New approaches for bioaugmentation as a remediation technology

Critical Reviews in Environmental Science and Technology

Volumn 34, Issue 5, 2004, Pages 447-494

  Gentry, Terry J ^a,b   Rensing, Christopher ^a   Pepper, Ian L ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Genetically engineered microorganism; Immobilized cell; Phytoaugmentation; Phytoremediation; Reporter gene; Suicide gene

Indexed keywords

BIOAUGMENTATION; CHAIN REACTIONS; INOCULANTS;

BIOMEDICAL ENGINEERING; CELLS; ENVIRONMENTAL ENGINEERING; GENES; IMPURITIES; MICROORGANISMS;

REMEDIATION;

BIOREMEDIATION; GENETICALLY MODIFIED ORGANISM; PHYTOREMEDIATION; WASTE MANAGEMENT;

BIOREMEDIATION; CELL ENCAPSULATION; DNA MODIFICATION; INOCULATION; MICROORGANISM; NONHUMAN; PHYTOREMEDIATION; REAL TIME POLYMERASE CHAIN REACTION; REPORTER GENE; REVIEW; RHIZOSPHERE;

EID: 4444339072     PISSN: 10643389     EISSN: None     Source Type: Journal    
DOI: 10.1080/10643380490452362     Document Type: Review

References (266)

1. Aggarwal, N., HogenEsch, H., Guo, P., North, A., Suckow, M., Mittal, S.K. Biodegradable alginate microspheres as a delivery system for naked DNA, Can. J. Vet. Res. 63, 148, 1999.
2. Ahrenholtz, I., Lorenz, M.G., and Wackernagel, W. A conditional suicide system in Escherichia coli based on the intracellular degradation of DNA, Appl. Environ. Microbiol. 60, 3746, 1994.
3. Alexander, M. Biodegradation and bioremediation, 2nd ed., p. 453. Academic Press, San Diego, CA, 1999.
4. Alfreider, A., Vogt, C., and Babel, W. Expression of chlorocatechol 1,2-dioxygenase and chlorocatechol 2,3-dioxygenase genes in chlorobenzene- contaminated subsurface samples, Appl. Environ. Microbiol. 69, 1372, 2003.
5. Amarger, N. Genetically modified bacteria in agriculture, Biochimie, 84, 1061, 2002.
6. Anderson, T.A., Guthrie, E.A., and Walton, B.T. Bioremediation in the rhizosphere, Environ. Sci. Technol. 27, 2630, 1993.
7. Atlas, R.M. Molecular methods for environmental monitoring and containment of genetically engineered microorganisms, Biodegradation 3, 137, 1992.
8. Bakermans, C., and Madsen, E.L. 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, 75, 2002.
9. Barbeau, C., Deschênes, L., Karamanev, D., Comeau, Y., and Samson, R. Bioremediation of pentachlorophenol-contaminated soil by bioaugmentation using activated soil, Appl. Microbiol. Biotechnol. 48, 745, 1997.
10. Bastos, A.E.R., Cassidy, M.B., Trevors, J.T., Lee, H., and Rossi, A. Introduction of green fluorescent protein gene into phenol-degrading Alcaligenes faecalis cells and their monitoring in phenol-contaminated soil, Appl. Microbiol. Biotechnol. 56, 255, 2001.
11. Beck, D.P. Suitability of charcoal-amended mineral soil as carrier for Rhizobium inoculants, Soil Biol. Biochem. 23, 41, 1991.
12. Bej, A.K., Perlin, M.H., and Atlas, R.M. Model suicide vector for containment of genetically engineered microorganisms, Appl. Environ. Microbiol. 54, 2472, 1988.
13. Ben Rebah, F., Tyagi, R.D., and Prevost, D. Wastewater sludge as a substrate for growth and carrier for rhizobia: The effect of storage conditions on survival of Sinorhizobium meliloti, Bioresour. Technol. 83, 145, 2002.
14. Bennett, J.W. Mycotechnology: The role of fungi in biotechnology, J. Biotechnol. 66, 101, 1998.
15. Bent, E., Tuzun, S., Chanway, C.P., and Enebak, S. Alterations in plant growth and in root hormone levels of lodgepole pines inoculated with rhizobacteria, Can. J. Microbiol. 47, 793, 2001.
16. Bevan, M.W., and Chilton, M.D. T-DNA of the Agrobacterium Ti and Ri plasmids, Annu. Rev. Genet. 16, 357, 1982.
17. Bhandari, A., and Xu, F. Impact of peroxidase addition on the sorption-desorption behavior of phenolic contaminants in surface soils, Environ. Sci. Technol. 35, 3163, 2001.
18. Bizily, S.P., Rugh, C.L., and Meagher, R.B. Phytodetoxification of hazardous organomercurials by genetically engineered plants, Nat. Biotechnol. 18, 213, 2000.
19. Bizily, S.P., Rugh, C.L., Summers, A.O., and Meagher, R.B. Phytoremediation of methylmercury pollution: merB expression in Arabidopsis thaliana confers resistance to organomercurials, Proc. Natl. Acad. Sci. USA 96, 6808, 1999.
20. Bloemberg, G.V., Wijfjes, A.H.M., Lamers, G.E.M., Stuurman, N., and Lugtenberg, B.J.J. Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: New perspectives for studying microbial communities, Mol. Plant Microbe Interact. 13, 1170, 2000.
21. Blumenroth, P., and Wagner-Döbler, I. Survival of inoculants in polluted sediments: Effect of strain origin and carbon source competition, Microb. Ecol. 35, 279, 1998.
22. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. Development and validation of a diagnostic microbial microarray for methanotrophs, Environ. Microbiol. 5, 566, 2003.
23. Bogan, B.W., Schoenike, B., Lamar, R.T., and Cullen, D. Manganese peroxidase mRNA and enzyme activity levels during bioremediation of polycyclic aromatic hydrocarbon-contaminated soil with Phanerochaete chrysosporium, Appl. Environ. Microbiol. 62, 2381, 1996.
24. Boon, N., De Gelder, L., Lievens, H., Siciliano, S.D., Top, E.M., and Verstraete, W. Bioaugmenting bioreactors for the continuous removal of 3-chloroaniline by a slow release approach, Environ. Sci. Technol. 36, 4698, 2002.
25. Boon, N., Top, E.M., Verstraete, W., and Siciliano, S.D. Bioaugmentation as a tool to protect the structure and function of an activated-sludge microbial community against a 3-chloroaniline shock load, Appl. Environ. Microbiol. 69, 1511, 2003.
26. Bouchez, T., Patureau, D., Dabert, P., Juretschko, S., Dore, J., Delgenes, P., Moletta, R., and Wagner, M. Ecological study of a bioaugmentation failure, Environ. Microbiol. 2, 179, 2000.
27. 301, in In situ and on-site bioremediation, vol. 4, pp. 513-518, Batelle Press, Columbus, OH, 1997.
28. Briglia, M., Nurmiaho-Lassila, E.-L., Vallini, G., and Salkinoja-Salonen, M. The survival of the pentachlorophenol-degrading Rhodococcus chlorophenolicus PCP-1 and Flavobacterium sp. in natural soil, Biodegradation 1, 273, 1990.
29. Brown, D.G., and Jaffé, P.R. Effects of nonionic surfactants on bacterial transport through porous media, Environ. Sci. Technol. 35, 3877, 2001.
30. Bruhlmann, F., and Chen, W. Tuning biphenyl dioxygenase for extended substrate specificity, Biotechnol. Bioeng. 63, 544, 1999.
31. Burchhardt, G., Schmidt, I., Cuypers, H., Petruschka, L., Volker, A., and Herrmann, H. Studies on spontaneous promoter-up mutations in the transcriptional activator-encoding gene phIR and their effects on the degradation of phenol in Escherichia coli and Pseudomonas putida, Mol. Gen. Genet. 254, 539, 1997.
32. Burlage, R.S. Emerging technologies: Bioreporters, biosensors, and microprobes, In Manual of environmental microbiology, ed. C.J. Hurst, pp. 115-123. ASM, Washington, DC, 1997.
