Cloning the metagenome: Culture-independent access to thediversity and functions of the uncultivated microbial world

Methods in Microbiology

Volumn 33, Issue , 2002, Pages 241-255

  Handelsman, Jo ^a   Liles, Mark ^a   Mann, David ^a   Riesenfeld, Christian ^a   Goodman, Robert M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 35448976959     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0580-9517(02)33014-9     Document Type: Review

References (72)

1. P.R. August T.H. Grossman C. Minor M.P. Draper I.A. MacNeil J.M. Pemberton K.M. Call D. Holt M.S. Osburne Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violacenim J. Mol. Microbiol. Biotechnol. 2 2000 513 519
2. O. Beja L. Aravind E.V. Koonin M. Suzuki A. Hadd L.P. Nguyen S.B. Jovanovich C.M. Gates R.A. Feldman J.L. Spudich E.N. Spudich E.F. DeLong Bacterial rhodopsin: evidence for a new type of phototrophy in the sea Science 289 2000 1902 1906
3. O. Beja 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 E.F. DeLong Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage Environ. Microbiol. 2 2000 516 529
4. O. Beja M.T. Suzuki J.F. Heidelberg W.C. Nelson C.M. Preston T. Hamada J.A. Eisen C.M. Fraser E.F. DeLong Unsuspected diversity among marine aerobic anoxygenic phototrophs Nature 415 2002 630 633
5. O. Beja E.V. Koonin L. Aravind L.T. Taylor H. Seitz J.L. Stein D.C. Bensen R.A. Feldman R.V. Swanson E.F. DeLong Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces Appl. Environ. Microbiol. 68 2002 335 345
6. S.B. Bintrim T.J. Donohue J. Handelsman G.P. Roberts R.M. Goodman Molecular phylogeny of Archaea from soil Proc. Nall Acad. Sci. USA 94 1997 277 282
7. C. Black J.A.M. Fyfe J.K. Davies A promoter associated with the neisserial repeat can be used to transcribe the uvrB gene from Neisseria gonorrhoeae J. Bacterial. 177 1995 1952 1958
8. J. Borneman P.W. Skroch K.M. O'Sullivan J.A. Palus N.G. Rumjanek J.L. Jansen J. Nienhuis E.W. Triplett Molecular microbial diversity of an agricultural soil in Wisconsin Appl. Environ. Microbiol. 62 1996 1935 1943
9. S.F. Brady J. Clardy Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA J. Am. Chem. Soc. 122 2000 12903 12904
10. S.F. Brady C.J. Chao J. Handelsman J. Clardy Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA Organic Lett. 3 2001 1981 1984
11. D.E. Cane C.T. Walsh C. Khosla Biochemistry — harnessing the biosynthetic code: combinations, permutations, and mutations Science 282 1998 63 68
12. S. Chávez J. Reyes C.F. Cahuvat F.J. Florencio P. Candau The NADP-glutamate dehydrogenase of the cyanobacterium Synechocystis 6803: cloning, transcriptional analysis and disruption of the gdhA gene Plant Mol. Biol. 28 1995 173 188
13. M.T. Cottrell J.A. Moore D.L. Kirchman Chitinases from uncultured marine microorganisms Appl. Environ. Microbiol. 65 1999 2553 2557
14. E.F. DeLong Archaea in coastal marine environments Proc. Nall. Acad. Sci. USA 89 1992 5685 5689
15. E.F. DeLong K.Y. Wu B.B. Prezelin R.V.M. Jovine High abundance of Archaea in Antarctic marine picoplankton Nature (London) 371 1994 695 697
16. E.F. DeLong L.T. Taylor T.L. Marsh C.M. Preston Visualization and enumeration of marine planktonic archaea and bacteria using polyribonucleotide probes and fluorescence in situ hybridization Appl. Environ. Microbiol. 65 1999 5554 5563
17. W.M. deVos Gene cloning and expression in lactic streptococci FEMS Microbiol. Rev. 46 1987 281 295
18. W.M. deVos M. Kleerebezem O. Kuipers Expression systems for industrial Gram-positive bacteria with low guanine and cytosine content Curr. Opin. Biotechnol. 8 1997 547 553
19. M. Ding D.B. Yelton Cloning and analysis of the leuB gene of Leptospira interrogans serovar pomona J. Gen. Microbiol. 139 1993 1093 1103
20. J.A. Eisen Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res. 8 1998 163 167
21. P. Entcheva W. Liebl A. Johann T. Hartsch W.R. Streit 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
22. R.G. Ferreyra F.C. Soncini A.M. Viale Cloning, characterization, and functional expression in Escherichia coli of chaperonin ( gro ESL) genes from the prototrophic sulfur bacterium Chronnatiurn vinosum J. Bacterial. 175 1993 1514 1523
