Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities

Methods in Microbiology

Volumn 34, Issue , 2004, Pages 331-368

  Schadt, Christopher W ^a,b   Liebich, Jost ^a,b   Chong, Song C ^a,b   Gentry, Terry J ^a,b   He, Zhili ^a,b   Pan, Hongbin ^a,b   Zhou, Jizhong ^a,b  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 36148940946     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0580-9517(04)34011-0     Document Type: Review

References (163)

1. A. Allen M.G. Booth M.E. Frischer P.G. Verity J.P. Zehr S. Zani Diversity and detection of nitrate assimilation genes in marine bacteria Appl. Environ. Microbiol 67 2001 5343 5348
2. S. Altschul T. Madden A. Schäffer J. Zhang W. Miller D. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 1997 3389 3402
3. V. Andreoni S. Bernasconi M. Colombo J.B. van Beilen L. Cavalca Detection of genes for alkane and naphthalene catabolism in Rhodococcus sp. strain 1BN Environ. Microbiol 2 2000 572 577
4. B.R. Baldwin C.H. Nakatsu L. Nies Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR Appl. Environ. Microbiol 69 2003 3350 3358
5. T. Barkay S.M. Miller A.O. Summers Bacterial mercury resistance from atoms to ecosystems FEMS Microbiol. Rev 27 2003 355 384
6. M. Beaulieu V. Becaert L. Deschenes R. Villemur Evolution of bacterial diversity during enrichment of PCP-degrading activated soils Microb. Ecol 40 2000 345 356
7. T. Beißbarth K. Fellenberg B. Brors R. Arribas-Prat J.M. Boer N.C. Hauser M. Scheideler J.D. Hoheisel G. Schütz A. Poustka M. Virgon Processing and quality control of DNA array hybridization data Bioinformatics 16 2000 1014 1022
8. L. Bodrossy N. Stralis-Pavese J.C. Jurrell S. Radejewski A. Weilharter A. Sessitsch Development and validation of a diagnostic microbial microarray for methanotrophs Environ. Microbiol 5 2003 566 582
9. E.S. Bogdanova I.A. Bass L.S. Minakhin M.A. Petrova S.Z. Mindlin A.A. Volodin E.S. Kalyaeva J.M. Tiedje J.L. Hobman N.L. Brown V.G. Nikiforov Horizontal spread of mer operons among Gram-positive bacteria in natural environments Microbiology 144 1998 609 620
10. R. Bosch E. Garcia-Valdes E.R.B. Moore Genetic characterization and evolutionary implications of a chromosomally encoded naphthalene-degradation upper pathway from Pseudomonas stutzeri AN10 Gene 236 1999 149 157
11. G. Braker J.M. Tiedje Nitric oxide reductase (norB) genes from pure cultures and environmental samples Appl. Environ. Microbiol 69 2003 3476 3483
12. K.D. Bruce A.M. Osborn A.J. Pearson P. Strike D.A. Ritchie Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria Mol. Ecol 4 1995 605 612
13. Cassidy, S. L. (2002). Microbial activity and biodiversity as indicators of hydrocarbon bioremediation. Thesis. University of London, United Kingdom.
