Exploring the microbial biodegradation and biotransformation gene pool

Trends in Biotechnology

Volumn 23, Issue 10, 2005, Pages 497-506

  Galvão, Teca Calcagno ^a   Mohn, William W ^b   De Lorenzo, Víctor ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIODEGRADATION; ENZYMES; MICROORGANISMS;

BIOTRANSFORMATION; MICROBIAL BIODEGRADATION; MICROBIAL LIFESTYLES;

BIOTECHNOLOGY;

GREEN FLUORESCENT PROTEIN; RIBOSOME RNA; STABLE ISOTOPE; XENOBIOTIC AGENT;

BIODEGRADABILITY; BIOLOGICAL ACTIVITY; BIOTRANSFORMATION; CATABOLISM; DIFFERENTIAL DISPLAY; DNA FINGERPRINTING; DNA LIBRARY; DNA MICROARRAY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE IDENTIFICATION; GENE POOL; GENE SEQUENCE; GENOME; MICROORGANISM; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PHYLOGENY; POLLUTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEOBACTERIA; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

BACTERIA; BIOTRANSFORMATION; GENE POOL; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION;

EID: 24944526639     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2005.08.002     Document Type: Review

References (83)

1. J.C. Venter Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74
2. C. Dong Crystal structure and mechanism of a bacterial fluorinating enzyme Nature 427 2004 561 565
3. D.L. Zechel Enzymatic synthesis of carbon-fluorine bonds J. Am. Chem. Soc. 123 2001 4350 4351
4. K.N. Timmis, and D.H. Pieper Bacteria designed for bioremediation Trends Biotechnol. 17 1999 200 204
5. A. Schmid Industrial biocatalysis today and tomorrow Nature 409 2001 258 268
6. L.B. Ellis The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining Nucleic Acids Res. 31 2003 262 265
7. Pazos, F. et al. (2005) MetaRouter: bioinformatics for bioremediation. Nucleic Acids Res. 33 Database Issue, D588-D592
8. H. Futamata Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation Appl. Environ. Microbiol. 67 2001 4671 4677
9. M.S. Wilson In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater Appl. Environ. Microbiol. 65 1999 80 87
10. B.R. Baldwin Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR Appl. Environ. Microbiol. 69 2003 3350 3358
11. H.M. Dionisi Abundance of dioxygenase genes similar to Ralstonia sp strain U2 nagAc is correlated with naphthalene concentrations in coal tar-contaminated freshwater sediments Appl. Environ. Microbiol. 70 2004 3988 3995
12. P.M. Taylor Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria FEMS Microbiol. Lett. 216 2002 61 66
13. N. Fromin Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns Environ. Microbiol. 4 2002 634 643
14. H. Junca, and D.H. Pieper Amplified functional DNA restriction analysis to determine catechol 2,3-dioxygenase gene diversity in soil bacteria J. Microbiol. Methods 55 2003 697 708
15. R. Amann The identification of microorganisms by fluorescence in situ hybridization Curr. Opin. Biotechnol. 12 2001 231 236
16. A. Moter, and U.B. Gobel Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms J. Microbiol. Methods 41 2000 85 112
17. A. Pernthaler, and R. Amann Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria Appl. Environ. Microbiol. 70 2004 5426 5433
18. P. Lebaron A new sensitive, whole-cell hybridization technique for detection of bacteria involving a biotinylated oligonucleotide probe targeting rRNA and tyramide signal amplification Appl. Environ. Microbiol. 63 1997 3274 3278
19. W. Schonhuber Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification Appl. Environ. Microbiol. 63 1997 3268 3273
20. C. Bakermans, and E.L. Madsen Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization with tyramide signal amplification J. Microbiol. Methods 50 2002 75 84
21. J.C. Dias Molecular diversity of mesophilic and thermophilic bacteria in a membrane bioreactor determined by fluorescent in situ hybridization with mxaF- and rRNA-targeted probes J. Basic Microbiol. 43 2003 202 209
