Our laboratory has examined microorganisms resident in soils and groundwater aquifers contaminated with manmade chemicals to understand their growth and metabolism with the idea that these organisms could be used to remediate contaminants. This work has resulted in technologies that are currently being practiced in the field for remediating groundwater contaminated with trichloroethene and tetrachloroethene. More recently, we have rationally engineered microorganisms to degrade nerve agents (phosphonofluoridates) for application to degrading chemical warfare agent stockpiles. Furthermore, structural similarity of nerve agents to prevalently-used pesticides may allow a microbial platform for environmental decontamination of pesticides.

FUNDING

ONR, DARPA

REPRESENTATIVE PUBLICATIONS
  • J. D. Keasling and G. A. Hupf. 1996. “Genetic manipulation of polyphosphate metabolism affects cadmium tolerance in Escherichia coli.” Appl. Environ. Microbiol. 62:743-746.
  • N. Shapiro and J. D. Keasling. 1996. “The recA gene and cadmium toxicity in Escherichia coli K-12.” Microbios 86:23-26.
  • S. Keyhani, J. L. Lopez, D. S. Clark, and J. D. Keasling. 1996. “Intracellular polyphosphate content and cadmium tolerance in Anacystis nidulans R2.” Microbios 88:105-114.
  • S. J. Van Dien, S. Keyhani, C. Yang, and J. D. Keasling. 1997. “Manipulation of independent synthesis and degradation of polyphosphate in Escherichia coli for investigation of phosphate secretion from the cell.” Appl. Environ. Microbiol. 63:1689-1695.
  • J. Elmen, W. Pan, S. Y. Leung, A. Magyarosy, and J. D. Keasling. 1997. “Kinetics of toluene degradation by a nitrate-reducing bacterium isolated from a groundwater aquifer.” Biotechnol. Bioeng. 55:82-90.
  • C. L. Wang, P. C. Michels, S. Dawson, S. Kitisakkul, J. A. Baross, J. D. Keasling, and D. S. Clark. 1997. “Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture.” Appl. Environ. Microbiol. 63:4075-4078.
  • J. D. Keasling, S. J. Van Dien, and J. Pramanik. 1998. “Engineering polyphosphate metabolism in Escherichia coli: implications for bioremediation of inorganic contaminants.” Biotechnol. Bioeng. 58:231-239.
  • J. Pramanik, P. L. Trelstad, and J. D. Keasling. 1998. “A flux-based stoichiometric model of enhanced biological phosphorus removal metabolism.” Wat. Sci. Tech. 37:609-613.
  • J. Pramanik, P. L. Trelstad, A. J. Schuler, D. Jenkins, and J. D. Keasling. 1998. “Development and validation of a flux-based stoichiometric model for enhanced biological phosphorus removal metabolism.” Water Research 33:462-476.
  • R. Brent Nielsen and J. D. Keasling. 1999. “Reductive dechlorination of chlorinated ethene DNAPLs by a culture enriched from contaminated groundwater.” Biotechnol. Bioeng. 62:160-165.
  • P. L. Trelstad, P. Purdhani, W. Geibdorfer, W. Hillen, and J. D. Keasling. 1999. “Polyphosphate kinase of Acinetobacter sp. Strain ADP1: purification and characterization of the enzyme and its role during changes in extracellular phosphate.” Appl. Environ. Microbiol. 65(9):3780-3786.
  • D. S. Reichmuth, J. L. Hittle, H. W. Blanch, and J. D. Keasling. 2000. “Biodesulfurization of dibenzothiophene in Escherichia coli is enhanced by expression of a Vibrio harveyi oxidoreductase gene.” Biotechnol. Bioeng. 67:72-79.
  • J. D. Keasling, S. J. Van Dien, P. Trelstad, N. Renninger, and K. McMahon. 2000. “Application of polyphosphate metabolism to environmental and biotechnological problems.” Biochemistry (Moscow). 65:324-331.
  • S.-W. Bang, D. S. Clark, and J. D. Keasling. 2000. “Engineering hydrogen sulfide production and cadmium removal by expression of the thiosulfate reductase gene (phsABC) from Salmonella enterica serovar Typhimurium in Escherichia coli.” Appl. Environ. Microbiol. 66:3939-3944.