14. H. Castro K.R. Reddy A. Ogram Composition and function of sulfate-reducing prokaryotes in eutrophic and pristine areas of the Florida Everglades Appl. Environ. Microbiol 68 2002 6129 6137
15. Y.J. Chang A.D. Peacock P.E. Long J.R. Stephen J.P. McKinley S.J. Macnaughton A.K. Hussain A.M. Saxton D.C. White Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site Appl. Environ. Microbiol 67 2001 3149 3160
16. Y. Chen E.R. Dougherty M. Bittner Ratio-based decisions and the quantitative analysis of cDNA microarray images J. Biomed. Opt 2 1996 364 374
17. Y.T. Chien S.H. Zinder Cloning, DNA sequencing, and characterization of a nifD-homologous gene from the archaeon Methanosarcina barkeri 227 which resembles nifD from the eubacterium Clostridium pasteurianum J. Bacteriol 176 1994 6590 6598
18. J.C. Cho J.M. Tiedje Quantitative detection of microbial genes by using DNA microarrays Appl. Environ. Microbiol 68 2002 1425 1430
19. D.R. Dean J.T. Bolin L.M. Zheng Nitrogenase metalloclusters: structures, organization, and synthesis J. Bacteriol 175 1993 6737 6744
20. V.J. Denef J. Park J.L.M. Rodrigues T.V. Tsoi S.A. Hashsham J.M. Tiedje Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities Environ. Microbiol 5 2003 933 943
21. P. Dennis E.A. Edwards S.N. Liss R. Fulthorpe Monitoring gene expression in mixed microbial communities by using DNA microarrays Appl. Environ. Microbiol 69 2003 769 778
22. S.A. Denome D.C. Stanley E.S. Olson K.D. Young Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains – complete DNA-sequence of an upper naphthalene catabolic pathway J. Bacteriol 175 1993 6890 6901
23. B. Deplancke K.R. Hristova H.A. Oakley V.J. McCracken R. Aminov R.I. Mackie H.R. Gaskins Molecular ecological analysis of the succession and diversity of sulfate-reducing bacteria in the mouse gastrointestinal tract Appl. Environ. Microbiol 66 2000 2166 2174
24. J.L. DeRisi V.R. Iyer P.O. Brown Exploring the metabolic and genetic control of gene expression on a genomic scale Science 278 1997 680 686
25. F. Diehl S. Grahlmann M. Beier J.D. Hoheisel Manufacturing DNA microarrays of high spot homogeneity and reduced background signal Nucleic Acids Res 29 2001 E38
26. G.F. Duarte A.S. Rosado L. Seldin W. de Araujo J.D. van Elsas Analysis of bacterial community structure in sulfurous-oil-containing soils and detection of species carrying dibenzothiophene desulfurization ( dsz ) genes Appl. Environ. Microbiol 67 2001 1052 1062
27. N. Dubilier C. Mulders T. Ferdelman D. de Beer A. Pernthaler M. Klein M. Wagner C. Erseus F. Thiermann J. Krieger O. Giere R. Amann Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm Nature 411 2001 298 302
28. A.M. Dudley J. Aach M.A. Steffen G.M. Church Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range Proc. Natl Acad. Sci 99 2002 7554 7559
29. P.F. Dunfield W. Liesack T. Henckel R. Knowles R. Conrad High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph Appl. Environ. Microbiol 65 1999 1009 1014
30. M.B. Eisen P.T. Spellman P.O. Brown D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl Acad. Sci 95 1998 14863 14868
31. H. Elsaied T. Naganuma Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms Appl. Environ. Microbiol 67 2001 1751 1765
32. S.J. Emrich M. Lowe A. Delcher PROBEmer: a web-based software tool for selecting optimal DNA oligos Nucleic Acids Res 31 2003 3746 3750
33. A.D.M. Felske W. Fehr B.V. Pauling H. von Canstein I. Wagner-Dobler Functional profiling of mercuric reductase ( mer A) genes in biofilm communities of a technical scale biocatalyzer BMC Microbiol 3 2003 22 (published online- http://www.biomedcentral.com/1471-2180/3/22 )
34. M. Ferrero E. Llobet-Brossa J. Lalucat E. Garcia-Valdes R. Rossello-Mora R. Bosch Coexistence of two distinct copies of naphthalene degradation genes in Pseudomonas strains isolated from the western Mediterranean region Appl. Environ. Microbiol 68 2002 957 962
