.. .. .. .. .. W. M. Keck Laboratory . PhytoTechnologies Catabolic . . . .Enzymes . . . and. Metabolic Pathways in Phytoremediation Final Report to the W. M. Keck Foundation by the University of Iowa July,2005 . Table of Contents I. Narrative Description of Progress ....................................................................................3 II. Problems Encountered or Unanticipated Developments in the Project/Program ...5 III. Further Progress Expected in Next 2 Years ……………………………………… 5 IV. Other Support Solicited/Received…………………………………………………………6 V. Structure of This Grant………………………………………………………………………7 VI. Related Activities…………………………………………………………………………….7 VII. Relevant Honors……………………………………………………………………………10 VIII. Budget Expenditures…………………………………………………………….............10 2 I. Narrative Description of Progress The University of Iowa project team for Catabolic Enzymes and Metabolic Pathways in Phytoremediation has been quite successful in its first two years of operation – publishing papers, discovering a new bacteria living inside hybrid poplar trees, and attracting new research funding. The W. M. Keck PhytoTechnologies Laboratory at the University of Iowa was initiated by a grant from the W.M. Keck Foundation for a two-year period: January, 2003 through December, 2004. This is the final report covering the last six-month-period of the project through December 31, 2004, and also summarizing activities for the 2-yr project period and through today. We have published additional research papers, entered into a new research area using microarray technology, updated our website (www.phytotechnologies.org), and formed new partnerships within the plant sciences community. All equipment under the Keck award has been purchased and the budget has been expended, including 100% of the matching funds from the University of Iowa. We have transitioned the salary from Collin Just, Senior Research Assistant, to other grants, and he will continue to oversee the Keck PhytoTechnologies Laboratory in his new role as Lab Director. The Keck funds have allowed our laboratory to make a major upgrade in liquid chromatography, electron microscopy, and plant molecular biology equipment and research. A new faculty member has joined the W. M. Keck PhytoTechnologies Laboratory and the University of Iowa: Assistant Professor Timothy E. Mattes, Department of Civil and Environmental Engineering. Tim received the Ph.D. degree from Cornell University under the supervision of Prof. Jim Gossett, Civil and Environmental Engineering. His expertise is in environmental microbiology and microbial biogeochemistry. He uses molecular biology techniques to investigate new enzymes and microorganisms, like the dehalorespirers that can degrade vinyl chloride. Tim suspects that one of his organisms, Nocardioides JS614 has a plantassociated lifestyle in the environment that will allow it to be effective in rhizosphere bioremediation. It can oxidize vinyl chloride to innocuous endproducts, a rather unusual and important metabolic capability. Tim replaces Professor Pedro Alvarez, who continues to collaborate with the Keck PhytoTechnologies Laboratory from his position as Professor and Chair at Rice University. In the six months since the last progress report, Dr. Jong Moon Yoon graduated with the Ph.D. degree in Environmental Engineering and accepted a postdoctoral associate position in phytoremediation with Dr. Jacqueline Shanks, Chemical Engineering, Iowa State University. Dr. Melissa Mezzari also graduated and began a postdoctoral position in the plant genetics laboratory of Prof. Janet Braam at Rice University. Dr. Mezzari is beginning to interview for faculty positions in her native country, Brazil New equipment at the W.M. Keck PhytoTechnologies Laboratory is being used extensively in several research projects. The Liquid Chromatograph – Mass Spectometer (LC/MS) has been particularly useful for tracking metabolites in plants. Real time quantitative polymerase chain reaction (RTQ-PCR) is used extensively in gene expression studies. The Bal-Tec High Pressure 3 Freezer (HPF) enables us to optimally preserve biological samples for structural characteristics, enzyme detection and immunolabeling. It is used in concert with a Leica