Dr. Madsen`s fundamental research interests are in documenting the "who", "what", "how", "where", "when", and "why" of microbiological processes in soil, water, sediments, and ground water. Microorganisms play a critical role in biogeochemical cycling of carbon , nutrients, and pollutant compounds in the soil habitat. Yet, methodological limitations of environmental microbiology are substantial. For instance, despite its relevance to society, proving that microbial populations are truly active in catalyzing biodegradation of toxic organic pollutants in a given habitat is a difficult task. A synthesis of toxicological, genetic, biochemical, physiological, analytical chemistry, and field-site research will successfully lead to progress in understanding how to measure, verify, and harness microbially-mediated processes that affect environmental quality. Ongoing research projects have objectives that include characterizing soil and subsurface (ground water) microorganisms and their activities, devising criteria for documenting detoxification processes in contaminated sites, discovering factors that govern reductive dechlorination reactions of halogenated organic compounds, using molecular biological methods to assess horizontal gene transfer and other mechanisms of microbial adaptation to pollutant compounds, understanding geochemical and physiological characteristics that may prevent or 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. Recent genome sequencing by the U.S.D.O.E. of Polaromonas naphthalenivorans (a bacterium active in situ in metabolizing naphthalene in polluted sediment) paves the way for studies aimed at identifying the genetic basis for ecological fitness.