35. S.M. Finegold H. Jousimies-Somer Recently described clinically important anaerobic bacteria: medical aspects Clin. Infect. Dis 25 Suppl. 2 1997 S88 S93
36. M.W. Friedrich Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphosulfate reductase genes among sulfate-reducing microorganisms J. Bacteriol 184 2002 278 289
37. S.L. Fuenmayor M. Wild A.L. Boyes P.A. Williams A gene cluster encoding steps in conversion of naphthalene to gentisate in Pseudomonas sp. strain U2 J. Bacteriol 180 1998 2522 2530
38. T. Furuchi G.W. Hwang A. Naganuma Overexpression of the ubiquitin-conjugating enzyme Cdc34 confers resistance to methylmercury in Saccharomyces cerevisiae Mol. Pharmacol 61 2002 738 741
39. A.D. Geiselbrecht B.P. Hedlund M.A. Tichi J.T. Staley Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of Puget Sound Cycloclasticus strains Appl. Environ. Microbiol 64 1998 4703 4710
40. D.R. Gilbert M. Schroeder J. van Helden Interactive visualization and exploration of relationships between biological objects Trends Biotechnol 18 2000 487 494
41. O. Gueldry M. Lazard F. Delort M. Dauplais I. Grigoras S. Blanquet P. Plateau Ycf1p-dependent Hg(II) detoxification in Saccharomyces cerevisiae Eur. J. Biochem 270 2003 2486 2496
42. H. Habe T. Omori Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria Biosci. Biotechnol. Biochem 67 2003 225 243
43. S.J. Hallam P.R. Girguis C.M. Preston P.M. Richardson E.F. DeLong Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea Appl. Environ. Microbiol 69 2003 5483 5491
44. C. Hamann J. Hegemann A. Hildebrandt Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization FEMS Microbiol. Lett 173 1999 255 263
45. M.C. Hart G.N. Elliott A.M. Osborn D.A. Ritchie P. Strike Diversity amongst Bacillus mer A genes amplified from mercury resistant isolates and directly from mercury polluted soil FEMS Microbiol. Ecol 27 1998 73 84
46. B.P. Hedlund A.D. Geiselbrecht T.J. Bair J.T. Staley Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov Appl. Environ. Microbiol 65 1999 251 259
47. B.P. Hedlund A.D. Geiselbrecht J.T. Staley Marinobacter strain NCE312 has a Pseudomonas -like naphthalene dioxygenase FEMS Microbiol. Lett 201 2001 47 51
48. P. Hegde R. Qi K. Abernathy C. Gay S. Dharap R. Gaspard J.E. Hughes E. Snesrud N. Lee J. Quackenbush A concise guide to cDNA microarray analysis BioTechniques 29 2000 548 560
49. J.B. Herrick K.G. StuartKeil W.C. Ghiorse E.L. Madsen Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site Appl. Environ. Microbiol 63 1997 2330 2337
50. S.G. Hilsenbeck W.E. Friedrichs R. Schiff P. O'Connell R.K. Hansen C.K. Osborne S.A. Fuqua Statistical analysis of array expression data as applied to the problem of tamoxifen resistance J. Natl Cancer Inst 91 1999 53 459
51. C. Holliger D. Hahn H. Harmsen W. Ludwig W. Schumacher B. Tindall F. Vazquez N. Weiss A.J. Zehnder Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration Arch. Microbiol 169 1998 313 321
52. A.J. Holmes A. Costello M.E. Lidstrom J.C. Murrell Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related FEMS Microbiol. Lett 132 1995 203 208
53. H.P. Horz M.T. Yimga W. Liesack Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA , mmoX , mxaF , and 16S rRNA and ribosomal DNA including pmoA -based terminal restriction fragment length polymorphism profiling Appl. Environ. Microbiol 67 2001 4177 4185
54. J.B. Howard D.C. Rees Structural basis of biological nitrogen fixation Chem. Rev 96 1996 2965 2982
55. H. Huber H. Jannasch R. Rachel T. Fuchs K.O. Stetter Archaeoglobus veneficus sp. nov., a novel facultative chemolithoautotrophic hyperthermophilic sulfite reducer, isolated from abyssal black smokers Syst. Appl. Microbiol 20 1997 374 380
