The Role of Methane- and Ammonia-Oxidizing Bacteria in the Emission of Greenhouse Gases from Agricultural Soils

Nitrous oxide production from N-impacted soils is highly influenced by rates of inorganic nitrogen metabolized by the soil microbial community. The processes of nitrification and denitrification convert soil nitrite into nitrous oxide either directly or via nitrate. Although methane-oxidizing bacteria (MOB) are predominantly involved in converting methane to carbon dioxide, their evolutionary linkage to ammonia-oxidizing bacteria (AOB) makes them dynamic players in the oxidation of ammonia and in the production of nitrous oxide. Little to nothing is known about the metabolism of inorganic nitrogen by MOB. Furthermore, ammonia oxidation by AOB has been extensively characterized in only a single bacterial strain. To understand the function of these bacteria in producing or consuming greenhouse gases in soils, techniques must be developed and utilized to directly link the native microbial population structure with its function. Through this project, we completed three objectives to close these gaps in knowledge: 1) we characterized the rates of ammonia and hydroxylamine oxidation to nitrite and the concomitant production of nitrous oxide by pure MOB cultures, 2) we characterized hydroxylamine oxidoreductase genes and rates of ammonia oxidation in two AOB species, and 3) we optimized and applied molecular tools and traditional techniques to link diversity, abundance, and function of AOB in native, N-impacted, forest soils. Our results demonstrated that each of four MOB species, even those with close taxonomic relationships, metabolized nitrogen differently. The two AOB species studied had similar hydroxylamine oxidoreductase gene structure, but not surprisingly, their metabolisms were highly tuned to their optimal growth conditions. Last, we demonstrated our ability to correlate AOB community structure with function in native N-impacted soils using 16S rDNA gene clone libraries, quantitative PCR, and nitrification activity assays. Accomplishing these objectives has brought us a large step forward towards understanding and quantifying the specific roles of MOB and AOB in soil nitrogen transformations. Using the techniques mastered and knowledge generated through this study, MOB and AOB populations and their roles in greenhouse gas production and consumption in soils can be directly targeted.