22. F. Chen In situ reverse transcription, an approach to characterize genetic diversity and activities of prokaryotes Appl. Environ. Microbiol. 63 1997 4907 4913
23. F. Chen Microscopic detection of the toluene dioxygenase gene and its expression inside bacterial cells in seawater using prokaryotic in situ PCR Hydrobiologia 401 1999 131 138
24. T. Hoshino Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process Appl. Environ. Microbiol. 67 2001 5261 5266
25. T. Hoshino In situ PCR for visualizing distribution of a functional gene 'amoA' in a biofilm regardless of activity J. Biotechnol. 105 2003 33 40
26. F. Maruyama Detection of bacteria carrying the stx2 gene by in situ loop-mediated isothermal amplification Appl. Environ. Microbiol. 69 2003 5023 5028
27. J. Zhou, and D.K. Thompson Challenges in applying microarrays to environmental studies Curr. Opin. Biotechnol. 13 2002 204 207
28. J. Zhou Microarrays for bacterial detection and microbial community analysis Curr. Opin. Microbiol. 6 2003 288 294
29. S.K. Rhee Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays Appl. Environ. Microbiol. 70 2004 4303 4317
30. B.D. Jenkins Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray Appl. Environ. Microbiol. 70 2004 1767 1776
31. G.F. Steward Development and testing of a DNA macroarray to assess nitrogenase (nifH) gene diversity Appl. Environ. Microbiol. 70 2004 1455 1465
32. S.M. Tiquia Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples Biotechniques 36 2004 664 675
33. L. Wu Development and evaluation of functional gene arrays for detection of selected genes in the environment Appl. Environ. Microbiol. 67 2001 5780 5790
34. N. Stralis-Pavese Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers Environ. Microbiol. 6 2004 347 363
35. P. Dennis Monitoring gene expression in mixed microbial communities by using DNA microarrays Appl. Environ. Microbiol. 69 2003 769 778
36. A. Okuta PCR isolation of catechol 2,3-dioxygenase gene fragments from environmental samples and their assembly into functional genes Gene 212 1998 221 228
37. P. Liang A decade of differential display Biotechniques 33 2002 338 346
38. P. Liang, and A.B. Pardee Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction Science 257 1992 967 971
39. D.M. Walters High-density sampling of a bacterial operon using mRNA differential display Gene 273 2001 305 315
40. P.C. Brzostowicz Simultaneous identification of two cyclohexanone oxidation genes from an environmental Brevibacterium isolate using mRNA differential display J. Bacteriol. 182 2000 4241 4248
41. P.C. Brzostowicz mRNA differential display in a microbial enrichment culture: simultaneous identification of three cyclohexanone monooxygenases from three species Appl. Environ. Microbiol. 69 2003 334 342
42. J.T. Fleming Optimization of differential display of prokaryotic mRNA: application to pure culture and soil microcosms Appl. Environ. Microbiol. 64 1998 3698 3706
43. M. Meselson, and F.W. Stahl The replication of DNA Cold Spring Harb. Symp. Quant. Biol. 23 1958 9 12
44. S. Radajewski Stable-isotope probing as a tool in microbial ecology Nature 403 2000 646 649
45. L.P. Wackett Stable isotope probing in biodegradation research Trends Biotechnol. 22 2004 153 154
46. P.D. Schloss, and J. Handelsman Biotechnological prospects from metagenomics Curr. Opin. Biotechnol. 14 2003 303 310
47. C.O. Jeon Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment Proc. Natl. Acad. Sci. U. S. A. 100 2003 13591 13596
48. 13- labeled soil DNA Appl. Environ. Microbiol. 69 2003 1614 1622
49. M. Manefield RNA stable isotope probing, a novel means of linking microbial community function to Phylogeny Appl. Environ. Microbiol. 68 2002 5367 5373
50. A. Tschech, and G. Fuchs Anaerobic degradation of phenol by pure cultures of newly isolated denitrifying pseudomonads Arch. Microbiol. 148 1987 213 217