Automatic Freeze Substitution unit (purchased with other funds by the Central Microscopy Research Facility) for processing frozen specimens through dehydrants and embedments. The availability of the HPF was noted in a successful grant application to the National Institutes of Health for funds to buy a new transmission electron microscope ($561,000). In addition, we are now using the new BioRad Multiphoton microscope for fixed and live samples analysis of fluorescently labeled specimens. Professor Keri Hornbuckle, with assistance from Craig Just, Richard Valentine, and Jerry Schnoor, was awarded a Major Research Instrumentation grant from NSF for analysis of volatile and emerging chemical contaminants using a tandem GC/MS/MS ($400,000). Ming-Che Shih was successful on obtaining a matching grant from the National Science Foundation and the University of Iowa Foundation to establish a new DNA-microarray facility in Biological Sciences at the University of Iowa. This will allow Keck researchers to make their own biochips and read their results at the microarray facility at low cost and in close proximity to the W. M. Keck PhytoTechnologies Laboratory. All this instrumentation is complementary and necessary for our faculty to study novel biological processes. Beginning in August 2004, Kenneth Moore, Director of the Electron Microscopy Facility, and Jerry Schnoor, Director of the W. M. Keck PhytoTechnology Laboratory, began to co-advise an award-winning undergraduate researcher, Rachael Collier, on use of the multiphoton and confocal microscopes. We currently have three undergraduate students working in the Keck Laboratory on phyto projects: Rachael Collier, Kate Merchie, and Pieter Beyer. In addition, the Keck PhytoTechnology Laboratory has proven to be effective in attracting high quality graduate student researchers to the University of Iowa. Primary faculty contributing to the Keck PhytoTechnologies Laboratory are: Jerald L. Schnoor, Principal Investigator and Professor in Civil and Environmental Engineering; Timothy Mattes, Assistant Professor in Civil and Environmental Engineering; John P. N. Rosazza, Professor of Medicinal and Natural Products Chemistry and Director of the Center for Biocatalysis and Bioprocessing; Craig L. Just, EES Research Scientist and Adjunct Assistant Professor in Civil and Environmental Engineering; Kenneth C. Moore, Director of the University Central Microscopy Research Facility and Co-Director of the Center for Genetic Therapy Cell Morphology Core; and Benoit Van Aken, Associate Research Scientist and Adjunct Assistant Professor in Civil and Environmental Engineering. Two staff members contribute significantly to the research of the laboratory: Collin Just, Research Assistant III Engineering; and Kathy Walters, University Central Microscopy Research Facility. In addition, we have close affiliation with Prof. Ming-Che Shih, Department of Biological Sciences at the University of Iowa; and Professor Gene F. Parkin, Civil and Environmental Engineering, collaborates on the use of phytoremediation for mitigating perchlorate contaminated groundwater. 4 II. Problems Encountered or Unanticipated Developments in the Project/Program In general, there are no major impediments or unanticipated developments in the program. We have made progress on all three objectives in the proposal to the Keck Foundation: 1) Identifying catabolic enzymes, metabolites and pathways in model plants for degrading xenobiotic chemicals; 2) Developing a screening methodology for systematic plant selection based on identification and expression of catabolic enzyme DNA-coding sequences using PCR; and 3) Transforming plant species useful for phytoremediation by introducing genes coding for useful catabolic enzymes. The second objective requires further research, but we have made progress. A recent publication by Van Aken et al. (2005), in press with Environmental Science and Technology, is our first using PCR screening techniques for gene expression of glutathione-Stransferase. Much more research will continue on this topic in future months. To accomplish the third objective, we are beginning to transform Arabadopsis thaliana with plant genes that code for nitroreductase and