1
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Jin D, Zhang X, Zhang X, Zhou L, Zhu Z, Deogratias UK, Wu Z, Zhang K, Ji X, Ju T, Zhu X, Gao B, Ji L, Zhao R, Ruth G, Wu P. A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174855. [PMID: 39034010 DOI: 10.1016/j.scitotenv.2024.174855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/13/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.
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Affiliation(s)
- Da Jin
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xiaonong Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xingxing Zhang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Li Zhou
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Zixuan Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Ufoymungu Kisa Deogratias
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Zhiqiang Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Kangyu Zhang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xu Ji
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Ting Ju
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Xurui Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Bo Gao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Luomiao Ji
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Rui Zhao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Guerra Ruth
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China
| | - Peng Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, No. 1 Kerui Road, Suzhou 215009, PR China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, No. 1 Kerui Road, Suzhou 215009, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, No. 1 Kerui Road, Suzhou 215009, PR China.
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2
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Ye W, Yan J, Yan J, Lin JG, Ji Q, Li Z, Ganjidoust H, Huang L, Li M, Zhang H. Potential electron acceptors for ammonium oxidation in wastewater treatment system under anoxic condition: A review. ENVIRONMENTAL RESEARCH 2024; 252:118984. [PMID: 38670211 DOI: 10.1016/j.envres.2024.118984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 04/28/2024]
Abstract
Anaerobic ammonium oxidation has been considered as an environmental-friendly and energy-efficient biological nitrogen removal (BNR) technology. Recently, new reaction pathway for ammonium oxidation under anaerobic condition had been discovered. In addition to nitrite, iron trivalent, sulfate, manganese and electrons from electrode might be potential electron acceptors for ammonium oxidation, which can be coupled to traditional BNR process for wastewater treatment. In this paper, the pathway and mechanism for ammonium oxidation with various electron acceptors under anaerobic condition is studied comprehensively, and the research progress of potentially functional microbes is summarized. The potential application of various electron acceptors for ammonium oxidation in wastewater is addressed, and the N2O emission during nitrogen removal is also discussed, which was important greenhouse gas for global climate change. The problems remained unclear for ammonium oxidation by multi-electron acceptors and potential interactions are also discussed in this review.
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Affiliation(s)
- Weizhuo Ye
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
| | - Jiaqi Yan
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
| | - Jia Yan
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China.
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Yang Ming Chiao Tung University, 1001 University Road, Hsinchu City, 30010, Taiwan
| | - Qixing Ji
- The Earth, Ocean and atmospheric sciences thrust (EOAS), Hong Gong University of Science and Technology (Guangzhou), 511442, Guangzhou, China
| | - Zilei Li
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
| | - Hossein Ganjidoust
- Faculty of Civil and Environmental Engineering, Tarbiat Modarres University, 14115-397, Tehran, Iran
| | - Lei Huang
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
| | - Meng Li
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
| | - Hongguo Zhang
- School of Environmental Science and Engineering, Guangzhou University, 510006, Guangzhou, China; Guangzhou University-Linköping University Research Center on Urban Sustainable Development, Guangzhou University, 510006, Guangzhou, China
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3
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Hu Y, Wang Y, Wang R, Wang X, Liu SJ. Dirammox-dominated microbial community for biological nitrogen removal from wastewater. Appl Microbiol Biotechnol 2024; 108:389. [PMID: 38904674 PMCID: PMC11192851 DOI: 10.1007/s00253-024-13214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/15/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024]
Abstract
Direct ammonia oxidation (Dirammox) might be of great significance to advance the innovation of biological nitrogen removal process in wastewater treatment systems. However, it remains unknown whether Dirammox bacteria can be selectively enriched in activated sludge. In this study, a lab-scale bioreactor was established and operated for 2 months to treat synthetic wastewater with hydroxylamine as a selection pressure. Three Dirammox strains (Alcaligenes aquatilis SDU_AA1, Alcaligenes aquatilis SDU_AA2, and Alcaligenes sp. SDU_A2) were isolated from the activated sludge, and their capability to perform Dirammox process was confirmed. Although these three Dirammox bacteria were undetectable in the seed sludge (0%), their relative abundances rapidly increased after a month of operation, reaching 12.65%, 0.69%, and 0.69% for SDU_A2, SDU_AA1, and SDU_AA2, respectively. Among them, the most dominant Dirammox (SDU_A2) exhibited higher nitrogen removal rate (32.35%) than the other two strains (13.57% of SDU_AA1 and 14.52% of SDU_AA2). Comparative genomic analysis demonstrated that the most dominant Dirammox bacterium (SDU_A2) possesses fewer complete metabolic modules compared to the other two less abundant Alcaligenes strains. Our findings expanded the understanding of the application of Dirammox bacteria as key functional microorganisms in a novel biological nitrogen and carbon removal process if they could be well stabilized. KEY POINTS: • Dirammox-dominated microbial community was enriched in activated sludge bioreactor. • The addition of hydroxylamine played a role in Dirammox enrichment. • Three Dirammox bacterial strains, including one novel species, were isolated.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.
| | - Runhua Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaokang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
- University of Chinese Academy of Sciences, Beijing, P. R. China.
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4
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Lenferink WB, Bakken LR, Jetten MSM, van Kessel MAHJ, Lücker S. Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification. SCIENCE ADVANCES 2024; 10:eadl3587. [PMID: 38848370 PMCID: PMC11160463 DOI: 10.1126/sciadv.adl3587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.
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Affiliation(s)
- Wouter B. Lenferink
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Mike S. M. Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Maartje A. H. J. van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, Netherlands
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5
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Yang Y, Gui X, Chen L, Li H, Li Z, Liu T. Acid-tolerant Pseudomonas citronellolis YN-21 exhibits a high heterotrophic nitrification capacity independent of the amo and hao genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116385. [PMID: 38772137 DOI: 10.1016/j.ecoenv.2024.116385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/17/2024] [Accepted: 04/21/2024] [Indexed: 05/23/2024]
Abstract
Heterotrophic nitrifying bacteria are found to be promising candidates for implementation in wastewater treatment systems due to their tolerance to extreme environments. A novel acid-resistant bacterium, Pseudomonas citronellolis YN-21, was isolated and reported to have exceptional heterotrophic nitrification capabilities in acidic condition. At pH 5, the highest NH4+ removal rate of 7.84 mg/L/h was displayed by YN-21, which was significantly higher than the NH4+ removal rates of other strains in neutral and alkaline environments. Remarkably, a distinct accumulation of NH2OH and NO3- was observed during NH4+ removal by strain YN-21, while traditional amo and hao genes were not detected in the genome, suggesting the possible presence of alternative nitrifying genes. Moreover, excellent nitrogen removal performance was displayed by YN-21 even under high concentrations of metal ion stress. Consequently, a broad application prospect in the treatment of leather wastewater and mine tailwater is offered by YN-21.
