Department of Microbiology
B57A Wing Hall
Ithaca, NY 14853-5701
Phone: (607) 255-2417
Fax: (607) 255-3904
Microorganisms in the Real World
My fundamental research interests are in documenting the "who", "what", "how", "where", "when", and "why" of microbiological processes in water, soil, sediments, and ground water. Microorganisms play a critical role in biogeochemical cycling of carbon, nutrients, and pollutant compounds in the biosphere. Yet, methodological limitations of environmental microbiology are severe. For instance, despite its relevance to society, proving that microbial populations are truly active in catalyzing biodegradation of organic pollutants in a given habitat is a difficult task. A synthesis of genetic, biochemical, physiological, analytical, and field-site research will successfully lead to progress in understanding how to measure, verify, and harness microbially-mediated processes that affect environmental quality.
One microbiological process of particular relevance to society is "bioremediation". For "bioremediation" to be transformed from the idea stage into a useful technology, collaboration between many disciplines is essential. In approaching a given contamination scenario, all available methods of pollutant removal and elimination (physical, chemical, microbiological using reactors and in situ techniques) should be considered. When appropriate, application of microbiological processes to eliminating environmental (especially organic) contaminants must follow a logical progression from site characterization and chemical analyses to laboratory and pilot scale verification of process feasibility.
My ongoing research projects have objectives that include characterizing soil and subsurface (ground water) microorganisms and their activities, use of molecular biology in discerning mechanisms of metabolic adaptation to pollutant compounds, understanding geochemical and physiological characteristics which both prevent and foster microbial activity, and developing a rapport with the biogeochemistry of field sites so that realism is an integral part of conceptual advancements in environmental microbiology.
The latest NSF-sponsored research project examines how the biogeochemical cycling of Carbon (biodegradation of organic contaminants) can interact with the cycling of other elements. The key hypothesis of the new project is that as microorganisms oxidize environmental pollutants, they simultaneously cause the accrual of reduced metabolic byproducts, such as Methane, Ammonia, and Sulfide. These, in turn, enrich for microbial populations that carry out new biogeochemical processes that would otherwise be absent from the study site. A major objective of the new project is to discover novel interactions between microbial populations and the processes they catalyze.
Eugene Madsen is an Professor in the Section of Microbiology. He was trained at the undergraduate level with bachelor's degrees in Chemistry (University of California at Santa Cruz) and soil science (Oregon State University). For his graduate education, he studied Rhizobium ecology in soil (MS) and metabolism of organic pollutants (Ph.D.) at Cornell University. Interest in field work led Madsen to a postdoctoral fellowship at Rutgers University where he studied transformation of iron and sulfur in fresh water streams. Interests in anaerobic metabolism of groundwater pollutants led to a postdoctoral appointment at Penn State University. A desire to explore the northwest led Madsen to an appointment as Senior Microbiologist at an environmental restoration firm in Bozeman Montana. After a year in industry Madsen accepted an appointment at Cornell that led to his current position. He serves as a member of the editorial board of Applied and Environmental Microbiology and has also been a member of two National Academy of Sciences committees on In situ Bioremediation.
Liou, J.S.-C. B. Szostek, C.M. DeRito, and E.L. Madsen. 2010. Investigating the biodegradability of perfluorooctanoic acid. Chemosphere 79: (in press)
Madsen, E.L. 2010. Stable Isotope probing techniques and bioremediation, pp . IN Stable isotope probing in microbial molecular ecology. J.C. Murrel and A. Whiteley (eds). American Society for Microbiology Press. Washington DC (in press)
Yagi, J.M., C.M. DeRito, J.M. Suflita, L. Geig, C.-O. Jeon, and E.L. Madsen. 2010. Subsurface microbial communities involved in in situ naphthalene catabolism carry out a complete N cycle via dissimilatory nitrate reduction to ammonia and nitrification. Appl. Environ Microbiol 76:3124-3134.
Yagi. J.M., D. Sims, T. Brettin, D. Bruce and E.L. Madsen. 2009. Remarkable physiologival versatility revealed by whole-genome analysis of the aromatic-hydrocarbon-degrading bacterium, Polaromonas naphthalenivorans. Environ Microbiol 11:2253-2270.
