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Hu P, Qian Y, Xu Y, Radian A, Yang Y, Gu JD. A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system. WATER RESEARCH X 2024; 24:100237. [PMID: 39155949 PMCID: PMC11327836 DOI: 10.1016/j.wroa.2024.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/29/2024] [Accepted: 07/09/2024] [Indexed: 08/20/2024]
Abstract
Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.
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Affiliation(s)
- Pengfei Hu
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Youfen Qian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
| | - Yanbin Xu
- School of Environmental Sciences and Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Adi Radian
- Civil and Environmental Engineering, Technion – Israel Institute of Technology, Haifa 320003, Israel
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong 510275, People’s Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People’s Republic of China
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Zhao Z, Zhao Y, Marotta F, Xamxidin M, Li H, Xu J, Hu B, Wu M. The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau. Front Microbiol 2024; 15:1424368. [PMID: 39132143 PMCID: PMC11312105 DOI: 10.3389/fmicb.2024.1424368] [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: 04/27/2024] [Accepted: 06/18/2024] [Indexed: 08/13/2024] Open
Abstract
The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.
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Affiliation(s)
- Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yuxiang Zhao
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Federico Marotta
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Huan Li
- Lab of Plateau Ecology and Nature Conservation, The Altun Mountain National Nature Reserve, Xinjiang, China
| | - Junquan Xu
- Lab of Plateau Ecology and Nature Conservation, The Altun Mountain National Nature Reserve, Xinjiang, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
| | - Min Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
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3
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Zhao ZC, Fan SQ, Lu Y, Tan X, Liu LY, Wang XW, Liu BF, Xing DF, Ren NQ, Xie GJ. Deep insights into the biofilm formation mechanism and nitrogen-transformation network in a nitrate-dependent anaerobic methane oxidation biofilm. ENVIRONMENTAL RESEARCH 2024; 252:118810. [PMID: 38552829 DOI: 10.1016/j.envres.2024.118810] [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: 02/03/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) process offers a promising solution for simultaneously achieving methane emissions reduction and efficient nitrogen removal in wastewater treatment. Although nitrogen removal at a practical rate has been achieved by n-DAMO biofilm process, the mechanisms of biofilm formation and nitrogen transformation remain to be elucidated. In this study, n-DAMO biofilms were successfully developed in the membrane aerated moving bed biofilm reactor (MAMBBR) and removed nitrate at a rate of 159 mg NO3--N L-1 d-1. The obvious increase in the content of extracellular polymeric substances (EPS) indicated that EPS production was important for biofilm development. n-DAMO microorganisms dominated the microbial community, and n-DAMO bacteria were the most abundant microorganisms. However, the expression of biosynthesis genes for proteins and polysaccharides encoded by n-DAMO archaea was significantly more active compared to other microorganisms, suggesting the central role of n-DAMO archaea in EPS production and biofilm formation. In addition to nitrate reduction, n-DAMO archaea were revealed to actively express dissimilatory nitrate reduction to ammonium and nitrogen fixation. The produced ammonium was putatively converted to dinitrogen gas through the joint function of n-DAMO archaea and n-DAMO bacteria. This study revealed the biofilm formation mechanism and nitrogen-transformation network in n-DAMO biofilm systems, shedding new light on promoting the application of n-DAMO process.
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Affiliation(s)
- Zhi-Cheng Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lu-Yao Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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4
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Downs DM, Poole RK. Interpreting the role of antioxidants in vivo: A cautionary tale. Mol Microbiol 2024; 122:129-132. [PMID: 38960396 PMCID: PMC11260230 DOI: 10.1111/mmi.15292] [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: 06/13/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
Bacteria have a remarkable ability to sense environmental stresses and to respond to these stressors by adapting their metabolism and physiology. In recent publications, investigators have suggested that multiple stresses that cause cell death share the mechanistic feature of stimulating the formation of reactive oxygen species (ROS). A central piece of evidence cited in these claims is the ability of exogenous antioxidant compounds to mitigate stress-related cell death. The validity of attributing a positive effect of exogenous antioxidants to ROS-mediated stress is challenged by an important study by Korshunov and Imlay in this issue of Molecular Microbiology. This study reports biochemical data that convincingly show that some commonly used antioxidants quench oxidants orders of magnitude too slowly to have a significant effect on the concentration of ROS in the cell. Under conditions where antioxidants minimize cell death, they also slow growth. Significantly, slowing cell growth by other means has the same restorative effect as adding an antioxidant. Based on the solid biochemical and genetic data, Korshunov and Imlay make the case for discarding the use of antioxidants to diagnose conditions that generate increased internal ROS production.