33. Caccavo, F., Jr., Ramsing, N.B., and Costerton, J.W. Morphological and metabolic responses to starvation by the dissimilatory metal-reducing bacterium Shewanella alga BrY, Appl. Environ. Microbiol. 62, 4678, 1996.
34. Casavant, N.C., Thompson, D., Beattie, G.A., Phillips, G.J., and Halverson, L.J. Use of a site-specific recombination-based biosensor for detecting bioavailable toluene and related compounds on roots, Environ. Microbiol. 5, 238, 2003.
35. Caspi, R., Pacek, M., Consiglieri, G., Helinski, D.R., Toukdarian, A., and Konieczny, I. A broad host range replicon with different requirements for replication initiation in three bacterial species, EMBO J. 20, 3262, 2001.
36. Cassidy M.B., Lee, H., and Trevors, J.T. Environmental applications of immobilized microbial cells: A review, J. Ind. Microbiol. 16, 79, 1996.
37. Cebolla, A., Sousa, C., and de Lorenzo, V. Rational design of a bacterial transcriptional cascade for amplifying gene expression capacity, Nucleic Acids Res. 29, 759, 2001.
38. Cho, J.-C., and Tiedje, J.M. Quantitative detection of microbial genes by using DNA microarrays, Appl. Environ. Microbiol. 68, 1425, 2002.
39. Christensen, B.B., Sternberg, C., Andersen, J.B., Eberl, L., Møller, S., Givskov, M., and Molin, S. Establishment of new genetic traits in a microbial biofilm community, Appl. Environ. Microbiol. 64, 2247, 1998.
40. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., Chandra, S., McGarrell, D.M., Schmidt, T.M., Garrity, G.M., and Tiedje, J.M. The ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy, Nucleic Acids Res. 31, 442, 2003.
41. Contreras, A., Molin, S., and Ramos, J.-L. Conditional-suicide containment system for bacteria which mineralize aromatics, Appl. Environ. Microbiol. 57, 1504, 1991.
42. Curl, E.A., and Truelove, B. The Rhizosphere, Springer-Verlag, Berlin, 1986, 288.
43. Dandie, C.E., Thomas, S.M., and McClure, N.C. Comparison of a range of green fluorescent protein-tagging vectors for monitoring a microbial inoculant in soil, Lett. Appl. Microbiol. 32, 26, 2001.
44. de Lorenzo, V., Herrero, M., Jakubzik, U., and Timmis, K.N. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative eubacteria, J. Bacteriol. 172, 6568, 1990.
45. De Wildeman, S., Linthout, G., Van Langenhove, H., and Verstraete, W. Complete lab-scale detoxification of groundwater containing 1,2-dichloroethane, Appl. Microbiol. Biotecbnol. 63, 609, 2004.
46. Dean, S.M., Jin, Y., Cha, D.K., Wilson, S.V., and Radosevich, M. Phenanthrene degradation in soils co-inoculated with phenanthrene-degrading and biosurfactant-producing bacteria, J. Environ. Qual. 30, 1126, 2001.
47. Dejonghe, W., Boon, N., Seghers, D., Top, E.M., and Verstraete, W. Bioaugmentation of soils by increasing microbial richness: Missing links, Environ. Microbiol. 3, 649, 2001.
48. Dejonghe, W., Goris, J., El Fantroussi, S., Höfte, M., De Vos, P., Verstraete, W., and Top, E.M. 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, 2000.
49. Dennis, P., Edwards, E.A., Liss, S.N., and Fulthorpe, R. Monitoring gene expression in mixed microbial communities by using DNA microarrays, Appl. Environ. Microbiol. 69, 769, 2003.
50. Devers, M., Soulas, G., and Martin-Laurent, F. Real-time reverse transcription PCR analysis of expression of atrazine catabolism genes in two bacterial strains isolated from soil, J. Microbiol. Metbods 56, 3, 2004.
51. Dhankher, O.P., Li, Y., Rosen, B.P., Shi, J., Salt, D., Senecoff, J.F., Sashti, N.A., and Meagher, R.B. Engineering tolerance and hyperaccumulation of arsenic in plants by combining arsenate reductase and γ-glutamylcysteine synthetase expression, Nat. Biotechnol. 20, 1140, 2002.
52. Diaz, E., Munthali, M., de Lorenzo, V., and Timmis, K.N. Universal barrier to lateral spread of specific genes among microorganisms, Mol. Microbiol. 13, 855, 1994.
53. DiGiovanni, G.D., Neilson, J.W., Pepper, I.L., and Sinclair, N.A. Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients, Appl. Environ. Microbiol. 62, 2521, 1996.
54. Dittmann, J., Heyser, W., and Bucking, H. Biodegradation of aromatic compounds by white rot and ectomycorrhizal fungal species and the accumulation of chlorinated benzoic acid in ectomycorrhizal pine seedlings, Chemosphere 49, 297, 2002.
55. Dong, H., Onstott, T.C., Deflaun, M.F., Fuller, M.E., Scheibe, T.D., Streger, S.H., Rothmel, R.K., and Mailloux, B.J. Relative dominance of physical versus chemical effects on the transport of adhesion-deficient bacteria in intact cores from South Oyster, Virgina, Environ. Sci. Technol. 36, 891, 2002.
56. Dong, Q., Springeal, D., Schoeters, J., Nuyts, G., Mergeay, M., and Diels, L. Horizontal transfer of bacterial heavy metal resistance genes and its applications to activated sludge systems, Water Sci. Tech. 37, 465, 1998.
57. Donnelly, P.K., Fletcher, J.S. Potential use of mycorrhizal fungi as bioremediation agents, In Bioremediation through rhizosphere technology, eds. T.A. Anderson and J.R. Coats, pp. 93-99. American Chemical Society, Washington, DC, 1994.
58. Dorn, J.G., Frye, R.J., and Maier, R.M. Effect of temperature, pH, and initial cell number on luxCDABE and nah gene expression during naphthalene and salicylate catabolism in the bioreporter organism Pseudomonas putida RB1353, Appl. Environ. Microbiol. 69, 2209, 2003.
59. Dröge, M., Pühler, A., and Selbitschka, W. Horizontal gene transfer as a biosafety issue: A natural phenomenon of public concern, J. Biotechnol. 64, 75, 1998.
60. Duba, A.G., Jackson, K.J., Jovanovich, M.C., Knapp, R.B., and Taylor, R.T. TCE remediation using in situ, resting-state bioaugmentation, Environ. Sci. Technol. 30, 1982, 1996.
61. Dunfield, K.E., and Germida, J.J. Diversity of bacterial communities in the rhizosphere and root interior of field-grown genetically modified Brassica napus, FEMS Microbiol. Ecol. 38, 1, 2001.
62. Duquenne, P., Chenu, C., Richard, G., and Catroux, G. Effect of carbon source supply and its location on competition between inoculated and established bacterial strains in sterile soil microcosm, FEMS Microbiol. Ecol. 29, 331, 1999.
63. Dybas, M.J., Bezborodinikov, S., Voice, T., Wiggert, D.C., Davies, S., Tiedje, J., Criddle, C.S., Kawka, O., Barcelona, M., and Mayotte, T. Evaluation of bioaugmentation to remediate an aquifer contaminated with carbon tetrachloride, in In situ and on-site bioremediation, vol. 4, pp. 507-512. Batelle Press, Columbus, OH, 1997.
64. Dybas, M.J., Hyndman, D.W., Heine, R., Tiedje, J., Linning, K., Wiggert, D., Voice, T., Zhao, X., Dybas, L., and Criddle, C.S. Development, operation, and long-term performance of a full-scale biocurtain utilizing bioaugmentation, Environ. Sci. Technol. 36, 3635, 2002.
65. Ellis, D.E., Lutz, E.J., Odom, J.M., Buchanan, R.J., Jr., Bartlett, C.L., Lee, M.D., Harkness, M.R., and Deweerd, K.A. Bioaugmentation for accelerated in situ anaerobic bioremediation, Environ. Sci. Technol. 34, 2254, 2000.