56. T. Hurek T. Egener B. Reinhold-Hurek Divergence in nitrogenases of Azoarcus spp., Proteobacteria of the beta subclass J. Bacteriol 179 1997 4172 4178
57. R.A. Hurt X. Qui L. Wu Y. Roh A.V. Palumbo J.M. Tiedje J. Zhou Simultaneous recovery of RNA and DNA from soils and sediments Appl. Environ. Microbiol 67 2001 4495 4503
58. C.O. Jeon W. Park P. Padmanabhan C. DeRito J.R. Snape E.L. Madsen Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment Proc. Natl Acad. Sci. USA 100 2003 13591 13596
59. B.B. Jørgensen Mineralization of organic-matter in the sea bed – the role of sulfate reduction Nature 296 1982 643 645
60. R.R. Karkhoff-Schweizer D.P. Huber G. Voordouw Conservation of the genes for dissimilatory sulfite reductase from Desulfovibrio vulgaris and Archaeoglobus fulgidus allows their detection by PCR Appl. Environ. Microbiol 61 1995 290 296
61. Y. Kasai K. Shindo S. Harayama N. Misawa Molecular characterization and substrate preference of a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5 Appl. Environ. Microbiol 69 2003 6688 6697
62. B. Kauppi K. Lee E. Carredano R.E. Parales D.T. Gibson H. Eklund S. Ramaswamy Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase Struct. Fold. Des 6 1998 571 586
63. G. Kholodii O. Yurieva S. Mindlin Z. Gorlenko V. Rybochkin V. Nikiforov Tn 5044 , a novel Tn3 family transposon coding for temperature-sensitive mercury resistance Res. Microbiol 151 2000 291 302
64. J.D. Kirshtein H.W. Paerl J. Zehy Amplification, cloning, and sequencing of a nifH segment from aquatic microorganisms and natural communities Appl. Environ. Microbiol 57 1991 2645 2650
65. J. Kleikemper M.H. Schroth W.V. Sigler M. Schmucki S.M. Bernasconi J. Zeyer Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer Appl. Environ. Microbiol 68 2002 1516 1523
66. M. Klein M. Friedrich A.J. Roger P. Hugenholtz S. Fishbain H. Abicht L.L. Blackall D.A. Stahl M. Wagner Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes J. Bacteriol 83 2001 6028 6035
67. Y. Koizumi J.J. Kelly T. Nakagawa H. Urakawa S. El-Fantroussi S. Al-Muzaini M. Fukui Y. Urushigawa D.A. Stahl Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA–DNA membrane hybridization, and DNA microarray technology Appl. Environ. Microbiol 68 2002 3215 3225
68. S. Kurkela H. Lehvaslaiho E.T. Palva T.H. Teeri Cloning, nucleotide-sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816 Gene 73 1988 355 362
69. R.A. Laddaga L.E. Chu T.K. Misra S. Silver Nucleotide sequence and expression of the mercurial-resistance operon from Staphylococcus aureus plasmid pI258 Proc. Natl Acad. Sci. USA 84 1987 5106 5110
70. M.J. Larkin C.C.R. Allen L.A. Kulakov D.A. Lipscomb Purification and characterization of a novel naphthalene dioxygenase from Rhodococcus sp. strain NCIMB12038 J. Bacteriol 181 1999 6200 6204
71. O. Larsen T. Lien N.K. Birkeland Dissimilatory sulfite reductase from Archaeoglobus profundus and Desulfotomaculum thermocisternum : phylogenetic and structural implications from gene sequences Extremophiles 3 1999 63 70
72. H. Laue M. Friedrich J. Ruff A.M. Cook Dissimilatory sulfite reductase (desulfoviridin) of the taurine-degrading, non-sulfate-reducing bacterium Bilophila wadsworthia RZATAU contains a fused DsrB–DsrD subunit J. Bacteriol 183 2001 1727 1733
73. A.B. Leaphart C.R. Lovell Recovery and analysis of formyltetrahydrofolate synthetase gene sequences from natural populations of acetogenic bacteria Appl. Environ. Microbiol 67 2001 1392 1395
74. F. Li G. Stormo Selection of optimal DNA oligos for gene expression arrays Bioinformatics 17 2001 1067 1076
75. X. Liu S.M. Tiquia G. Holguin L. Wu S.C. Nold A.H. Devol K. Luo A. Palumbo J.M. Tiedje J. Zhou Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the pacific coast of Mexico Appl. Environ. Microbiol 69 2003 3549 3560
