Genomics, physiology, and ecology of microbial nitrogen metabolism

微生物氮循环在地球早期进化，为所有生命提供可用的氮。然而，人类从农业和工业中大量输入的氮严重改变了氮循环的平衡。一些氮循环微生物不会将未被吸收的氮作为惰性二氮返回大气，而是作为氮负荷增加的功能，有利于产生和释放活性氮中间体（RNI），如亚硝酸盐、硝酸盐、一氧化氮和氧化亚氮。RNI对环境有显著的负面影响，包括地表水富营养化、平流层臭氧破坏和全球变暖。拟议中的研究重点是微生物产生一氧化二氮，一种温室气体，在全球变暖潜力方面比二氧化碳强约300倍。在厌氧代谢，即反硝化过程中，氧化亚氮很容易被消耗，产生二氮作为最终产物。相反，好氧氨氧化菌在n负荷高、氧浓度低时产生并释放一氧化二氮作为终产物。例如，氨氧化剂是受农业径流影响的农业土壤和水体中氧化亚氮的重要全球生产者。有趣的是，氨氧化菌产生一氧化二氮的基因和途径在很大程度上仍未被表征，我们所知道的几乎所有信息都来自于对单个氨氧化菌的研究。基于我们进一步了解微生物氮循环的工作原理和我们对微生物氮循环的持续影响的迫切需要，提出的研究目标是：1)广泛识别和表征RNI产生和代谢的微生物基因；2)确定RNI代谢基因在氨氧化细菌中的生理作用；3)检测环境样品中氨氧化剂基因的存在和表达水平。这种从生物信息学、生物体到环境尺度的多方面方法将进一步加深我们对微生物氮循环、RNI产生和代谢途径以及大气中氧化亚氮来源的理解。

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.