Use of genetically engineered microorganisms (GEMs) for the bioremediation of contaminants

Critical Reviews in Biotechnology

Volumn 26, Issue 3, 2006, Pages 145-164

  Urgun Demirtas, Meltem ^a   Stark, Benjamin ^b   Pagilla, Krishna ^a  

^a ILLINOIS INSTITUTE OF TECHNOLOGY   (United States)

^b Illinois Institute of Technology   (United States)

Author keywords

Bioremediation; Contaminants; Genetically engineered microorganisms

Indexed keywords

BACTERIAL HEMOGLOBIN (VHB); ENZYME SPECIFICITY; GENETICALLY ENGINEERED MICROORGANISMS (GEM); MINERALIZATION;

AROMATIC COMPOUNDS; BACTERIA; BIOREMEDIATION; ENZYME KINETICS; GENETIC ENGINEERING; HEMOGLOBIN; IMPURITIES;

MICROORGANISMS;

BACTERIAL HEMOGLOBIN; HEMOGLOBIN; ORGANIC COMPOUND; OXYGEN; UNCLASSIFIED DRUG;

AEROBIC BACTERIUM; BACTERIAL GROWTH; BINDING AFFINITY; BIOREMEDIATION; ENZYME SPECIFICITY; GENE TRANSFER; GENETIC ENGINEERING; GENETICALLY ENGINEERED MICROORGANISM; HYPOXIA; MICROORGANISM; MINERALIZATION; NONHUMAN; POLLUTANT; POLLUTION CONTROL; PRIORITY JOURNAL; REVIEW; SCIENTIFIC LITERATURE;

BACTERIA; BACTERIAL PROTEINS; BACTERIOLOGICAL TECHNIQUES; BIODEGRADATION, ENVIRONMENTAL; ENVIRONMENTAL POLLUTANTS; GENE TRANSFER, HORIZONTAL; HEMOGLOBINS; METALS, HEAVY; ORGANISMS, GENETICALLY MODIFIED; RECOMBINANT FUSION PROTEINS; XENOBIOTICS;

BACTERIA (MICROORGANISMS);

EID: 33750009593     PISSN: 07388551     EISSN: 15497801     Source Type: Journal    
DOI: 10.1080/07388550600842794     Document Type: Review

References (161)