glutathione-S-transferase. It is through our collaboration with Professor Ming-Che Shih in the Department of Biological Sciences, who has extensive experience in plant genetics, genomics, and transforming Arabadopsis. Following success with Arabadopsis, we will try to transform poplar. III. Further Progress Expected We will continue to research all three objectives over the coming years at the W. M. Keck PhytoTechnologies Laboratory. In the next few months, we will begin using microarrays (Affymetrix) and toxicogenomics to compare our gene expression results using RTQ-PCR. In addition, we continue to investigate the metabolites of TNT, RDX, and HMX in hybrid poplar and poplar tissue cultures; the ecotoxicology of these metabolites in plant tissues and in earthworms; molecular techniques for tracking the enzymes and metabolites of pesticides and explosives degradation by plants (using RTQ-PCR and liquid chromatography-mass spectrometry (LC-MS), immunocytochemistry, immunohistochemistry, and confocal microscopy); the cometabolism of PCBs by rhizosphere bacteria; and field demonstrations of phytoremediation of petroleum hydrocarbons and perchlorate in groundwater. In addition, we are embarking on a new avenue of phytotechnology research: the use of nano/microporous thinfilms to enhance the growth of plants, transpiration, and protection from pest species. Dr. Craig Just has designed our website to report the activities of the W.M. Keck PhytoTechologies Laboratory at the University of Iowa. It is available at www.phytotechnologies.org. We have posted more content in the form of Power Point presentations of the progress of our Keck Laboratory and publication citations. The website helps to build awareness of the W. M. Keck PhytoTechnologies Laboratory and to disseminate information about phytoremediation. The website will continue to develop as the Laboratory makes progress. 5 IV. Other Support Solicited/Received Our new member of the Keck PhytoTechnologies team, Assistant Professor Timothy Mattes, received a research grant for three years from the National Science Foundation (NSF) Center for Environmentally Beneficial Catalysis (CEBC), “Development of Alkene Monooxygenase Systems for Biocatalytic Applications”. The NSF CEBC Center is led by Prof. Bala Subramaniam, Kansas University, and its Co-Director is a member of the Keck PhytoTechnologies team, Dr. Jack Rosazza. The recent collaboration between Jerry Schnoor, Director of the Keck PhytoTechnologies Laboratory, and Professor Ming-Che Shih, Biological Sciences at the University of Iowa, has resulted in another new grant award for three years from the National Science Foundation Center for Environmentally Beneficial Catalysis (CEBC), “Development of a Transgenic Plant System for Production of Monooxygenases Engineered for Biocatalytic Oxidations of Organic Compounds.” Ming-Che Shih, Jerry Schnoor, Benoit Van Aken, Lydia Wagner and Brittany Flokstra began collaboration on plant genetics required for Arabadopsis thaliana to degrade TNT. Funding is from the University of Iowa Biosciences Initiative ($50,000). We are focusing on the identification and characterization of genes involved in the uptake, transport, and assimilation of TNT in Arabidopsis. We will isolate Arabidopsis mutants that are either more tolerant or overly sensitive to TNT. Map-based cloning or other molecular techniques will be used to clone the genes that are affected by these mutations. Gene expression profiling of wild-type and mutants will be performed to examine the effects of TNT on plant gene expression at the genomic scale. In addition, metabolic profiling of wild-type and mutant plants will be compared to trace the fate of TNT. Results from these experiments will allow us to determine the metabolic pathways affected by TNT and the functional roles of key enzymes in the detoxification of explosives. Based on this information, we will construct transgenic poplars that over-express these key enzymes and test their ability to uptake and degrade TNT in laboratory and filed studies. We have found that there are three similar nitroreductase genes in the Arabidopsis genome, and our preliminary results indicate that one of them induces production of OPR2 to a high level by