66. Elväng, A.M., Westerberg, K., Jernberg, C., and Jansson, J.K. Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil, Environ. Microbiol. 3, 32, 2001.
67. European Parliament and The Council of the European Community, Directive 2001/18/EC [Online], available at http://europa.eu.int/eur-lex/pri/en/oj/dat/ 2001/1_106/1_10620010417en00010038.pdf, 2001 (verified 14 February 2004).
68. Fang, M., and Wong, J.W. Seeding effect on cocomposting wastewater biosolids with coal ash, Water Environ. Res. 73, 633, 2001.
69. Fleming, J.T., Yao, W.H., and Sayler, G.S. Optimization of differential display of prokaryotic mRNA: Application to pure culture and soil microcosms, Appl. Environ. Microbiol. 64, 3698, 1998.
70. Ford, C.Z., Sayler, G.S., and Burlage, R.S. Containment of a genetically engineered microorganism during a field bioremediation application, Appl. Microbiol. Biotechnol. 51, 397, 1999.
71. Fray, R.G., Throup, J.P., Daykin, M., Wallace, A., Williams, P., Stewart, G.S.A.B., and Grierson, D. Plants genetically modified to produce N-acylhomoserine lactones communicate with bacteria, Nat. Biotechnol. 17, 1017, 1999.
72. French, C.E., Rosser, S.J., Davies, G.J., Nicklin, S., and Bruce, N.C. Biodegradation of explosives by transgenic plants expressing pentaerythritol tetranitrate reductase, Nat. Biotechnol. 17, 491, 1999.
73. Ganguli, A., and Tripathi, A.K. Bioremediation of toxic chromium from electroporating effluent by chromate-reducing Pseudomonas aeruginosa A2Chr in two bioreactors, Appl. Microbiol. Biotechnol. 58, 416, 2002.
74. Garcia-Junco, M., Gomez-Lahoz, C., Niqui-Arroyo, J.L., and Ortega-Calvo, J.J. Biosurfactant- and biodegradation-enhanced partitioning of polycyclic aromatic hydrocarbons from nonaqueous-phase liquids, Environ. Sci. Technol. 37, 2988, 2003.
75. Gardin, H., and Pauss, A. K-Carrageenan/gelatin gel beads for the co-immobilization of aerobic and anaerobic microbial communities degrading 2,4,6-trichlorophenol under air-limited conditions, Appl. Microbiol. Biotechnol. 56, 517, 2001.
76. Gentry, T.J., Josephson, K.L., and Pepper, I.L. Functional establishment of introduced chlorobenzoate degraders following bioaugmentation with newly activated soil, Biodegradation 15, 67, 2004.
77. Gentry, T.J., Newby, D.T., Josephson, K.L., and Pepper, I.L. Soil microbial population dynamics following bioaugmentation with a 3-chlorobenzoate-degradaing bacterial culture, Biodegradation 12, 349, 2001.
78. Gisbert, C., Ros, R., De Haro, A., Walker, D.J., Pilar Bernal, M., Serrano, R., and Navarro-Avino, J. A plant genetically modified that accumulates Pb is especially promising for phytoremediation, Biochem. Biophys. Res. Commun. 303, 440, 2003.
79. Gleba, D., Borisjuk, N.V., Borisjuk, L.G., Kneer, R., Poulev, A., Skarzhinskaya, M., Dushenkov, S., Logendra, S., Gleba, Y.Y., and Raskin, I. Use of plant roots for phytoremediation and molecular farming, Proc. Natl. Acad. Sci. USA 96, 5973, 1999.
80. Glick, B.R. and Pasternak, J.J. Molecular Biotechnology - Principles and Applications of Recombinant DNA, 2nd ed., p. 683. ASM Press, Washington, DC, 1998.
81. Gordon, M., Choe, N., Duffy, J., Ekuan, G., Heilman, P., Muiznieks, I., Ruszaj, M., Shurtleff, B.B., Strand, S., Wilmoth, J., and Newman, L.A. Phytoremediation of trichloroethylene with hybrid poplars, Environ. Health Perspect. 106(suppl. 4), 1001, 1998.
82. Gotfredson, M., and Gerdes, K. The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family, Mol. Microbiol. 29, 1065, 1998.
83. Graupner, S., and Wackernagel, W. A broad-host-range expression vector series including Ptac test plasmid and its application in the expression of the dod gene of Serratia marcescens (coding for ribulose-5-phosphate 3-epimerase) in Pseudomonas stutzeri, Biomol. Eng. 17, 11, 2000.
84. Gu, A.Z., Hedlund, B.P., Staley, J.T., Strand, S.E., and Stensel, H.D. Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE, Environ. Microbiol. 6, 45, 2004.
85. Gugerli, R., Cantana, E., Heinzen, C., von Stockar, U., and Marison, I.W. Quantitative study of the production and properties of alginate/poly-L-lysine microcapsules, J. Microencapsulation 19, 571, 2002.
86. Haby, P.A., and Crowley, D.E. Biodegradation of 3-chlorobenzoate as affected by rhizodeposition and selected carbon substrates, J. Environ. Qual. 25, 304, 1996.
87. Hajji, K.T., Lépine, F., Bisaillon, J.-G., Beaudet, R., Hawari, J., and Guiot, S.R. Effects of bioaugmentation strategies in UASB reactors with a methanogenic consortium for removal of phenolic compounds, Biotechnol. Bioeng. 67, 417, 2000.
88. Hamid, M., Siddiqui, I.A., and Shahid Shaukat, S. Improvement of Pseudomonas fluorescens CHAO biocontrol activity against root-knot nematode by the addition of ammonium molybdate, Lett. Appl. Microbiol. 36, 239, 2003.
89. Harkness, M.R., Bracco, A.A., Brennan, M.J., Jr., Deweerd, K.A., and Spivack, J.L. Use of bioaugmentation to stimulate complete reductive dechlorination of trichloroethene in dover soil columns, Environ. Sci. Technol. 33, 1100, 1999.
90. Heid, C.A., Stevens, J., Livak, K.J., and Williams, P.M. Real time quantitative PCR, Genome Res. 6, 986, 1996.
91. Hendrickson, E.R., Payne, J.A., Young, R.M., Starr, M.G., Perry, M.P., Fahnestock, S., Ellis, D.E., and Ebersole, R.C. Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe, Appl. Environ. Microbiol. 68, 485, 2002.
92. Herrero, M., de Lorenzo, V., and Timmis, K.N. 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, 1990.
93. Herrick, J.B., Stuart-Keil, K.G., Ghiorse, W.C., and Madsen, E.L. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site, Appl. Environ. Microbiol. 63, 2330, 1997.
94. Hestbjerg, H., Willumsen, P.A., Christensen, M., Andersen, O., and Jacobsen, C.S. Bioaugmentation of tar-contaminated soils under field conditions using Pleurotus ostreatus refuse from commercial mushroom production, Environ. Toxicol. Chem. 22, 692, 2003.
95. Hoang, T.T., Kutchma, A.J., Becher, A., and Schweizer, H.P. Integration-proficient plasmids for Pseudomonas aeruginosa: Site-specific integration and use for engineering of reporter and expression strains, Plasmid 43, 59, 2000.
96. Holden, P.A., LaMontagne, M.G., Bruce, A.K., Miller, W.G., and Lindow, S.E. Assessing the role of Pseudomonas aeruginosa surface-active gene expression in hexadecane biodegradation in sand, Appl. Environ. Microbiol. 68, 2509, 2002.
97. Hong, K.J., Tokunaga, S., and Kajiuchi, T. Evaluation of remediation process with plant-derived biosurfactant for recovery of heavy metals from contaminated soils, Chemosphere 49, 379, 2002.
98. Hooker, B.S., and Skeen, R.S. Transgenic phytoremediation blasts onto the scene, Nat. Biotechnol. 17, 428, 1999.
99. Hristova, K.R., Lutenegger, C.M., and Scow, K.M. Detection and quantification of methyl tert-butyl ether-degrading strain PM1 by real-time TaqMan PCR, Appl. Environ. Microbiol. 67, 5154, 2001.