  • C. L. Wang, P. D. Maratukulam, A. M. Lum, D. S. Clark, and J. D. Keasling. 2000. “Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface.” Appl. Environ. Microbiol. 66:4497-4502.
  • S. E. Cowan, E. Gilbert, D. Liepmann, and J. D. Keasling. 2000. “Commensal interactions in a dual-species biofilm exposed to mixed organic compounds.” Appl. Environ. Microbiol. 66:4481-4485.
  • S.-W. Bang, D. S. Clark, and J. D. Keasling. 2000. “Cadmium, lead, and zinc removal by expression of the thiosulfate reductase gene from Salmonella typhimurium in Escherichia coli.” Biotechnol. Lett. 22:1331-1335.
  • C. L. Wang, A. M. Lum, S. C. Ozuna, D. S. Clark, and J. D. Keasling. 2001. “Aerobic sulfide production and cadmium precipitation by Escherichia coli expressing the Treponema denticola cysteine desulfhydrase gene.” Appl. Microbiol. Biotechnol. 56:425-430.
  • C. L. Wang, D. S. Clark, and J. D. Keasling. 2001. “Analysis of an engineered sulfate reduction pathway and cadmium precipitation on the cell surface.” Biotechnol. Bioeng. 75:285-291.
  • N. Renninger, K. D. McMahon, R. Knopp, H. Nitsche, D. S. Clark, and J. D. Keasling. 2002. “Uranyl precipitation by biomass from an enhanced biological phosphorus removal reactor.” Biodegradation 12:401-410.
  • C. L. Wang, S. C. Ozuna, D. S. Clark, and J. D. Keasling. 2002. “A deep-sea hydrothermal vent isolate, Pseudomonas aeruginosa CW961, requires thiosulfate for Cd2+ tolerance and precipitation.” Biotechnol. Lett. 24:637-641.
  •   A. W. Walker and J. D. Keasling. 2002. “Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source.” Biotechnol. Bioeng. 78:715-721.
  • A. Magyarosy, R. D. Laidlaw, R. Kilaas, C. Echer, D. S. Clark, and J. D. Keasling. 2002. “Nickel accumulation and nickel oxalate precipitation by Aspergillus niger.” Appl. Microbiol. Biotechnol. 59:381-388.
  • K. D. McMahon, D. Jenkins, and J. D. Keasling. 2002. “Polyphosphate kinase genes from activated sludge carrying out enhanced biological phosphorus removal.” Water Sci. Technol. 46:155-162.
  • K. D. McMahon, M. A. Dojka, N. R. Pace, D. Jenkins, and J. D. Keasling. 2002. “Polyphosphate kinase from activated sludge performing enhanced biological phosphorus removal.” Appl. Environ. Microbiol. 68:4971-4978.
  • S. K. Tehara and J. D. Keasling. 2003. “Gene cloning, purification, and characterization of a phosphodiesterase from Delftia acidovorans.” Appl. Envir. Microbiol. 69:504-508.
  • E. S. Gilbert, A. W. Walker and J. D. Keasling. 2003. “A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion.” Appl Microbiol Biotechnol. 61:77-81.
  • R. Knopp, P. J. Panak, L. A. Wray, N. S. Renninger, J. D. Keasling, and H. Nitsche. 2003. “Laser spectroscopic studies of U(VI) with bacterial phosphate species.” Chem. Eur. J. 9:2812-2818.
  • D. S. Reichmuth, H. W. Blanch, and J. D. Keasling. 2004. “Dibenzothiophene desulfurization pathway improvement using diagnostic GFP fusions.” Biotechnol. Bioeng. 88:94-99.
  • N. Renninger, R. Knopp, H. Nitsche, D.S. Clark, J. D. Keasling. 2004. “Uranyl precipitation by Pseudomonas aeruginosa via controlled polyphosphate metabolism.” Appl. Environ. Microbiol. 70:7404-7412.
