Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

Meng-Ru Wu; Ting-Ting Hou; Ying Liu; Li-Li Miao; Guo-Min Ai; Lan Ma; Hai-Zhen Zhu; Ya-Xin Zhu; Xi-Yan Gao; Craig W Herbold; Michael Wagner; De-Feng Li; Zhi-Pei Liu; Shuang-Jiang Liu

doi:10.1111/1462-2920.15751

Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

Meng-Ru Wu
, Ting-Ting Hou
, Ying Liu
, Li-Li Miao
, Guo-Min Ai
, Lan Ma
, Hai-Zhen Zhu
, Ya-Xin Zhu
, Xi-Yan Gao
, Craig W Herbold
, Michael Wagner
, De-Feng Li
, Zhi-Pei Liu (Corresponding author)
, Shuang-Jiang Liu (Corresponding author)

Department of Microbiology and Ecosystem Science

Publications: Contribution to journal › Article › Peer Reviewed

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 .

Original language	English
Pages (from-to)	6965-6980
Number of pages	16
Journal	Environmental Microbiology
Volume	23
Issue number	11
DOIs	https://doi.org/10.1111/1462-2920.15751
Publication status	Published - 26 Nov 2021

Funding

This research was supported by grants from the National Key R&D Program of China (2019YFA0905500; 2016YFD0501409) and National Natural Science Foundation of China (NSFC grant Nos. 31861133002; 91951101; 31870103), Chinese Academy of Science (KFZD\u2010SW\u2010219\u20103; KFZD\u2010SW\u2010309) and CAS Key Technology Talent Program (to GMA). We thank Dr. Sebastian L\u00FCcker at the Department of Microbiology, Radboud University, the Netherlands, and Dr. Holger Daims at the University of Vienna for helpful discussions on this research. This research was supported by grants from the National Key R&D Program of China (2019YFA0905500; 2016YFD0501409) and National Natural Science Foundation of China (NSFC grant Nos. 31861133002; 91951101; 31870103), Chinese Academy of Science (KFZD-SW-219-3; KFZD-SW-309) and CAS Key Technology Talent Program (to GMA). We thank Dr. Sebastian L?cker at the Department of Microbiology, Radboud University, the Netherlands, and Dr. Holger Daims at the University of Vienna for helpful discussions on this research.

Austrian Fields of Science 2012

106014 Genomics
106022 Microbiology

Keywords

Alcaligenes ammonioxydans sp. nov.
heterotrophic nitrifier
wastewater
direct ammonia oxidation (Dirammox)
OXIDATION
HETEROTROPHIC NITRIFICATION
THIOSPHAERA-PANTOTROPHA
AEROBIC DENITRIFICATION
PYRUVIC-OXIME
PURIFICATION
NITROGEN
REDUCTASE
FAECALIS
HYDROXYLAMINE OXIDASE

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Cite this

Wu, M.-R., Hou, T.-T., Liu, Y., Miao, L.-L., Ai, G.-M., Ma, L., Zhu, H.-Z., Zhu, Y.-X., Gao, X.-Y., Herbold, C. W., Wagner, M., Li, D.-F., Liu, Z.-P., & Liu, S.-J. (2021). Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway. Environmental Microbiology, 23(11), 6965-6980. https://doi.org/10.1111/1462-2920.15751

@article{c704656104864713891e428e5660abcb,

title = "Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway",

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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author = "Meng-Ru Wu and Ting-Ting Hou and Ying Liu and Li-Li Miao and Guo-Min Ai and Lan Ma and Hai-Zhen Zhu and Ya-Xin Zhu and Xi-Yan Gao and Herbold, \{Craig W\} and Michael Wagner and De-Feng Li and Zhi-Pei Liu and Shuang-Jiang Liu",

note = "Publisher Copyright: {\textcopyright} 2021 Society for Applied Microbiology and John Wiley \& Sons Ltd.",

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month = nov,

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doi = "10.1111/1462-2920.15751",

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Wu, M-R, Hou, T-T, Liu, Y, Miao, L-L, Ai, G-M, Ma, L, Zhu, H-Z, Zhu, Y-X, Gao, X-Y, Herbold, CW, Wagner, M, Li, D-F, Liu, Z-P & Liu, S-J 2021, 'Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway', Environmental Microbiology, vol. 23, no. 11, pp. 6965-6980. https://doi.org/10.1111/1462-2920.15751

TY - JOUR

T1 - Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

AU - Wu, Meng-Ru

AU - Hou, Ting-Ting

AU - Liu, Ying

AU - Miao, Li-Li

AU - Ai, Guo-Min

AU - Ma, Lan

AU - Zhu, Hai-Zhen

AU - Zhu, Ya-Xin

AU - Gao, Xi-Yan

AU - Herbold, Craig W

AU - Wagner, Michael

AU - Li, De-Feng

AU - Liu, Zhi-Pei

AU - Liu, Shuang-Jiang

PY - 2021/11/26

Y1 - 2021/11/26

N2 - 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 .

AB - 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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KW - direct ammonia oxidation (Dirammox)

KW - OXIDATION

KW - HETEROTROPHIC NITRIFICATION

KW - THIOSPHAERA-PANTOTROPHA

KW - AEROBIC DENITRIFICATION

KW - PYRUVIC-OXIME

KW - PURIFICATION

KW - NITROGEN

KW - REDUCTASE

KW - FAECALIS

KW - HYDROXYLAMINE OXIDASE

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DO - 10.1111/1462-2920.15751

M3 - Article

C2 - 34581470

SN - 1462-2912

VL - 23

SP - 6965

EP - 6980

JO - Environmental Microbiology

JF - Environmental Microbiology

IS - 11

ER -

Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

Abstract

Funding

Austrian Fields of Science 2012

Keywords

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