Progress 10/01/08 to 09/30/09
Outputs
OUTPUTS: My research group continues to focus on microorganisms capable of metabolizing organic environmental pollutants in soil and groundwater. We are examining relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of naphthalene (a representative of polycyclic aromatic hydrocarbons), benzoate, benzene, and related aromatic pollutants. New molecular biological, microscopic, and analytical chemistry procedures continue to be developed and provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions can influence broader cycles of carbon and nitrogen in groundwater habitats. PARTICIPANTS: Students: Jane Yagi, Buck Hanson, Graham Pumphrey (Graduate Students in the Department of Microbiology) Collaborators: Sims, D., Brettin, T., Bruce, D., Neuhauser, E. F., Ripp,J. A., Azzolina, A. N. A. Chandra, S. [US DOE, National Grid LLC, Cornell University] TARGET AUDIENCES: Researchers interested in environmental clean-up of polluted groundwater, bioremediation, biogeochemistry, microbial ecology PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
This work extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Yagi, J.M. and Madsen, E. L. 2009. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer Appl. Environ. Microbiol. 75: 6478-6487.
- Yagi. J. M., Sims, D., Brettin, T.,Bruce, D., and Madsen, E. L. 2009. Remarkable physiological versatility revealed by whole-genome analysis of the aromatic-hydrocarbon-degrading bacterium, Polaromonas naphthalenivorans. Environ Microbiol 11: 2253-2270.
- Neuhauser, E. F., Ripp, J. A., Azzolina, A. N. A., Madsen, E. L., Mauro, D. M., and Taylor, T. 2009. Monitored natural attenuation of manufactured gas plant tar mono- and polycyclic aromatic hydrocarbons in ground water: A 14-year field study. Groundwater Monit. Remed. 29 (3): 66-76.
- Pumphrey, G. M., Hanson, B. T., Chandra, S., and Madsen, E. L. 2009. Dynamic secondary ion mass spectrometry (SIMS) imaging of microbial populations utilizing 13C-labeled substrates in pure culture and in soil. Environ. Microbiol. 11: 220-229.
- Madsen, E.L. 2009. Exclude unculturable from taxonomic microbiology literature. Microbe 4: 351.
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Progress 10/01/07 to 09/30/08
Outputs
OUTPUTS: My research group has continued to focus on microorganisms capable of metabolizing organic environmental pollutants in soil and groundwater. We are examining relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of naphthalene (a representative of polycyclic aromatic hydrocarbons), benzoate, benzene, and related aromatic pollutants. New molecular biological, microscopic, and analytical chemistry procedures continue to be developed and provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions can influence broader cycles of carbon and nitrogen in groundwater habitats. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
This work extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Madsen E.L. 2008. Environmental Microbiology: From Genomes to Biogeochemistry. Wiley Blackwell. Oxford UK, 479 pp.
- Kim, J.M., N. T. Le, B. S. Chung, J. H. Park, J.-W. Bae, E. L. Madsen, and Che Ok Jeon. 2008. Influence of soil components on the biodegradation of benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl. Environ. Microbiol. 74: 7313-7320.
- Chandra, S., G. Pumphrey. J.M.Abraham, and E. L.Madsen. 2008. Dynamic SIMS ion microscopy imaging of individual bacterial cells for studies of isotopically labeled molecules. Appl. Surface Sci. 255: 847-851.
- Pumphrey, G. M and E. L. Madsen. 2008. Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganisms and their in situ growth in agricultural soil. Appl. Environ. Microbiol. 74: 4111-4118.
- J. S-C. Liou, C.M. DeRito, and E.L. Madsen. 2008. Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metabolizing microorganisms in freshwater sediment. Environ. Microbiol. 10: 1964-1977.
- Liou, J. and E.L.Madsen. 2008. Microbial ecological processes : Aerobic / Anaerobic. IN Encyclopedia of Ecology (S.E. Jorgensen ed.) Elsevier Science Ltd. Oxford UK.
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Progress 10/01/06 to 09/30/07
Outputs
My research group has continued to focus on microorganisms capable of metabolizing organic environmental pollutants in soil and upon the pollutants, themselves. We are examining relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of naphthalene (a representative of polycyclic aromatic hydrocarbons), benzene, and phenol. New molecular biological, microscopic, and analytical chemistry procedures continue to be developed and provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions with soil constituents influence the bioavailability of pollutants.
Impacts
This work extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Pumphrey, G.M. and E.L.Madsen. 2007. Naphthalene metabolism and growth inhibition by naphthalene in Polaraomonas naphthalenivorans strain CJ2. Microbiology 153:3739-3747.
- Park, M., Y. Jeon, Y., H.-S. Ro., W. Park, E. L. Madsen and C.- O. Jeon. 2007. Molecular and Biochemical Characterization of 3-Hydroxybenzoate 6-hydroxylase from Polaromonas naphthalenivorans CJ2. Appl. Environ. Microbiol. 73: 5146-5152.