  • A. Mukhopadhyay, Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Qiang He, H.-Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang , H.-C. Yen, J. Zhou, and J. D. Keasling. 2006. “Salt stress in Desulfovibrio vulgaris Hildenborough: An integrated genomics approach.” J. Bacteriol. 188:4068-4078.
  • A. M. Redding, A. Mukhopadhyay, D. Joyner, T. C. Hazen, and J. D. Keasling. 2006. “Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics.” Brief. Funct. Genom. Proteom. 5:133-43.
  • Y. J. Tang, D. Laidlaw, K. Gani, and J. D. Keasling. 2006. “Evaluation of the effects of various culture conditions on Cr(VI) reduction by Shewanella oneidensis MR-1 in a novel high-throughput mini-bioreactor.” Biotechnol. Bioeng. 95:176-184.
  • M. Mattozzi, S. Tehara, and J. D. Keasling. 2006. “Mineralization of paraoxon and use as a sole C and P source by a rationally designed catabolism in Pseudomonas putida.” Appl. Environ. Microbiol. 72:6699-6706.
  • Y. J. Tang, A. L. Meadows, and J. D. Keasling. 2007. “A kinetic model describing Shewanella oneidensis MR-1 growth, substrate consumption, and product secretion”. Biotechnol. Bioeng. 96:125-133.
  • Y. J. Tang, A. L. Meadows, J. Kirby, and J. D. Keasling. 2007. “Anaerobic central metabolic pathways in Shewanella oneidensis MR-1 reinterpreted in the light of isotopic metabolite labeling.” J. Bacteriol. 189:894-901.
  •   Y. J. Tang, F. Pingitore, A. Mukhopadhyay, R. Phan, T. C. Hazen, and J. D. Keasling. 2007. “Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using GC-MS and FT-ICR mass spectrometry. J. Bacteriol. 189:940-949.
  • Y. J. Tang, J. S. Hwang, D. E. Wemmer, and J. D. Keasling. 2007. “The Shewanella oneidensis MR-1 fluxome under various oxygen conditions.” Appl. Environ. Microbiol. 73:718-729.
  • Y. J. Tang, R. Chakraborty, H. G. Mart?n, J. Chu, T, C. Hazen, and J. D. Keasling. 2007. “Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid.” Appl. Environ. Microbiol. 73:3859-3864.
  • A. Mukhopadhyay, A. M. Redding, M. P. Joachimiak, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. J. Martin, J. D. Wall, Z. K. Yang, J. Zhou, and J. D. Keasling. 2007. “Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough.” J. Bacteriol. 189:5996-6010.
  • K. D. McMahon, S. Yilmaz, S. He, D. L. Gall, D. Jenkins, and J. D. Keasling. 2007. “Polyphosphate kinase genes from full-scale activated sludge plants.” Appl. Microbiol. Biotechnol. 77:167-173.
  • S. Mahendra, C. J. Petzold, E. E. Baidoo, J. D. Keasling, and L. Alvarez-Cohen. 2007. “Identification of the intermediates of in vivo oxidation of 1,4-dioxane by monooxygenase-containing bacteria.” Environ. Sci. Technol. 144:7330-7336.
  • S. P. Gaucher, A. M. Redding, A. Mukhopadhyay, J. D. Keasling, and A. K. Singh. 2008. “Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins.” J. Proteome Res. 7:2320-2331.
  • Y. J. Tang, H. G. Martin, P. S. Dehal, A. Deutschbauer, X. Llora, A. Meadows, A. Arkin, and J. D. Keasling. 2009. “Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism.” Biotechnol. Bioeng. 102:1161-1169.
  •   Y. J. Tang, R. Sapra, D. Joyner, T. C. Hazen, S. Myers, D. Reichmuth, H. Blanch, and J. D. Keasling. 2009. “Analysis of metabolic pathways and fluxes in a newly discovered thermophilic and ethanol-tolerant Geobacillus strain.” Biotechnol. Bioeng. 102:1377-1386.
  • D. A. Elias, A. Mukhopadhyay, M. P. Joachimiak, E. C. Drury, A. M. Redding, H. C. Yen, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Keasling, J. D. Wall. 2009. “Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.” Nucl. Acids Res. 37:2926-2939.