100. Hurt, R.A., Qiu, X., Wu, L., Roh, Y., Palumbo, A.V., Tiedje, J.M., and Zhou, J. Simultaneous recovery of RNA and DNA from soils and sediments, Appl. Environ. Microbiol. 67, 4495, 2001.
101. Jensen, L.B., Ramos, J.-L., Kaneva, Z., and Molin, S. A substrate-dependent biological containment system for Pseudomonasputida based on the Escherichia coli gef gene, Appl. Environ. Microbiol. 59, 3713, 1993.
102. Jernberg, C., and Jansson, J.K. Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure, FEMS Microbiol. Ecol. 42, 387, 2002.
103. Jitnuyanont, P., Sayavedra-Soto, L.A., and Semprini, L. Bioaugmentation of butane-utilizing microorganisms to promote cometabolism of 1,1,1-trichloroethane in groundwater microcosms, Biodegradation 12, 11, 2001.
104. Jones, R.W., Pettit, R.E., and Taber, R.A. Lignite and stillage: Carrier and substrate for application of fungal biocontrol agents to soil, Phytopathology 74, 1167, 1984.
105. Kaplan, D.L., Mello, C., Sano, T., Cantor, C., and Smith, C. Streptavidin-based containment systems for genetically engineered microorganisms, Biomol. Eng. 16, 135, 1999.
106. Karthikeyan, R., and Kulakow, P.A. Soil plant microbe interactions in phytoremediation, Adv. Biochem. Eng. Biotechnol. 78, 51, 2003.
107. Kay, E., Vogel, T.M., Bertolla, F., Nalin, R., and Simonet, P. In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria, Appl. Environ. Microbiol. 68, 3345, 2002.
108. Kikuchi, T., Iwasaki, K., Nishihara, H., Takamura, Y., and Yagi, O. Quantitative and rapid detection of the trichloroethylene-degrading bacterium Methylocystis sp. M in groundwater by real-time PCR, Appl. Microbiol. Biotechnol. 59, 731, 2002.
109. Kloos, D.U., Stratz, M., Guttler, A., Steffan, R.J., and Timmis, K.N. Inducible cell lysis system for the study of natural transformation and environmental fate of DNA released by cell death, J. Bacteriol. 176, 7352, 1994.
110. Knudsen, S., Saadbye, P., Hansen, L.H., Collier, A., Jacobsen, B.L., Schlundt, J., and Karlström, O.H. Development and testing of improved suicide functions for biological containment of bacteria, Appl. Environ. Microbiol. 61, 985, 1995.
111. Koch, B., Jensen, L.E., and Nybroe, O. A panel of TN7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site, J. Microbiol. Methods 45, 187, 2001.
112. Köhler, S., Belkin, S., and Schmid, R.D. Reporter gene bioassays in environmental analysis, Fresenius. J. Anal. Chem. 366, 769, 2000.
113. Kok, C.J., Hageman, P.E.J., Maas, P.W.T., Postma, J., Roozen, N.J.M., and van Vuurde, J.W.L. Processed manure as carrier to introduce Trichoderma harzianum: Population dynamics and biocontrol effects on Rhizoctonia solani, Biocontrol Sci. Technol. 6, 147, 1996.
114. Kota, M., Daniell, H., Varma, S., Garczynski, S.F., Gould, F., and Moar, W.J. Overexpression of the Bacillus thuringiensis (Bt) Cry2Aa2 protein in chloroplasts confers resistance to plants against susceptible and Bt-resistant insects, Proc. Natl. Acad. Sci. USA 96, 1840, 1999.
115. Kowalchuk, G.A., Buma, D.S., de Boer, W., Klinkhamer, P.G.L., and van Veen, J.A. Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms, Antonie van Leeuwenhoek 81, 509, 2002.
116. Krutz, L.J., Beyrouty, C.A., Gentry, T.J., Wolf, D.C., and Reynolds, C.M. Selective enrichment of a pyrene degrader population and enhanced pyrene degradation in bermudagrass rhizosphere, Biol. Fert. Soils. 2004(submitted).
117. Kuiper, I., Kravchenko, L.V., Bloemberg, G.V., and Lugtenberg, B.J. Pseudomonas putida strain PCL1444, selected for efficient root colonization and naphthalene degradation, effectively utilizes root exudate components, Mol. Plant Microbe Interact. 15, 734, 2002.
118. Lamar, R.T., Davis, M.W., Dietrich, D.M., and Glaser, J.A. Treatment of a pentachlorophenol- and creosote-contaminated soil using the lignin-degrading fungus Phanerochaete sordida: A field demonstration, Soil Biol. Biochem. 26, 1603, 1994.
119. Lamar, R.T., and Dietrich, D.M., In situ depletion of pentachlorophenol from contaminated soil by Phanerochaete spp., Appl. Environ. Microbiol. 56, 3093, 1990.
120. Lamar, R.T., Schoenike, B., Vanden Wymelenberg, A., Stewart, P., Dietrich, D.M., and Cullen, D. Quantitation of fungal mRNAs in complex substrates by reverse transcription PCR and its application to Phanerochaete chrysosporium-colonized soil, Appl. Environ. Microbiol. 61, 2122, 1995.
121. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses, Proc. Natl. Acad. Sci. USA 82, 6955, 1985.
122. Lappin-Scott, H.M., and Costerton, J.W. Ultramicrobacteria and their biotechnological applications, Curr. Opin. Biotechnol. 3, 283, 1992.
123. Laramee, L., Lawrence, J.R., and Greer, C.W. Molecular analysis and development of 16S rRNA oligonucleotide probes to characterize a diclofop-methyl-degrading biofilm consortium, Can. J. Microbiol. 46, 133, 2000.
124. Lassner, M.W., and McElroy, D. Directed molecular evolution: Bridging the gap between genomics leads and commercial products, OMICS 6, 153, 2002.
125. Lau, P.C.K., and de Lorenzo, V. Genetic engineering: The frontier of bioremediation, Environ. Sci. Technol. 33, 124A, 1999.
126. Lawford, H.G., and Rousseau, J.D. Cellulosic fuel ethanol: Alternative fermentation process designs with wild-type and recombinant Zymomonas mobilis, Appl. Biochem. Biotechnol. 105-108, 457, 2003.
127. Leeson, A., and Alleman, B.C. Eds. Phytoremediation and Innovative Strategies for Specialized Remedial Applications, p. 340. Battelle Press, Columbus, OH, 1999.
128. Lehrbach, P.R., Zeyer, J., Reineke, W., Knackmuss, H.-J., and Timmis, K.N. Enzyme recruitment in vitro: Use of cloned genes to extend the range of haloaromatics degraded by Pseudomonas sp. strain B13, J. Bacteriol. 158, 1025, 1984.
129. Lendvay, J.M., Löffler, F.E., Dollhopf, M., Aiello, M.R., Daniels, G., Fathepure, B.Z., Gebhard, M., Heine, R., Helton, R., Shi, J., Krajmalnik-Brown, R., Major, C.L., Jr., Barcelona, M.J., Petrovskis, E., Hickey, R., Tiedje, J.M., and Adriaens, P. Bioreactive barriers: A comparison of bioaugmentation and biostimulation for chlorinated solvent remediation, Environ. Sci. Technol. 37, 1422, 2003.
130. Leveau, J.H.J., and Lindow, S.E. Bioreporters in microbial ecology, Curr. Opin. Microbiol. 5, 259, 2002.
131. Li, Q., and Logan, B.E. Enhancing bacterial transport for bioaugmentation of aquifers using low ionic strength solutions and surfactants, Water Res. 33, 1090, 1999.
132. Loh, J., Pierson, E.A., Pierson, L.S., III, Stacey, G., and Chatterjee, A. Quorum sensing in plant-associated bacteria, Curr. Opin. Plant Biol. 5, 1, 2002.