- Kang, Y.-S., Y. Lee, H. Jung, C.-O. Jeon, E. L. Madsen, and W. Park. 2007. Overexpressing antioxidant enzymes enhances naphthalene biodegradation in Pseudomonas sp. Strain As1. Microbiology 153: 3246-3254.
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Progress 01/01/06 to 12/31/06
Outputs
My research group has continued to focus on microorganisms capable of metabolizing organic environmental pollutants in soil and upon the pollutants, themselves. We are examining relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of naphthalene (a representative of polycyclic aromatic hydrocarbons) and phenol. New molecular biological and analytical chemistry procedures continue to be developed and provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions with soil constituents influence the bioavailability of pollutants.
Impacts
This work extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Lee, Y., E. Ahn, S. Park, E.L.Madsen, C. Jeon, and W. Park. 2006. Construction of a reporter strain Pseudomonas putida for the detection of oxidative stress caused by environmental pollutants. J. Microrbiol. Biotechnol. 16: 386-390.
- Jeon , C.-O, M. Park, H.-S. Rob, W. Park, and E. L. Madsen. 2006. The naphthalene catabolic (nag) genes of Polaromonas naphthalenivorans CJ2: Evolutionary implications for two gene clusters and novel regulatory control. Appl. Environ. Microbiol. 72: 1086-1095.
- Madsen. E.L. 2006. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr. Opin. Biotechnol. 17: 92-97.
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Progress 01/01/05 to 12/31/05
Outputs
During the past year, my research group has focused on microorganisms capable of metabolizing organic environmental pollutants in soil and upon the pollutants, themselves. We have examined relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of naphthalene (a representative of polycyclic aromatic hydrocarbons) and phenol. New molecular biological and analytical chemistry procedures continue to be developed and provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions with soil constituents influence the bioavailability of pollutants.
Impacts
The major impact of this work is that it extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- DeRito, C. M., G. M. Pumphrey, and E. L. Madsen. 2005. Using field-based stable isotope probing to identify adapted populations and to track carbon flow through a phenol-degrading soil microbial community. Appl. Environ. Microbiol.71:7858-7865.
- Madsen, E. L. 2005. Identifying microorganisms responsible for ecological significant biogeochemical processes. Nature Microbiol. Rev. 3:439-446.
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Progress 01/01/04 to 12/31/04
Outputs
During the past year, my research group has focused on microorganisms capable of metabolizing organic environmental pollutants in soil and upon the pollutants, themselves. We have examined relationships between geochemical setting and in situ physiological reactions carried out by microbial communities involved in metabolism of methane (a key greenhouse gas). Molecular biological and analytical chemistry procedures continue to provide insights into the identity and diversity of microorganisms carrying out biodegradation reactions and how reactions with soil constituents influence the bioavailability of pollutants.
Impacts
The major impact of this work is that it extends knowledge about how genetic, physiological, and geochemical factors control microbial metabolism of organic environmental pollutants. This information, in turn, determines both technology and policy issues pertinent to remediation of polluted sites. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen: Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Park, W. and Madsen, E.L. 2004. Characterization of nah in Pseudomonas putida Cg1 and its role in bacterial survival in soil. Appl. Microbiol. Biotechnol. 66:209-216.
- Jeon, C.-O., Park, W., Ghiorse, W.C. and Madsen, E.L. 2004. Polaromonas naphthalenivorans gen. nov., sp. nov., a naphthalene-degrading bacterium from naphthalene-contaminated sediment. Intl. J. Syst. Evol. Microbiol.54:93-97.
- Weiss, J.M., McKay, A.J., DeRito, C. Watanabe, C., Thorn, K.A., and Madsen, E. L. 2004. Development and application of pyrolysis-gas chromatography/mass spectrometry for the analysis of bound trinitrotoluene residues in soil. Environ. Sci. Technol. 38:2167-2174.
- Park, W., Jeon, C.-O., Cadillo, H., DeRito, C., and Madsen, E.L. 2004. Survival of naphthalene-degrading Pseudomonas putida NCIB 9816-04 in naphthalene-amended soil: Toxicity of naphthalene and its metabolites. Appl. Microbiol. Biotechnol. 64:429-435.
- Miller, D.N., Yavitt, J.B., Madsen, E.L., and Ghiorse, W.C. 2004. Methanotrophic activity, abundance, and diversity in forest swamp pools: spatiotemporal dynamics and influences on methane fluxes. Geomicrobiol. J. 21:257-271.
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Progress 01/01/03 to 12/31/03
Outputs
During the past year, investigations examining microorganisms dwelling in a contaminated subsurface site have continued. We have continued to examine relationships between geochemical setting and in situ physiological reactions carried out by subsurface microorganisms. Molecular biological procedures continue to provide insights into the identity and diversity of naturally-occurring microbial communities carrying out biodegradation reactions.
Impacts
The major impact of this work is that it extends knowledge about how naturally occurring microbial communities metabolize organic environmental pollutants. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen. Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Padmanabhan, P., S. Padmanabhan, C. DeRito, A. Gray, D. Gannon, J. R. Snape, C.S. Tsai, W. Park, C. Jeon, and E. L. Madsen. 2003. Respiration of 13C-labeled substrate added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Appl. Environ. Microbiol. 69:1614-1622.