51. C.S. Harwood, and J. Gibson Anaerobic and aerobic metabolism of diverse aromatic compounds by the photosynthetic bacterium Rhodopseudomonas palustris Appl. Environ. Microbiol. 54 1988 712 717
52. A.S. Whiteley Bacterial community structure and physiological analyses of Pseudomonad species within a phenol remediation system J. Microbiol. Methods 44 2000 79 88
53. A.S. Whiteley, and M.J. Bailey Bacterial community structure and physiological state within an industrial phenol bioremediation system Appl. Environ. Microbiol. 66 2000 2400 2407
54. M. Manefield 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
55. S. Radajewski Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms Curr. Opin. Biotechnol. 14 2003 296 302
56. R. Daniel The soil metagenome - a rich resource for the discovery of novel natural products Curr. Opin. Biotechnol. 15 2004 199 204
57. M.A. Schneegurt Direct extraction of DNA from soils for studies in microbial ecology Curr. Issues Mol. Biol. 5 2003 1 8
58. S. Courtois Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products Appl. Environ. Microbiol. 69 2003 49 55
59. A. Martinez 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 2004 2452 2463
60. G.Y. Wang Novel natural products from soil DNA libraries in a streptomycete host Org. Lett. 2 2000 2401 2404
61. E.M. Gabor Quantifying the accessibility of the metagenome by random expression cloning techniques Environ. Microbiol. 6 2004 879 886
62. J.P. Goddard, and J.L. Reymond Enzyme assays for high-throughput screening Curr. Opin. Biotechnol. 15 2004 314 322
63. W.R. Streit Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms Curr. Opin. Biotechnol. 15 2004 285 290
64. P.B. Warren, and P.R. ten Wolde Statistical analysis of the spatial distribution of operons in the transcriptional regulation network of Escherichia coli J. Mol. Biol. 342 2004 1379 1390
65. T. Uchiyama Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes Nat. Biotechnol. 23 2005 88 93
66. I. Cases, and V. de Lorenzo The black cat/white cat principle of signal integration in bacterial promoters EMBO J. 20 2001 1 11
67. J. Garmendia À la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors Mol. Microbiol. 42 2001 47 59
68. L.L. Looger Computational design of receptor and sensor proteins with novel functions Nature 423 2003 185 190
69. S. Becker Ultra-high-throughput screening based on cell-surface display and fluorescence-activated cell sorting for the identification of novel biocatalysts Curr. Opin. Biotechnol. 15 2004 323 329
70. S. Radajewski Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing Microbiology. 148 2002 2331 2342
71. S.A. Morris Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing Appl. Environ. Microbiol. 68 2002 1446 1453
72. J.L. Lin Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing Environ. Microbiol. 6 2004 1049 1060
73. E. Hutchens Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing Environ. Microbiol. 6 2004 111 120
74. M.P. Ginige Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community Appl. Environ. Microbiol. 70 2004 588 596
75. T. Lueders Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rice field soil Environ. Microbiol. 6 2004 60 72
76. M.R. Rondon Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl. Environ. Microbiol. 66 2000 2541 2547
77. 12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures Appl. Environ. Microbiol. 69 2003 3048 3060
78. S. Voget Prospecting for novel biocatalysts in a soil metagenome Appl. Environ. Microbiol. 69 2003 6235 6242
79. A. Knietsch 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 2003 46 56
80. A. Knietsch 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 2003 1408 1416
81. A. Henne 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
82. H. Junca Difference in kinetic behaviour of catechol 2,3-dioxygenase variants from a polluted environment Microbiology 150 2004 4181 4187
83. R.S. Poretsky Analysis of microbial gene transcripts in environmental samples Appl. Environ. Microbiol. 71 2005 4121 4126