23. M. Fiandt Construction of an environmental genomic DNA library from soil using the EpiFCS fosmid library production kit Epicentre Forum 7 2000 6
24. D.E. Gillespie S.F. Brady A.D. Bettermann N.P. Cianciotto M.R. Liles M.R. Rondon J. Clardy R.M. Goodman J. Handelsman Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA Appl. Environ. Microbiol. 2002 (in press)
25. S.J. Giovannoni T.B. Britschgi C.L. Meyer K.G. Field Genetic diversity in Sargasso Sea bacterioplankton Nature 345 1990 60 63
26. B.S. Griffiths K. Ritz L.A. Glover Broad-scale approaches to the determination of soil microbial community structure: application of the community DNA hybridization technique Microbial Ecol. 31 1996 269 280
27. D.G. Guiney E. Yakobsen Location and nucleotide sequence of the transfer origin of the broad range host plasmid RK2 Proc. Natl Acad. Sci. USA 80 1983 3595 3598
28. J. Handelsman M.R. Rondon S. Brady J. Clardy R.M. Goodman Molecular biology provides access to the chemistry of unknown soil microbes: a new frontier for natural products Chem. Biol. 5 1998 R245 R249
29. I.M. Head J.R. Saunders R.W. Pickup Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms Microb. Ecol. 35 1998 1 21
30. A. Henne R. Daniel R.A. Schmitz G. Gottschalk Construction of environmental DNA libraries in Eschericlua coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate Appl. Environ. Microbiol. 65 1999 3901 3907
31. A. Henne R.A. Schmitz M. Bomeke G. Gottschalk R. Daniel Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli Appl. Environ. Microbiol. 66 2000 3113 3116
32. P. Hugenholtz B.M. Goebel N.R. Pace Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity J. Bacterial. 180 1998 4765 4774
33. P. Joseph J.R. Fantino M.L. Herbaud F. Denizot Rapid orientated cloning in a shuttle vector allowing modulated gene expression in Bacillus subtilis FEMS Microbiol. Lett. 205 2001 91 97
34. S. Karlin J. Mrazek A. Campbell D. Kaiser Characterizations of highly expressed genes of four fast-growing bacteria J. Bacterial. 183 2001 5025 5040
35. M. Krsek E.M.H. Wellington Comparison of different methods for the isolation and purification of total community DNA from soil J. Microbiol. Meth. 39 1999 1 16
36. H. Leonhardt J.C. Alonso S1 mapping of the pC194 encoded chloramphenicol gene in Bacillus subtilis Nucleic Acids Res. 16 1988 1618
37. V. Lindahl Improved soil dispersion procedures for total bacterial counts, extraction of indigenous bacteria and cell survival J. Microbiol. Meth. 25 1996 279 286
38. I.A. MacNeil T.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 M.S. Osburne Expression and isolation of antimicrobial small molecules from soil DNA libraries J. Mol. Microbiol. Biotechnol. 3 2001 301 308
39. + antiporter activity on Escherichia coli : characterization of the recovered genes and the corresponding gene products J. Bacteriol. 183 2001 6645 6653
40. M.O. McInerney M. Wilkinson J.W. Patching T.M. Embley R. Powell Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder Appl. Environ. Microbiol. 61 1995 1646 1648
41. J.R. Newman C. Fuqua Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator Gene 227 1999 197 203
42. N.R. Pace New perspective on the natural microbial world: molecular microbial ecology ASM News 62 1996 463 470
43. B.A. Pfeifer S.J. Admiraal H. Gramajo D.E. Cane C. Khosla Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli Science 291 2001 1790 1792
44. C. Poyart P. Trieu-Cuot A broad-host-range mobilizable shuttle vector for the construction of transcriptional fusions to beta-galactosidase in Grampositive bacteria FEMS Microbiol. Lett. 156 1997 193 198
45. M.R. Rondon R.M. Goodman J. Handelsman The Earth's bounty: assessing and accessing soil microbial diversity Trends Biotechnol. 17 1999 403 409
46. M.R. Rondon S.J. Raffel R.M. Goodman J. Handelsman 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 1999 6451 6455