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Affiliation(s)
- Yuran Yang
- Chongqing Key Laboratory of Interfacial Processes and Soil Health, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Xuwei Gui
- Chongqing Key Laboratory of Interfacial Processes and Soil Health, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Liuyi Chen
- Hanhong college, southwest university, Chongqing 400716, China
| | - Huimiao Li
- Chongqing Key Laboratory of Plant Disease Biology, college of Plant Protection, Southwest University, Chongqing 400716, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Interfacial Processes and Soil Health, College of Resources and Environment, Southwest University, Chongqing 400716, China.
| | - Tuohong Liu
- Chongqing Key Laboratory of Interfacial Processes and Soil Health, College of Resources and Environment, Southwest University, Chongqing 400716, China
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6
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Sánchez-Arroyo A, Plaza-Vinuesa L, de Las Rivas B, Mancheño JM, Muñoz R. Structural and functional analysis of the key enzyme responsible for the degradation of ochratoxin A in the Alcaligenes genus. Int J Biol Macromol 2024; 267:131342. [PMID: 38574921 DOI: 10.1016/j.ijbiomac.2024.131342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The potential to degrade ochratoxin A (OTA), a highly poisonous mycotoxin, was investigated in cultures from Alcaligenes-type strains. Genome sequence analyses from different Alcaligenes species have permitted us to demonstrate a direct, causal link between the gene coding a known N-acyl-L-amino acid amidohydrolase from A. faecalis (AfOTH) and the OTA-degrading activity of this bacterium. In agreement with this finding, we found the gene coding AfOTH in two additional species included in the Alcaligenes genus, namely, A. pakistanensis, and A. aquatilis, which also degraded OTA. Notably, A. faecalis subsp. faecalis DSM 30030T was able to transform OTα, the product of OTA hydrolysis. AfOTH from A. faecalis subsp. phenolicus DSM 16503T was recombinantly over-produced and enzymatically characterized. AfOTH is a Zn2+-containing metalloenzyme that possesses structural features and conserved residues identified in the M20D family of enzymes. AfOTH is a tetramer in solution that shows both aminoacylase and carboxypeptidase activities. Using diverse potential substrates, namely, N-acetyl-L-amino acids and carbobenzyloxy-L-amino acids, a marked preference towards C-terminal Phe and Tyr residues could be deduced. The structural basis for this specificity has been determined by in silico molecular docking analyses. The amidase activity of AfOTH on C-terminal Phe residues structurally supports its OTA and OTB degradation activity.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Blanca de Las Rivas
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain.
| | - Rosario Muñoz
- Bacterial Biotechnology Laboratory, Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain.
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7
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Zhang H, Ma L, Li Y, Yan S, Tong Z, Qiu Y, Zhang X, Yong X, Luo L, Wong JWC, Zhou J. Control of nitrogen and odor emissions during chicken manure composting with a carbon-based microbial inoculant and a biotrickling filter. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 357:120636. [PMID: 38552514 DOI: 10.1016/j.jenvman.2024.120636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 04/14/2024]
Abstract
Although aerobic composting is usually utilized in livestock manure disposal, the emission of odorous gases from compost not only induces harm to the human body and the environment, but also causes loss of nitrogen, sulfur, and other essential elements, resulting in a decline in product quality. The impact of biotrickling filter (BTF) and insertion of carbon-based microbial agent (CBMA) on compost maturation, odor emissions, and microbial population during the chicken manure composting were assessed in the current experiment. Compared with the CK group, CBMA addition accelerated the increase in pile temperature (EG group reached maximum temperature 10 days earlier than CK group), increased compost maturation (GI showed the highest increase of 41.3% on day 14 in EG group), resulted in 36.59% and 14.60% increase in NO3--N content and the total nitrogen retention preservation rate after composting. The deodorization effect of biotrickling filter was stable, and the removal rates of NH3, H2S, and TVOCs reached more than 90%, 96%, and 56%, respectively. Furthermore, microbial sequencing showed that CBMA effectively changed the microbial community in compost, protected the ammonia-oxidizing microorganisms, and strengthened the nitrification of the compost. In addition, the nitrifying and denitrifying bacteria were more active in the cooling period than they were in the thermophilic period. Moreover, the abundance of denitrification genes containing nirS, nirK, and nosZ in EG group was lower than that in CK group. Thus, a large amount of nitrogen was retained under the combined drive of BTF and CBMA during composting. This study made significant contributions to our understanding of how to compost livestock manure while reducing releases of odors and raising compost quality.
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Affiliation(s)
- Haorong Zhang
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Liqian Ma
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Yinchao Li
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Su Yan
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Zhenye Tong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Yue Qiu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xueying Zhang
- College of Environmental Science and Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Xiaoyu Yong
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China
| | - Liwen Luo
- Institute of Bioresource and Agriculture, And Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Jonathan W C Wong
- Institute of Bioresource and Agriculture, And Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, Jiangsu 211816, China.
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8
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Chen Z, Wu Y, Dolfing J, Zhuang S, Wang B, Li D, Huang S, Rittmann BE. Complex ammonium oxidation demands visualized resolution. Sci Bull (Beijing) 2024:S2095-9273(24)00210-X. [PMID: 38604937 DOI: 10.1016/j.scib.2024.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China.