1. Abebe, H. M., Seidler, R. J., Lindow, S. E., Short, K. A., Clark, E., and King, R. J. 1997. Relative expression and stability of a chromosomally integrated and plasmid-borne marker gene fusion in environmentally competent bacteria. Curr. Microbiol. 34: 71-78.
2. Alvarez, A. J., Yumet, G. M., Santiago, C. L., and Toranzos, G. A. 1996. Stability of manipulated plasmid DNA in aquatic environments. Environ. Toxicol. Water Qual. 11: 129-135.
3. Ang, E. L., Zhao, H., and Obbard, J. P. 2005. Recent advances in the bioremediation of persistent organic pollutants via molecular engineering. Enzyme Microb. Technol. 37: 487-496.
4. Arp, D. J., Yeager, C. M., and Hyman, M. R. 2001. Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation. 12: 81-103.
5. Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F. C. H., Bagdasarian, M. M., Frey, J., and Timmis, K. N. 1981. Broad host range, high copy number, RSFS1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16: 237-247.
6. Birnbaum, S., and Bailey, J.E. 1991. Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli. Biotechnol. Bioeng. 37: 736-745.
7. Boe, L., Gerdes, K., and Molin, S. 1987. Effects of genes exerting growth inhibition and plasmid stability on plasmid maintenance. J. Bacteriol. 169: 4646-4650.
8. Boye, M., Ahl, T., and Molin, S. 1995. Application of strain-specific rRNA oligonucleotide probe targeting Pseudomonas fluorescens Ag1 in a mesocosm study of bacterial release into the environment. Appl. Environ. Microbiol. 61: 1384-1390.
9. Brockman, F. J. 1995. Nucleic-acid based methods for monitoring the performance of in situ bioremediation. Mol. Ecol. 4: 567-578.
10. Bruins, M. R., Kapil, S., and Oehme, F. W. 2000. Pseudomonas pickettii: A common soil and groundwater aerobic bacteria with pathogenic and biodegradation properties. Ecotoxicol. Environ. Saf. 47: 105-111.
11. Bulter, T., Alcalde, M., Sieber, V., Meinhold, P., Schlachtbauer, C., and Arnold, F. H. 2003. Functional expression of a fungal laccase in Saccharomyces cerevisiae by directed evolution. Appl. Environ. Microbiol. 69: 987-995.
12. Caulcott, C. A., Dunn, A., Heather, A. R., Cooper, N. S., Brown, M. E., and Rhodes, P. M. 1987. Investigation of the effect of growth environment on the stability of low-copy-number plasmids in Escherichia coli. J. Gen. Microbiol. 133: 1881-1889.
13. Chandler, D. P. 1998. Redefining relativity: quantitative PCR at low template concentrations for industrial and environmental microbiology. J. Ind. Microbiol. Biotechnol. 21: 128-140.
14. Cheah, U. E., Weigand, W. A., and Stark, B. C. 1987. Effects of recombinant plasmid size on cellular processes in Escherichia coli. Plasmid. 18: 127-134.
15. Chen, W., Brühlman, F., Richins, R. D., and Mulchandani, A. 1999. Engineering of improved microbes and enzymes for bioremediation. Curr. Opin. Biotechnol. 10: 137-141.
16. Cho, J-C., and Tiedje, J. M. 2002. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68: 1425-1430.
17. Chung, J. W., Webster, D. A., Pagilla, K. R., and Stark, B. C. 2001. Chromosomal integration of the Vitreoscilla hemoglobin gene in Burkholderia and Pseudomonas for the purpose of producing stable engineered strains with enhanced bioremediating ability. J. Ind. Microbiol. Biotechnol. 27: 27-33.
18. Crameri, A., Dawes, G., Rodriquez, E., Silver, S., and Stemmer, W. P. C. 1997. Molecular evolution of an arsenate detoxification pathway by DNA shuffling. Nat. Biotechnol. 15: 436-438.
19. Davison, J. 1999. Genetic exchange between bacteria in the environment. Plasmid. 42: 73-91.
20. Dechesne, A., Pallud, C., Bertolla, F., and Grundmann, G. L. 2005. Impact of the microscale distribution of Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria. Appl. Environ. Microbiol. 71: 8123-8131.
21. Dejonghe, W., Goris, J., Fantroussi, S. E., Höfte, M., De Vos, P., Verstraete, W., and Top, E. M. 2000. Effect of dissemination of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids on 2,4-D degradation and on bacterial community structure in two different soil horizons. Appl. Environ. Microbiol. 66: 3297-3304.
22. De Lorenzo, V., Herrero, M., Sánchez, J. M., and Timmis, K. N. 1998. Mini-transposons in microbial ecology and environmental biotechnology. FEMS Microbiol. Ecol. 27: 211-224.
23. De Lorenzo, V., Herrero, M., Metzke, M., and Timmis, K. N. 1991. An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid. EMBO J. 10(5): 1159-1167.
24. De Modena J. A., Gutierrez, S., Velasco, J., Fernandez, F. J., Fachini, R. A., Galazzo, J. L., Hughes, D. E., and Martin, J. F. 1993. The production of cephalosporin C by Acremonium chrysogenium is improved by the intracellular expression of a bacterial hemoglobin. Bio/Technol. 11: 926-929.