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Affiliation(s)
- Diana M. Downs
- Department of Microbiology, University of Georgia, Athens, GA
| | - Robert K Poole
- School of Biosciences, University of Sheffield, Sheffield, UK
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5
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Chrysochoidis V, Andersen MH, Remigi EU, Faragó M, Smets BF, Domingo-Félez C, Valverde-Pérez B. Critical evaluation of different mass transfer equations to model N 2O emissions from water resource recovery facilities with diffuse aeration. ENVIRONMENTAL TECHNOLOGY 2024; 45:3339-3353. [PMID: 37191950 DOI: 10.1080/09593330.2023.2215454] [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: 12/23/2022] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
N2O measurements by liquid sensors in aerated tanks are an input to gas-liquid mass-transfer models for the prediction of N2O off-gas emissions. The prediction of N2O emissions from Water Resource Recovery Facilities (WRRFs) was evaluated by three different mass-transfer models using Benchmark Simulation Model 1 (BSM1) as a reference model. Inappropriate selection of mass-transfer model may result in miscalculation of carbon footprints based on soluble N2O online measurements. The film theory considers a constant mass-transfer expression, while more complex models suggest that emissions are affected by the aeration type, efficiency, and tank design characteristics. The differences among model predictions were 10-16% at dissolved oxygen (DO) concentration of 0.6 g/m3, when biological N2O production was the highest, while the flux of N2O was 20.0-24 kg N2O-N/d. At lower DO, the nitrification rate was low, while at DO higher than 2 g/m3, the N2O production was reduced leading to higher rates of complete nitrification and a flux of 5 kg N2O-N/d. The differences increased to 14-26% in deeper tanks, due to the pressure assumed in the tanks. The predicted emissions are also affected by the aeration efficiency when KLaN2O depends on the airflow instead of the KLaO2. Increasing the nitrogen loading rate under DO concentration of 0.50-0.65 g/m3 increased the differences in predictions by 10-20% in both alpha 0.6 and 1.2. A sensitivity analysis indicated that the selection of different mass-transfer models did not affect the selection of biochemical parameters for N2O model calibration.
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Affiliation(s)
| | | | | | - Maria Faragó
- Climate Adaptation and Green Infrastructure, Ramboll, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Denmark
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
- Infrastructure and Environment, School of Engineering, University of Glasgow, University Avenue, Glasgow, UK
| | - Borja Valverde-Pérez
- Department of Environmental Engineering, Technical University of Denmark, Miljøvej, Denmark
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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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7
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Beeckman F, Annetta L, Corrochano-Monsalve M, Beeckman T, Motte H. Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition. Trends Microbiol 2024; 32:590-601. [PMID: 37973432 DOI: 10.1016/j.tim.2023.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Laure Annetta
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Departamento de Genética, Antropología Física y Fisiología Animal, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Leioa, Spain; Instituto Multidisciplinar Para el Estudio del Medio 'Ramon Margalef', Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Spain
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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Luo L, Cohan DS, Gurung RB, Venterea RT, Ran L, Benson V, Yuan Y. Impacts assessment of nitrification inhibitors on U.S. agricultural emissions of reactive nitrogen gases. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:121043. [PMID: 38723497 PMCID: PMC11261242 DOI: 10.1016/j.jenvman.2024.121043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
Fertilizer-intensive agriculture leads to emissions of reactive nitrogen (Nr), posing threats to climate via nitrous oxide (N2O) and to air quality and human health via nitric oxide (NO) and ammonia (NH3) that form ozone and particulate matter (PM) downwind. Adding nitrification inhibitors (NIs) to fertilizers can mitigate N2O and NO emissions but may stimulate NH3 emissions. Quantifying the net effects of these trade-offs requires spatially resolving changes in emissions and associated impacts. We introduce an assessment framework to quantify such trade-off effects. It deploys an agroecosystem model with enhanced capabilities to predict emissions of Nr with or without the use of NIs, and a social cost of greenhouse gas to monetize the impacts of N2O on climate. The framework also incorporates reduced-complexity air quality and health models to monetize associated impacts of NO and NH3 emissions on human health downwind via ozone and PM. Evaluation of our model against available field measurements showed that it captured the direction of emission changes but underestimated reductions in N2O and overestimated increases in NH3 emissions. The model estimated that, averaged over applicable U.S. agricultural soils, NIs could reduce N2O and NO emissions by an average of 11% and 16%, respectively, while stimulating NH3 emissions by 87%. Impacts are largest in regions with moderate soil temperatures and occur mostly within two to three months of N fertilizer and NI application. An alternative estimate of NI-induced emission changes was obtained by multiplying the baseline emissions from the agroecosystem model by the reported relative changes in Nr emissions suggested from a global meta-analysis: -44% for N2O, -24% for NO and +20% for NH3. Monetized assessments indicate that on an annual scale, NI-induced harms from increased NH3 emissions outweigh (8.5-33.8 times) the benefits of reducing NO and N2O emissions in all agricultural regions, according to model-based estimates. Even under meta-analysis-based estimates, NI-induced damages exceed benefits by a factor of 1.1-4. Our study highlights the importance of considering multiple pollutants when assessing NIs, and underscores the need to mitigate NH3 emissions. Further field studies are needed to evaluate the robustness of multi-pollutant assessments.