Yagi J.M., E.F. Neuhauser, J. Ripp, D. Mauro and E. L. Madsen. 2009. Subsurface ecosystem resilience: Long-term attenuation of subsurface contaminants supports an elaborate eukaryotic food chain and a dynamic microbial community. ISME Journal 4:131-143.
Madsen, E.L. 2009. Exclude "unculturable" from the taxonomic microbiology literature (Letter to Editor). Microbe 4:351.
Yagi, J.M. and E.L. Madsen. 2009. Diversity and spatial/temporal variability of oxygenase genes and nah/nag mRNA transcripts in a shallow contaminated aquifer. Appl Environ Microbiol 75:6478-6487.
DeRito, C.M. and E.L. Madsen. 2009. Stable isotope probing reveals Trichosporon yeast to be active in situ in soil phenol metabolism. ISME Journal ISME Journal 3:477-485.
Pumphrey, G.M., B.T. Hanson, S. Chandra, and E.L. Madsen. 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. 2008. Environmental Microbiology: From Genomes to Biogeochemistry. Wiley Blackwell. Malden MA, 479 pp.
Kim, J.M., N.T. Le, B.S. Chung, J.H. Park, J.-W. Bae, E.L. Madsen, and C.-O. Jeon. 2008. Influence of soil components on the biodegradation of benzene, toluene, ethbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl. Environ. Microbiol. 74:7313-7320.
Chandra, S., G.M. 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 microorganism 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-metablolizing microorganisms in freshwater sediment. Environ. Microbiol. 10:1964-1977.
Liou, J. and E.L. Madsen. 2008. Microbioal ecological processrs: Aerobic/Anaerobic. IN Encyclopedia of Ecology (S.E. Jorgensen ed.) Elsevier Science Ltd. Oxford UK.
Pumphrey, G.M. and E.L.Madsen 2007. Naphthalene metabolism and growth inhibition by naphthalene in Polaraomonas naphthlenivorans 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.
Madsen. E.L. 2006. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr. Opin. Biotechnol. 17: 92-97.
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 naphthalenivoransCJ2: Evolutionary implications for two gene clusters and novel regulatory control. Appl. Environ. Microbiol. 72: 1086-1095.
Madsen, E. L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Reviews Microbiology 3:439-446.
Park, W. and E. L. Madsen. 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., W. Park, W. C. Ghiorse, and E. L. Madsen. 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., A. J. McKay, C. DeRito, C. Watanabe, K. A. Thorn, and E. L. Madsen. 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., C.-O. Jeon, H. Cadillo, C. DeRito, and E. L. Madsen. 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., J. B. Yavitt, E. L. Madsen, and W. C. Ghiorse. 2004. Methanotrophic activity, abundance, and diversity in forest swamp pools: spatiotemporal dynamics and influences on methane fluxes. Geomicrobiol. J. 21:257-271.
Jeon, C.-O., W. Park, P. Padmanabhan, C. DeRito, J. R. Snape, and E. L. Madsen. 2003. Discovery of a novel bacterium with distinctive dioxygenase that is responsible for in situ biodegradation in a contaminated sediment. Proc. Natl. Acad. Sci. USA 100:13591-13596.
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.
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, and E. L. Madsen. 2002. Interaction of NahR, a LysR-type transcriptional regulator, with the alpha subunit of RNA polymerase in the naphthalene degrading bacterium, Pseudomonas putida NCIB 9816-4. FEMS Microbiol. Lett 213:159-165.
Park, W., P. Padmanabhan, S. Padmanabhan, G. J. Zylstra, and E. L. Madsen. 2002. nahR, encoding a LysR-type transcriptional activator, is highly conserved among naphthalene degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA. Microbiol. 148:2319-2329.
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.
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.
Madsen, E. 2002. Horizontal transfer of naphthalene catabolic genes in a contaminated aquifer, pp. 35-42. In: M. Syvanen and C. I. Kato (Eds.)Horizontal Gene Transfer, 2nd ed. Chapman and Hall, New York, NY.