25. Dennis, J. J. 2005. The evolution of IncP catabolic plasmids. Curr. Opin. Biotechnol. 16: 291-298.
26. De Souza, M., Seffernick, J., Martinez, B., Sadowsky, M. J., and Wackett, L. P. 1998. The atrazine catabolism genes atzABC are widespread and highly conserved. J. Bacteriol. 180: 1951-1954.
27. Diaz-Ricci, J. C., and Hernandez, M. E. 2000. Plasmid effects on Escherichia coli metabolism. Crit. Rev. Biotechnol. 20: 79-108.
28. Di Giovanni, G. D., Neilson, J. W., Pepper, I. L., and Sinclair, N. A. 1996. Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients. Appl. Environ. Microbiol. 62: 2521-2526.
29. Dikshit, R. P., Dikshit, K. L., Liu, Y. X., and Webster, D. A. 1992. The bacterial hemoglobin from Vitreoscilla can support the aerobic growth of Escherichia coli. Arch. Biochem. Biophys. 293: 241-245.
30. Diviacco, S., Norio, P., Zentiilin, L., Menzo, S., Clementi, M., Biamonti, G., Riva, S., Falaschi, A., and Giacca, M. 1992. A novel procedure for quantitative polymerase chain reaction by coamplification of competitive templates. Gene. 122: 313-320.
31. Doblhoff-Dier, O., Bachmayer, H., Bennett, A., Brunius, G., Bürki, K., Cantley, M., Collins, C., Crooy, P., Elmqvist, A., Frontali-Botti, C., Havenaar, R., Haymerle, H., Lelieveld, H., Lex, M., Mahler, J. L., Martinez, L., Mosgaard, C., Olsen, L., Pazlarova J., Rudan, F., Sarvas, M., Stepankova, H., Tzotzos, G., Wagner, K., and Werner, R. 1999. Safe biotechnology 9: Values in risk assessment for the environmental application of microorganisms. TIBTEC. 17: 307-311.
32. Ensley, B. D. 1991. Biochemical diversity of trichloroethylene metabolism. Annu. Rev. Microbiol. 45: 440-449.
33. Feliciano, J., Liu, Y., and Daunert, S. 2006. Novel reporter gene in a fluorescent-based whole cell sensing system. Biotechnol. Bioeng. 93: 989-997.
34. Fish, P. A., Webster, D. A., and Stark, B. C. 2001. Vitreoscilla hemoglobin enhances the first step in 2,4-dinitrotoluene degradation in vitro and at low aeration in vivo. J. Mol. Catal. B. 9: 75-82.
35. Fulthorpe, R. R., and Wyndham, R. C. 1992. Involvement of a chlorobenzoate-catabolic transposon, Tn5271, in community adaptation to chlorobiphenyl, chloroaniline, and 2,4-dichlorophenoxyacetic acid in a freshwater ecosystem. Appl. Environ. Microbiol. 58: 314-325.
36. Furukawa, K. 2000a. Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs). J. Gen. Appl. Microbiol. 46: 283-296.
37. Furukawa, K. 2000b. Engineering dioxygenases for efficient degradation of environmental pollutants. Curr. Opin. Biotechnol. 11: 244-249.
38. Furukawa, K., Suenaga, H., and Goto, M. 2004. Biphenyl dioxygenases: Functional versatilities and directed evolution. J. Bacteriol. 186: 5189-5196.
39. Gallardo, M. E., Fernandez, A., de Lorenzo, V., Garcia, J. L., and Diaz, E. 1997. Designing recombinant Pseudomonas strains to enhance biodesulfurization. J. Bacteriol. 179: 7156-7160.
40. Gentry, T. J., Rensing, C., and Pepper, I. L. 2004. New approaches for bioaugmentation as a remediation technology. Crit. Rev. Env. Sci. Technol. 34: 447-494.
41. Gibson, D. T., and Parales, R. E. 2000. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr. Opin. Biotechnol. 11: 236-243.
42. Gupta, R., Sharma, P., and Vyas, V. V. 1995. Effect of growth environment on the stability of a recombinant shuttle plasmid, pCPPS-31, in Escherichia coli. J. Biotechnol. 41: 4129-4137.
43. Görgens, J. F., van Zyl, W. H., Knotze, J. H., and Hahn-Hagerdal, B. 2001 The metabolic burden of the pgk1 and adh2 promoter systems for heterologous xylanase production by Saccharomyces cerevisiae in defined medium. Biotechnol. Bioeng. 73: 239-245.
44. Hedenstierna, K. O. F., Lee, Y.-H., Yang, Y., and Fox, G. E. 1993. A prototype stable RNA identification cassette for monitoring plasmids of genetically engineered microorganisms. Sys. Appl. Microbiol. 16: 280-286.
45. Hempel, C., Erb, R. W., Deckwer, W. D., and Hecht, V. 1998. Plasmid stability of recombinant Pseudomonas sp. B13 FR1 pFRC20P in continuous culture. Biotechnol. Bioeng. 57: 62-70.
46. Herrero, M., de Lorenzo, V., and Timmis, K. N. 1990. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol. 172: 6557-6567.
47. Holmberg, N., Lilius, G., Bailey, J. E., and Bülow, L. 1997. Transgenic tobacco expressing Vitreoscilla hemoglobin exhibits enhanced growth and altered metabolite production. Nat. Biotechnol. 15: 244-247.
48. Hrywna, Y., Tsoi, T. V., Maltseva, O. V., Quensen, J. F. III, and Tiedje, J. M. 1999. Construction and characterization of two recombinant bacteria that grow on ortho-and para-substituted chlorobiphenyls. Appl. Environ. Microbiol. 65: 2163-2169.
49. Inamori, Y., Murakami, K., Sudo, R., Kurihara, Y., and Tanaka, N. 1992. Environmental assessment method for field release of genetically engineered microorganisms using microcosm systems. Water Sci. Technol. 26: 2161-2164.