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Affiliation(s)
- Lina Luo
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA
| | - Daniel S Cohan
- Department of Civil and Environmental Engineering, Rice University, Houston, TX 77005, USA.
| | - Ram B Gurung
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Rodney T Venterea
- Soil and Water Management Research Unit, USDA-ARS, St. Paul, MN 55108, USA
| | - Limei Ran
- Nature Resources Conservation Service, United States Department of Agriculture, Greensboro, NC 27401, USA
| | | | - Yongping Yuan
- US Environmental Protection Agency, Office of Research and Development, Research Triangle Park, NC, 27711, USA
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9
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Zhang M, He T, Wu Q, Chen M, Liang X. Hydroxylamine supplementation accelerated the rates of cell growth, aerobic denitrification and nitrous oxide emission of Pseudomonas taiwanensis EN-F2. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120826. [PMID: 38608579 DOI: 10.1016/j.jenvman.2024.120826] [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: 12/09/2023] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Hydroxylamine can disrupt the protein translation process of most reported nitrogen-converting bacteria, and thus hinder the reproduction of bacteria and nitrogen conversion capacity. However, the effect of hydroxylamine on the denitrification ability of strain EN-F2 is unclear. In this study, the cell growth, aerobic denitrification ability, and nitrous oxide (N2O) emission by Pseudomonas taiwanensis were carefully investigated by addition of hydroxylamine at different concentrations. The results demonstrated that the rates of nitrate and nitrite reduction were enhanced by 2.51 and 2.78 mg/L/h after the addition of 8.0 and 12.0 mg/L hydroxylamine, respectively. The N2O production from nitrate and nitrite reaction systems were strongly promoted by 4.39 and 8.62 mg/L, respectively, through the simultaneous acceleration of cell growth and both of nitrite and nitrate reduction. Additionally, the enzymatic activities of nitrate reductase and nitrite reductase climbed from 0.13 and 0.01 to 0.22 and 0.04 U/mg protein when hydroxylamine concentration increased from 0 to 6.0 and 12.0 mg/L. This may be the main mechanism for controlling the observed higher denitrification rate and N2O release. Overall, hydroxylamine supplementation supported the EN-F2 strain cell growth, denitrification and N2O emission rates.
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Affiliation(s)
- Manman Zhang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China.
| | - Qifeng Wu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Mengping Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Xiwen Liang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science, Guizhou University, Guiyang, 550025, Guizhou Province, China
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10
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Welle M, Niether W, Stöhr C. The underestimated role of plant root nitric oxide emission under low-oxygen stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1290700. [PMID: 38379951 PMCID: PMC10876902 DOI: 10.3389/fpls.2024.1290700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024]
Abstract
The biotic release of nitric oxide (NO), a greenhouse gas, into the atmosphere contributes to climate change. In plants, NO plays a significant role in metabolic and signaling processes. However, little attention has been paid to the plant-borne portion of global NO emissions. Owing to the growing significance of global flooding events caused by climate change, the extent of plant NO emissions has been assessed under low-oxygen conditions for the roots of intact plants. Each examined plant species (tomato, tobacco, and barley) exhibited NO emissions in a highly oxygen-dependent manner. The transfer of data obtained under laboratory conditions to the global area of farmland was used to estimate possible plant NO contribution to greenhouse gas budgets. Plant-derived and stress-induced NO emissions were estimated to account for the equivalent of 1 to 9% of global annual NO emissions from agricultural land. Because several stressors induce NO formation in plants, the actual impact may be even higher.
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Affiliation(s)
- Marcel Welle
- Plant Physiology, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
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11
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Zhang S, Li C, Lv H, Cui B, Zhou D. Anammox activity improved significantly by the cross-fed NO from ammonia-oxidizing bacteria and denitrifying bacteria to anammox bacteria. WATER RESEARCH 2024; 249:120986. [PMID: 38086204 DOI: 10.1016/j.watres.2023.120986] [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: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Nitric oxide (NO) has been suggested as an obligate intermediate in anaerobic ammonium oxidation (anammox), nitrification and denitrification. At the same time, ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (DNB) are always existed in anammox flora, so what is the role of NO produced from AOB and DNB? Could it accelerate nitrogen removal via the anammox pathway with NO as an electron acceptor? To investigate this hypothesis, nitrogen transforming of an anammox biofilter was analyzed, functional gene expression of anammox bacteria (AnAOB), AOB and DNB were compared, and NO source was verified. For anammox biofilter, anammox contributed to 91.3 % nitrogen removal with only 14.4 % of AnAOB being enriched, while DNB was dominant. Meta-omics analysis and batch test results indicated that AOB could provide NO to AnAOB, and DNB also produced NO via up-regulating nirS/K and down-regulating nor. The activation of the anammox pathway of NH4++NO→N2 caused the downregulation of nirS and nxr in Ca. Kuenenia stuttgartiensis. Additionally, changes in nitrogen transforming pathways affected the electron generation and transport, limiting the carbon metabolism of AnAOB. This study provided new insights into improving nitrogen removal of the anammox system.
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Affiliation(s)
- Sixin Zhang
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Chunrui Li
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Han Lv
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, School of Environment, Northeast Normal University, Changchun, 130117, China
| | - Bin Cui
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, School of Environment, Northeast Normal University, Changchun, 130117, China.
| | - Dandan Zhou
- Engineering Research Center of Low-Carbon Treatment and Green Development of Polluted Water in Northeast China, Ministry of Education, School of Environment, Northeast Normal University, Changchun, 130117, China.
