Biotechnological prospects from metagenomics

Current Opinion in Biotechnology

Volumn 14, Issue 3, 2003, Pages 303-310

  Schloss, Patrick D ^a   Handelsman, Jo ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; MICROBIAL ENZYME; STREPTOMYCIN; TURBOMYCIN; UNCLASSIFIED DRUG;

ANALYTIC METHOD; BIOTECHNOLOGY; CELL ACTIVITY; CHEMICAL ANALYSIS; DNA SEQUENCE; ENZYME ACTIVITY; GENE EXPRESSION; GENE FUNCTION; GENE LIBRARY; GENETIC CODE; GENOME; GENOME ANALYSIS; GENOMICS; MICROBIAL ACTIVITY; MICROBIAL POPULATION DYNAMICS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; REVIEW; TECHNIQUE;

EID: 0037805644     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(03)00067-3     Document Type: Review

References (51)

1. Rondon M.R., August P.R., Bettermann A.D., Brady S.F., Grossman T.H., Liles M.R., Loiacono K.A., Lynch B.A., MacNeil I.A., Minor C.et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 66:2000;2541-2547 The authors report the construction and functional screening of a metagenomic library from soil containing 1 Gb of DNA in a bacterial artificial chromosome vector. The library contained diverse functions and was derived from diverse taxa, as indicated by analysis of 16S rRNA genes.
2. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 59:1995;143-169.
3. Pace N.R., Stahl D.A., Lane D.J., Olsen G.J. Analyzing natural microbial populations by rRNA sequences. ASM News. 51:1985;4-12.
4. Waksman S.A., Foster J.W. Associative and antagonistic effects of microorganisms: II. Antagonistic effects of microorganisms grown on artificial substrates. Soil Sci. 43:1937;69-76.
5. Waksman S.A., Curtis R.E. The actinomyces of the soil. Soil Sci. 1:1916;99-134.
6. Gillespie D.E., Brady S.F., Bettermann A.D., Cianciotto N.P., Liles M.R., Rondon M.R., Clardy J., Goodman R.M., Handelsman J. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol. 68:2002;4301-4306.
7. August P.R., Grossman T.H., Minor C., Draper M.P., MacNeil I.A., Pemberton J.M., Call K.M., Holt D., Osburne M.S. Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violaceum. J Mol Microbiol Biotechnol. 2:2000;513-519.
8. Brady S.F., Chao C.J., Clardy J. New natural product families from an environmental DNA (eDNA) gene cluster. J Am Chem Soc. 124:2002;9968-9969 The authors describe the discovery of a new class of aminoacylated antibiotics from a metagenomic library constructed from soil.
9. Brady S.F., Chao C.J., Handelsman J., Clardy J. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett. 3:2001;1981-1984.
10. Brady S.F., Clardy J. Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J Am Chem Soc. 122:2000;12903-12904.
11. MacNeil I.A., Tiong C.L., Minor C., August P.R., Grossman T.H., Loiacono K.A., Lynch B.A., Phillips T., Narula S., Sundaramoorthi R.et al. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J Mol Microbiol Biotechnol. 3:2001;301-308.
12. Wang G.Y., Graziani E., Waters B., Pan W., Li X., McDermott J., Meurer G., Saxena G., Andersen R.J., Davies J. Novel natural products from soil DNA libraries in a streptomycete host. Org Lett. 2:2000;2401-2404.
13. Courtois S., Cappellano C.M., Ball M., Francou F.X., Normand P., Helynck G., Martinez A., Kolvek S.J., Hopke J., Osburne M.S.et al. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol. 69:2003;49-55.
14. Piel J. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc Natl Acad Sci USA. 99:2002;14002-14007.
15. Diaz-Torres M.L., McNab R., Spratt D.A., Villedieu A., Hunt N., Wilson M., Mullany P. Novel tetracycline resistance determinant from the oral metagenome. Antimicrob Agents Chemother. 47:2003;1430-1432.
16. Henne A., Schmitz R.A., Bomeke M., Gottschalk G., Daniel R. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl Environ Microbiol. 66:2000;3113-3116 The paper presents two screens for lipolytic activity, which were applied to metagenomic libraries constructed from soil. One screen led to the identification of one lipolytic clone out of 730 000 screened clones; the other led to the identification of three out of 286 000 clones, indicating the relatively low frequency of functionally active clones.
17. Cottrell M.T., Moore J.A., Kirchman D.L. Chitinases from uncultured marine microorganisms. Appl Environ Microbiol. 65:1999;2553-2557.
18. + antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol. 183:2001;6645-6653.
19. Henne A., Daniel R., Schmitz R.A., Gottschalk G. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Appl Environ Microbiol. 65:1999;3901-3907.
20. Entcheva P., Liebl W., Johann A., Hartsch T., Streit W.R. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol. 67:2001;89-99.
21. Beja O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues C., Jovanovich S.B.et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol. 2:2000;516-529.
22. Beja O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L.et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:2000;1902-1906 The authors report the isolation of a new rhodopsin, the first derived from bacteria, that was discovered in a genomic library constructed from microorganisms in seawater.