50. Jank, B., and Gaugitsch, H. 2001. Assessing the environmental impacts of transgenic plants. Trends Biotechnol. 19: 371-372.
51. Jansson, J. K. 1995. Tracking genetically engineered microorganisms in nature. Curr. Opin. Biotechnol. 6: 275-283.
52. Jansson, J. K., and Prosser, J. I. 1997. Quantification of the presence and activity of specific microorganisms in nature. Mol. Biotechnol. 7: 103-120.
53. Joshi, M., and Dikshit, K. L. 1994. Oxygen dependent regulation of Vitreoscilla globin gene: Evidence for positive regulation by fnr. Biochem. Biophys. Res. Commun. 202: 535-542.
54. Kallio, P. T., and Bailey, J. E. 1996. Intracellular expression of Vitreoscilla hemoglobin (VHb) enhances total protein secretion and improves the production of alpha-amylase and neutral protease in Bacillus subtilis. Biotechnol. Progr. 12: 31-39.
55. Kallio, P. T., Kim, D. J., Tsai, P. S., and Bailey, J. E. 1994. Intracellular expression of Vitreoscilla hemoglobin alters Escherichia coli energy metabolism under oxygen-limited conditions. Eur. J. Biochem. 219: 201-208.
56. Kang, D. G., Choi, S. S., and Cha, H. J. 2006. Enhanced biodegradation of toxic organophosphate compounds using recombinant Escherichia coli with sec pathway driven periplasmic secretion of organophosphorous hydrolase. Biotechnol. Progr. 22: 406-410.
57. Kang, D. G., Kim, J. Y. H., and Cha, H. J. 2002. Enhanced detoxification of organophosphates using recombinant Escherichia coli with co-expression of organophosphorous hydrolase and bacterial hemoglobin. Biotechnol. Lett. 24: 879-883.
58. Kawabata, Z., Min, M.-G., Matsui, K., and Ishii, N. 1998. Factors effecting the survival of genetically engineered Escherichia coli bearing a plasmid in a paddy field microcosm. Int. J. Environ. Stud. 55: 271-285.
59. Khosravi, M., Webster, D. A., and Stark, B. C. 1990. Presence of the bacterial hemoglobin gene improves alpha-amylase production of a recombinant Escherichia coli strain. Plasmid. 24: 190-194.
60. Kim, Y., Webster, D. A., and Stark, B. C. 2005. Improvement of bioremediation by Pseudomonas and Burkholderia by mutants of the Vitreoscilla hemoglobin gene (vgb) integrated into their chromosomes. J. Ind. Microbiol. Biotechnol. 32: 148-154.
61. Krooneman, J., Wieringa, E. B. A., Moore, E. R. B., Gerritse, J., Prins, R. A., and Gottschal, J. C. 1996. Isolation of Alcaligenes sp. strain L6 at low oxygen concentrations and degradation of 3-chlorobenzoate via a pathway not involving (chloro) catechols. Appl. Environ. Microbiol. 62: 2427-2434.
62. Lange, C. C., Wackett, L. P., Minton, K. W., and Daly, M. J. 1998. Engineering a recombinant Deinococcus radiodurans for organopollutant degradation in radioactive mixed waste environments. Nat. Biotechnol. 16: 929-933.
63. Lee, S. Y., Stark, B. C., and Webster, D. A. 2004. Structure-function studies of the Vitreoscilla hemoglobin D-region. Biochem. Biophys. Res. Commun. 316: 1101-1106.
64. Lin, J. M., Stark, B. C., and Webster, D. A. 2003. Effects of Vitreoscilla hemoglobin on the 2,4-dinitrotoluene (DNT) dioxygenase activity of Burkholderia and on DNT degradation in two-phase bioreactors. J. Ind. Microbiol. Biotechnol. 30: 362-368.
65. Lindow, S. E. 1995. The use of reporter genes in the study of microbial ecology. Mol. Ecol. 4: 555-566.
66. Liu, S. C., Liu, X. Y., Webster, D. A., and Stark, B. C. 1994. Sequence of the region downstream of the Vitreoscilla hemoglobin gene: vgb is not part of a multigene operon. Appl. Microbiol. Biotechnol. 42: 304-308.
67. Liu, S. C., Webster, D. A., and Stark, B. C. 1995. Cloning and expression of the Vitreoscilla hemoglobin gene in Pseudomonads: Effects on cell growth. Appl. Environ. Microbiol. 44: 419-424.
68. Liu, S. C., Liu, X. Y., Webster, D. A., and Stark, B. C. 1996. Genetic engineering to contain the Vitreoscilla hemoglobin gene enhances degradation of benzoic acid by Xanthomonas maltophillia. Biotechnol. Bioeng. 49: 101-105.
69. Magnolo, S. K., Leenutaphong, D. L., De Modena, J. A., Curtis, J. E., Bailey, J. E., Galazzo, J. L., and Hughes, D. E. 1991. Actinorhodin production by Streptomyces coelicolor and growth of Streptomyces lividans are improved by the expression of a bacterial hemoglobin. Bio/Technol. 9: 473-476.
70. Matheson, V. G., Forney, L. J., Suwa, Y., Nakatsu, C. H., Sewtone, A. J., and Holben, W. E. 1996. Evidence for acquisition in nature of a chromosomal 2,4-dichlorophenooxyacetic acid/ketoglutarate dioxygenase gene by different Burkholderia sp. Appl. Environ. Microbiol. 62: 2457-2463.
71. McGowan, C., Fulthorpe, R., Wright, A., and Tiedje, J. M. 1998. Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders. Appl. Environ. Microbiol. 64: 4989-4092.