TNT. Further collaboration on this topic is envisioned with Drs. Janet Braam and Melissa Mezzari, Plant Genetics Department, Rice University. Ming-Che Shih, Biological Sciences, and Jerry Schnoor have submitted a proposal to the National Science Foundation Biological Science Directorate, IOB Functional & Regulatory Systems program for $606,168 entitled, “Detoxification pathways of nitro-based explosives TNT and RDX in Arabadopsis”. A National Science Foundation Graduate Research Supplement (GRS) is in process of being awarded to a Ph.D. student of Jerry Schnoor, Ms. Laura Brentner, for 2005-2006; and a new grant for $717,839 has been announced in response to the proposal by Jerry Schnoor and Benoit Van Aken, “Phytoremediation for the Containment and Treatment of Energetic and Propellant 6 Material Releases on Testing and Training Ranges”, by the Strategic Environmental Research and Development Program (SERDP). Jerry Schnoor; Pedro Alvarez, Rice University; and Marc Anderson, University of Wisconsin, are preparing a preliminary proposal to the Defense Agency Research Projects Administration (DARPA) on the utility and effects of nano/microporous thin-films on plants for enhancing light capture and biomass production in light systems. In addition, they are considering the role of nanofilms on plants as a plant protection system – the target agency is U. S. Department of Agriculture. Larry Robertson, Keri Hornbuckle, Benoit Van Aken, and Jerry Schnoor have submitted a multimillion dollar Superfund Basic Research Program proposal to the National Institutes of Environmental Health Sciences (NIEHS) on the fate, transport, and phytoremediation of airborne polychlorinated biphenyls (PCBs) in the environment. V. Structure of This Grant The Administrative structure has worked well, and the original objectives of the W. M. Keck PhytoTechnologies Laboratory have been achieved. We have made significant progress on all the objectives of the grant, and we have published many papers listed below. We will continue to cite the W.M. Keck Foundation for funding the W. M. Keck PhytoTechnologies Laboratory in our research papers, and we will update the Foundation on our progress periodically, as requested. VI. Related Activities Publications: C. L. Just and J. L. Schnoor (2004). Phytophotolysis of Hexahydro-1,3,5-trinitro-1,3,5-triazine in leaves of reed canary grass. Environ. Sci. Technol., 38(1):290-295. R. Kamath, J. A. Rentz, J. L. Schnoor, and P. J. J. Alvarez (2004). Phytoremediation of hydrocarbon-contaminated soils: principles and applications. In: R. Vazquez-Duhalt and R. Quintero-Ramirez (Eds.), Petroleum Biotechnology Developments and Perspectives, 151. Elsevier, ISBN: 0-444-51699-9. R. Kamath, J. L. Schnoor, P. J. J. Alvarez (2004). Effect of root-derived substrates on the expression of nah-lux genes in Pseudomonas fluorescens HK44 – implications for PAH biodegradation in the rhizosphere. Environ. Sci. Technol., 38:1740-1745. R. Kamath, J. L. Schnoor, P. J. J. Alvarez (2005). Effect of simulated rhizodeposition on the fate of phenanthrene in aged contaminated soils, (in preparation). S.C. McCutcheon and J. L. Schnoor, Eds. (2003). Phytoremediation: Transformation and Control of Contaminants, Wiley Interscience, Hoboken, New Jersey, 987 pp. 7 M. P. Mezzari, B. Van Aken, J. M. Yoon, C. L. Just, J. L. Schnoor (2004). Mathematical modeling of RDX and HMX metabolism in Poplar (Populus deltoides x nigra DN34) Tissue Culture. Intl. J. Phytoremediation, 6:323-345. M. P. Mezzari, M. Jelinkova, M-C. Shih, C. L. Just, and J.L. Schnoor (2005). Glutathione STransferase and nitroreductase gene induction in Arabadopsis exposed to chloroacetanilide herbicides and explosive compounds: a phytoremediation approach. Plant Physiology 138(2):858-870. R. A. Ney, T. A. Meyers, A. Espina, J. L. Schnoor (2005). How many samples are required to evaluate a model verification of carbon sequestration in a hybrid poplar buffer strip? Environmental Monitoring and Assessment 102(1-3):375-388. K. D. Precht, J. A. Rentz, and J. L. Schnoor (2005). Greenhouse treatability studies that guide phytoremediation nutrient management. Int. J. Phytoremediation, (in preparation). J.A. Rentz, P. J. J. Alvarez, and J. L. Schnoor (2005). Salicylate