt. 2008. Transcription of foreign DNA in Escherichia coli. Genome Res. 18: 1798–1805.10.1101/gr.080358.108Search in Google Scholar PubMed PubMed Central

Wexler, M., P.L. Bond, D.J. Richardson and A.W. Johnston. 2005. A wide host range metagenomic library from a wastewater treatment plant yields a novel alcohol/aldehyde dehydrogenase. Environ. Microbiol. 7: 1917–1926.10.1002/9781118010549.ch44Search in Google Scholar

Wild, J., Z. Hradecna and W. Szybalski. 2002. Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome. Res. 12: 1434–1444.10.1101/gr.130502Search in Google Scholar PubMed PubMed Central

Wooley, J.C., A. Godzik and I. Friedberg. 2010. A primer on metagenomics. PLoS Comput Biol. 6: e1000667.10.1371/journal.pcbi.1000667Search in Google Scholar PubMed PubMed Central

Xu, M., X. Xiao and F. Wang. 2008. Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment. Extremophiles 12: 255–262.10.1007/s00792-007-0122-xSearch in Google Scholar PubMed

Yamada, K., T. Terahara, S. Kurata, T. Yokomaku, S. Tsuneda and S. Harayama. 2008. Retrieval of entire genes from environmental DNA by inverse PCR with pre-amplification of target genes using primers containing locked nucleic acids. Environ. Microbiol. 10: 978–987.10.1111/j.1462-2920.2007.01518.xSearch in Google Scholar PubMed PubMed Central

Yin, B., D. Crowley, G. Sparovek, W.J. De Melo and J. Borneman. 2000. Bacterial functional redundancy along a soil reclamation gradient. Appl. Environ. Microbiol. 66: 4361–4365.10.1128/AEM.66.10.4361-4365.2000Search in Google Scholar PubMed PubMed Central

Yung, P.Y., C. Burke, M. Lewis, S. Egan, S. Kjelleberg and T. Thomas. 2009. Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion. Nucleic Acid Res. 37: e144.10.1093/nar/gkp746Search in Google Scholar PubMed PubMed Central