72. Min, M.-G., Kawabata, Z., Ishii, N., Takata, R., and Furukawa, K. 1998. Fate of a PCBs degrading recombinant Pseudomonas putida AC30 (PMFB2) and its effect on the densities of microbes in marine microcosms contaminated with PCBs. Int. J. Environ. Stud. 55: 271-285.
73. Molin, S., Boe, L., Jensen, L. B., Kristensen, C. S., Givskov, M., Ramos, J. L., and Bej, A. K. 1993. Suicidal genetic elements and their use in biological containment of bacteria. Annu. Rev. Microbiol. 47: 139-66.
74. Molina, L., Ramos, C., Ronchel, M. C., Molin, S., and Ramos, J. L. 1998. Construction of an efficient biologically contained Pseudomonas putida strain and its survival in outdoor assays. Appl. Environ. Microbiol. 64: 2072-2078.
75. Mondello, F. J., Turcich, M. P., Lobos, J. H., and Erickson, B. D. 1997. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl. Environ. Microbiol. 63: 3096-3103.
76. Monti, M. R., Smania, A. M., Fabro, G., Alvarez, M. E., and Argarana, C. E. 2005. Engineering Pseudomonas fluorescens for biodegradation of 2,4-dinitrotoluene. Appl. Environ. Microbiol. 71: 8864-8872.
77. Mulchandani, A., Kaneva, I., and Chen, W. 1999. Detoxification of organophosphorus nerve agents by immobilized Escherichia coli with surface-expressed organophosphorus hydrolase. Biotechnol. Bioeng. 63: 216-223.
78. Müller, T. A., Werlen, C., Spain, J., and van der Meer, J. R. 2003. Evolution of a chlorobenzene degradative pathway among bacteria in a contaminated groundwater mediated by a genomic island in Ralstonia. Environ. Microbiol. 3: 163-173.
79. Nasr, M. A., Hwang, K.-W., Akbas, M., Webster, D. A., and Stark, B. C. 2001. Effects of culture conditions on enhancement of 2,4-dinitrotoluene degradation by Burkholderia engineered with the Vitreoscilla hemoglobin gene. Biotechnol. Progr. 17: 359-361.
80. Newby, D. T., Gentry, T. J., and Pepper, I. L. 2000a. Comparison of 2,4-dichlorophenoxyacetic acid degradation and plasmid transfer in soil resulting from bioaugmentation with two different pJP4 donors. Appl. Env. Microbiol. 66: 3399-3407.
81. Newby, D. T., Josephson, K. L., and Pepper, I. L. 2000b. Detection and characterization of plasmid pJP4 transfer to indigenous soil bacteria. Appl. Env. Microbiol. 66: 290-296.
82. Ohtsubo, Y., Shimura, M., Delawary, M., Kimbara, K., Takagi, M., Kudo, T., Ohta, A., and Nagata, Y. 2003. Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: Promoter implantation by homologous recombination. Appl. Environ. Microbiol. 69: 146-153.
83. Pandey, G., Paul, D., and Jain, R. K. 2005. Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications. Biochem. Biophys. Res. Commun. 327: 637-639.
84. Panke, S., Sanchez-Romero, J. M., and de Lorenzo, V. 1998. Engineering of quasi natural Pseudomonas putida strains for toluene metabolism through an ortho-cleavage degradation pathway. Appl. Environ. Microbiol. 64: 748-751.
85. Parales, R. E., Bruce, N. C., Schmid, A., and Wackett, L. P. 2002. Biodegradation, biotransformation, and biocatalysis (B3). Appl. Environ. Microbiol. 68: 4699-4709.
86. Park, K. W., Kim, K. J., Howard, A. J., Stark, B. C., and Webster, D. A. 2002. Vitreoscilla hemoglobin binds to subunit i of cytochrome bo ubiquinol oxidases. J. Biol. Chem. 277: 33334-33337.
87. Patel, S. M., Stark, B. C., Hwang, K.-W., Dikshit, K. L., and Webster, D. A. 2000. Cloning and expression of Vitreoscilla hemoglobin gene in Burkholderia sp. strain DNT for enhancement of 2,4-dinitrotoluene degradation. Biotechnol. Progr. 16: 26-30.
88. Paul, D., Pandey, G., Pandey, J., and Jain, R. K. 2005a. Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol. 23: 135-142.
89. Paul, D., Pandey, G., and Jain, R. K. 2005b. Suicidal genetically engineered microorganisms for bioremediation: Need and perspectives. BioEssays. 27: 563-573.
90. Pendse, G. J., and Bailey, J. E. 1994. Effect of Vitreoscilla hemoglobin expression on growth and specific tissue plasminogen activator productivity in recombinant Chinese hamster ovary cells. Biotechnol. Bioeng. 44: 1367-1370.
91. Peters, M., Heinauru, E., Talpsep, E. W., Stoottmeister, U., Heinaru, A., and Nurk, A. 1997. Acquisition of a deliberately introduced phenol degradation operon, pheba, by different indigenous Pseudomonas species. Appl. Environ. Microbiol. 63: 4899-4906.
92. Picard, C., Nesme, X., and Sinomet, P. 1996. Detection and enumeration of soil bacteria using the MPN-PCR technique, In: van Elsas, J. D. (ed.) Molecular Ecology Manual. 2: 1-9. Kluwer, Dordrecht, Netherlands.
93. Pieper, D. H., and Reineke, W. 2000. Engineering bacteria for bioremediation. Curr. Opin. Biotechnol. 11: 262-270.
94. Qin, J., Song, L., Brim, H., Daly, M. J., and Summers, A. O. 2006. Hg(II) sequestration and protection by the MerR metal-binding domain (MBD). Microbiology. 152: 709-719.