76. Y. Liu J. Zhou M. Omelchenko A. Beliaev A. Venkateswaran J. Stair L. Wu D.K. Thompson D. Xu I.B. Rogozin E.K. Gaidamakova M. Zhai K.S. Makarova E.V. Koonin M.J. Daly Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation Proc. Natl Acad. Sci. USA 100 2003 4191 4196
77. G. Lloyd-Jones A.D. Laurie D.W.F. Hunter R. Fraser Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils FEMS Microbiol. Ecol 29 1999 69 79
78. D.J. Lockhart H. Dong M.C. Byrne M.T. Follettie M.V. Gallo M.S. Chee M. Mittmann C. Wang M. Kobayashi H. Horton E.L. Brown Expression monitoring by hybridization to high-density oligonucleotide arrays Nat. Biotechnol 14 1996 1675 1680
79. D.R. Lovley Potential for anaerobic bioremediation of BTEX in petroleum-contaminated aquifers J. Ind. Microbiol. Biotechnol 18 1997 75 81
80. D.R. Lovley M.J. Klug Sulfate reducers can out-compete methanogens at fresh-water sulfate concentrations Appl. Environ. Microbiol 45 1983 187 192
81. J.I. Lyons S.Y. Newell A. Buchan M.A. Moran Diversity of ascomycete laccase gene sequences in a southeastern U.S. salt marsh Microb. Ecol 45 2003 270 281
82. W. Manz M. Eisenbrecher T.R. Neu U. Szewzyk Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides FEMS Microbiol. Ecol 25 1998 43 61
83. J.R. Marchesi A.J. Weightman Comparing the dehalogenase gene pool in cultivated α-halocarboxylic acid-degrading bacteria with the environmental metagene pool Appl. Environ. Microbiol 69 2003 4375 4382
84. F. Martin-Laurent S. Piutti S. Hallet I. Wagschal L. Philippot G. Catroux G. Soulas Monitoring of atrazine treatment on soil bacterial, fungal and atrazine-degrading communities by quantitative competitive PCR Pest. Manag. Sci 59 2003 259 268
85. R.P. Mason W.F. Fitzgerald F.M.M. Morel The biogeochemical cycling of elemental mercury – anthropogenic influences Geochim. Cosmochim. Acta 58 1994 3191 3198
86. C. McGowan R. Fulthorpe A. Wright J.M. Tiedje Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders Appl. Environ. Microbiol 64 1998 4089 4092
87. K.D. McMahon M.A. Dojka N.R. Pace D. Jenkins J.D. Keasling Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal Appl. Environ. Microbiol 68 2002 4971 4978
88. R.J. Melcher S.E. Apitz B.B. Hemmingsen Impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies Appl. Environ. Microbiol 68 2002 2858 2868
89. A.C. Metcalfe M. Krsek G.W. Gooday J.I. Prosser E.M.H. Wellington Molecular analysis of a bacterial chitinolytic community in an upland pasture Appl. Environ. Microbiol 68 2002 5042 5050
90. M. Molitor C. Dahl I. Molitor U. Schafer N. Speich R. Huber R. Deutzmann H.G. Truper A dissimilatory sirohaem-sulfite-reductase-type protein from the hyperthermophilic archaeon Pyrobaculum islandicum Microbiology 144 1998 529 541
91. K. Mori H. Kim T. Kakegawa S. Hanada A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense , gen. nov., sp. nov., a new thermophilic isolate from a hot spring Extremophiles 7 2003 283 290
92. J.C. Murrell B. Gilbert I.R. McDonald Molecular biology and regulation of methane monooxygenase Arch. Microbiol 173 2000 325 332
93. J.C. Murrell I.R. McDonald D.G. Bourne Molecular methods for the study of methanotroph ecology FEMS Microbiol. Ecol 27 1998 103 114
94. E.W. Myers Ninth Combinatorial Pattern Matching Conference 1998 Springer Piscataway, NJ pp. 1–13
95. T. Nakagawa S. Nakagawa F. Inagaki K. Takai K. Horikoshi Phylogenetic diversity of sulfate-reducing prokaryotes in active deep-sea hydrothermal vent chimney structures FEMS Microbiol. Lett 232 2004 145 152
96. A.M. Nascimento E. Chartone-Souza Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments Genet. Mol. Res 2 92 2003 101
97. N.T. Nguyên-nhu B. Knoops Alkyl hydroperoxide reductase 1 protects Saccharomyces cerevisiae against metal ion toxicity and glutathione depletion Toxicol. Lett 135 2002 219 228