133. Mae, A., Montesano, M., Koiv, V., and Palva, E.T. Transgenic plants producing the bacterial pheromone N-acyl-homoserine lactone exhibit enhanced resistance to the bacterial phytopathogen Erwinia carotovora, Mol. Plant Microbe Interact. 14, 1035, 2001.
134. Maier, R.M., Neilson, J.W., Artiola, J.F., Jordan, F.L., Glenn, E.P., and Descher, S.M. Remediaton of metal-contaminated soil and sludge using biosurfactant technology, Int. J. Occup. Med. Environ. Health 14, 241, 2001.
135. Major, D.W., McMaster, M. L., Cox, E.E., Edwards, E.A., Dworatzek, S.M., Hendrickson, E.R., Starr, M.G., Payne, J.A., and Buonamici, L.W. Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene, Environ. Sci. Technol. 36, 5106, 2002.
136. Marlowe, E.M., Wang, J.M., Pepper, I.L., and Maier, R.M. Application of a reverse transcription- PCR assay to monitor regulation of the catabolic nahAc gene during phenanthrene degradation, Biodegradation 13, 251, 2002.
137. Mata-Sandoval, J.C., Karns, J., and Torrents, A. Influence of rhamnolipids and Triton X-100 on the desorption of pesticides from soils, Environ. Sci. Technol. 36, 4669, 2002.
138. Meharg, A.A., and Cairney, J.W.G. Ectomycorrhizas-Extending the capabilities of rhizosphere remediation?, Soil Biol. Biochem. 32, 1475, 2000.
139. Meharg, A.A., Cairney, J.W.G., and Maguire, N. Mineralization of 2,4-dichlorophenol by ectomycorrhizal fungi in axenic culture and in symbiosis with pine, Chemosphere 34, 2495, 1997.
140. Meharg, A.A., and Macnair, M.R. Genetic correlation between arsenate tolerance and the rate of influx of arsenate and phosphate in Holcus lanatus L., Heredity 69, 336, 1992.
141. Middeldorp, P.J.M., Briglia, M., and Salkinoja-Salonen, M.S. Biodegradation of pentachlorophenol in natural soil by inoculated Rhodococcus chlorophenolicus, Microb. Ecol. 20, 123, 1990.
142. Miethling, R., Wieland, G., Backhaus, H., and Tebbe, C.C. Variation of microbial rhizosphere communities in response to crop species, soil origin, and inoculation with Sinorhizobium meliloti L33, Microb. Ecol. 41, 43, 2000.
143. Misko, A.L., and Germida, J.J. Taxonomic and functional diversity of pseudomonads isolated from the roots of field-grown canola, FEMS Microbiol. Ecol. 42, 399, 2002.
144. Molin, S. Environmental potential of suicide genes, Curr. Opin. Biotechnol. 4, 299, 1993.
145. Molin, S., and Givskov, M. Application of molecular tools for in situ monitoring of bacterial growth activity, Environ. Microbiol. 1, 383, 1999.
146. Molina, L., Ramos, C., Ronchel, M.-C., Molin, S., and Ramos, J.-L. Construction of an efficient biologically contained Pseudomonasputida strain and its survival in outdoor assays, Appl. Environ. Microbiol. 64, 2072, 1998.
147. Monib, M., Abd-el-Malek, Y., Hosny, I., and Fayez, M. Effect of Azotobacter inoculation on plant growth and soil nitrogen, Zentralbl. Bakteriol. Naturwiss. 134, 140, 1979.
148. Morrissey, J.P., Walsh, U.F., O'Donnell, A., Moënne-Loccoz, Y., and O'Gara, F. Exploitation of genetically modified inoculants for industrial ecology applications, Antonie van Leeuwenhoek 81, 599, 2002.
149. Moslemy, P., Neufeld, R.J., and Guiot, S.R. Biodegradation of gasoline by gellan gum-encapsulated bacterial cells, Biotechnol. Bioeng. 80, 175, 2002.
150. Moslemy, P., Neufeld, R.J., Millette, D., and Guiot, S.R. Transport of gellan gum microbeads through sand: An experimental evaluation for encapsulated cell bioaugmentation, J. Environ. Manage. 69, 249, 2003.
151. Moter, A., and Gobel, U.B. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms, J. Microbiol. Methods 41, 85, 2000.
152. Mueller, J.G., Resnick, S.M., Shelton, M.E., and Pritchard, P.H. Effect of inoculation on the biodegradation of weathered Prudhoe Bay crude oil, J. Indust. Microbiol. 10, 95, 1992.
153. Narasimhan, K., Basheer, C., Bajic, V.B., and Swarup, S. Enhancement of plant-microbe interactions using a rhizosphere metabolomics-driven approach and its application in the removal of polychlorinated biphenyls, Plant Physiol. 132, 146, 2003.
154. Neilson, J.W., Pierce, S.A., and Maier, R.M. Factors influencing expression of luxCDABE and nah genes in Pseudomonas putida RB1353 (NAH7, pUTK9) in dynamic systems, Appl. Environ. Microbiol. 65, 3473, 1999.
155. Newby, D.T., Gentry, T.J., and Pepper, I.L. Comparison of 2,4-dichlorophenoxyacetic acid degradation and plasmid transfer in soil resulting from bioaugmentation with two different pJP4 donors, Appl. Environ. Microbiol. 66, 3399, 2000a.
156. Newby, D.T., Josephson, K.L., and Pepper, I.L. Detection and characterization of plasmid pJP4 transfer to indigenous soil bacteria, Appl. Environ. Microbiol. 66, 290, 2000b.
157. Niemi, K., Vuorinen, T., Ernstsen, A., and Häggman, H. Ectomycorrhizal fungi and exogenous auxins influence root and mycorrhiza formation of Scots pine hypocotyl cuttings in vitro, Tree Physiol. 22, 1231, 2002.
158. Normander, B., and Hendriksen, N.B. Effective dose of a microbial inoculant is one to four cells in the rhizosphere, Can. J. Microbiol. 48, 940, 2002.
159. Ochman, H., Lawrence, J.G., and Groisman, E.A. Lateral gene transfer and the nature of bacterial innovation, Nature 405, 299, 2000.
160. Ogawa, N., and Miyashita, K. Recombination of a 3-chlorobenzoate catabolic plasmid from Alcaligenes eutrophus NH9 mediated by direct repeat elements, Appl. Environ. Microbiol. 61, 3788, 1995.
161. Oger, P.M., Mansouri, H., Nesme, X., and Dessaux, Y. Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere, Microb. Ecol., published online, available at http://springerlink.metapress.com/openurl. asp?genre=article&id=doi:10.1007/s00248-003-2012-9, 2003.
162. Ohtsubo, Y., Shimura, M., Delawary, M., Kimbara, K., Takagi, M., Kudo, T., Ohta, A., and Nagata, Y. Novel approach to the improvement of biphenyl and polychlorinated biphenyl degradation activity: Promoter implantation by homologous recombination, Appl. Environ. Microbiol. 69, 146, 2003.
163. Olexa, T.J., Gentry, T.J., Hartel, P.G., Wolf, D.C., Fuhrmann, J.J., and Reynolds, C.M. Mycorrhizal colonization and microbial community structure in the rhizosphere of annual ryegrass grown in pyrene-amended soils, Int. J. Phytoremediation 2, 213, 2000.
164. Olsen, P.E., Rice, W-A., Bordeleau, L.M., Demidoff, A.H., Collins, M.M. Levels and identities of nonrhizobial microorganisms found in commercial legume inoculant made with nonsterile peat carrier, Can. J. Microbiol. 42, 72, 1996.
165. O'Reilley, K.T., and Crawford, R.L. Degradation of pentachlorophenol by polyurethane immobilized Flavobacterium cells, Appl. Environ. Microbiol. 55, 2113, 1989.
166. Patureau, D., Helloin, E., Rustrian, E., Bouchez, T., Delgenes, J.P., and Moletta, R. Combined phosphate and nitrogen removal in a sequencing batch reactor using the aerobic denitrifier, Microvirgula aerodenitrificans, Wat. Res. 35, 189, 2001.