95. Ramandeep, Hwang, K. W., Raje, M., Kim, K. J., Stark, B. C., Dikshit, K. L., and Webster, D. A. 2001. Vitreoscilla hemoglobin: intracellullar localization and binding to membranes. J. Biol. Chem. 27: 24781-24789.
96. Ravatn, R., Zehnder, A. J. B., and van der Meer, J. R. 1998. Low-frequency horizontal transfer of an element containing the chlorocatechol degradation genes from Pseudomonas sp strain B13 to Pseudomonas putida F1 and to indigenous bacteria in laboratory-scale activated-sludge microcosms. Appl. Environ. Microbiol. 64: 2126-2132.
97. Reichmuth, D. S., Blanch, H. W., and Keasling, J. D. 2004. Dibenzothiopene biodesulfurization pathway improvement using diagnostic GFP fusions. Biotechnol. Bioeng. 88: 94-99.
98. Reineke, W. 1998. Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu. Rev. Microbiol. 52: 287-331.
99. Renninger, N., Knopp, R., Nitsche, H., Clark, D. S., and Keasling J. D. 2004. Uranyl precipitation by Pseudomonas aeruginosa via controlled polyphosphate metabolism. Appl. Environ. Microbiol. 70: 7404-7412.
100. Rensing, C., Newby, D. T., and Pepper, I. L. 2002. The role of selective pressure and selfish DNA in horizontal gene transfer and soil microbial community adaptation. Soil Biol. Biochem. 34: 285-296.
101. Richins, R. D., Kaneva, I., Mulchandani, A., and Chen,W. 1997. Biodegradation of organophosphorus pesticides by surface expressed organophosphorus hydrolase. Nat. Biotechnol. 15: 984-987.
102. Riley, P. A., and Hoffmann, L. 1999. Value-enhanced crops: Biotechnology's next stage. Agricul. Outlook. Economic Research Service/USDA, March, pp. 18-22
103. Ripp, S., Nivens, D. E., Ahn, Y., Werner, C., Jarrell IV, J., Easter, J. P., Cox, C. D., Burlage, R. S., and Sayler, G. S. 2000. Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control. Environ. Sci. Technol. 34: 846-853.
104. Rittmann, B. E., Smets, B. F., and Stahl, D. A. 1990. The role of genes in biological processes. Environ. Sci. Technol. 24: 23-29.
105. Rittmann, B. E., Smets, B. F., MacDonald, J. A., and Stahl, D. A. 1995. Plasmid transfer enhancing degradation capabilities. Environ. Health Issues. 103(S5): 23-29.
106. Ronchel, M. C., Ramos, C., Jensen, L. B., Molin, S., and Ramos, J. L. 1995. Construction and behavior of biologically contained bacteria for environmental applications in bioremediation. Appl. Environ. Microbiol. 61: 2990-2994.
107. Ronchel, M. C., Molina, L., Witte, A., Lutbiz, W., Molin, S., Ramos, J. L., and Ramos, C. 1998. Characterization of cell lysis in Pseudomonas putida induced upon expression of heterologous killing genes. Appl. Environ. Microbiol. 64: 4904-4911.
108. Ronchel, M. C., and Ramos, J. L. 2000. Retrotransfer of DNA in the rhizosphere. Environ. Microbiol. 2: 319-323.
109. Ronchel, M. C., and Ramos, J. L. 2001. Dual system to reinforce biological containment of recombinant bacteria designed for rhizoremediation. Appl. Environ. Microbiol. 67: 2649-2656.
110. Roos, V., Andersson, C. I. J., and Bulow, L. 2004. Gene expression profiling of Escherichia coli expressing double Vitreoscilla hemoglobin. Biotechnology 114: 107-120.
111. Sanchez-Romero, J. M., Diaz-Orejas, R., and de Lorenzo, V. 1998. Resistance to tellurite as a selection marker for genetic manipulations of Pseudomonas strains. Appl. Environ. Microbiol. 64: 4040-4046.
112. Sayler, G. S., and Ripp, S. 2000. Field applications of genetically engineered microorganisms for bioremediation processes. Curr. Opin. Biotechnol. 11: 286-289.
113. Scanferlato, V. S., Orvos, D. R., Cairns, J. Jr., and Lacy, G. H. 1989. Genetically engineered Erwinia carotovora in aquatic microcosms: survival and effects on functional groups of indigenous bacteria. Appl. Environ. Microbiol. 55: 1477-1482.
114. Sharp, J. O., Wood, K. W., and Alvarez-Cohen, A. 2005. Aerobic biodegradation of N-nitrosodimethylamine (NDMA) by axenic bacterial strains. Biotechnol. Bioeng. 89: 608-618.
115. Sharp, R. R., Bryers, J. D., Jones, W. G., and Shields, M. S. 1998. Activity and stability of a recombinant plasmid-borne TCE degradative pathway in suspended cultures. Biotechnol. Bioeng. 57: 287-296.
116. Shingleton, J. T., Applegate, B. M., Nagel, A. C., Bienkowski, P. R., and Sayler, G. S. 1998. Induction of the tod operon by trichloroethylene in Pseudomonas putida TVA8. Appl. Environ. Microbiol. 64: 5049-5052.
117. Short, K. A., Doyle, J. D., King, R. J., Seidler, R. J., Stotzky, G., and Olsen, R. H. 1991. Effect of 2,4-dichlorophenol, a metabolite of a genetically engineered bacterium, and 2,4-dichlorophenoxyacetate on some microorganism-mediated ecological processes in soil. Appl. Environ. Microbiol. 57: 412-418.