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Dan Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton NJ 08540, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe AZ 85287-5701, USA
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9
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Lv JL, Min D, Cheng ZH, Zhang JX, Li WW, Mu Y, Liu SJ, Liu DF. Direct ammonia oxidation (Dirammox) is favored over cell growth in Alcaligenes ammonioxydans HO-1 to deal with the toxicity of ammonium. Biotechnol Bioeng 2024; 121:980-990. [PMID: 38088435 DOI: 10.1002/bit.28623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 02/20/2024]
Abstract
Bacteria capable of direct ammonia oxidation (Dirammox) play important roles in global nitrogen cycling and nutrient removal from wastewater. Dirammox process, NH3 → NH2 OH → N2 , first defined in Alcaligenes ammonioxydans HO-1 and encoded by dnf gene cluster, has been found to widely exist in aquatic environments. However, because of multidrug resistance in Alcaligenes species, the key genes involved in the Dirammox pathway and the interaction between Dirammox process and the physiological state of Alcaligenes species remain unclear. In this work, ammonia removal via the redistribution of nitrogen between Dirammox and microbial growth in A. ammonioxydans HO-1, a model organism of Alcaligenes species, was investigated. The dnfA, dnfB, dnfC, and dnfR genes were found to play important roles in the Dirammox process in A. ammonioxydans HO-1, while dnfH, dnfG, and dnfD were not essential genes. Furthermore, an unexpected redistribution phenomenon for nitrogen between Dirammox and cell growth for ammonia removal in HO-1 was revealed. After the disruption of the Dirammox in HO-1, more consumed NH4 + was recovered as biomass-N via rapid metabolic response and upregulated expression of genes associated with ammonia transport and assimilation, tricarboxylic acid cycle, sulfur metabolism, ribosome synthesis, and other molecular functions. These findings deepen our understanding of the molecular mechanisms for Dirammox process in the genus Alcaligenes and provide useful information about the application of Alcaligenes species for ammonia-rich wastewater treatment.
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Affiliation(s)
- Jun-Lu Lv
- School of Life Science, University of Science and Technology of China, Hefei, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Zhou-Hua Cheng
- School of Life Science, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Zhang
- School of Life Science, University of Science and Technology of China, Hefei, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 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
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
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10
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Karmann C, Mágrová A, Jeníček P, Bartáček J, Kouba V. Advances in nitrogen removal and recovery technologies from reject water: Economic and environmental perspectives. BIORESOURCE TECHNOLOGY 2024; 391:129888. [PMID: 37914052 DOI: 10.1016/j.biortech.2023.129888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
This review critically assesses nitrogen removal technologies applied in the reject water treatment, across different stages of technological development, with a focus on their economic and environmental impacts. The prevalent use of biological processes raises concerns due to potential environmental impacts caused by N2O emissions. However, partial nitritation-anaerobic ammonium oxidation demonstrated economic benefits and the potential for positive environmental outcomes when properly operated and controlled. Furthermore, reject water, in many cases, provides sufficient nitrogen concentrations for nitrogen recovery processes, such as ammonia stripping, substituting production of industrial fertilizers and contributing to a circular economy. Nonetheless, their financial competitiveness is subject to various conditions, including the nitrogen concentration or reject water flow. As the environmental benefits of bioprocesses and economic benefits of nitrogen recovery processes may vary, it is crucial to further optimize both and investigate novel promising technologies such as electrochemical systems, denitrifying anaerobic methane oxidation or direct ammonia oxidation.
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Affiliation(s)
- Christina Karmann
- University of Chemistry and Technology Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Anna Mágrová
- University of Chemistry and Technology Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Pavel Jeníček
- University of Chemistry and Technology Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Jan Bartáček
- University of Chemistry and Technology Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Vojtěch Kouba
- University of Chemistry and Technology Prague, Technická 5, Prague 166 28, Czech Republic.
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11
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Xie Y, Tian X, He Y, Dong S, Zhao K. Nitrogen removal capability and mechanism of a novel heterotrophic nitrification-aerobic denitrification bacterium Halomonas sp. DN3. BIORESOURCE TECHNOLOGY 2023; 387:129569. [PMID: 37517711 DOI: 10.1016/j.biortech.2023.129569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Recently, the functional microorganisms capable of eliminating nitrogenous waste have been applied in mariculture systems. As a potential candidate for treating mariculture wastewater, strain DN3 eliminated 100% of ammonia and nitrate and 96.61%-100% of nitrite within 72 h, when single nitrogen sources at concentrations of 0-50 mg/L. Strain DN3 also exhibited the efficient removal performance of mixed-form nitrogen (ammonia, nitrate, and nitrite) at salinity 30 ‰, C/N ratio 20, and 180 rpm. The nitrogen assimilation pathway dominated inorganic nitrogen metabolism, with less nitrogen (14.23%-25.02% of TN) lost into the air via nitrification and denitrification, based on nitrogen balance analysis. Moreover, the bacterial nitrification pathway was explored by enzymatic assays and inhibition assays. These complex nitrogen assimilation and dissimilation processes were further revealed by bacterial genome analysis. These results provide important insight into nitrogen metabolism of Halomonas sp. and theoretical support for treating mariculture wastewater with strain DN3.
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Affiliation(s)
- Yumeng Xie
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266000, PR China
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266000, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, PR China.
| | - Yu He
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266000, PR China
| | - Shuanglin Dong
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266000, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, PR China
| | - Kun Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266000, PR China
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12
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Leng J, Lu J, Hai C, Liu X, Wu P, Sun Y, Yuan C, Zhao J, Hu B. Exploring influence mechanism of small-molecule carbon source on heterotrophic nitrification-aerobic denitrification process from carbon metabolism, nitrogen metabolism and electron transport process. BIORESOURCE TECHNOLOGY 2023; 387:129681. [PMID: 37586428 DOI: 10.1016/j.biortech.2023.129681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
The heterotrophic nitrification-aerobic denitrification (HNAD) process can remove nitrogen and organic carbon under aerobic conditions. To get the in-depth mechanism of the HAND process, a strain named Acinetobacter johnsonii ZHL01 was isolated, and enzyme activity, electron transport, energy production, and gene expression of the strain were studied with small-molecule carbon sources, including sodium citrate, sodium acetate, sodium fumarate, and sodium succinate. The HNAD pathway of ZHL01 was NH4+→NH2OH → NO, and nitrogen balance analysis shows that ZHL01 could assimilate and denitrify 58.29 ± 1.05 % and 16.58 ± 1.07 % of nitrogen, respectively. The assimilation, the nitrification/denitrification, and the respiration processes were regulated by the concentration of reduced nicotinamide adenine dinucleotide (NADH) produced from the different metabolic pathways of small-molecule carbon sources. The HNAD process occurs to reduce intracellular redox levels related to NADH concentrations. This discovery provides a theoretical basis for the practical application of HAND bacteria.