23. Beja O., Spudich E.N., Spudich J.L., Leclerc M., DeLong E.F. Proteorhodopsin phototrophy in the ocean. Nature. 411:2001;786-789.
24. Beja O., Koonin E.V., Aravind L., Taylor L.T., Seitz H., Stein J.L., Bensen D.C., Feldman R.A., Swanson R.V., DeLong E.F. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol. 68:2002;335-345.
25. Quaiser A., Ochsenreiter T., Klenk H.P., Kletzin A., Treusch A.H., Meurer G., Eck J., Sensen C.W., Schleper C. First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol. 4:2002;603-611 The authors identified clones carrying Crenarchaeota 16S rRNA genes in a soil metagenomic library and sequenced the flanking DNA to begin to compile genomic information about this poorly understood and, as yet, uncultured group of prokaryotes.
26. Schleper C., Swanson R.V., Mathur E.J., DeLong E.F. Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol. 179:1997;7803-7811.
27. Schleper C., DeLong E.F., Preston C.M., Feldman R.A., Wu K.Y., Swanson R.V. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol. 180:1998;5003-5009.
28. Stein J.L., Marsh T.L., Wu K.Y., Shizuya H., DeLong E.F. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol. 178:1996;591-599.
29. Suzuki M.T., Beja O., Taylor L.T., Delong E.F. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol. 3:2001;323-331.
30. Vergin K.L., Urbach E., Stein J.L., DeLong E.F., Lanoil B.D., Giovannoni S.J. Screening of a fosmid library of marine environmental genomic DNA fragments reveals four clones related to members of the order Planctomycetales. Appl Environ Microbiol. 64:1998;3075-3078.
31. Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM: A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 2003: in press.
32. Cane D.E., Walsh C.T., Khosla C. Harnessing the biosynthetic code: combinations, permutations, and mutations. Science. 282:1998;63-68.
33. Beja O., Suzuki M.T., Heidelberg J.F., Nelson W.C., Preston C.M., Hamada T., Eisen J.A., Fraser C.M., DeLong E.F. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature. 415:2002;630-633 The paper presents an elegant study of the diversity of photosynthetic operons in a marine assemblage of prokaryotes using conserved sequences to screen a metagenomic library for pufL and pufM, the genes encoding the reaction center complex.
34. Sandler S.J., Hugenholtz P., Schleper C., DeLong E.F., Pace N.R., Clark A.J. Diversity of radA genes from cultured and uncultured archaea: comparative analysis of putative RadA proteins and their use as a phylogenetic marker. J Bacteriol. 181:1999;907-915.
35. Clark M.A., Baumann L., Thao M.L., Moran N.A., Baumann P. Degenerative minimalism in the genome of a psyllid endosymbiont. J Bacteriol. 183:2001;1853-1861.
36. Tamas I., Klasson L., Canback B., Naslund A.K., Eriksson A.S., Wernegreen J.J., Sandstrom J.P., Moran N.A., Andersson S.G. 50 million years of genomic stasis in endosymbiotic bacteria. Science. 296:2002;2376-2379 The paper discusses the genomic sequence of an obligate endosymbiotic bacterium, Buchnera aphidicola. The sequence was obtained by constructing a genomic library from a single homogenized Schizaphis graminum female.
37. Wernegreen J.J., Ochman H., Jones I.B., Moran N.A. Decoupling of genome size and sequence divergence in a symbiotic bacterium. J Bacteriol. 182:2000;3867-3869.
38. Preston C.M., Wu K.Y., Molinski T.F., DeLong E.F. A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. Proc Natl Acad Sci USA. 93:1996;6241-6246.
39. Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 406:2000;477-483.
40. Torsvik V., Goksoyr J., Daae F.L. High diversity in DNA of soil bacteria. Appl Environ Microbiol. 56:1990;782-787.
41. Urbach E., Vergin K.L., Giovannoni S.J. Immunochemical detection and isolation of DNA from metabolically active bacteria. Appl Environ Microbiol. 65:1999;1207-1213.
42. Borneman J. Culture-independent identification of microorganisms that respond to specified stimuli. Appl Environ Microbiol. 65:1999;3398-3400.
43. Yin B., Crowley D., Sparovek G., De Melo W.J., Borneman J. Bacterial functional redundancy along a soil reclamation gradient. Appl Environ Microbiol. 66:2000;4361-4365.
44. 4. Methods Mol Biol. 179:2002;149-157.
45. Morris S.A., Radajewski S., Willison T.W., Murrell J.C. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol. 68:2002;1446-1453.
46. Radajewski S., Webster G., Reay D.S., Morris S.A., Ineson P., Nedwell D.B., Prosser J.I., Murrell J.C. Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology. 148:2002;2331-2342.
47. Murrell J.C., Radajewski S. Cultivation-independent techniques for studying methanotroph ecology. Res Microbiol. 151:2000;807-814.
48. 12C labeled DNA fractions before cloning.
49. Manefield M., Whiteley A.S., Griffiths R.I., Bailey M.J. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol. 68:2002;5367-5373.
50. Manefield M., Whiteley A.S., Ostle N., Ineson P., Bailey M.J. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun Mass Spectrom. 16:2002;2179-2183.
51. Abraham W.R., Nogales B., Golyshin P.N., Pieper D.H., Timmis K.N. Polychlorinated biphenyl-degrading microbial communities in soils and sediments. Curr Opin Microbiol. 5:2002;246-253.