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.
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: Geochemical and microbial controls on in situ reductive dechlorination. Environ. Sci. Technol.35:4449-4456.
Madsen, E.L. 2001. Natural Attenuation of Organic Contaminants, pp. 249-278. In: J. K. Fredrickson and M. Fletcher (ed.) Subsurface Microbiology and Biogeochemistry. John Wiley and Sons, NY.
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.
National Research Council. 2000. Natural attenuation for groundwater remediation. National Academic Press. Washington, DC.
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.
Miller, D. N., J. E. Bryant, E. L. Madsen, and W. C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:4715-4724.
Kalogeraki, V., J. Zhu, A. Eberhard, E. L. Madsen, and S. C. Winans. 1999. The phenolic vir gene inducer ferulic acid is O-demethylated by the VirH2 protein of an Agrobacterium tumefaciens Ti plasmid. Molec. Microbiol. 34:512-522.
Wilson, M.S., C. Bakermans, and E. L. Madsen. 1999. In situ, real-time catabolic gene expression: Extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl. Environ. Microbiol. 65:80-87.
Madsen, E. L. 1998. Theoretical and Applied Aspects of Bioremediation: The Influence of Microbiological Processes on Organic Compounds in Field Sites, pp. 354-407. In: R. Burlage, R. Atlas, D. Stahl, G. Geesey, G. Sayler (eds.)Techniques in Microbial Ecology. Oxford University Press. New York, NY.
Stuart-Keil, K.G., A.M. Hohnstock, K.P. Drees, J.B. Herrick. and E. L. Madsen. 1998. Plasmids responsible for horizontal transfer of naphthalene catabolic genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from Pseudomonas putida 9816-4. Appl. Environ. Microbiol. 64: 3633-3640.
Madsen, E. L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32: 429-539.
Madsen, E. L. 1997. Themes and variations of aromatic hydrocarbon catabolism by microorganisms in a contaminated field site. In: Progress in Microbial Ecology. Proceedings of the 7th International Symposium on Microbial Ecology. M. T. Martins et al., (eds).pp. 587-596.
Yager, R. M., S. E. Bilotta, C. L. Mann, and E. L. Madsen. 1997. Metabolic adaptation and In situ attenuation of chlorinated ethenes by naturally-occurring microorganisms in a fractured dolomite aquifer near Niagara Falls, NY. Environ. Sci. Technol. 31:3138-3147.
Herrick, J. B., K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen. 1997. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native a contaminated field site. Appl. Environ. Microbiol. 63:2330-2337.
Herrick, J. B., D. N. Miller, E. L. Madsen, and W. C. Ghiorse. 1997. Extraction, purification, and PCR amplification of microbial DNA from sediments and soils. In: J. Burke (ed.) PCR: Essential Techniques. Bios Scientific Publishers, Oxford.
Williams, R. A., K. A. Shuttle, J. L. Kunkler, E. L. Madsen, and S. W. Hooper. 1997. Intrinsic bioremediation in a solvent - contaminated alluvium. J. Ind. Microbiol. Biotechnol. 18:177-188.
Madsen, E. L. 1997. Methods for determining biodegradability. In: C. J. Hurst, et al. (ed.). Manual of Environmental Microbiology. American Society for Microbiology, Washington, DC, pp. 709-720.
Sandoli, R. S., W. C. Ghiorse, and E. L. Madsen. 1996. Regulation of microbial phenanthrene mineralization in sediments by sorbent- sorbate contact time, inoculum, and gamma irradiation-induced sterilization artifacts. Environ. Toxicol. Chem.15:1901-1907.
Madsen, E. L., C. L. Mann, and S. Bilotta. 1996. Oxygen limitations and aging as explanation for the persistence of naphthalene in coal-tar contaminated surface sediments. Environ. Toxicol. Chem. 15:1876-1882.
Madsen, E. L., C. T. Thomas, M. S. Wilson, R. L. Sandoli, and S. B. Best. 1996. In situ dynamics of aromatic hydrocarbons (AHs) and bacteria capable of AH metabolism in a coal tar waste-contaminated field site. Environ. Sci. Technol. 30:2412-2416.