167. Pepper, I.L., Gentry, T.J., Newby, D.T., Roane, T.M., and Josephson, K.L. The role of cell bioaugmentation and gene bioaugmentation in the remediation of co-contaminated soils, Environ. Health Perspect. 110(Suppl. 6), 943, 2002.
168. Perlak, F.J., Oppenhuizen, M., Gustafson, K., Voth, R., Sivasupramaniam, S., Heering, D., Carey, B., Ihrig, R.A., and Roberts, J.K. Development and commercial use of Bollgard® cotton in the USA-Early promises versus today's reality, Plant J. 27, 489, 2001.
169. Pierson, L.S., III, Expanding the club: Engineering plants to talk to bacteria, Trends Plant. Sci. 5, 89, 2000.
170. Porteous, L.A., Widmer, F., and Seidler, R.J. Multiple enzyme restriction fragment length polymorphism analysis for high resolution distinction of Pseudomonas (sensu stricto) 16S rRNA genes, J. Microbiol. Methods. 51, 337, 2002.
171. Poulsen, L.K., Larsen, N.W., Molin, S., and Andersson, P. A family of genes encoding a cell-killing function may be conserved in all Gram-negative bacteria, Mol. Microbiol. 3, 1463, 1989.
172. Pritchard, P.H. Use of inoculation in bioremediation, Curr. Opin. Biotech. 3, 232, 1992.
173. Quan, X., Shi, H., Wang, J., and Qian, Y. Biodegradation of 2,4-dichlorphenol in sequencing batch reactors augmented with immobilized mixed culture, Chemosphere 50, 1069, 2003.
174. Rahman, K.S., Rahman, T.J., Kourkoutas, Y., Petsas, I., Marchant, R., and Banat, I.M. Enhanced bioremediation of n-alkane in petroleum sludge using bacterial consortium amended with rhamnolipid and micronutrients, Bioresour. Technol. 90, 159, 2003.
175. Ramos, H.J., Roncato-Maccari, L.D., Souza, E.M., Soares-Ramos, J.R., Hung, M., and Pedrosa, F.O. Monitoring Azospirillum-wheat interactions using the gfp and gusA genes constitutively expressed from a new broad-host range vector, J. Biotechnol 97, 243, 2002.
176. Ramos, J.L., Stolz, A., Reineke, W., and Timmis, K.N. Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria, Proc. Natl. Acad. Sci. USA 83, 8467, 1986.
177. Regan, J.M., Oldenburg, P.S., Park, H.D., Harrington, G.W., and Noguera, D.R. Simultaneous determination of bacterial viability and identity in biofilms using ethidium monoazide and fluorescent in situ hybridization, Water Sci. Technol. 47, 123, 2003.
178. Rensing C., Newby D.T., and Pepper I.L. The role of selective pressure and selfish DNA in horizontal gene transfer and soil microbial community adaptation, Soil. Biol. Biochem. 34, 285, 2002.
179. Richardson, R.E., Bhupathiraju, V.K., Song, D.L., Goulet, T.A., and Alvarez-Cohen, L. Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques, Environ. Sci. Technol. 36, 2652, 2002.
180. Ripp, S., Nivens, D.E., Ahn, Y., Wemer, C., Jarrell, J. IV., Easter, J.P., Cox, C.D., Burlage, R.S., and Sayler, G.S. Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control, Environ. Sci. Technol. 34, 846, 2000.
181. Roane, T.M., Josephson, K.L., and Pepper, I.L. Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil, Appl. Environ. Microbiol. 67, 3208, 2001.
182. Rodrigues, J.L.M., Aiello, M.R., Urbance, J.W., Tsoi, T.V., and Tiedje, J.M. Use of both 16S rRNA and engineered functional genes with real-time PCR to quantify an engineered, PCB-degrading Rhodococcus in soil, J. Microbiol. Methods 51, 181, 2002.
183. Ronchel, M.C., Molina, L., Witte, A., Lutbiz, W., Molin, S., Ramos, J.L., and Ramos, C. Characterization of cell lysis in Pseudomonas putida induced upon expression of heterologous killing genes, Appl. Environ. Microbiol. 64, 4904, 1998.
184. Ronchel, M.C., and Ramos, J.L. Dual system to reinforce biological containment of recombinant bacteria designed for rhizoremediation, Appl. Environ. Microbiol. 67, 2649, 2001.
185. Ronchel, M.C., Ramos, C., Jensen, L.B., Molin, S., and Ramos, J.L. Construction and behavior of biologically contained bacteria for environmental applications in bioremediation, Appl. Environ. Microbiol. 61, 2990, 1995.
186. Rose, P., Harkin, J.M., and Hickey, W.J. Competitive touchdown PCR for estimation of Escherichia coli DNA recovery in soil DNA extraction, J. Microbiol. Methods 52, 29, 2003.
187. Rosochacki, S.J., and Matejczyk, M. Green fluorescent protein as a molecular marker in microbiology, Acta. Microbiol. Pol. 51, 205, 2002.
188. Ross, N., Villemur, R., Marcandella, É., and Deschênes, L. Assessment of changes in biodiversity when a community of ultramicrobacteria isolated from groundwater is stimulated to form a biofilm, Microb. Ecol. 42, 56, 2001.
189. Runes, H.B., Jenkins, J.J., and Bottomley, P.J. Atrazine degradation by bioaugmented sediment from constructed wetlands, Appl. Microbiol. Biotechnol. 57, 427, 2001.
190. Rutledge, R.G., and Cote, C. Mathematics of quantitative kinetic PCR and the application of standard curves, Nucleic Acids Res. 31, e93, 2003.
191. Salanitro, J.P., Johnson, P.C., Spinnler, G.E., Maner, P.M., Wisniewski, H.L., and Bruce, C. Field-scale demonstration of enhanced MTBE bioremediation through aquifer bioaugmentation and oxygenation, Environ. Sci. Technol. 34, 4152, 2000.
192. Sambrook, J., and Russell, D. Molecular Cloning-A Laboratory Manual, 3rd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 2001, 2344.
193. Sandrin, T.R., Chech, A.M., and Maier, R.M. A rhamnolipid biosurfactant reduces cadmium toxicity during naphthalene biodegradation, Appl. Environ. Microbiol. 66, 4585, 2000.
194. Savka, M.A., Dessaux, Y., Oger, P., and Rossbach, S. Engineering bacterial competitiveness and persistence in the phytosphere, Mol. Plant Microbe Interact. 15, 866, 2002.
195. Savka, M.A., and Farrand, S.K. Modification of rhizobacterial populations by engineering bacterium utilization of a novel plant-produced resource, Nat. Biotechnol. 15, 363, 1997.
196. Sayler, G.S., Fleming, J.T., and Nivens, D.E. Gene expression monitoring in soils by mRNA analysis and gene lux fusions, Curr. Opin. Biotechnol. 12, 455, 2001.
197. Sayler, G.S., and Ripp, S. Field applications of genetically engineered microorganisms for bioremediation processes, Curr. Opin. Biotechnol. 11, 286, 2000.
198. Scheel, T., Hofer, M., Ludwig, S., and Holker, U. Differential expression of manganese peroxidase and laccase in white-rot fungi in the presence of manganese or aromatic compounds, Appl. Microbiol. Biotechnol. 54, 686, 2000.
199. Schippers, C., Gessner, K., Muller, T., and Scheper, T. Microbial degradation of phenanthrene by addition of a sophorolipid mixture, J. Biotechnol. 83, 189, 2000.
200. Schwartz, E., and Scow, K.M. Repeated inoculation as a strategy for the remediation of low concentrations of phenanthrene in soil, Biodegradation 12, 201, 2001.
201. Schweizer, H.P. Vectors to express foreign genes and techniques to monitor gene expression in Pseudomonads, Curr. Opin. Biotechnol. 12, 439, 2001.
202. Schwieger, F., and Tebbe, C.C. Effect of field inoculation with Sinorhiobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album)-Linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria, Appl. Environ. Microbiol. 66, 3556, 2000.