118. Short, K. A., Seidler, R. J., and Olsen, R. H. 1990. Survival and degradative capacity of Pseudomonas putida induced or constitutively expressing plasmid-mediated degradation of 2,4-dichlorophenoxyacetate in soil. Can. J. Microbiol. 36: 821-826.
119. Singh, A., Billingsley, K., and Ward, O. 2006. Composting: A potential safe process for disposal of genetically modified organisms. Crit. Rev. Biotechnol. 26: 1-16.
120. Small, J., Call, D. R., Brockman, F. J., Straub, T. M., and Chandler, D. P. 2001. Direct detection of 16 rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67: 4708-4716.
121. Smets, B. F., Rittmann, B. E., and Stahl, D. A. 1994. The specific growth rate of Pseudomonas putida PAW1 influences the conjugal transfer rate of the TOL plasmid Appl. Environ. Microbiol. 59: 3430-3437.
122. Smets, B. F., Rittmann, B. E., and Stahl, D. A. 1990. The role of genes in biological processes. Part 2 of a two-part particle. Environ. Sci. Technol. 24: 162-169.
123. So, J., Webster, D. A., Stark, B. C., and Pagilla, K. R. 2004. Enhancement of 2,4-dinitrotoluene biodegradation by Burkholderia sp. in sand bioreactors using bacterial hemoglobin technology. Biodegradation. 15: 161-171.
124. Sobecky, P. A., Schell, M. A., Moran, M. A., and Hodson, R. E. 1996. Impact of a genetically engineered bacterium with enhanced alkaline phosphatase activity on marine phytoplankton communities. Appl. Environ. Microbiol. 62: 6-12.
125. Sobecky, P. A., Schell, M. A., Moran, M. A., and Hodson, R. E. 1992. Adaptation of model genetically engineered microorganisms to lake water: Growth rate enhancements and plasmid loss. Appl. Environ. Microbiol. 58: 3630-3637.
126. Spanggord, R. J., Spain, J. C., Nishino, S. F., and Mortelmans, K. E. 1991. Biodegradation of 2,4-dinitrotoluene by a Pseudomonas sp. Appl. Environ. Microbiol. 57: 3200-3205.
127. Springael, D., Peys, K., Ryngaert, A., van Roy, S., Hooyberghs, L., Ravatn, R., Heyndrick, M., van der Meer, J. R., Vandecasteele, C., Mergeay, M., and Diels, L. 2002. Community shifts in a seeded 3-chlorobenzoate degrading membrane biofilm reactor: Indications for involvement of in situ horizontal transfer of the clc-element from inoculum to contaminant bacteria. Environ. Microbiol. 4: 70-80.
128. Springael, D., and Top, E. M. 2004. Horizontal gene transfer and microbial adaptation to xenobiotics: New types of mobile genetic elements and lessons from ecological studies. Trends Microbiol. 12: 53-58.
129. cam. New J. Chem. 22: 551-552.
130. Strong, L. C., McTavish, H., Sadowsky, M. J., and Wackett, L. P. 2000. Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase. Environ. Microbiol. 2: 91-98.
131. Suen, W. C., and Spain, J. C. 1993. Cloning and characterization of Pseudomonas sp. strain DNT genes for 2,4-dinitrotoluene degradation. J. Bacteriol. 175: 1831-1837.
132. Suidan, M. T., Esperanza, M., Zein, M., McCauley, P., Brenner, R. C., and Venosa, A. D. 2005. Challenges in biodegradation of trace organic contaminants-gasoline oxygenates and sex hormones. Water Environ. Res. 77: 4-11.
133. Szafranski, P., Mello, C. M., Sano, T., Smith, C. L., Kaplan, D. L., and Cantor, C. R. 1997. A new approach for containment of microorganisms: dual control of streptavidin expression by antisense RNA and the T7 transcription system. Proc. Natl. Acad. Sci. USA. 94(4): 1059-1063.
134. Tiedje, J. M., Colwell, R. K., Grossman, Y. L., Hodson, R. E., Lenski, R. E., Mack, R. N., and Regal, P. J. 1989. The planed introduction of genetically engineered organisms: Ecological considerations and recommendations. Ecol. 70: 298-315.
135. Timmis, K. N., and Pieper D. H. 1999. Bacteria designed for bioremediation. Trends Biotechnol. 17: 200-204.
136. Top, E. M., Springael, D., and Boon, N. 2002. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol. Ecol. 42: 199-208.
137. Top, E., van Daele, P., De Saeyer, N., and Forney, L. J. 1998. Enhancement of 2,4-dichlorophenoxyacetic acid degradation in soil by dissemination of catabolic plasmids. Antonie Leeuwenhoek Int. J. G. 73: 87-94.
138. Tsai, P. S., Kallio, P. T., and Bailey, J. E. 1995. Fnr, a global transcriptional regulator of Escherichia coli, activates the Vitreoscilla hemoglobin (VHb) promoter and intracellular VHb expression increases cytochrome d promoter activity. Biotechnol. Progr. 11(3): 288-293.
139. Tsai, P. S., Hatzimanikatis, V., and Bailey, J. E. 1996. Effect of Vitreoscilla hemoglobin dosage on microaerobic Escherichia coli carbon and energy metabolism. Biotechnol. Bioeng. 49: 139-150.
140. Urgun-Demirtas, M., Pagilla, K. R., Stark, B. C., and Webster, D. A. 2003. Biodegradation of 2-chlorobenzoate by recombinant Burkholderia cepacia expressing Vitreoscilla hemoglobin under variable levels of oxygen availability. Biodegradation. 14: 357-365.