  • Z. He, A. Zhou, E. Baidoo, Q. He, M. P. Joachimiak, P. Benke, R. Phan, A. Mukhopadhyay, C. L. Hemme, K. Huang, E. J. Alm, M. W. Fields, J. Wall, D. Stahl, T. C. Hazen, J. D. Keasling, A. P. Arkin, and J. Zhou. 2010. “Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation.” Appl. Environ. Microbiol. 76:1574-1586.
  • M. de la Pena Mattozzi and J. D. Keasling. 2010. “Rationally engineered biotransformation of p-nitrophenol.” Biotechnol. Prog. 26:616-621.
  • Q. He, Z. He, D. C. Joyner, M. Joachimiak, M. N. Price, Z. K. Yang, H.-C. B. Yen, C. L. Hemme, W. Chen, M. M. Fields, D. A. Stahl, J. D. Keasling, M. Keller, A. P. Arkin, T. C. Hazen, J. D. Wall, and J. Zhou. 2010. “Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris.” ISME J. 4:1386-1397.
  • A. Zhou, Z. He, A. M. Redding-Johanson, A. Mukhopadhyay, C. L. Hemme, M. P. Joachimiak, F. Lou, Y. Deng, K. S. Bender, Q. He, J. D. Keasling, D. A. Stahl, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J. Zhou. 2010. “Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.” Environ. Microbiol. 12:2645-2657.
  • S. R. Chhabra, M. P. Joachimiak, C. J. Petzold, G. M. Zane, M. N. Price, S. A. Reveco, V. Fok, A. R. Johanson, T. S. Batth, M. Singer, J. M. Chandonia, D. Joyner, T. C. Hazen, A, P. Arkin, J. D. Wall, A. K. Singh, and J. D. Keasling. 2011. “Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.” PLoS One 6:e21470.
  • S. R. Chhabra, G. Butland, D. Elias, J.-M. Chandonia, O.-Y. Fok, T. Juba, A. Gorur, S. Allen, C. M. Leung, K. Keller, S. Reveco, G. Zane, E. Semkiw, R. Prathapam, B. Gold, M. Singer, M. Ouellet, E. Szakal, D. Jorgens, M. Price, E. Witkowska, H. Beller, T. C. Hazen, M. D. Biggin, M. Auer, J. Wall, and J. D. Keasling. 2011. “Generalized schemes for high throughput manipulation of the Desulfovibrio vulgaris Hildenborough genome”. Appl. Environ. Microbiol. 77:7595-7604.
  • M. E. Clark, Z. He, A. M. Redding, M. P. Joachimiak, J. D. Keasling, J. Zhou, A. P. Arkin, A. Mukhopadhyay, and M. W. Fields. 2012. “Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.” BMC Genomics 13:138.
  • C. B. Walker, A. M. Redding-Johanson, E. Baidoo, L. Rajeev, Z. He, E. L Hendrickson, M.P. Joachimiak, S. Stolyar, A. P. Arkin, J. A. Leigh, J. Zhou, J. D. Keasling, A. Mukhopadhyay, and D. A. Stahl. 2012. “Functional response of methanogenic archaea to syntrophic growth.” ISME J. 6:2045-2055.
  • A. Zhou, E. Baidoo, Z. He, A. Mukhopadhyay, J. K. Baumohl, P. Benke, M. P Joachimiak, M. Xie, R. Song, A. P. Arkin, T. C. Hazen, J. D. Keasling, J. D. Wall, D. A. Stahl and J. Zhou. 2013. “Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.” ISME J. 7(9):1790-1802.
  • A. Ghosh, J. Nilmeier, D. Weaver, P. D. Adams, J. D. Keasling, A. Mukhopadhyay, C. J. Petzold, H. G. Martin. 2014. “A peptide-based method for 13C metabolic flux analysis in microbial communities.” PLoS Comp Biol 10(9):e1003827. doi:10.1371/journal.pcbi.1003827
  • M. E. Brown, A. Mukhopadhyay, J. D. Keasling. 2016. “Engineering bacteria to catabolize the carbonaceous component of the chemical warfare agent sarin.” Submitted to ACS Synth. Biol.