47. M.R. Rondon P.R. August A.D. Bettermann S.F. Brady T.H. Grossman M.R. Liles K.A. Loiacono B.A. Lynch I.A. MacNeil M.S. Osburne J. Clardy J. Handelsman R.M. Goodman Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl. Environ. Microbiol. 66 2000 2541 2547
48. S.J. Sandler P. Hugenholtz C. Schleper E.F. DeLong N.R. Pace A.J. Clark 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
49. C. Schleper R.V. Swanson E.J. Mathur E.F. DeLong Characterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum J. Bacteriol. 179 1997 7803 7811
50. C. Schleper E.F. DeLong C.M. Preston R.A. Feldman K.Y. Wu R.V. Swanson Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum J. Bacteriol. 180 1998 5003 5009
51. H. Shizuya B. Birren U.-J. Kim V. Mancino T. Slepak Y. Tachiri M. Simon Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Proc. Natl Acad. Sci. USA 89 1992 8794 8797
52. H.M. Simon J. Dodsworth R.M. Goodman Crenarchaeota colonize terrestrial plant roots Environ. Microbiol. 2 2000 495 505
53. J.E.M. Stach S. Bathe J.P. Clapp R.G. Burns PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods FEMS Microbiol. Ecol. 36 2001 139 151
54. D.A. Stahl The natural history of microorganisms ASM News 59 1993 609 613
55. D.A. Stahl D.J. Lane G.J. Olsen N.R. Pace Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences Appl. Environ. Microbiol. 49 1985 1379 1384
56. J.L. Stein T.L. Marsh K.Y. Wu H. Shizuya E.F. DeLong 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
57. M. Steinmetz R. Richter Plasmids designed to alter the antibiotic resistance expressed by insertion mutations in Bacillus subtilis , through in vivo recombination Gene 142 1994 79 83
58. M.T. Suzuki M.S. Rappe Z.W. Haimberger H. Winfield N. Adair J. Strobel S.J. Giovannoni Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample Appl. Environ. Microbiol. 63 1997 983 989
59. L. Tang S. Shah L. Chung J. Carney L. Katz C. Khosla B. Julien Cloning and heterologous expression of the epothilone gene cluster Science 287 2000 640 642
60. V. Torsvik J. Goksoyr F.L. Daae High diversity in DNA of soil bacteria Appl. Environ. Microbiol. 56 1990 782 787
61. V. Torsvik R. Sorheim J. Goksoyr Total bacterial diversity in soil and sediment communities — a review J. Indust. Microbiol. Biotech. 17 1996 170 178
62. P. Trieu-Cuot C. Carlier P. Martin P. Courvalin Plasmid transfer by conjugation from Escherichia coli to Gram-positive bacteria FEMS Microbiol. Lett. 48 1987 289 294
63. T. Uozumi A. Ozaki T. Beppu K. Arima New cryptic plasmid of Bacillus subtilis and restriction analysis of other plasmids found by general screening J. Bacteriol. 142 1980 315 318
64. K.L. Vergin E. Urbach J.L. Stein E.F. DeLong B.D. Lanoil S.J. Giovannoni 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
65. G.L. Wang R. Warren Construction of an Arabidopsis BAC library and isolation of clones hybridizing with disease-resistance, gene-like sequences Plant Mol. Biol. Reporter 14 1996 107
66. G.-Y.-S. Wang E. Graziani B. Waters W. Pan X. Li J. McDermott G. Meurer G. Saxena J. Andersen J. Davies Novel natural products from soil DNA libraries in a Streptomycete host Organic Lett. 2 2000 2401 2404
67. D.M. Ward R. Weller M.M. Bateson 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community Nature 345 1990 63 65
68. W.B. Whitman D.C. Coleman W.J. Wiebe Prokaryotes: the unseen majority Proc. Natl Acad. Sci. USA 95 1998 6578 6583
69. J. Wild M. Sektas Z. Hradecna W. Szybalski Targeting and retrofitting pre-existing libraries of transposon insertions with FRT and oriV elements for in-vivo generation of large quantities of any genomic fragment Gene 223 1998 55 66
70. J. Wild Z. Hradecna W. Szybalski On command amplification of large genomic fragments cloned in pBeloBAC/oriV vectors The 1999 Molecular Genetics of Bacteria and Phages Meeting Madison, WI 1999 44
71. E.A. Yakobson D.G. Guiney Conjugal transfer of bacterial chromosomes mediated by the RK2 plasmid transfer origin cloned into transposon Tn5 J. Bacteriol. 160 1984 451 453
72. J. Zhou M.A. Bruns J.M. Tiedje DNA recovery from soils of diverse composition Appl. Environ. Microbiol. 62 1996 316 322