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Wu MR, Hou TT, Liu Y, Miao LL, Ai GM, Ma L, Zhu HZ, Zhu YX, Gao XY, Herbold CW, Wagner M, Li DF, Liu ZP, Liu SJ. Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N 2 with a previously unknown pathway. Environ Microbiol 2021; 23:6965-6980. [PMID: 34581470 DOI: 10.1111/1462-2920.15751] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/02/2021] [Accepted: 08/29/2021] [Indexed: 11/28/2022]
Abstract
Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N2 gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N2 and N2 O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N2 production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to 15 N2 from (15 NH4 )2 SO4 . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N2 .
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Affiliation(s)
- Meng-Ru Wu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ting-Ting Hou
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ya-Xin Zhu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.,Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
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