Genomics, physiology, and ecology of microbial nitrogen metabolism

微生物的氮循环在地球上很早就进化了，为所有生命提供了可用的氮素。然而，人类从农业和工业中大量输入的氮素严重改变了氮循环的平衡。一些氮循环微生物不是将未被同化的氮作为惰性氮返回大气，而是随着氮负荷的增加而有利地产生和释放活性氮中间体(RNI)，如亚硝酸盐、硝酸盐、一氧化氮和一氧化二氮。RNI对环境有显著的负面影响，包括地表水的富营养化、平流层臭氧的破坏和全球变暖。这项拟议中的研究重点是一氧化二氮的微生物生产，一氧化二氮是一种温室气体，其全球变暖潜力大约是二氧化碳的300倍。在厌氧代谢中，即反硝化作用中，一氧化二氮很容易被消耗，作为最终产物产生氮素。相比之下，好氧氨氧化细菌在氮负荷高、氧气浓度低的情况下，会产生并释放作为最终产物的一氧化二氮。例如，氨氧化剂是农业土壤和受农业径流影响的水体中一氧化二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确定，我们所知道的几乎所有信息都来自于单一的氨氧化菌。基于我们迫切需要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，拟议研究的目标是：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，以及3)检测环境样本中氨氧化菌基因的存在和表达水平。这种从生物信息学到生物体再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产生和代谢的途径以及大气中一氧化二氮来源的了解。

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.