Genomics, physiology, and ecology of microbial nitrogen metabolism

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The microbial nitrogen cycle evolved early on Earth to provide usable forms of nitrogen to all of life. However, massive human inputs of nitrogen from agriculture and industry have severely altered the balance of the nitrogen cycle. Rather than returning unassimilated nitrogen to the atmosphere as inert dinitrogen, some N-cycling microorganisms favorably produce and release reactive nitrogen intermediates (RNI) like nitrite, nitrate, nitric oxide and nitrous oxide as a function of increased N-loading. RNI have significant negative effects on the environment including eutrophication of surface water, destruction of stratospheric ozone, and global warming. The proposed research focuses on the microbial production of nitrous oxide, a greenhouse gas that is ca. 300 times more potent than carbon dioxide in global warming potential. In anaerobic metabolism, i.e. denitrification, nitrous oxide is readily consumed to produce dinitrogen as a terminal product. In contrast, the aerobic ammonia-oxidizing bacteria produce and release nitrous oxide as a terminal product when N-loads are high and oxygen concentrations are low. For instance, ammonia-oxidizers are significant global producers of nitrous oxide in agricultural soils and water bodies impacted by agricultural runoff. Interestingly, the genes and pathways for nitrous oxide production by ammonia-oxidizers remain largely uncharacterized, and nearly all of what we know is from work with a single ammonia-oxidizing isolate. Based on our vital need to further understand the workings of, and our continued impact on the microbial nitrogen cycle, objectives of the proposed research are to: 1) broadly identify and characterize microbial genes for RNI production and metabolism, 2) determine the physiological role of RNI metabolism genes in ammonia-oxidizing bacteria, and 3) detect the presence and expression levels of genes from ammonia oxidizers in environmental samples. This multifaceted approach from the bioinformatics, to the organism, to the environmental scales will further our understanding of the microbial nitrogen cycle, pathways for RNI production and metabolism, and sources of nitrous oxide to the atmosphere.