induced benzo[a]pyrene cometabolism by Sphingomonas yanoikuyae JAR02. (in preparation). J.A. Rentz, P. J. J. Alvarez, and J. L. Schnoor (2005). Benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: Implications for phytoremediation. Environmental Pollution 136(3):477-484. J. A. Rentz, B. Chapman, P.J.J. Alvarez, and J. L. Schnoor (2003). Stimulation of hybrid poplar growth in petroleum-contaminated soils through oxygen addition and soil nutrient amendments. Int. J. Phytoremediation 5(1): 57-72. J. A. Rentz, P. J. J. Alvarez, and J. L. Schnoor (2004). Repression of Pseudomonas putida phenanthrene degrading activity by plant root extracts and exudates. Environmental Microbiology 6(6):574-583. J. L. Schnoor, M. L. Seppanen, J. D. Shrout, G. F. Parkin, and C. L. Just (2005). Demonstration Project of Phytoremediation and Rhizodegradation of Perchlorate in Groundwater at the Longhorn Army Ammunition Plant, Final Report to the Industrial Operations Support Command, U. S. Army, Rock Island, Illinois, 39 pp. J. D. Shrout, G. F. Parkin, and J. L. Schnoor (2005). Stimulation of bacterial perchlorate rhizodegradation with plant-produced electron donors. Environ. Sci. Technol. (in review). B. Van Aken, L. Brentner, C. M. Peres, J. M. Yoon, and J. L. Schnoor (2005). Expression of glutathione S-transferase in poplar trees (Populus trichocarpa) exposed to 2,4,6-trinitrotoluene (TNT). (in preparation). B. Van Aken, C. M. Peres, S. Lafferty-Doty, J.M. Yoon, and J. L. Schnoor (2004). Methylobacterium sp. nov.: a new aerobic, pink-pigmented, facultatively methylotrophic 8 bacterium from poplar trees (Populus deltoides x nigra DN34). Intl. J. Systematic & Evolutionary Microbiology, 54: 2796-2804. B. Van Aken, J.M. Yoon, and J. L. Schnoor (2004). Biodegradation of nitro-substituted explosives TNT, RDX, and HMX by a phytosymbiotic Methylobacterium sp. associated with Poplar Tissues (Populus deltoides x nigra DN34). Applied and Environmental Microbiology, 70 (1): 508-517. B. Van Aken, J. M. Yoon, C. L. Just, and J. L. Schnoor (2004). Metabolism and mineralization of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) inside poplar tissues (Populus deltoides x nigra DN34). Environ. Sci. Technol., 38 (17): 4572-4579. J. M. Yoon, B. Van Aken, and J. L. Schnoor (2004). Leaching of contaminated leaves following uptake and phytoremediation of RDX, HMX, and TNT by poplar. International Journal of Phytoremediation, (in review). Presentations: C. L. Just and J. L. Schnoor (2003). Phytophotolysis of RDX in reed canary grass. Preprints of Extended Abstracts, 225th American Chemical Society National Meeting, New Orleans, LA (March 25, 2003). R. Kamath, J. L. Schnoor, and P. J. J. Alvarez (2003). Effect of root extracts on the expression of nah-lux genes in Pseudomonas fluorescens HK44 implications for PAH biodegradation in the rhizosphere. International Applied Phytotechnologies Conference. U. S. Environmental Protection Agency, Chicago, Illinois, March 3-5, 2003. J. D. Shrout, M. Seppanen, G. F. Parkin, and J. L. Schnoor (2003). Utilization of plant-produced electron donors for bacterial perchlorate degradation. National Meeting of the American Waste Management Association, San Diego, CA (June 30, 2003). J. L. Schnoor (2003). Phytoremediation of soils and sediments. Presented at the Chemicals in Sediments Meeting, U. S. Army Corps of Engineers, San Diego, CA (April 9, 2003). J. L. Schnoor (2003). Phytoremediation: From lab to field and back again. Presented at the U. S. Army Corps of Engineers, Waterways Experiment Station, Vicksburg, MS (June 23, 2003). J. L. Schnoor and B. Van Aken (2003). Identification of metabolic routes and catabolic enzymes involved in phytoremediation of the nitro-substituted explosives. Presented at the SERDP & ESTCP Joint Annual Spring In-Progress Review, Arlington, VA (April 24, 2003). B. Van Aken, J.