- Park, W., C.-O. Jeon, A. M. Hohnstock-Ashe, S. C. Winans, B. J. Zylstra, and E. L. Madsen. 2003. Identification and characterization of the conjugal transfer region of the pCg1 plasmid from naphthalene-degrading Pseudomonas putida Cg1. Appl. Environ. Microbiol. 69:3263-3271.
- Wilson, M. S., J. B. Herrick, C. O Jeon, D. E. Hinman, and E. L. Madsen. 2003. Horizontal transfer of phn-Ac dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments. Appl. Environ. Microbiol. 69:2172-2181.
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Progress 01/01/02 to 12/31/02
Outputs
During the past year, investigations examining microorganisms dwelling in a contaminated subsurface site have continued. We have continued to examine relationships between geochemical setting and in situ physiological reactions carried out by subsurface microorganisms. Molecular biological procedures continue to provide insights into the identity and diversity of naturally-occurring microbial communities carrying out biodegradation reactions.
Impacts
The major impact of this work is that it extends knowledge about how naturally occurring microbial communities metabolize organic environmental pollutants. The impact is exemplified by a book written by a National Research Council committee that included E. Madsen. Natural Attenuation for Groundwater Remediation. 2000. National Academy Press, Washington, DC.
Publications
- Madsen, E. 2002. Methods for Assessing Biodegradability: Field and Laboratory, pp. 475-484. In: G. Bitton (Ed.) Encyclopedia of Environmental Microbiology. Wiley, New York, NY.
- Madsen, E.L. 2002. Methods for determining biodegradability, pp. 903-913. In: C. J. Hurst, et al. (ed.). Manual of Environmental Microbiology, 2nd ed. ASM, Washington, DC.
- Lowe, M., F. Robb, E. L. Madsen, and R. Halden. 2002. Geochemistry and microbial diversity of a trichloroethene-contaminated superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbial Ecol. 40:123-134.
- Bakermans, C. and E. L. Madsen. 2002. Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization (FISH) with tyramide signal amplification (TSA). J. Microbiol. Meth. 50:75-84.
- Bakermans, C., A. M. Hohnstock-Ashe, S. Padmanabhan, P. Padmanabhan, and E. L. Madsen. 2002. Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar wastes by subsurface microorganisms. Microb. Ecol. 44:107-117.
- Bakermans, C. and E. L. Madsen. 2002. Diversity of 16S rRNA as naphthalene dioxygenase genes from a coal tar waste-contaminated aquifer waters. Microb. Ecol. 44:95-106.
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Progress 01/01/01 to 12/31/01
Outputs
During the past year, investigations examining microorganisms dwelling in a contaminated subsurface site have continued. We have continued to examine relationships between geochemical setting and in situ physiological reactions carried out by subsurface microorganisms. Molecular biological procedures continue to provide insights into the identity and diversity of naturally-occurring microbial communities carrying out biodegradation reactions.
Impacts
(N/A)
Publications
- Madsen, E. L. 2001. Methods for determining biodegradability, pp. 903-915. In: C. J. Hurst, et al. (ed.). Manual of Environmental Microbiology, 2nd ed. American Society for Microbiology, Washington, DC. (In Press).
- Madsen, E.L. 2001. Intrinsic bioremediation of organic subsurface contaminants, pp. 249-278. In: J. K. Fredrickson and M. Fletcher (ed.) Subsurface Microbiology and Biogeochemistry. John Wiley and Sons, NY.
- Hohnstock-Ashe, A. M., Plummer, S. M., R. M. Yager, P. Baveye, and E. L. Madsen. 2001. Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: Electron source and microbial communities involved in reductive dechlorination. Environ. Sci. Technol. 35:4449-4456.
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Progress 01/01/00 to 12/31/00
Outputs
During the past year, several types of investigations examining microorganisms dwelling in a contaminated subsurface site have been carried out. We have characterized the geochemical setting to document in situ physiological reactions carried out by subsurface microorganisms. We also have examined factors that allow and prevent exchange of biodegradation genes between site microorganisms. Furthermore, we have developed a microscopy-based set of procedures for visualizing cells in naturally occurring microbial communities capable of carrying out biodegradation reactions.
Impacts
(N/A)
Publications
- Madsen, E. L. 2000. Verifying Bioremediation: How do I know if it is taking place?. In: J. J. Valdes (ed.) Bioremediation. Kluwer Academic Publ., Netherlands (In Press).
- Bakermans, C. and E. L. Madsen. 2000. Use of substrate responsive direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community. J. Microbiol. Meth. 43:81-90.
- Hohnstock, A. M., K. G. Stuart-Keil, E. E. Kull, and E. L. Madsen. 2000. Naphthalene and donor cell density influence field conjugation of naphthalene catabolic plasmids. Appl. Environ. Microbiol. 66:3088-3092.
- Madsen , E.L. 2000. Nucleic acid procedures for characterizing the identity and activity of subsurface microorganisms. Invited contribution to special issue of Hydrogeology Journal, B. Bekins, ed. Hydrogeol. J. 8:112-125.
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