98. H.B. Nielsen R. Wernersson S. Knudsen Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays Nucleic Acids Res 31 2003 3491 3496
99. S.C. Nold J.Z. Zhou A.H. Devol J.M. Tiedje Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the Proteobacteria Appl. Environ. Microbiol 66 2000 4532 4535
100. P. Normand J. Bousquet Phylogeny of nitrogenase sequences in Frankia and other nitrogen-fixing microorganisms J. Mol. Evol 29 1989 436 447
101. P. Normand M. Gouy B. Cournoyer P. Simonet Nucleotide sequence of nifD from Frankia alni strain ARI3: phylogenetic inferences Mol. Biol. Evol 9 1992 495 506
102. C. Oger J. Mahillon F. Petit Distribution and diversity of a cadmium resistance ( cadA ) determinant and occurrence of IS257 insertion sequences in Staphylococcal bacteria isolated from a contaminated estuary (Seine, France) FEMS Microbol. Ecol 43 2003 173 183
103. A.M. Osborn K.D. Bruce P. Strike D.A. Ritchie Distribution, diversity and evolution of the bacterial mercury resistance ( mer ) operon FEMS Microbiol. Rev 19 1997 239 262
104. R.E. Parales M.D. Emig N.A. Lynch D.T. Gibson Substrate specificities of hybrid naphthalene and 2,4-dinitrotoluene dioxygenase enzyme systems J. Bacteriol 180 1998 2337 2344
105. R.E. Parales K. Lee S.M. Resnick H.Y. Jiang D.J. Lessner D.T. Gibson Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme J. Bacteriol 182 2000 1641 1649
106. W. Park P. Padmanabhan S. Padmanabhan G.J. Zylstra E.L. Madsen nahR , encoding a LysR-type transcriptional regulator, is highly conserved among naphthalene-degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA Microbiology 148 2002 2319 2329
107. L. Philippot S. Piutti F. Martin-Laurent S. Hallet J.C. Germon Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils Appl. Environ. Microbiol 68 2002 6121 6128
108. G. Piétu O. Alibert V. Guichard B. Lamy F. Bois E. Leroy R. Mariage-Samson R. Houlgatte P. Soularue C. Auffray Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array Genome Res 6 1996 492 503
109. R. Rabus T. Hansen F. Widdel The dissimilatory sulfate- and sulfur reducing Prokaryotes M. Dworkin The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community 3rd edn. 2000 Springer New York release 3.3, http://link.springer-ny.com/link/service/books/10125/
110. A. Relogio C. Schwager A. Richter W. Ansorge A. Valcarcel Optimization of oligonucleotide-based DNA microarrays Nucleic Acids Res 30 2002 e51
111. D. Reniero E. Mozzon E. Galli P. Barbieri Two aberrant mercury resistance transposons in the Pseudomonas stutzeri plasmid pPB Gene 208 1998 37 42
112. C. Rensing D.T. Newby I.L. Pepper The role of selective pressure and selfish DNA in horizontal gene transfer and soil microbial community adaptation Soil Biol. Biochem 34 2002 285 296
113. N. Reymond H. Charles L. Duret F. Calevro G. Beslon J.-M. Fayard ROSO: optimizing oligonucleotide probes for microarrays Bioinformatics 20 2004 271 273
114. S.K. Rhee X. Liu L. Wu S.C. Chong X. Wan J. Zhou Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays Appl. Environ. Microbiol 70 2004 4303 4317
115. C.S. Richmond J.D. Glasner R. Mau H. Jin F.R. Blattner Genome-wide expression profiling in Escherichia coli K-12 Nucleic Acids Res 27 1999 3821 3835
116. M.F. Romine L.C. Stillwell K.K. Wong S.J. Thurston E.C. Sisk C. Sensen T. Gaasterland J.K. Fredrickson J.D. Saffer Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199 J. Bacteriol 181 1999 1585 1602
117. J.-M. Rouillard C. Herbert M. Zuker OligoArray: genome-scale oligonucleotide design for microarrays Bioinformatics 18 2002 486 487
118. J.-M. Rouillard M. Zuker E. Gulari OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using thermodynamic approach Nucleic Acids Res 31 2003 3057 3062
119. S. Rozen H.J. Skaletsky Primer3 on the WWW for general users and for biologist programmers Meth. Mol. Biol 13 2000 365 386