203. Sefton, M.V., Dawson, R.M., Broughton, R.L., Blysniuk, J., and Sugamori, M.E. Microencapsulation of mammalian cells in a water-soluble polyacrylate by coextrusion and interfacial precipitation, Biotechnol. Bioeng. 29, 1135, 1987.
204. Sekelsky, A.M., and Shreve, G.S. Kinetic model of biosurfactant-enhanced hexadecane biodegradation by Pseudomonas aeruginosa, Biotechnol. Bioeng. 63, 401, 1999.
205. Sessitsch, A., Gyamfi, S., Stralis-Pavese, N., Weilharter, A., and Pfeifer, U. RNA isolation from soil for bacterial community and functional analysis: Evaluation of different extraction and soil conservation protocols, J. Microbiol. Methods 51, 171, 2002.
206. Sheeja, R.Y., and Murugesan, T. Mass transfer studies on the biodegradation of phenols in up-flow packed bed reactors, J. Hazard. Mater. B89, 287, 2002.
207. Shimizu, M., Kimura, T., Koyama, T., Suzuki, K., Ogawa, N., Miyashita, K., Sakka, K., and Ohmiya, K. Molecular breeding of transgenic rice plants expressing a bacterial chlorocatechol dioxygenase gene, Appl. Environ. Microbiol. 68, 4061, 2002.
208. Siciliano, S.D., and Germida, J.J. Bacterial inoculants of forage grasses that enhance degradation of 2-chlorobenzoic acid in soil, Environ. Toxicol. Chem. 16, 1098, 1997.
209. Siciliano, S.D., and Germida, J.J. Biolog analysis and fatty acid methyl ester profiles indicate that pseudomonad inoculants that promote phytoremediation alter the root-associated microbial community of Bromus biebersteinii, Soil Biol. Biochem. 30, 1717, 1998.
210. Siciliano, S.D., and Germida, J.J. Degradation of chlorinated benzoic acid mixtures by plant-bacterial associations, Environ. Toxicol. Chem. 17, 728, 1998.
211. Siciliano, S.D., and Germida, J.J. Taxonomic diversity of bacteria associated with the roots of field-grown transgenic Brassica napus cv. Quest, compared to the non-transgenic B. napus cv. Excel and B. rapa cv. Parkland, FEMS Microbiol. Ecol. 29, 263, 1999.
212. Siciliano, S.D., and Greer, C.W. Plant-bacterial combinations to phytoremediate soil contaminated with high concentrations of 2,4,6-trinitrotoluene, J. Environ. Qual. 29, 311, 2000.
213. Sidhu, R.S., Hammond, B.G., Fuchs, R.L., Mutz, J.-N., Holden, L.R., George, B., and Olson, T. Glyphosate-tolerant corn: The composition and feeding value of grain from glyphosate-tolerant corn is equivalent to that of conventional corn (Zea mays L.), J. Agric. Food Chem. 48, 2305, 2000.
214. Silva, E., Fialho, A.M., Sa-Correia, I., Burns, R.G., and Shaw, L.J. Combined bioaugmentation and biostimulation to cleanup soil contaminated with high concentrations of atrazine, Environ. Sci. Technol. 38, 632, 2004.
215. Singer, A.C., Smith, D., Jury, W.A., Hathuc, K., and Crowley, D.E. Impact of the plant rhizosphere and augmentation on remediation of polychlorinated biphenyl contaminated soil, Environ. Toxicol. Chem. 22, 1998, 2003.
216. Smit, E., Wolters, A.C., Lee, H., Trevors, J.T., and van Elsas, J.D. Interactions between a genetically marked Pseudomonasfluorescens strain and bacteriophage φR2f in soil: Effects of nutrients, alginate encapsulation, and the wheat rhizosphere, Microb. Ecol. 31, 125, 1996.
217. Springael, D., Diels, L., Hooyberghs, L., Kreps, S., and Mergeay, M. Construction and characterization of heavy metal-resistant haloaromatic- degrading Alcaligenes eutrophus strains, Appl. Environ. Microbiol. 59, 334, 1993.
218. Steffan, R.J., Sperry, K.L., Walsh, M.T., Vainberg, S., and Condee, C.W. Field-scale evaluation of in situ bioaugmentation for remediation of chlorinated solvents in groundwater, Environ. Sci. Technol. 33, 2771, 1999.
219. Steidle, A., Sigl, K., Schuhegger, R., Ihring, A., Schmid, M., Gantner, S., Stoffels, M., Riedel, K., Givskov, M., Hartmann, A., Langebartels, C., and Eberl, L. Visualization of N-acylhomoserine lactone-mediated cell-cell communication between bacteria colonizing the tomato rhizosphere, Appl. Environ. Microbiol. 67, 5761, 2001.
220. Steinberg, S.M., Poziomek, E.J., Engelmann, W.H., and Rogers, K.R. A review of environmental applications of bioluminescence measurements, Chemosphere, 30, 2155, 1995.
221. Steinle, P., Thalmann, P., Höhener, P., Hanselmann, K.W., and Stucki, G. Effect of environmental factors on the degradation of 2,6-dichlorophenol in soil, Environ. Sci. Technol. 34, 771, 2000.
222. Streger, S.H., Vainberg, S., Dong, H., and Hartzinger, P.B., Enhancing transport of Hydrogenophaga flava ENV735 for bioaugmentation of aquifers contaminated with methyl tert-butyl ether, Appl. Environ. Microbiol. 68, 5571, 2002.
223. Strong, L.C., McTavish, H., Sadowsky, M.J., and Wackett, L.P. Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase, Environ. Microbiol. 2, 91, 2000.
224. Stutzman-Engwall, K., Conlon, S., Fedechko, R., Kaczmarek, F., McArthur, H., Krebber, A., Chen, Y., Minshull, J., Raillard, S.A., and Gustafsson, C. Engineering the aveC gene to enhance the ratio of doramectin to its CHC-B2 analogue produced in Streptomyces avermitilis, Biotechnol. Bioeng. 82, 359, 2003.
225. Suenaga, H., Goto, M., and Furukawa, K. Emergence of multifunctional oxygenase activities by random priming recombination, J. Biol. Chem. 276, 22500, 2001.
226. Szafranski, P., Mello, C.M., Sano, T., Smith, C.L., Kaplan, D.L., and Cantor, C.R. A new approach for containment of microorganisms: Dual control of streptavidin expression of antisense RNA and the T7 transcription system, Proc. Natl. Acad. Sci. USA 94, 1059, 1997.
227. Taylor, C.C., Ranjit, N.J., Mills, J.A., Neylon, J.M., and Kung, L. Jr. The effect of treating whole-plant barley with Lactobacillus buchneri 40788 on silage fermentation, aerobic stability, and nutritive value for dairy cows, J. Dairy Sci. 85, 1793, 2002.
228. Temprano, F.J., Albareda, M., Camacho, M., Daza, A., Santamaria, C., and Rodriguez-Navarro, D.N. Survival of several Rhizobium/Bradyrhizobium strains on different inoculant formulations and inoculated seeds, Int. Microbiol. 5, 81, 2002.
229. Teplitski, M., Robinson, J.B., and Bauer, W.D. Plants secrete substances that mimic bacterial N-acyl homoserine lactone signal activities and affect population density-dependent behaviors in associated bacteria, Mol. Plant Microbe Interact. 13, 637, 2000.
230. Thiem, S.M., Krumme, M.L., Smith, R.L., and Tiedje, J.M. Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer, Appl. Environ. Microbiol. 60, 1059, 1994.
231. Thomas, J.C., Davies, E.C., Malick, F.K., Endreszl, C., Williams, C.R., Abbas, M., Petrella, S., Swisher, K., Perron, M., Edwards, R., Ostenkowski, P., Urbanczyk, N., Wiesend, W.N., and Murray, K.S. Yeast metallothionein in transgenic tobacco promotes copper uptake from contaminated soils, Biotechnol. Prog. 19, 273, 2003.
232. Thurnheer, T., Gmur, R., and Guggenheim, B. Multiplex FISH analysis of a six-species bacterial biofilm, J. Microbiol. Methods. 56, 37, 2004.
