基于宏基因组技术获得的对厌氧氨氧化菌代谢的新理解

New Understanding on Metabolism of Anaerobic Ammonium Oxidation Bacteria Based on Metagenomics Technology

厌氧氨氧化菌(Anaerobic ammonium oxidation bacteria,AAOB)是化能自养菌,由于其生理代谢的奇异性、细胞结构的特殊性以及对氮素循环的重要性,已成为环境工程、微生物以及海洋生物学等领域的研究热点.然而,AAOB未能实现纯培养的现状已成为AAOB代谢途径研究的巨大障碍.近年来兴起的宏基因组技术(Metagenomics)为AAOB代谢途径的研究提供了新手段.采用宏基因组技术,可直接研究微生物群体中某特定微生物基因组的结构与功能,摆脱了传统微生物学研究对纯培养的依赖,使未培养微生物的认识和开发成为可能.本文首先简述获取AAOB宏基因组信息的过程,然后通过比较由传统代谢研究方法和宏基因组技术获得的AAOB代谢途径的研究成果,论述基于宏基因组技术获得的对AAOB代谢的新理解,得出以下结果和结论:1)AAOB的碳素固定途径为乙酰辅酶A途径,碳素固定的还原力来自NADH或者QH2;2)AAOB氮素转化的重要中间产物是NO,而非NH2OH,并提出了以NO为核心的AAOB代谢的改进模型;3)AAOB的ATP合成途径为氧化磷酸化,推测的电子传递途径为N2H4—QH2—细胞色素bc1复合体;细胞色素bc1复合体再将电子用于NO2-还原和N2H4合成.AAOB的宏基因组技术使AAOB代谢途径的研究更具方向性.随着分子生物学理论和技术的不断发展,宏基因组学的升级技术(如宏转录组学、宏蛋白质组学)将为AAOB代谢途径的研究提供新的方法与平台.

Anaerobic ammonium oxidation bacteria （AAOB） belong to chemolitho-autotrophs. AAOB have become one of the research hotspots in the field of environmental engineering, microbiology and oceanography because of their specificities in metabolism, cell structure and nitrogen cycle. However, AAOB can not been cultivated in pure culture, which has become a great obstacle to study their metabolic pathways in further. Nowadays, fast-developing metagenomics provides us a new solution to study AAOB’s metabolism. Metagenomics mainly focuses on the structure and function relationships of particular genomes in a specific mixed microorganism population, which does not need traditional pure cultivation of microorganisms but makes it possible to recognize and exploit the uncultured microorganisms. Here we firstly summarize how the AAOB’s genomic information is gathered. Then we further review the new understanding on the AAOB’s metabolic pathways based on metagenomics by comparing with the conventional methods. Particularly, progresses on the carbon fixation, nitrogen conversion and ATP synthesis of AAOB are discussed in details in order to give some instructions for AAOB’s metabolism studies. Some constructive results and conclusions are reported as follows： 1） The carbon fixation pathway in AAOB is through reductive acetyl CoA pathway, and the reducing power originates from NADH or reduced ubiquinone （QH2）. 2） Nitric oxide （NO） is an important intermediate product in nitrogen conversion, but not hydroxylamine （NH2OH）. A new modified model based on nitric oxide is proposed. 3） The ATP synthetic pathway is through oxidative phosphorylation. The deduced electron transport chain is as follows： Hydrazine （N2H4） releases electrons to reduced ubiquinone, and then passes to cytochrome bc1 complex.The electrons are used to reduce nitrite （NO2-） or produce N2H4. The studies on AAOB’s metabolism based on metagenomics technology will be more directive. With the development of theories and methods on molecular biology, new technologies including metatranscriptomics and metaproteomics will provide more new methods and accurate information for studies on AAOB’s metabolism. Fig 3, Tab 1, Ref 51