120. D. Scala L.J. Kerkhof Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments Appl. Environ. Microbiol 65 1999 1681 1687
121. J. Schelert V. Dixit V. Hoang J. Simbahan M. Drozda P. Blum Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption J. Bacteriol 2 2004 427 437
122. M. Schena D. Shalon R.W. Davis P.O. Brown Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 270 1995 467 470
123. M. Schena D. Shalon R. Heller A. Chai P.O. Brown R.W. Davis Parallel human genome analysis: microarray-based expression monitoring of 1000 genes Proc. Natl Acad. Sci. USA 93 1996 10614 10619
124. A. Schluter H. Heuer R. Szczepanowski L.J. Forney C.M. Thomas A. Puhler E.M. Top The 64 508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1β group Microbiology 149 2003 3139 3153
125. S. Schneiker M. Keller M. Droge E. Lanka A. Puhler W. Selbitschka The genetic organization and evolution of the broad host range mercury resistance plasmid pSB102 isolated from a microbial population residing in the rhizosphere of alfalfa Nucleic Acids Res 29 2001 5169 5181
126. J. Schuchhardt D. Beule A. Malik E. Wolski H. Eickhoff H. Lehrach H. Herzel Normalization strategies for cDNA microarrays Nucleic Acids Res 28 2000 E47
127. R. Singleton Jr. The sulfate-reducing bacteria: an overview J.M. Odom R. Singleton Jr. The Sulfate-Reducing Bacteria: Contemporary Perspectives Brock/Springer Series in Contemporary Bioscience 1993 Springer New York 1 20
128. M. Sota H. Kawasaki M. Tsuda Structure of haloacetate-catabolic IncP-1β plasmid pUO1 and genetic mobility of its residing haloacetate-catabolic transposon J. Bacteriol 185 2003 6741 6745
129. E. Spanakis D. Brouty-Boyé Discrimination of fibroblast subtypes by multivariate analysis of gene expression Int. J. Cancer 71 1997 402 409
130. J.E.M. Stach R.G. Burns Enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities Environ. Microbiol 4 2002 169 182
131. J.P. Sullivan D. Dickinson H.A. Chase Methanotrophs, Methylosinus trichosporium OB3b, sMMO, and their application to bioremediation Crit. Rev. Microbiol 24 1998 335 373
132. C.G. Sun C.E. Snape C. McRae A.E. Fallick Resolving coal and petroleum-derived polycyclic aromatic hydrocarbons (PAHs) in some contaminated land samples using compound-specific stable carbon isotope ratio measurements in conjunction with molecular fingerprints Fuel 82 2003 2017 2023
133. N. Takizawa T. Iida T. Sawada K. Yamauchi Y.W. Wang M. Fukuda H. Kiyohara Nucleotide sequences and characterization of genes encoding naphthalene upper pathway of Pseudomonas aeruginosa PaK1 and Pseudomonas putida OUS82 J. Biosci. Bioeng 87 1999 721 731
134. N. Takizawa N. Kaida S. Torigoe T. Moritani T. Sawada S. Satoh H. Kiyohara Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82 J. Bacteriol 176 1994 2444 2449
135. A.M. Talaat S.T. Howard W. Hale IV R. Lyons H. Garner S.A. Jonston Genomic DNA standards for gene expression profiling in Mycobacterium tuberculosis Nucleic Acids Res 30 2002 e104
136. P. Tamayo D. Slonim J. Mesirov Q. Zhu S. Kitareewan E. Dmitrovsky E.S. Lander T.R. Golub Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation Proc. Natl Acad. Sci 96 1999 2907 2912
137. G. Taroncher-Oldenburg E.M. Griner C.A. Francis B.B. Ward Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment Appl. Environ. Microbiol 69 2002 1159 1171
138. J.G. Thomas J.M. Olson S.J. Tapscott L.P. Zhao An efficient and robust statistical modeling approach to discover differentially expressed genes using genomic expression profiles Genome Res 11 2001 1227 1236
139. D.K. Thompson A.S. Beliaev C.S. Giometti S.L. Tollaksen T. Khare D.P. Lies K.H. Nealson H. Lim J. Yates III C.C. Brandt J.M. Tiedje J. Zhou Transcriptional and proteomic analysis of a ferric uptake regulator (Fur) mutant of Shewanella oneidensis : possible involvement of Fur in energy metabolism, transcriptional regulation, and oxidative stress Appl. Environ. Microbiol 68 2002 881 892