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Affiliation(s)
- Juntong Leng
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Jiyan Lu
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Chao Hai
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Xinyi Liu
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Pei Wu
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China.
| | - Yan Sun
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Chunbo Yuan
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Jianqiang Zhao
- Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; School of Water and Environment, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China
| | - Bo Hu
- School of Civil Engineering, Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development Chang'an University, The Middle Section of the South 2(nd) Ring Road, 710064 Xi'an, Shaanxi Province, China.
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13
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Gao Y, Zhu J, Wang K, Ma Y, Fang J, Liu G. Discovery of a heterotrophic aerobic denitrification Pseudomonas sp. G16 and its unconventional nitrogen metabolic pathway. BIORESOURCE TECHNOLOGY 2023; 387:129670. [PMID: 37591467 DOI: 10.1016/j.biortech.2023.129670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
From the aerobic pond of the farm, the Pseudomonas sp. G16 was screened and isolated, which was confirmed to exhibit heterotrophic nitrification and aerobic denitrification. The removal rates of Ammonia (100 mg/L), nitrate (120 mg/L), and nitrite (100 mg/L) by the strain were 94.13%, 92.62%, and 85.67%, and the nitrogen metabolism pathway of strain G16 was analyzed by whole genome sequencing combined with its nitrification-denitrification intermediate products, it was found that the strain had independent nitrification-denitrification ability and no nitrite accumulation. Under the conditions of carbon source of sodium succinate hexahydrate, C/N ratio of 15, pH of 7.5, temperature of 15 °C, and DO of 210 rpm, strain G16 showed excellent denitrification performance. Strain G16 was prepared into biochar-based immobilized bacterial particles, which successfully improved its nitrogen removal efficiency and stability. Therefore, the application of strain G16 in the field of real wastewater treatment has very necessary research value.
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Affiliation(s)
- Yu Gao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Junwen Zhu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Keyu Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Yong Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China.
| | - Gang Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Engineering Laboratory for Pollution Control and Waste, Utilization in Swine Production, Changsha 410128, China
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14
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Tsujino S, Masuda R, Shimizu Y, Azuma Y, Kanada Y, Fujiwara T. Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification. Antonie Van Leeuwenhoek 2023; 116:1037-1055. [PMID: 37596503 DOI: 10.1007/s10482-023-01862-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.
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Affiliation(s)
- Shuhei Tsujino
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo, 060-8638, Japan
| | - Ryota Masuda
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yoshiyuki Shimizu
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yuichi Azuma
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yutaro Kanada
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Taketomo Fujiwara
- Department of Environment and Energy Systems, Graduate School of Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Biological Sciences, Faculty of Science, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oh-ya, Suruga-ku, Shizuoka, 422-8529, Japan.
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15
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Khanthong K, Jang H, Kadam R, Jo S, Lee J, Park J. Bioelectrochemical system for nitrogen removal: Fundamentals, current status, trends, and challenges. CHEMOSPHERE 2023; 339:139776. [PMID: 37567277 DOI: 10.1016/j.chemosphere.2023.139776] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Biological nitrogen removal (BNR) is essential for the treatment of nitrogen-containing wastewater. However, the requirement for aeration and the addition of external carbon sources, resulting in greenhouse gas emissions and additional costs, are disadvantages of the traditional BNR process. Alternative technologies have been devised to overcome these drawbacks. Bioelectrochemical nitrogen removal (BENR) has been proposed for efficient nitrogen removal, demonstrating flexibility and versatility. BENR can be performed by combining nitrification, denitrification, anaerobic ammonium oxidation (ANAMMOX), or organic carbon oxidation. Bioelectrochemical-ANAMMOX (BE-ANAMMOX) is the most promising method for nitrogen removal, as it can directly convert NH4+ to N2 and H2 in one step when the electrode is arranged as an electron acceptor. High-value-added hydrogen can potentially be recovered with efficient nitrogen removal using this concept, maximizing the benefits of BENR. Using alternative electron acceptors, such as electrodes and metal ions, for complete total nitrogen removal is a promising technology to substitute NO2- production from NH4+ oxidation by aeration. However, the requirement of electron donors for NO3- reduction, low NH4+ removal efficiency, and low competitiveness of exoelectrogenic bacteria still remain the main obstacles. The future direction for successful BENR should aim to achieve complete anaerobic NH4+ oxidation without any electron acceptor and to maximize selectivity in H2 production. Therefore, the bioelectrochemical pathways and balances between efficient nitrogen removal and high-value-added chemical production should be further studied for carbon and energy neutralities.
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Affiliation(s)
- Kamonwan Khanthong
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea.
| | - Heewon Jang
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Rahul Kadam
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Sangyeol Jo
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Jonghwa Lee
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea
| | - Jungyu Park
- Department of Advanced Energy Engineering, Chosun University, Gwangju, 61457, Republic of Korea.
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16
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Xie Y, Tian X, Liu Y, Zhao K, Li Y, Luo K, Wang B, Dong S. Nitrogen removal capability and mechanism of a novel heterotrophic nitrifying-aerobic denitrifying strain H1 as a potential candidate in mariculture wastewater treatment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:106366-106377. [PMID: 37728674 DOI: 10.1007/s11356-023-29666-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
The nitrogen removal performance and mechanisms of Bacillus subtilis H1 isolated from a mariculture environment were investigated. Strain H1 efficiently removed NH4+-N, NO2--N, and NO3--N in simulated wastewater with removal efficiencies of 85.61%, 90.58%, and 57.82%, respectively. Strain H1 also efficiently degraded mixed nitrogen (NH4+-N mixed with NO2--N and/or NO3--N) and had removal efficiencies ranging from 82.39 to 89.54%. Nitrogen balance analysis revealed that inorganic nitrogen was degraded by heterotrophic nitrification-aerobic denitrification (HN-AD) and assimilation. 15N isotope tracing indicated that N2O was the product of the HN-AD process, while N2 as the final product was only detected during the reduction of 15NO2--N. The nitrogen assimilation and dissimilation pathways by strain H1 were further clarified using complete genome sequencing, nitrification inhibitor addition, and enzymatic activity measurement, and the ammonium oxidation process was speculated as NH4+ → NH2OH → NO → N2O. These results showed the application prospect of B. subtilis H1 in treating mariculture wastewater.
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Affiliation(s)
- Yumeng Xie
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China.