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12
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Ma X, Feng ZT, Zhou JM, Sun YJ, Zhang QQ. Regulation mechanism of hydrazine and hydroxylamine in nitrogen removal processes: A Comprehensive review. CHEMOSPHERE 2024; 347:140670. [PMID: 37951396 DOI: 10.1016/j.chemosphere.2023.140670] [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: 07/20/2023] [Revised: 10/09/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
As the new fashioned nitrogen removal process, short-cut nitrification and denitrification (SHARON) process, anaerobic ammonium oxidation (anammox) process, completely autotrophic nitrogen removal over nitrite (CANON) process, partial nitrification and anammox (PN/A) process and partial denitrification and anammox (PD/A) process entered into the public eye due to its advantages of high nitrogen removal efficiency (NRE) and low energy consumption. However, the above process also be limited by long-term start-up time, unstable operation, complicated process regulation and so on. As intermediates or by-metabolites of functional microorganisms in above processes, hydroxylamine (NH2OH) and hydrazine (N2H4) improved NRE of the above processes by promoting functional enzyme activity, accelerating electron transport efficiency and regulating distribution of microbial communities. Therefore, this review discussed effects of NH2OH and N2H4 on stability and NRE of above processes, analyzed regulatory mechanism from functional enzyme activity, electron transport efficiency and microbial community distribution. Finally, the challenges and limitations for nitric oxide (NO) and nitrous oxide (N2O) produced from regulation of NH2OH and N2H4 are discussed. In additional, perspectives on future trends in technology development are proposed.
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Affiliation(s)
- Xin Ma
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China
| | - Ze-Tong Feng
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China
| | - Jia-Min Zhou
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China
| | - Ying-Jun Sun
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China
| | - Qian-Qian Zhang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region of the Ministry of Education, Chang'an University, Xi'an, 710054, China; Key Laboratory of Eco-hydrology and Water Security in Arid and Semi-arid Regions of Ministry of Water Resources, Chang'an University, Xi'an, 710054, China.
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13
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Pold G, Bonilla-Rosso G, Saghaï A, Strous M, Jones CM, Hallin S. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME COMMUNICATIONS 2024; 4:ycae020. [PMID: 38584645 PMCID: PMC10999283 DOI: 10.1093/ismeco/ycae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 04/09/2024]
Abstract
The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.
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Affiliation(s)
- Grace Pold
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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14
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Wang JF, Huang JW, Cai ZX, Li QS, Sun YY, Zhou HZ, Zhu H, Song XS, Wu HM. Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms. ENVIRONMENT INTERNATIONAL 2024; 183:108369. [PMID: 38070437 DOI: 10.1016/j.envint.2023.108369] [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: 07/25/2023] [Revised: 11/26/2023] [Accepted: 12/03/2023] [Indexed: 01/25/2024]
Abstract
Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4+-N or NO3--N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3--N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m2·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4+-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m2·h)). Furthermore, NH4+-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4+-N or NO3--N at different COD/N ratios.
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Affiliation(s)
- Jun-Feng Wang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jia-Wei Huang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ze-Xiang Cai
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Qu-Sheng Li
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yun-Yun Sun
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Huan-Zhan Zhou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Xin-Shan Song
- State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile Industry, College of Environmental Science and Engineering, Donghua University, Shanghai 201600, China
| | - Hai-Ming Wu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China.
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15
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Oshiki M, Saito T, Nakaya Y, Satoh H, Okabe S. Growth of the Nitrosomonas europaea cells in the biofilm and planktonic growth mode: Responses of extracellular polymeric substances production and transcriptome. J Biosci Bioeng 2023; 136:430-437. [PMID: 37925312 DOI: 10.1016/j.jbiosc.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 11/06/2023]
Abstract
Nitrosomonas europaea, an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
| | - Takahiro Saito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Yuki Nakaya
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
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16
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [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: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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17
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Chamba G, Rissanen M, Barthelmeß T, Saiz-Lopez A, Rose C, Iyer S, Saint-Macary A, Rocco M, Safi K, Deppeler S, Barr N, Harvey M, Engel A, Dunne E, Law CS, Sellegri K. Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific. Proc Natl Acad Sci U S A 2023; 120:e2308696120. [PMID: 37991941 PMCID: PMC10691324 DOI: 10.1073/pnas.2308696120] [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: 05/25/2023] [Accepted: 10/04/2023] [Indexed: 11/24/2023] Open
Abstract
Our understanding of ocean-cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air-sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.
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Affiliation(s)
- Guillaume Chamba
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Matti Rissanen
- Aerosol Physics Laboratory, Faculty of Engineering and Natural Sciences, University of Tampere, Tampere33720, Finland
- Chemistry Department, Molecular Research Unit, University of Helsinki, Helsinki00014, Finland
| | - Theresa Barthelmeß
- Research Center for Marine Geosciences, Helmholtz Centre for Ocean Research Kiel, Kiel24105, Germany
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Blas Cabrera, Consejo Superior de Investigaciones Científicas, Madrid28006, Spain
| | - Clémence Rose
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Siddharth Iyer
- Aerosol Physics Laboratory, Faculty of Engineering and Natural Sciences, University of Tampere, Tampere33720, Finland
| | - Alexia Saint-Macary
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
- Department of Marine Sciences, University of Otago, Dunedin9016, New Zealand
| | - Manon Rocco
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
| | - Karl Safi
- National Institute of Water and Atmospheric Research, Hamilton3216, New Zealand
| | - Stacy Deppeler
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Neill Barr
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Mike Harvey
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
| | - Anja Engel
- Research Center for Marine Geosciences, Helmholtz Centre for Ocean Research Kiel, Kiel24105, Germany
| | - Erin Dunne
- Commonwealth Scientific and Industrial Research Organisation Environment, AspendaleVIC3195, Australia
| | - Cliff S. Law
- National Institute of Water and Atmospheric Research, Wellington6021, New Zealand
- Department of Marine Sciences, University of Otago, Dunedin9016, New Zealand
| | - Karine Sellegri
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, Clermont-FerrandF-63000, France
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18
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Beeckman F, Drozdzecki A, De Knijf A, Corrochano-Monsalve M, Bodé S, Blom P, Goeminne G, González-Murua C, Lücker S, Boeckx P, Stevens CV, Audenaert D, Beeckman T, Motte H. Drug discovery-based approach identifies new nitrification inhibitors. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 346:118996. [PMID: 37725864 DOI: 10.1016/j.jenvman.2023.118996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/24/2023] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.