233. Top, E.M., Maila, M.P., Clerinx, M., Goris, J., De Vos, P., and Verstraete, W. Methane oxidation as a method to evaluate the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) from soil by plasmid mediated bioaugmentation, FEMS Microb. Ecol. 28, 203, 1999.
234. Top, E.M., Springael, D., and Boon, N. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soil and waters, FEMS Microb. Ecol. 42, 199, 2002.
235. Top, E.M., Van Daele, P., De Saeyer, N., and Forney, L.J. Enhancement of 2,4-dichlorophenoxyacetic acid (2,4-D) degradation in soil by dissemination of catabolic plasmids, Antonie Van Leeuwenhoek. 73, 87, 1998.
236. Trevors, J.T., van Elsas, J.D., Lee, H., and van Overbeek, L.S. Use of alginate and other carriers for encapsulation of microbial cells for use in soil, Microb. Releases 1, 61, 1992.
237. Unge, A., Tombolini, R., Molbak, L., and Jansson, J.K. Simultaneous monitoring of cell number and metabolic activity of specific bacterial populations with a dual gfp-luxAB marker system, Appl. Environ. Microbiol. 65, 813, 1999.
238. U.S. EPA, Biotechnology Program Under Toxic Substances Control Act (TSCA), Notifications, FY98 to Present [Online], available at http://www.epa.gov/opptintr/biotech/submiss.htm, 2003 (verified 14 February 2004).
239. U.S. EPA, Microbial Products of Biotechnology; Final Regulation Under the Toxic Substances Control Act [Online], available at http://www.epa.gov/ fedrgstr/EPA-TOX/1997/April/Day-11/t8669.htm, 1997 (verified 14 February 2004).
240. U.S. EPA, Phytoremediation Resource Guide, Publication 542-B-99-003, 1999.
241. van der Gast, C.J., Whiteley, A.S., Starkey, M., Knowles, C.J., and Thompson, I.P. Bioaugmentation strategies for remediating mixed chemical effluents, Biotechnol. Prog. 19, 1156, 2003.
242. Van Dyke, M.I., and Prosser, J.I. Enhanced survival of Pseudomonas fluorescens in soil following establishment of inoculum in a sterile soil carrier, Soil Biol. Biochem. 32, 1377, 2000.
243. van Veen, J.A., van Overbeek, L.S., and van Elsas, J.D. Fate and activity of microorganisms introduced into soil, Microbiol. Mol. Biol. Rev. 61, 121, 1997.
244. Vassilev, N., Vassileva, M., Azcon, R., and Medina, A. Application of free and Ca-alginate-entrapped Glomus deserticola and Yarowia lipolytica in a soil-plant system, J. Biotechnol. 91, 237, 2001.
245. Vogel, T.M. Bioaugmentation as a soil bioremediation approach, Curr. Opin. Biotech. 7, 311, 1996.
246. Wackett, L.P., Sadowsky, M.J., Martinez, B., and Shapir, N. Biodegradation of atrazine and related s-triazine compounds: From enzymes to field studies, Appl. Microbiol. Biotechnol. 58, 39, 2002.
247. Wang, G., Gentry, T.J., Grass, G., Josephson, K., Rensing, C., and Pepper, I.L. Real-time PCR quantification of a GFP-labeled, genetically engineered Pseudomonas putida strain during 2-chlorobenzoate degradation in soil, FFMS Microbiol. Lett. 233, 307, 2004.
248. Wantanabe, K., Hino, S., Onodera, K., Kajie, S., and Takahashi, N. Effects of exogenous phenol-degrading bacteria on performance and ecosystem of activated sludge, J. Ferment. Bioeng. 82, 291, 1996.
249. Wantanabe, K., Teramoto, M., and Harayama, S. Stable augmentation of activated sludge with foreign catabolic genes harboured by an indigenous dominant bacterium, Environ. Microbiol. 4, 577, 2002.
250. Weir, S.C., Dupuis, S.P., Providenti, M.A., Lee, H., and Trevors, J.T. Nutrient-enhanced survival of and phenanthrene mineralization by alginate-encapsulated and free Pseudomonas sp. UG14Lr cells in creosote-contaminated soil slurries, Appl. Microbiol. Biotechnol. 43, 946, 1995.
251. Weir, S.C., Providenti, M.A., Lee, H., and Trevors, J.T. Effect of alginate encapsulation and selected disinfectants on survival of and phenanthrene mineralization by Pseudomonas sp UG14Lr in creosote-contaminated soil, J. Ind. Microbiol. 16, 62, 1996.
252. Wenderoth, D.F., Rosenbrock, P., Abraham, W.-R., Pieper, D.H., and Höfle, M.G. Bacterial community dynamics during biostimulation and bioaugmentation experiments aiming at chlorobenzene degradation in groundwater, Microb. Ecol. 46, 161, 2003.
253. Whitehead, N.A., Barnard, A.M.L., Slater, H., Simpson, N.J.L., and Salmond, G.P.C. Quorum-sensing in Gram-negative bacteria, FEMS Microbiol. Rev. 25, 365, 2001.
254. Whiting, S.N., de Souza, M.P., and Terry, N. Rhizosphere bacteria mobilize Zn for hyperaccumulation by Thlaspi caerulescens, Environ. Sci. Technol. 35, 3144, 2001.
255. Widada, J., Nojiri, H., Kasuga, K., Yoshida, T., Habe, H., and Omori, T. Quantification of carbazole 1,9a-dioxygenase gene by real-time competitive PCR combined with co-extraction of internal standards, FEMS Microbiol. Lett. 202, 51, 2001.
256. Widada, J., Nojiri, H., Yoshida, T., Habe, H., and Omori, T. Enhanced degradation of carbazole and 2,3-dichlorodibenzo-p-dioxin in soils by Pseudomonas resinovorans strain CA10, Chemosphere, 49, 485, 2002.
257. Winther-Larsen, H.C., Josefsen, K.D., Brautaset, T., and Valla, S. Parameters affecting gene expression from the Pm promoter in gram-negative bacteria, Metab. Eng. 2, 79, 2000.
258. Witt, M.E., Dybas, M.J., Worden, R.M., and Criddle, C.S. Motility-enhanced bioremediation of carbon tetrachloride-contaminated aquifer sediments, Environ. Sci. Technol. 33, 2958, 1999.
259. Wu, L., Thompson, D.K., Li, G., Hurt, R.A., Tiedje, J.M., and Zhou, J. Development and evaluation of functional gene arrays for detection of selected genes in the environment, Appl. Environ. Microbiol. 67, 5780, 2001.
260. Yang, Y., and Zeyer, J. Specific detection of Dehalococcoides species by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes, Appl. Environ. Microbiol. 69, 2879, 2003.
261. Yee, D.C., Maynard, J.A., and Wood, T.K. Rhizoremediation of trichloroethylene by a recombinant, root-colonizing Pseudomonasfluorescens strain expressing toluene ortho-monooxygenase constitutively, Appl. Environ. Microbiol. 64, 112, 1998.
262. Zhao, S., Arthur, E.L., and Coats, J.R. Influence of microbial inoculation (Pseudomonas sp. strain ADP), the enzyme atrazine chlorohydrolase, and vegetation on the degradation of atrazine and metolachlor in soil, J. Agric. Food Chem. 51, 3043, 2003.
263. Zhou, J. Microarrays for bacterial detection and microbial community analysis, Curr. Opin. Microbiol. 6, 288, 2003.
264. Zhou, J., and Thompson, D.K. Challenges in applying microarrays to environmental studies, Curr. Opin. Biotechnol. 13, 204, 2002.
265. Zhou, J.-Z., and Tiedje, J.M. Gene transfer from a bacterium injected into an aquifer to an indigenous bacterium, Mol. Ecol. 4, 613, 1995.
266. Zouboulis, A.I., Loukidou, M.X., and Christodoulou, K. Enzymatic treatment of sanitary landfill leachate, Chemosphere 44, 1103, 2001.