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kun Zhao
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Yongmei Li
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Bo Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
| | - Shuanglin Dong
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Yushan Road 5, Qingdao, 266000, People's Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, People's Republic of China
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17
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Pedrosa-Silva F, Venancio TM. Comparative Genomics Reveals Novel Species and Insights into the Biotechnological Potential, Virulence, and Resistance of Alcaligenes. Genes (Basel) 2023; 14:1783. [PMID: 37761923 PMCID: PMC10530903 DOI: 10.3390/genes14091783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Alcaligenes is a cosmopolitan bacterial genus that exhibits diverse properties which are beneficial to plants. However, the genomic versatility of Alcaligenes has also been associated with the ability to cause opportunistic infections in humans, raising concerns about the safety of these microorganisms in biotechnological applications. Here, we report an in-depth comparative analysis of Alcaligenes species using all publicly available genomes to investigate genes associated with species, biotechnological potential, virulence, and resistance to multiple antibiotics. Phylogenomic analysis revealed that Alcaligenes consists of at least seven species, including three novel species. Pan-GWAS analysis uncovered 389 species-associated genes, including cold shock proteins (e.g., cspA) and aquaporins (e.g., aqpZ) found exclusively in the water-isolated species, Alcaligenes aquatilis. Functional annotation of plant-growth-promoting traits revealed enrichment of genes for auxin biosynthesis, siderophores, and organic acids. Genes involved in xenobiotic degradation and toxic metal tolerance were also identified. Virulome and resistome profiles provide insights into selective pressures exerted in clinical settings. Taken together, the results presented here provide the grounds for more detailed clinical and ecological studies of the genus Alcaligenes.
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Affiliation(s)
| | - Thiago M. Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, Brazil;
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18
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Wang T, Chen M, Zhu J, Li N, Wang X. Anodic ammonium oxidation in microbial electrolysis cell: Towards nitrogen removal in low C/N environment. WATER RESEARCH 2023; 242:120276. [PMID: 37392506 DOI: 10.1016/j.watres.2023.120276] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023]
Abstract
Biological nitrogen removal in low C/N environment is challenging in wastewater treatment for a long time. Autotrophic ammonium oxidation is promising due to the no need of carbon source addition, but alternative electron acceptors other than oxygen has to be widely investigated. Recently, microbial electrolysis cell (MEC), which applies a polarized inert electrode as the electron harvester, has been proved effective to oxidize ammonium with electroactive biofilm. That is, anodic microbes stimulated by exogenous low power can extract electron from ammonium and transfer electron to electrodes. This review aims to consolidate the recent advances in anodic ammonium oxidation in MEC. Various technologies based on different functional microbes and mechanisms of these processes are reviewed. Thereafter, the crucial factors influencing the ammonium oxidation technology are discussed. Challenges and prospects of anodic ammonium oxidation in ammonium-containing wastewater treatment are also proposed to provide valuable insights on the technologic reference and potential value of MEC in ammonium-containing wastewater treatment.
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Affiliation(s)
- Tuo Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Jiaxuan Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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19
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Pous N, Bañeras L, Corvini PFX, Liu SJ, Puig S. Direct ammonium oxidation to nitrogen gas (Dirammox) in Alcaligenes strain HO-1: The electrode role. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2023; 15:100253. [PMID: 36896143 PMCID: PMC9988695 DOI: 10.1016/j.ese.2023.100253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 05/14/2023]
Abstract
It has been recently suggested that Alcaligenes use a previously unknown pathway to convert ammonium into dinitrogen gas (Dirammox) via hydroxylamine (NH2OH). This fact alone already implies a significant decrease in the aeration requirements for the process, but the process would still be dependent on external aeration. This work studied the potential use of a polarised electrode as an electron acceptor for ammonium oxidation using the recently described Alcaligenes strain HO-1 as a model heterotrophic nitrifier. Results indicated that Alcaligenes strain HO-1 requires aeration for metabolism, a requirement that cannot be replaced for a polarised electrode alone. However, concomitant elimination of succinate and ammonium was observed when operating a previously grown Alcaligenes strain HO-1 culture in the presence of a polarised electrode and without aeration. The usage of a polarised electrode together with aeration did not increase the succinate nor the nitrogen removal rates observed with aeration alone. However, current density generation was observed along a feeding batch test representing an electron share of 3% of the ammonium removed in the presence of aeration and 16% without aeration. Additional tests suggested that hydroxylamine oxidation to dinitrogen gas could have a relevant role in the electron discharge onto the anode. Therefore, the presence of a polarised electrode supported the metabolic functions of Alcaligenes strain HO-1 on the simultaneous oxidation of succinate and ammonium.
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Affiliation(s)
- Narcís Pous
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Carrer Maria Aurèlia Capmany, 69, E-17003, Girona, Spain
| | - Lluis Bañeras
- Group of Environmental Microbial Ecology, Institute of Aquatic Ecology, University of Girona, C/Maria Aurèlia Capmany, 40, E-17003, Girona, Spain
| | - Philippe F.-X. Corvini
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, 4132, Switzerland
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resource at Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sebastià Puig
- Laboratory of Chemical and Environmental Engineering (LEQUiA), Institute of the Environment, University of Girona, Carrer Maria Aurèlia Capmany, 69, E-17003, Girona, Spain
- Corresponding author.
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20
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Tang Q, Zeng M, Zou W, Jiang W, Kahaer A, Liu S, Hong C, Ye Y, Jiang W, Kang J, Ren Y, Liu D. A new strategy to simultaneous removal and recovery of nitrogen from wastewater without N 2O emission by heterotrophic nitrogen-assimilating bacterium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162211. [PMID: 36791849 DOI: 10.1016/j.scitotenv.2023.162211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/23/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Biological assimilation that recovery the nitrogen from wastewater in the form of biomass offers a more environmentally friendly solution for the limitations of the conventional wastewater treatments. This study reported the simultaneous removal and recovery of nitrogen from wastewater without N2O emission by a heterotrophic nitrogen-assimilating Acinetobacter sp. DN1 strain. Nitrogen balance, biomass qualitative analysis, genome and enzyme studies have been performed to illustrate the mechanism of nitrogen conversion by strain DN1. Results showed that the ammonium removal followed one direct pathway (GOGAT/GDH) and three indirect pathways (NH4+ → NH2OH → NO → NO2- → NH4+ → GOGAT/GDH; NH4+ → NH2OH → NO → NO2- → NO3- → NO2- → NH4+ → GOGAT/GDH; NH4+ → NH2OH → NO → NO3- → NO2- → NH4+ → GOGAT/GDH). Nitrogen balance and biomass qualitative analysis showed that over 70 % of the ammonium in the wastewater was converted into intracellular nitrogen-containing compounds and stored in the cells of strain DN1. Traditional denitrification pathway was not detected and the ammonium was removed through assimilation, which makes it more energy-saving for nitrogen recovery when compared with Haber-Bosch process. This study provides a new direction for simultaneous nitrogen removal and recovery without N2O emission by the heterotrophic nitrogen-assimilating bacterium.