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Affiliation(s)
- Fabian Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Andrzej Drozdzecki
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Alexa De Knijf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Mario Corrochano-Monsalve
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Samuel Bodé
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country-UPV/EHU, Apdo. 644, Bilbao, E-48080, Spain
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, the Netherlands
| | - Pascal Boeckx
- Laboratory of Applied Physical Chemistry (ISOFYS), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Christian V Stevens
- Synthesis, Bioresources and Bioorganic Chemistry Research Group (SynBioC), Department of Green Chemistry and Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dominique Audenaert
- Ghent University Centre for Bioassay Development and Screening (C-BIOS), 9052, Ghent, Belgium; VIB Screening Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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19
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Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [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: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
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20
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Zhao Y, Duan H, Erler D, Yuan Z, Ye L. Decoupling the simultaneous effects of NO 2-, pH and free nitrous acid on N 2O and NO production from enriched nitrifying activated sludge. WATER RESEARCH 2023; 245:120609. [PMID: 37713792 DOI: 10.1016/j.watres.2023.120609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/09/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
In the pursuit of energy and carbon neutrality, nitrogen removal technologies have been developed featuring nitrite (NO2-) accumulation. However, high NO2- accumulations are often associated with stimulated greenhouse gas (i.e., nitrous oxide, N2O) emissions. Furthermore, the coexistence of free nitrous acid (FNA) formed by NO2- and proton (pH) makes the consequence of NO2- accumulation on N2O emissions complicated. The concurrent three factors, NO2-, pH and FNA may play different roles on N2O and nitric oxide (NO) emissions simultaneously, which has not been systematically studied. This study aims to decouple the effects of NO2- (0-200 mg N/L), pH (6.5-8) and FNA (0-0.15 mg N/L) on the N2O and NO production rates and the production pathways by ammonia oxidizing bacteria (AOB), with the use of a series of precisely executed batch tests and isotope site-preference analysis. Results suggested the dominant factors affecting the N2O production rate were NO2- and FNA concentrations, while pH alone played a relatively insignificant role. The most influential factor shifted from NO2- to FNA as FNA concentrations increased from 0 to 0.15 mg N/L. At concentrations below 0.0045 mg HNO2-N/L, nitrite rather than FNA played a significant role stimulating N2O production at elevated nitrite concentrations. The inhibition effect of FNA emerged with further increase of FNA between 0.0045-0.015 mg HNO2-N/L, weakening the promoting effect of increased nitrite. While at concentrations above 0.015 mg HNO2-N/L, FNA inhibited N2O production especially from nitrifier denitrification pathway with the level of inhibition linearly correlated with the FNA concentration. pH and the nitrite concentration regulated the production pathways, with elevated pH promoting the nitrifier nitrification pathway, while elevated NO2- concentrations promoting the nitrifier denitrification pathway. In contrast to N2O, NO emission was less susceptible to FNA at concentrations up to 0.015 mg N/L but was stimulated by increasing NO2- concentrations. This study, for the first time, distinguished the effects of pH, NO2- and FNA on N2O and NO production, thereby providing support to the design and operation of novel nitrogen removal systems with NO2- accumulation.
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Affiliation(s)
- Yingfen Zhao
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Haoran Duan
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia; The Australian Centre for Water and Environmental Biotechnology (ACWEB), The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Dirk Erler
- Centre for Coastal Biogeochemistry, School of Environmental Science and Engineering, Southern Cross University, Lismore, New South Wales 2480, Australia
| | - Zhiguo Yuan
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Liu Ye
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia.
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21
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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22
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Gao S, Das A, Alfonzo E, Sicinski KM, Rieger D, Arnold FH. Enzymatic Nitrogen Incorporation Using Hydroxylamine. J Am Chem Soc 2023; 145:20196-20201. [PMID: 37671894 PMCID: PMC10560455 DOI: 10.1021/jacs.3c08053] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Hydroxylamine-derived reagents have enabled versatile nitrene transfer reactions for introducing nitrogen-containing functionalities in small-molecule catalysis, as well as biocatalysis. These reagents, however, result in a poor atom economy and stoichiometric organic waste. Activating hydroxylamine (NH2OH) for nitrene transfer offers a low-cost and sustainable route to amine synthesis, since water is the sole byproduct. Despite its presence in nature, hydroxylamine is not known to be used for enzymatic nitrogen incorporation in biosynthesis. Here, we report an engineered heme enzyme that can utilize hydroxylammonium chloride, an inexpensive commodity chemical, for nitrene transfer. Directed evolution of Pyrobaculum arsenaticum protoglobin generated efficient enzymes for benzylic C-H primary amination and styrene aminohydroxylation. Mechanistic studies supported a stepwise radical pathway involving rate-limiting hydrogen atom transfer. This unprecedented activity is a useful addition to the "nitrene transferase" repertoire and hints at possible future discovery of natural enzymes that use hydroxylamine for amination chemistry.