-M. Yoon, S. Tanaka, B. R. Flokstra, J. L. Schnoor (2004). Mineralization of HMX and RDX by Hybrid Poplar Tissue Cultures and the potential for endo-phytoremediation 9 of organic contaminants. Presented at the Conference on Sustainable Range Management, Battelle Business of Innovation, New Orleans, LA (January 5-8, 2004). B. Van Aken, J. L. Schnoor (2003). A endosymbiotic Methylobacterium sp. isolated from hybrid poplar trees (Populus deltoides x nigra) mineralizes the toxic explosive RDX: Implications for phytoremediation. In Proceedings of the 103rd General Meeting of the American Society for Microbiology (ASM). ASM. May 18-22, 2003. Washington, DC (USA). Abstract Q-302 p 568569. VII. Relevant Honors and Awards Jerry Schnoor was the invited keynote speaker at the Soil Science Society of America National Meeting in Seattle on November 1, 2004. He presented a paper, “Phytoremediation: From the Molecular Scale to the Field”. A related keynote address was presented (with practical field applications) at the International Conference on PhytoTechnologies, sponsored by the U.S. Environmental Protection Agency on April 20-22, 2005, in Atlanta, Georgia. Schnoor also delivered the keynote paper on PhytoTechnologies at the 3rd Bioremediation Conference of the European Union in Chania, Crete, Greece, on July 4-7, 2005. Jerry and colleagues were awarded the Best Theoretical Paper Award by the Environmental Water Resources Institute, American Society of Civil Engineers, at the World Water & Environmental Resources Congress 2004, in Salt Lake City, Utah, on June 29, 2004. The exact citation for the paper is given below. G. M. Pierzynski, J. L. Schnoor, A. Youngman, L. Licht, and L. E. Erickson, Poplar trees for phytostabilization of abandoned zinc-lead smelter wastes. ASCE Practice Periodical of Hazardous, Toxic, and Radioactive Waste Management, Vol. 6, No. 3, July 2002, pp. 177-183. VIII. Budget Expenditures Expenditures from the Keck award during the past two years are listed on the enclosed Financial Management Summary from the Office of Sponsored Programs, University of Iowa. All of the funds have been expended or encumbered as per the original budget plan. Also, the matching funds from the University of Iowa ($300,000) have been expended on equipment as planned. 10 New Member Resume: Timothy E. Mattes Timothy E. Mattes Assistant Professor Department of Civil and Environmental Engineering The University of Iowa Iowa City, IA 52242 Phone: (319) 335-5065 Fax: (319) 335-5660 Email: tim-mattes@uiowa.edu EDUCATION Doctor of Philosophy, 2004. School of Civil and Environmental Engineering, Cornell University, Ithaca, NY. Master of Science in Engineering, 1995. Department of Geography and Environmental Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD. Bachelor of Science in Civil Engineering, 1994. Department of Civil Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD. PROFESSIONAL APPOINTMENTS Assistant Professor, The University of Iowa, Iowa City, IA (8/04-present). Graduate Research Assistant, Cornell University, Ithaca, NY (8/99-8/04) Teaching Assistant, Cornell University, Ithaca, NY (8/98-8/99) Design Engineer, Gannett Fleming Inc. Baltimore, MD (8/97-8/98). Design Engineer, Beavin Company. Baltimore, MD (6/95-8/97). PROFESSIONAL REGISTRATION Professional Engineer in Maryland since 1999. Registration #200383. PUBLICATIONS (Journal Article Peer Reviewed) Mattes, T., Coleman, N., Spain, J., and Gossett, J. Characterization of the vinyl chloride and ethene starvation response in Nocardioides Strain JS614. Submitted. Chartrand, M., Waller, A., Mattes, T., Elsner, M., Lacrampe-Couloume, G., Gossett, J., Edwards, E., and Lollar, B. Carbon isotopic fractionation during aerobic vinyl chloride degradation. Environmental Science and Technology, Jan. 6, 2005 web release. Mattes, T., Coleman, N., Spain, J., and Gossett, J. Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. JS614. Archives of Microbiology, Dec. 15, 2004 web release. 11 Coleman, N., Mattes, T, Gossett, J., and Spain, J., 2002. Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites. Applied and Environmental Microbiology (68:6162-6171). Coleman, N., Mattes, T, Gossett, J., and Spain, J., 2002. Biodegradation of cis-dichloroethene as sole carbon source by a β-proteobacterium, strain JS666. Applied and Environmental Microbiology (68:27262730). SYNERGISTIC ACTIVITIES Faculty Member – Center for Biocatalysis and Bioprocessing, The University of Iowa. Member of American Society for Microbiology, American Society for Civil Engineers, and Association of Environmental Engineering and Science Professors 12