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Affiliation(s)
- Qian Tang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Mengjie Zeng
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China; Wuhan Municipal Engineering Design & Research Institute Co., Ltd, No. 52 Optics Valley Avenue, Wuhan 430074, PR China
| | - Wugui Zou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Wenyu Jiang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Alimu Kahaer
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Shixi Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Chol Hong
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China; Heat Engineering Faculty, Kim Chaek University of Technology, Pyongyang 999093, Democratic People's Republic of Korea
| | - Yuanyao Ye
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Wei Jiang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Jianxiong Kang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Yongzheng Ren
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China
| | - Dongqi Liu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430074, PR China.
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21
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Pan Y, Liu DF. Tapping the Potential of Wastewater Treatment with Direct Ammonia Oxidation (Dirammox). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7106-7108. [PMID: 37114903 DOI: 10.1021/acs.est.3c02342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Yuan Pan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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22
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Huang MQ, Cui YW, Yang HJ, Xu MJ, Cui Y, Chen Z. A halophilic aerobic-heterotrophic strain Halomonas venusta SND-01: Nitrogen removal by ammonium assimilation and heterotrophic nitrification-aerobic denitrification. BIORESOURCE TECHNOLOGY 2023; 374:128758. [PMID: 36801440 DOI: 10.1016/j.biortech.2023.128758] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Nitrogen (N) removal from high-salinity wastewater is a major challenge. The aerobic-heterotrophic nitrogen removal (AHNR) process has been demonstrated to be feasible for treating hypersaline wastewater. In this study, Halomonas venusta SND-01, a halophilic strain capable of performing AHNR, was isolated from saltern sediment. The strain achieved ammonium, nitrite, and nitrate removal efficiencies of 98%, 81%, and 100%, respectively. The N balance experiment suggests that this isolate removes N mainly via assimilation. Various functional genes related to N metabolism were found in the genome of the strain, establishing a complex AHNR pathway that includes ammonium assimilation, heterotrophic nitrification-aerobic denitrification, and assimilatory nitrate reduction. Four key enzymes in the N removal process were successfully expressed. The strain exhibited high-adaptability under C/N ratios of 5-15, salinities of 2%-10% (m/v), and pH of 6.5-9.5. Therefore, the strain shows high potential for treating saline wastewater with different inorganic N compositions.
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Affiliation(s)
- Mei-Qi Huang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - You-Wei Cui
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Hou-Jian Yang
- Beijing Municipal Pollution Source Management Center, Beijing 100089, China
| | - Meng-Jiao Xu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yubo Cui
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian 116600, China
| | - Zhaobo Chen
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Dalian Minzu University, Dalian 116600, China
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23
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Hu C, Sun X, Zhang L, Wang H, Dong L, Li S. Long-term stability of reactor microbiome through bioaugmentation with Alcaligenes aquatilis AS1 promotes nitrogen removal of piggery wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117146. [PMID: 36586372 DOI: 10.1016/j.jenvman.2022.117146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Bioaugmentation is considered as an attractive method for nitrogen removal in water treatment, but its effectiveness in actual high-strength piggery wastewater has not been adequately verified and the mechanism of bioaugmentation in actual wastewater treatment system is not very clear especially from the perspectives of microbial communities and functional genes. This study investigated the mechanisms of a heterotrophic nitrifying-aerobic denitrifying strain Alcaligenes aquatilis AS1 in the bioaugmentation of continuous biological nitrogen removal of actual piggery wastewater at laboratory scale. The addition of strain AS1 significantly improved the nitrogen removal efficiency (more than 95% of NH4+-N and 75% of TN were removed) and raised the activated sludge resistance to shock loading. AS1 addition also significantly shifted the microbiota structure and interactions among microbial networks were enhanced to obtain the stable bacterial communities. Moreover, strain AS1 achieved effective proliferation and long-term colonization in activated sludge with a relative abundance of genus Alcaligenes more than 70% during the whole operation process and played a dominant role in biological nitrogen removal, while different genera were respectively enriched and involved in pollutants removal at different stages in the control group. In addition, the abundances of most functional genes involved in carbon (C) degradation, carbon fixation and nitrogen (N), phosphorus (P), sulfur (S) cycling in activated sludge were significantly increased in reactor AS1, indicating that strain AS1 not only relied on its unique C and N metabolic activities, but also recruited microorganisms with diverse functions to jointly remove pollutants in wastewater, which could be a common bioaugmentation mechanism in open reactors. This study proves the promising application prospect of strain AS1 in the treatment of high-strength piggery wastewater and shows great importance for guiding bioaugmentation application of functional strains in practical wastewater treatment systems.
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Affiliation(s)
- Chengcheng Hu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Long Zhang
- Shandong Jinniu Group Co., Ltd., Jinan, 250001, China
| | - Hongzhi Wang
- Xinjiang Herun Water Industry Co., Ltd., Urumqi, 830000, China
| | - Liang Dong
- Xinjiang Herun Water Industry Co., Ltd., Urumqi, 830000, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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24
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Xu SQ, Wang X, Xu L, Wang KX, Jiang YH, Zhang FY, Hong Q, He J, Liu SJ, Qiu JG. The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135. Environ Microbiol 2023; 25:675-688. [PMID: 36527381 DOI: 10.1111/1462-2920.16318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Microbial ammonia oxidation is vital to the nitrogen cycle. A biological process, called Dirammox (direct ammonia oxidation, NH3 →NH2 OH→N2 ), has been recently identified in Alcaligenes ammonioxydans and Alcaligenes faecalis. However, its transcriptional regulatory mechanism has not yet been fully elucidated. The present study characterized a new MocR-like transcription factor DnfR that is involved in the Dirammox process in A. faecalis strain JQ135. The entire dnf cluster was composed of 10 genes and transcribed as five transcriptional units, that is, dnfIH, dnfR, dnfG, dnfABCDE and dnfF. DnfR activates the transcription of dnfIH, dnfG and dnfABCDE genes, and represses its own transcription. The intact 1506-bp dnfR gene was required for activation of Dirammox. Electrophoretic mobility shift assays and DNase I footprinting analyses showed that DnfR has one binding site in the dnfH-dnfR intergenic region and two binding sites in the dnfG-dnfA intergenic region. Three binding sites of DnfR shared a 6-bp repeated conserved sequence 5'-GGTCTG-N17 -GGTCTG-3' which was essential for the transcription of downstream target genes. Cysteine and glutamate act as possible effectors of DnfR to activate the transcription of transcriptional units of dnfG and dnfABCDE, respectively. This study provided new insights in the transcriptional regulation mechanism of Dirammox by DnfR in A. faecalis JQ135.