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Affiliation(s)
- Shilong Gao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Anuvab Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Edwin Alfonzo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kathleen M. Sicinski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Dominic Rieger
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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23
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Wright CL, Lehtovirta-Morley LE. Nitrification and beyond: metabolic versatility of ammonia oxidising archaea. THE ISME JOURNAL 2023; 17:1358-1368. [PMID: 37452095 PMCID: PMC10432482 DOI: 10.1038/s41396-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.
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Affiliation(s)
- Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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24
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Choi E, Chaudhry SI, Martens-Habbena W. Role of Nitric Oxide in Hydroxylamine Oxidation by Ammonia-Oxidizing Bacteria. Appl Environ Microbiol 2023; 89:e0217322. [PMID: 37439697 PMCID: PMC10467338 DOI: 10.1128/aem.02173-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
An important role of nitric oxide (NO) as either a free intermediate in the NH3 oxidation pathway or a potential oxidant for NH3 or NH2OH has been proposed for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively. However, tracing NO metabolism at low concentrations remains notoriously difficult. Here, we use electrochemical sensors and the mild NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) to trace apparent NO concentration and determine production rates at low micromolar concentrations in the model AOB strain Nitrosomonas europaea. In agreement with previous studies, we found that PTIO does not affect NH3 oxidation instantaneously in both Nitrosospira briensis and Nitrosomonas europaea, unlike inhibitors for ammonia oxidation such as allylthiourea and acetylene, although it effectively scavenged NO from the cell suspensions. Quantitative analysis showed that NO production by N. europaea amounted to 3.15% to 6.23% of NO2- production, whereas N. europaea grown under O2 limitation produced NO equivalent to up to 40% of NO2- production at high substrate concentrations. In addition, we found that PTIO addition to N. europaea grown under O2 limitation abolished N2O production. These results indicate different turnover rates of NO during NH3 oxidation under O2-replete and O2-limited growth conditions in AOB. The results suggest that NO may not be a free intermediate or remain tightly bound to iron centers of enzymes during hydroxylamine oxidation and that only NH3 saturation and adaptation to O2 limitation may lead to significant dissociation of NO from hydroxylamine dehydrogenase. IMPORTANCE Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria (AOB) is thought to contribute significantly to global nitrous oxide (N2O) emissions and leaching of oxidized nitrogen, particularly through their activity in nitrogen (N)-fertilized agricultural production systems. Although substantial efforts have been made to characterize the N metabolism in AOB, recent findings suggest that nitric oxide (NO) may play an important mechanistic role as a free intermediate of hydroxylamine oxidation in AOB, further implying that besides hydroxylamine dehydrogenase (HAO), additional enzymes may be required to complete the ammonia oxidation pathway. However, the NO spin trap PTIO was found to not inhibit ammonia oxidation in AOB. This study provides a combination of physiological and spectroscopic evidence that PTIO indeed scavenges only free NO in AOB and that significant amounts of free NO are produced only during incomplete hydroxylamine oxidation or nitrifier denitrification under O2-limited growth conditions.
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Affiliation(s)
- Eunkyung Choi
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
| | - Sana I. Chaudhry
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Microbiology & Cell Science Department, University of Florida, Davie, Florida, USA
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25
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Li J, Zhao C, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, He X, Qiu Z, Wang J. Multidrug-resistant plasmid RP4 increases NO and N 2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation. WATER RESEARCH 2023; 242:120266. [PMID: 37421866 DOI: 10.1016/j.watres.2023.120266] [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: 01/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.
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Affiliation(s)
- Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
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26
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Bollmeyer MM, Majer SH, Coleman RE, Lancaster KM. Outer coordination sphere influences on cofactor maturation and substrate oxidation by cytochrome P460. Chem Sci 2023; 14:8295-8304. [PMID: 37564409 PMCID: PMC10411619 DOI: 10.1039/d3sc02288a] [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: 05/04/2023] [Accepted: 06/22/2023] [Indexed: 08/12/2023] Open
Abstract
Product selectivity of ammonia oxidation by ammonia-oxidizing bacteria (AOB) is tightly controlled by metalloenzymes. Hydroxylamine oxidoreductase (HAO) is responsible for the oxidation of hydroxylamine (NH2OH) to nitric oxide (NO). The non-metabolic enzyme cytochrome (cyt) P460 also oxidizes NH2OH, but instead produces nitrous oxide (N2O). While both enzymes use a heme P460 cofactor, they selectively oxidize NH2OH to different products. Previously reported structures of Nitrosomonas sp. AL212 cyt P460 show that a capping phenylalanine residue rotates upon ligand binding, suggesting that this Phe may influence substrate and/or product binding. Here, we show via substitutions of the capping Phe in Nitrosomonas europaea cyt P460 that the bulky phenyl side-chain promotes the heme-lysine cross-link forming reaction operative in maturing the cofactor. Additionally, the Phe side-chain plays an important role in modulating product selectivity between N2O and NO during NH2OH oxidation under aerobic conditions. A picture emerges where the sterics and electrostatics of the side-chain in this capping position control the kinetics of N2O formation and NO binding affinity. This demonstrates how the outer coordination sphere of cyt P460 is tuned not only for selective NH2OH oxidation, but also for the autocatalytic cross-link forming reaction that imbues activity to an otherwise inactive protein.