Madsen, E. L. 1996. Hydrogen-based microbial ecosystems - a clarification. Technical comment Science (272:896).
Madsen, E. L. 1996. A critical analysis of methods for determining the composition and biogeochemical activities of soil microbial communities in situ. In: G. Stotzky and J.-M. Bollag (eds.). Soil Biochemistry, Vol. 9:287-370.
Wilson, M. S., and E. L. Madsen. 1996. Field extraction of a unique intermediary metabolite indicative of real time In situ pollutant biodegradation. Environ. Sci. Technol. 30:2099-2103.
Ghiorse, W. C., J. B. Herrick, R. L. Sandoli, and E. L. Madsen. 1995. Natural selection of PAH-degrading bacterial guilds at coal tar disposal sites. Environmental Health Perspectives 103(5):107-111.
Madsen, E. L. 1995. Impacts of agricultural practices on subsurface microbial ecology. In: D. Sparks (ed.). Advances in Agronomy Vol. 54, pp. 1-67.
Madsen, E. L., S. E. Bilotta-Best, and W. C. Ghiorse. 1995. Development of a rapid 14C-based field method for assessing potential biodegradation of organic compounds in soil and sediment samples. J. Microbiol. Meth. 21:317-327.
Moré, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
National Research Council. 1993. In situ Bioremediation: When Does It Work? B. E. Rittmann, J. M. Tiedje, R. Brown (Executive Committee); E. L. Madsen (Rapporteur). National Academy Press, Washington, DC.
Madsen, E. L. and W. C. Ghiorse. 1993. Ground Water Microbiology: Subsurface ecosystem processes. pp. 167-213. In: Ford, T. (ed.) Aquatic Microbiology: An Ecological Approach. Blackwell Scientific Publications, Cambridge, MA.
Herrick, J. B., E. L. Madsen, C. A. Batt, and W. C. Ghiorse. 1993. Polymerase chain reaction amplification of naphthalene catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59:687-694.
Madsen, E. L., A. Winding, K. Malachowsky, C. T. Thomas, and W. C. Ghiorse. 1992. Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and urban coal tar disposal site. Microb. Ecol. 24:199-213.
Madsen, E. L. 1991. Determining in situ biodegradation: Facts and challenges. Environ. Sci. Technol. 25:1662-1673.
Madsen, E. L., J. L. Sinclair and W. C. Ghiorse. 1991. In situ biodegradation: Microbiological patterns in a contaminated aquifer. Science 252:830-833.
Madsen, E. L. and J.-M. Bollag. 1989. Pathway of indole metabolism by a denitrifying microbial community. Arch. Microbiol. 151:71-76.
Madsen, E. L. and J.-M. Bollag. 1989. Aerobic and anaerobic microbial activity in deep subsurface sediments from the Savannah River Plant. Geomicrobiol. J. 7:93-102.
Madsen, E. L., A. J. Francis, and J.-M. Bollag. 1988. Environmental factors affecting indole metabolism under anaerobic conditions. Appl. Environ. Microbiol. 54:74-78.
Berry, D. F., E. L. Madsen, and J.-M. Bollag. 1987. Conversion of indole to oxindole under methanogenic conditions. Appl. Environ. Microbiol. 53:180-182.
Madsen, E. L., M. D. Morgan, and. R. E. Good. 1986. Simultaneous photoreduction and microbial oxidation of iron in a stream in the New Jersey Pinelands. Limnol. Oceanogr. 31:832-838.
Madsen, E. L. and M. Alexander. 1985. Effects of chemical speciation on the mineralization of organic compounds by microorganisms. Appl. Environ. Microbiol. 50:342-349.
Wang, Y. S., E. L. Madsen, and M. Alexander. 1985. Microbial degradation by mineralization or cometabolism determined by chemical concentration and environment. J. Ag. Food Chem. 33:495-499.
Madsen, E. L. and M. Alexander. 1982. Transport of Rhizobium and Pseudomonas through soil. Soil Sci. Soc. Am. J. 46:557-560.