140. S.M. Tiquia L. Wu S.C. Chong S. Passovets D. Xu Y. Xu J. Zhou Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples BioTechniques 36 2004 664 675
141. E.M. Top D. Springael The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds Curr. Opin. Biotechnol 14 2003 262 269
142. T. Ueda Y. Suga N. Yahiro T. Matsuguchi Genetic diversity of N2-fixing bacteria associated with rice roots by molecular evolutionary analysis of a nifD library Can. J. Microbiol 41 1995 235 240
143. M.M. Venkatesan M.B. Goldberg D.J. Rose E.J. Grotbeck V. Burland F.R. Blattner Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri Infect. Immun 69 2001 3271 3285
144. P.M. Vitousek R.W. Howarth Nitrogen limitation on land and in the sea: how can it occur? Biogeochemistry 13 1991 87 115
145. L.P. Wackett Mechanism and applications of Rieske non-heme iron dioxygenases Enzyme Microb. Technol 31 2002 577 587
146. M. Wagner A.J. Roger J.L. Flax G.A. Brusseau D.A. Stahl Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration J. Bacteriol 180 1998 2975 2982
147. X. Wang B. Seed Selection of oligonucleotide probes for protein coding sequences Bioinformatics 19 2003 796 802
148. J. Westwater N.F. McLaren U.H. Dormer D.J. Jamieson The adaptive response of Saccharomyces cerevisiae to mercury exposure Yeast 19 2002 233 239
149. F. Widmer B.T. Shaffer L.A. Porteous R.J. Seidler Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon Cascade mountain range Appl. Environ. Microbiol 65 1999 374 380
150. M.S. Wilson C. Bakermans E.L. Madsen In situ, real-time catabolic gene expression: extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater Appl. Environ. Microbiol 65 1999 80 87
151. M.S. Wilson J.B. Herrick C.O. Jeon D.E. Hinman E.L. Madsen Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments Appl. Environ. Microbiol 69 2003 2172 2181
152. L.Y. Wu D.K. Thompson G. Li R.A. Hurt J.M. Tiedje J. Zhou Development and evaluation of functional gene arrays for detection of selected gene in the environment Appl. Environ. Microbiol 67 2001 5780 5790
153. D. Xu G. Li L. Wu J. Zhou Y. Xu PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis Bioinformatics 18 11 2002 1432 1437
154. R.W. Ye W. Tao L. Beddzyk T. Young M. Chen L. Li Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions J. Bacteriol 182 2000 4458 4465
155. O. Yurieva G. Kholodii L. Minakhin Z. Gorlenko E. Kalyaeva S. Mindlin V. Nikiforov Intercontinental spread of promiscuous mercury-resistance transposons in environmental bacteria Mol. Microbiol 24 1997 321 329
156. J.H. Zar Biostatistical Analysis 1999 Prentice-Hall Englewood Cliffs, NJ
157. J.P. Zehr L.A. McReynolds Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium spp Appl. Environ. Microbiol 55 1989 2522 2526
158. J.P. Zehr M. Mellon S. Braun W. Litaker T. Steppe H.W. Paerl Diversity of heterotrophic nitrogen fixation genes in a marine cyanobacterial mat Appl. Environ. Microbiol 61 1995 2527 2532
159. J. Zhou Microarrays for bacterial detection and microbial community analysis Curr. Opin. Microbiol 6 2003 288 294
160. J. Zhou D.K. Thompson Challenges in applying microarrays to environmental studies Curr. Opin. Biotechnol 13 2002 204 207
161. J. Zhou M.A. Bruns J.M. Tiedje DNA recovery from soils of diverse composition Appl. Environ. Microbiol 62 1996 461 468
162. Zhu, J., Bozdech, Z. and DeRisi, J. (2003). ArrayOligoSelector . http://sourceforge.net/projects/arrayoligosel/ .
163. M. Zuker D.H. Mathews D.H. Turner Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide J. Barciszewski B.F.C. Clark RNA Biochemistry and Biotechnology 1999 Kluwer Academic Publishers Dordrecht 11 43