Dan Arp

Dean, College of Agricultural Sciences
Professor, Botany and Plant Pathology
Affiliate Faculty, Microbiology

Office: Strand Agricultural Hall 227B
Email: Dan.J.Arp@oregonstate.edu
Phone: (541) 737-1297
Arp Lab
Pub Med

Ph.D. 1980, University of Wisconsin-Madison

KEYWORDS: N Cycles; Nitrification; Bioremediation; Butane Metabolism

The research projects in my laboratory are in the following three areas:

1) Nitrification: Oxidation of ammonia to nitrite.
Nitrification is the microbial process whereby ammonia is oxidized to nitrite and nitrate. In general, this process is detrimental to agriculture where large amounts of ammonia or urea-based fertilizers are applied to croplands. The nitrates that are formed are readily leached from the soil, leading to eutrophication of surface waters and contamination of ground waters, which often serve as a source of water for human consumption. Furthermore, nitrate and nitrite are substrates for denitrification, which results in their loss from the soil in gaseous form. We study ammonia oxidation in the model organism, Nitrosomonas europaea. Our investigations are at the molecular and physiological level. Recently, the genome sequence for N. europaea was completed. The sequence has given us new insights into the physiology and metabolism of this organism. We are currently investigating the basis of obligate chemolithoautotrophy in this organism. From the genome sequence, a putative fructose transporter was identified. This led us to investigate fructose as a carbon and energy source for N. europaea. Consistent with previous reports with other organic compounds, fructose cannot serve as the sole energy source for these bacteria. However, fructose can replace CO2 as the sole carbon source. This result provides the first indication of chemolithoorganotrophic growth of this organism. We are engaged in a project to produce microarrays representing all the genes of the N. europaea genome to study gene expression under various conditions of nutrient stress.

2) Bioremediation: Cometabolic degradation of enviromental pollutants.
Cometabolism is defined as the transformation of a non-growth-supporting compound in the obligate presence of a growth-supporting substrate or other transformable compound. When the non-growth-supporting compound is an environmental pollutant, cometabolism offers a means to use organisms to clean up contaminated environments, i.e. bioremediation. The substrate range of ammonia monooxygenase, the enzyme that initiates the metabolism of ammonia in N. europaea, extends to halogenated aliphatics (many of which are environmental pollutants). We have identified over thirty halogenated aliphatics and aromatics that are transformed by ammonia monooxygenase including trichloroethylene, chlorobenzene, vinyl chloride and dibromochloropropane. While ammonia oxidizing bacteria are not likely to find widespread application in bioremediation schemes, N. europaea has, nonetheless, been a useful model organism in examining the mechanism of cometabolism. We are also studying other groups of organisms, which do show more potential for use in bioremediation schemes. All have in common the requirement for a monooxygenase to harvest their growth substrate and initiate the degradation of pollutants. For example, we have studied the physiological consequences of trichloroethylene metabolism by toluene-oxidizing bacteria. We are also investigating the consequences of cometabolism by butane-oxidizing bacteria.

3) Butane metabolism by microorganisms.
Butane is used as an energy source by a number of bacteria. The pathway for butane metabolism involves oxidation to butanol, followed by conversion to butyaldehyde, and then to butyric acid which is metabolized as a fatty acid. We are studying butane metabolism at the molecular level in three butane grown bacteria. Three different types of butane monooxygenases are present in these three bacteria. The enzyme from Mycobacterium vaccae is membrane associated and likely to harbor a diiron center, the enzyme from Pseudomonas butanovora is soluble and contains a diiron center, and the enzyme from our isolate, Nocardioides CF8, likely contains copper. We have characterized the genes for butane metabolism from P. butanovora and have purified butane monooxygenase and two distinct butanol dehydrogenases. The butanol dehydrogenases belong to a unique class of enzymes that utilize pyrolloquinolinequinone (PQQ) as their cofactor. With butane monooxygenase, we are engaged in a study to determine the basis of the specificity of butane and other gaseous alkanes. Although at the structure and sequence level, butane monooxygenase is similar to soluble methane monooxygenase, butane monooxygenase does not oxidize methane efficiently.