141. Urgun-Demirtas, M., Pagilla, K. R., and Stark, B. C. 2004. Enhanced kinetics of genetically engineered Burkholderia cepacia: the role of vgb in the hypoxic cometabolism of 2-CBA. Biotechnol. Bioeng. 87: 110-118.
142. Urgun-Demirtas, M., Stark, B. C., and Pagilla, K. R. Comparison of 2-chlorobenzoic acid biodegradation in a membrane bioreactor by B. cepacia and B. cepacia bearing the bacterial hemoglobin gene. Water Res. In press.
143. van der Meer, J. R., and Sentchilo, V. 2003. Genomic islands and the evolution of catabolic pathways in bacteria. Curr. Opin. Biotechnol. 14: 248-254.
144. Velkov, V. V. 2001. Stress-induced evolution and the biosafety of genetically modified microorganisms released into the environment. J. Biosci. 26: 667-683.
145. Villacieros, M., Whelan, C., Mackova, M., Molgaard, J., Sanchez-Conteras, M., Lloret, J., de Carcer, D. A., Orueazabal, R. I., Bolanos, L., Macek, T., Karlson, U., Dowling, D. N., Martin, M., and Rivilla, R. 2005. Polychlorinated biphenyl rhizoremediation by Pseudomonas fluoresecens F113 derivatives, using a Sinorhizobium melioti nod system to derive bph gene expression. Appl. Environ. Microbiol. 71: 2687-2694.
146. Vollmer, M. D., Hoier, H., Hecht, H. J., Schell, U., Groning, J., Goldman, A., and Schlomann, M. 1998. Substrate specificity of and product formation by muconate cycloisomerases: An analysis of wild-type enzymes and engineered variants. Appl. Environ. Microbiol. 64: 3290-3299.
147. Wang, A. A., Chen, W., and Mulchandani, A. 2005. Detoxification of organophosphate nerve agents by immobilized dual functional biocatalysts in a cellulose hollow fiber bioreactor. Biotechnol. Bioeng. 91: 379-386.
148. Wang, A. A., Mulchandani, A., and Chen, W. 2002. Specific adhesion to cellulose and hydrolysis of organophosphate nerve agents by a genetically engineered Escherichia coli strain with a surface-expressed cellulose-binding domain and organophosphorus hydrolase. Appl. Env. Microbiol., 68: 1684-1689.
149. Webster, D. 1987. Structure and function of bacterial hemoglobin and related proteins. In: Eichorn, G. C., Marzilli, L. G. (Ed.) Advances in Inorganic Biochemistry. 7: 245-265. Elsevier, New York.
150. Wei, M. L., Webster, D. A., and Stark, B. C. 1998a. Genetic engineering of Serratia marcescens with bacterial hemoglobin gene: effects on growth, oxygen utilization, and cell size. Biotechnol Bioeng. 57: 477-483.
151. Wei, M.-L.,Webster, D. A., and Stark, B. C. 1998b. Metabolic engineering of Serratia marcescens with the bacterial hemoglobin gene: alterations in fermentation pathways. Biotechnol Bioeng. 59: 640-646.
152. Widada, J., Nojiri, H., and Omori, T. 2002. Recent developments in molecular techniques for identification and monitoring of xenobiotic-degrading bacteria and their catabolic genes in bioremediation. Appl. Microbiol. Biotechnol. 60: 45-59.
153. Widada, J., Nojiri, H., Kasuga, K., Yoshida, T., Hiroshi, H., and Omori, T. 2001. Quantification of the carbazole 1,9a-dioxygenase gene by real time competitive PCR combined with co-extraction of internal standards. FEMS Microbiol. Lett. 202: 51-57.
154. Wiles, S., Ferguson, K., Stefanidou, M., Young, D. B., and Robertson, B. D. 2005. Alternative luciferase for monitoring bacterial cells under adverse conditions. Appl. Environ. Microbiol. 71: 3427-3432.
155. Willardson, B. M., Wilkins, J. F., Rand, T. A., Schupp, J. M, Hill, K. K., Keim, P., and Jackson, P. J. 1998. Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Appl. Environ. Microbiol. 64: 1006-1012.
156. Wu, J.-F., Jiang, C., Wang, B., Liu, Z., and Liu, S. 2006. Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl. Environ. Microbiol. 72: 1759-1765.
157. Wu, L., Thompson, D. K., Li, G., Hurt, R. A., Tiedje, J. M., and Zhou, J. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67: 5780-5790.
158. Yang, J., Webster, D. A., and Stark, B. C. 2005. ArcA works with Fnr as a positive regulator of Vitreoscilla (bacterial) hemoglobin gene expression in Escherichia coli. Microbiolog. Res. 160: 405-415.
159. Yee, D. C., Maynard, J. A., and Wood, T. K. 1998. Rhizoremediation of trichloroethylene by a recombinant root-colonizing Pseudomonas fluorescens strain expressing toluene ortho-monooxygenase constitutively. Appl. Environ. Microbiol. 64: 112-118.
160. Yildirim, S., Franco, T. T., Wohlgemuth, R., Kohler, H. E., Witholt, B., and Schmid, A. 2005. Recombinant chlorobenzene dioxygenase from Pseudomonas sp. P51: A biocatalyst for regioselective oxidation of aromatic nitriles. Adv. Synth. Catal. 347: 1060-1072.
161. Zaat, S. A. J., Slegtenhorst-Eegdeman, K., Tommassen, J., Geli, V., Wijfelman, C. A., and Lugtenberg, B. J. J. 1994. Construction of phoE-caa, a novel PCR- and immunologically detectable marker gene for Pseudomonas putida. Appl. Environ. Microbiol. 60: 913-920.