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Affiliation(s)
- Melissa M Bollmeyer
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Sean H Majer
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Rachael E Coleman
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
| | - Kyle M Lancaster
- Baker Laboratory Department of Chemistry and Chemical Biology Cornell University 162 Sciences Drive Ithaca NY 14853 USA
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27
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Yan X, Liu D, Klok JBM, de Smit SM, Buisman CJN, ter Heijne A. Enhancement of Ammonium Oxidation at Microoxic Bioanodes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11561-11571. [PMID: 37498945 PMCID: PMC10413939 DOI: 10.1021/acs.est.3c02227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Bioelectrochemical systems (BESs) are considered to be energy-efficient to convert ammonium, which is present in wastewater. The application of BESs as a technology to treat wastewater on an industrial scale is hindered by the slow removal rate and lack of understanding of the underlying ammonium conversion pathways. This study shows ammonium oxidation rates up to 228 ± 0.4 g-N m-3 d-1 under microoxic conditions (dissolved oxygen at 0.02-0.2 mg-O2/L), which is a significant improvement compared to anoxic conditions (120 ± 21 g-N m-3 d-1). We found that this enhancement was related to the formation of hydroxylamine (NH2OH), which is rate limiting in ammonium oxidation by ammonia-oxidizing microorganisms. NH2OH was intermediate in both the absence and presence of oxygen. The dominant end-product of ammonium oxidation was dinitrogen gas, with about 75% conversion efficiency in the presence of a microoxic level of dissolved oxygen and 100% conversion efficiency in the absence of oxygen. This work elucidates the dominant pathways under microoxic and anoxic conditions which is a step toward the application of BESs for ammonium removal in wastewater treatment.
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Affiliation(s)
- Xiaofang Yan
- Environmental
Technology, Wageningen University &
Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Dandan Liu
- Paqell
B.V., Reactorweg 301, 3542 AD Utrecht, The Netherlands
| | - Johannes B. M. Klok
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Sanne M. de Smit
- Environmental
Technology, Wageningen University &
Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Cees J. N. Buisman
- Environmental
Technology, Wageningen University &
Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
- Wetsus,
European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, The Netherlands
| | - Annemiek ter Heijne
- Environmental
Technology, Wageningen University &
Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
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28
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Zhang IH, Sun X, Jayakumar A, Fortin SG, Ward BB, Babbin AR. Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones. ISME COMMUNICATIONS 2023; 3:76. [PMID: 37474642 PMCID: PMC10359470 DOI: 10.1038/s43705-023-00284-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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Affiliation(s)
- Irene H Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Xin Sun
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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29
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Allagulova CR, Lubyanova AR, Avalbaev AM. Multiple Ways of Nitric Oxide Production in Plants and Its Functional Activity under Abiotic Stress Conditions. Int J Mol Sci 2023; 24:11637. [PMID: 37511393 PMCID: PMC10380521 DOI: 10.3390/ijms241411637] [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: 06/15/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Nitric oxide (NO) is an endogenous signaling molecule that plays an important role in plant ontogenesis and responses to different stresses. The most widespread abiotic stress factors limiting significantly plant growth and crop yield are drought, salinity, hypo-, hyperthermia, and an excess of heavy metal (HM) ions. Data on the accumulation of endogenous NO under stress factors and on the alleviation of their negative effects under exogenous NO treatments indicate the perspectives of its practical application to improve stress resistance and plant productivity. This requires fundamental knowledge of the NO metabolism and the mechanisms of its biological action in plants. NO generation occurs in plants by two main alternative mechanisms: oxidative or reductive, in spontaneous or enzymatic reactions. NO participates in plant development by controlling the processes of seed germination, vegetative growth, morphogenesis, flower transition, fruit ripening, and senescence. Under stressful conditions, NO contributes to antioxidant protection, osmotic adjustment, normalization of water balance, regulation of cellular ion homeostasis, maintenance of photosynthetic reactions, and growth processes of plants. NO can exert regulative action by inducing posttranslational modifications (PTMs) of proteins changing the activity of different enzymes or transcriptional factors, modulating the expression of huge amounts of genes, including those related to stress tolerance. This review summarizes the current data concerning molecular mechanisms of NO production and its activity in plants during regulation of their life cycle and adaptation to drought, salinity, temperature stress, and HM ions.