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Affiliation(s)
- Si-Qiong Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xiao Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Lu Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ke-Xin Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yin-Hu Jiang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fu-Yin Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qing Hong
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jian He
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, 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
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ji-Guo Qiu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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25
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Quach NT, Loan TT, Nguyen TTA, Nguyen Vu TH, Pham QA, Chu HH, Phi QT, Thuoc DV. Phenotypic and genomic characterization provide new insights into adaptation to environmental stressors and biotechnological relevance of mangrove Alcaligenes faecalis D334. Res Microbiol 2023; 174:103994. [PMID: 36240959 DOI: 10.1016/j.resmic.2022.103994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/07/2022]
Abstract
Alcaligenes faecalis D334 was determined in this study as a salt-tolerant bacterium isolated from mangrove sediment. In response to 6% (w/v) NaCl, strain D334 produced the highest ectoines of 14.14 wt%. To understand adaptive features to mangrove environment, strain D334 was sequenced using Pacific BioScience platform, resulting in a circular chromosome of 4.23 Mb. Of note, D334 genome harbored 81 salt-responsive genes, among which two membrane-associated genes ompc and eric were absent in 3 selected A. faecalis genomes. Apart from that, a complete pathway for ectoine and 5-hydroxyectoine synthesis was predicted. To resist 40 mM H2O2, 46 genetic determinants contributing to oxidative stress response were employed. Moreover, two operons involved in polyhydroxyalkanoate (PHA) production were identified in the D334 genome, resulting in maximum PHA content of 5.03 ± 0.04 wt% and PHA concentration of 0.13 ± 0.001 g/L. A large flagellar biosynthesis operon contributing to swimming motility was found to be conserved in D334 and 8 other A. faecalis genomes. These findings shed light for the first time on the high versatility of A. faecalis D334 genome to adapt to mangrove lifestyle and the possibility to develop D334 as an industrial platform for PHA and 5-hydroxyectoine production.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Tran Thi Loan
- Department of Microbiology, Faculty of Biology, University of Science, Vietnam National University, Hanoi (VNU), Hanoi 100000, Viet Nam; Department of Biotechnology and Microbiology, Faculty of Biology, Hanoi National University of Education, Hanoi 100000, Viet Nam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Quynh Anh Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam
| | - Quyet-Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 100000, Viet Nam.
| | - Doan Van Thuoc
- Department of Biotechnology and Microbiology, Faculty of Biology, Hanoi National University of Education, Hanoi 100000, Viet Nam.
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26
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Xu T, Song S, Ren B, Li J, Yang J, Bai L, Piao Z. Fungus Pichia kudriavzevii XTY1 and heterotrophic nitrifying bacterium Enterobacter asburiae GS2 cannot efficiently transform organic nitrogen via hydroxylamine and nitrite. Front Microbiol 2022; 13:1038599. [PMID: 36569078 PMCID: PMC9772036 DOI: 10.3389/fmicb.2022.1038599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Heterotrophic nitrification is a process of organic nitrogen degradation completed by the participation of heterotrophic nitrifying microorganisms, which can accelerate the nitrogen transformation process. However, the current research mainly focuses on heterotrophic nitrifying bacteria and their ammonium degradation capacities. And there is little accumulation of research on fungi, the main force of heterotrophic nitrification, and their capacities to transform organic nitrogen. In this study, novel heterotrophic nitrifying fungus (XTY1) and bacterium (GS2) were screened and isolated from upland soil, and the strains were identified and registered through GenBank comparison. After 24 h single nitrogen source tests and 15N labeling tests, we compared and preliminarily determined the heterotrophic nitrification capacities and pathways of the two strains. The results showed that XTY1 and GS2 had different transformation capacities to different nitrogen substrates and could efficiently transform organic nitrogen. However, the transformation capacity of XTY1 to ammonium was much lower than that of GS2. The two strains did not pass through NH2OH and NO2 - during the heterotrophic nitrification of organic nitrogen, and mainly generated intracellular nitrogen and low N2O. Other novel organic nitrogen metabolism pathways may be existed, but they remain to be further validated.
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Lee YJ, Lin BL, Lei Z. Nitrous oxide emission mitigation from biological wastewater treatment - A review. BIORESOURCE TECHNOLOGY 2022; 362:127747. [PMID: 35964917 DOI: 10.1016/j.biortech.2022.127747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide (N2O) emitted from wastewater treatment processes has emerged as a focal point for academic and practical research amidst pressing environmental issues. This review presents an updated view on the biological pathways for N2O production and consumption in addition to the critical process factors affecting N2O emission. The current research trends including the strain and reactor aspects were then outlined with discussions. Last but not least, the research needs were proposed. The holistic life cycle assessment needs to be performed to evaluate the technical and economic feasibility of the proposed mitigation strategies or recovery options. This review also provides the background information for the proposed future research prospects on N2O mitigation and recovery technologies. As pointed out, dilution effects of the produced N2O gas product would hinder its use as renewable energy; instead, its use as an effective oxidizing agent is proposed as a promising recovery option.
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Affiliation(s)
- Yu-Jen Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10649, Taiwan
| | - Bin-le Lin
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Zhongfang Lei
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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28
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Wu MR, Miao LL, Liu Y, Qian XX, Hou TT, Ai GM, Yu L, Ma L, Gao XY, Qin YL, Zhu HZ, Du L, Li SY, Tian CL, Li DF, Liu ZP, Liu SJ. Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N 2. J Biol Chem 2022; 298:102372. [PMID: 35970391 PMCID: PMC9478400 DOI: 10.1016/j.jbc.2022.102372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrogen (N2) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed “Dirammox” (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N2. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of 15N-labeled hydroxylamine to 15N2. This conversion did not happen under oxygen (O2)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a Km of 92.9 ± 3.0 μM for hydroxylamine and a kcat of 0.028 ± 0.001 s−1. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N2.
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Affiliation(s)
- Meng-Ru Wu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Qian
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting-Ting Hou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lu Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Xi-Yan Gao
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Ya-Ling Qin
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Sheng-Ying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China
| | - Chang-Lin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China; The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, and Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, 230026, Hefei, Anhui, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, China 100049; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266273, China.
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29
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Gao XY, Xie W, Liu Y, Ma L, Liu ZP. Alcaligenes ammonioxydans HO-1 antagonizes Bacillus velezensis via hydroxylamine-triggered population response. Front Microbiol 2022; 13:920052. [PMID: 35935184 PMCID: PMC9355588 DOI: 10.3389/fmicb.2022.920052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Antagonism is a common behavior seen between microbes in nature. Alcaligenes ammonioxydans HO-1 converts ammonia to nitrogen under aerobic conditions, which leads to the accumulation of extracellular hydroxylamine (HA), providing pronounced growth advantages against many bacterial genera, including Bacillus velezensis V4. In contrast, a mutant variant of A. ammonioxydans, strain 2-29, that cannot produce HA fails to antagonize other bacteria. In this article, we demonstrate that cell-free supernatants derived from the antagonistic HO-1 strain were sufficient to reproduce the antagonistic behavior and the efficiency of this inhibition correlated strongly with the HA content of the supernatant. Furthermore, reintroducing the capacity to produce HA to the 2-29 strain or supplementing bacterial co-cultures with HA restored antagonistic behavior. The HA-mediated antagonism was dose-dependent and affected by the temperature, but not by pH. HA caused a decline in biomass, cell aggregation, and hydrolysis of the cell wall in exponentially growing B. velezensis bulk cultures. Analysis of differential gene expression identified a series of genes modulating multicellular behavior in B. velezensis. Genes involved in motility, chemotaxis, sporulation, polypeptide synthesis, and non-ribosomal peptide synthesis were all significantly downregulated in the presence of HA, whereas autolysis-related genes showed upregulation. Taken together, these findings indicate that HA affects the population response of coexisting strains and also suggest that A. ammonioxydans HO-1 antagonize other bacteria by producing extracellular HA that, in turn, acts as a signaling molecule.
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Affiliation(s)
- Xi-Yan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhi-Pei Liu
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Cao X, Zhao B, Wu Y, Huang J, Wang H, Sun X, Li S. Characterization of Alcaligenes aquatilis as a novel member of heterotrophic nitrifier-aerobic denitrifier and its performance in treating piggery wastewater. BIORESOURCE TECHNOLOGY 2022; 354:127176. [PMID: 35439558 DOI: 10.1016/j.biortech.2022.127176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
A novel strain AS1 with heterotrophic nitrifying-aerobic denitrifying capacity in the species of Alcaligenes aquatilis was isolated from the aerobic activated sludge. It showed a great capability of ammonia removal, and the aerobic metabolic pathways to yield gaseous-nitrogen by hydroxylamine oxidation and nitrite denitrification were proposed. AS1 could efficiently remove ammonia under a wide range of environmental conditions, including the ratio of chemical oxygen demand to total nitrogen: 15-30, pH: 6-10, NaCl: 0-60 g/L, shaking speed of 0-180 rpm, and succinate, acetate, or citrate as carbon source. In the treatment of actual piggery wastewater, 95.3%, 95.1% and 84.9% of NH4+-N was removed by AS1 when the initial ammonia concentration was 500, 1300, and 2000 mg/L, respectively, with the maximum NH4+-N removal rate of 30.5 mg/L/h and 569.7 mg/L/d. Furthermore, plate colony-counting showed that AS1 achieved an efficient proliferation. These results imply the application potential of AS1 in treating high-ammonia wastewater.
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Affiliation(s)
- Xianhe Cao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binhan Zhao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongming Wu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Jun Huang
- Shandong Jinniu Group Company Limited, Jinan 250001, China
| | - Hongzhi Wang
- Xinjiang Herun Water Industry Company Limited, Urumqi 830000, China
| | - Xianyun Sun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaojie Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330096, China.
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Hou TT, Miao LL, Peng JS, Ma L, Huang Q, Liu Y, Wu MR, Ai GM, Liu SJ, Liu ZP. Dirammox Is Widely Distributed and Dependently Evolved in Alcaligenes and Is Important to Nitrogen Cycle. Front Microbiol 2022; 13:864053. [PMID: 35633697 PMCID: PMC9136411 DOI: 10.3389/fmicb.2022.864053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrogen cycle is an essential process for environmental health. Dirammox (direct ammonia oxidation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes. Under 20% O2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal–plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.
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Affiliation(s)
- Ting-Ting Hou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Li-Li Miao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ji-Sen Peng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lan Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Meng-Ru Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Zhi-Pei Liu,
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Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N 2 and MocR-like Transcriptional Regulator DnfR in Alcaligenes faecalis JQ135. Appl Environ Microbiol 2022; 88:e0226121. [PMID: 35108103 DOI: 10.1128/aem.02261-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ammonia oxidation is an important process of both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH3→NH2OH→N2) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes and its genetic regulation remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N2 via NH2OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N2 in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N2O and trace amounts of N2 with nitrite as sole nitrogen source. Deletion of genes nirK and nosZ that are essential for denitrification did not impair the capability of JQ135 to oxidize ammonia to N2 (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 5'-TGGTCTGT-3' in the promotor region. Bioinformatic survey showed that homologs to dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that besides A. ammonioxydans, Dirammox also occurs in other bacteria, and is regulated by the MocR-family transcriptional regulator DnfR. Importance Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previous known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation (Anammox), and complete ammonia oxidation (Comammox)) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N2 (Dirammox), has been identified in the heterotrophic bacterium Alcaligenes ammonioxydans HO-1. This paper shows that in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by dnf genes, which are independent of the denitrification pathway. Bioinformatic survey suggests that homologs to dnf genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N2.
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