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Affiliation(s)
- Chulpan R Allagulova
- Institute of Biochemistry and Genetics-Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Alsu R Lubyanova
- Institute of Biochemistry and Genetics-Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Azamat M Avalbaev
- Institute of Biochemistry and Genetics-Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
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30
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Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P. Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasit Vectors 2023; 16:226. [PMID: 37415204 DOI: 10.1186/s13071-023-05842-w] [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: 03/13/2023] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial. METHODS In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions. RESULTS First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release. CONCLUSION These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Lei S, Zhang J, Hu B, Zhao J, Yang W, Shi B, Chen Y, Zhao J. Improving nutrients removal of Anaerobic-Anoxic-Oxic process via inhibiting partial anaerobic mixture with nitrite in side-stream tanks: role of nitric oxide. BIORESOURCE TECHNOLOGY 2023; 382:129207. [PMID: 37217148 DOI: 10.1016/j.biortech.2023.129207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
A side-stream tank which was in parallel with the anoxic tank was used to improve the performance of the Anaerobic-Anoxic-Oxic process. The partial mixtures from the anaerobic tank were injected into the side-stream tank with the initial nitrite nitrogen (NO2--N) concentrations of 10 mg/L and 20 mg/L. When the initial NO2--N concentration in the tank was 20 mg/L, total nitrogen and total phosphorus removal efficiencies of the A2/O process increased from 72% and 48% to 90% and 89%, respectively. 2.23 mg/L of nitric oxide (NO) were observed in the side-stream tank. The abundance of Nitrosomonas sp. and Nitrospira sp. were varied from 0.98% and 6.13% to 2.04% and 1.13%, respectively. The abundances of Pseudomonas sp. and Acinetobacter sp. were increased from 0.81% and 0.74% to 6.69% and 5.48%, respectively. NO plays an important role for improving the nutrients removal of the A2/O process in the side-stream nitrite-enhanced strategy.
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Affiliation(s)
- Shuhan Lei
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
| | - Ju Zhang
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
| | - Bo Hu
- School of Civil Engineering, Chang' an University, Xi' an 710064, Shaanxi, China.
| | - Junkai Zhao
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
| | - Wenjuan Yang
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
| | - Bingfeng Shi
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
| | - Ying Chen
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China
| | - Jianqiang Zhao
- School of Water and Environment, Chang' an University, Xi'an 710064, Shaanxi, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Xi'an 710064, Shaanxi, China
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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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Zhou H, Cheng L, Xia L, Deng G, Zhang Y, Shi X. Rapid simultaneous removal of nitrogen and phosphorous by a novel isolated Pseudomonas mendocina SCZ-2. ENVIRONMENTAL RESEARCH 2023; 231:116062. [PMID: 37149028 DOI: 10.1016/j.envres.2023.116062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Nitrogen (N) and phosphorous (P) removal by a single bacterium could improve the biological reaction efficiency and reduce the operating cost and complexity in wastewater treatment plants (WWTPs). Here, an isolated strain was identified as Pseudomonas mendocina SCZ-2 and showed high performance of heterotrophic nitrification (HN) and aerobic denitrification (AD) without intermediate accumulation. During the AD process, the nitrate removal efficiency and rate reached a maximum of 100% and 47.70 mg/L/h, respectively, under optimal conditions of sodium citrate as carbon source, a carbon-to-nitrogen ratio of 10, a temperature of 35 °C, and shaking a speed of 200 rpm. Most importantly, the strain SCZ-2 could rapidly and simultaneously eliminate N and P with maximum NH4+-N, NO3--N, NO2--N, and PO43--P removal rates of 14.38, 17.77, 20.13 mg N/L/h, and 2.93 mg P/L/h, respectively. Both the N and P degradation curves matched well with the modified Gompertz model. Moreover, the amplification results of functional genes, whole genome sequencing, and enzyme activity tests provided theoretical support for simultaneous N and P removal pathways. This study deepens our understanding of the role of HN-AD bacteria and provides more options for simultaneous N and P removal from actual sewage.
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Affiliation(s)
- Hongfeng Zhou
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Lei Cheng
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
| | - Lisong Xia
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Guozhi Deng
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China
| | - Youde Zhang
- Anhui Xinyu Environmental Protection Technology Co., Ltd., Hefei, 230051, China
| | - Xianyang Shi
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
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Gao P, Zhang X, Huang X, Chen Z, Marietou A, Holmkvist L, Qu L, Finster K, Gong X. Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling. BMC Genomics 2023; 24:209. [PMID: 37076818 PMCID: PMC10116758 DOI: 10.1186/s12864-023-09297-2] [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: 08/11/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.
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Affiliation(s)
- Ping Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Xiaoting Zhang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Xiaomei Huang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Lars Holmkvist
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
| | - Lingyun Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, 8000, Aarhus, Denmark
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China.
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Al-Hazmi HE, Lu X, Grubba D, Majtacz J, Badawi M, Mąkinia J. Sustainable nitrogen removal in anammox-mediated systems: Microbial metabolic pathways, operational conditions and mathematical modelling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161633. [PMID: 36669661 DOI: 10.1016/j.scitotenv.2023.161633] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Anammox-mediated systems have attracted considerable attention as alternative cost-effective technologies for sustainable nitrogen (N) removal from wastewater. This review comprehensively highlights the importance of understanding microbial metabolism in anammox-mediated systems under crucial operation parameters, indicating the potentially wide applications for the sustainable treatment of N-containing wastewater. The partial nitrification-anammox (PN-A), simultaneous PN-A and denitrification (SNAD) processes have demonstrated sustainable N removal from sidestream wastewater. The partial denitrification-anammox (PD-A) and denitrifying anaerobic methane oxidation-anammox (DAMO-A) processes have advanced sustainable N removal efficiency in mainstream wastewater treatment. Moreover, N2O production/emission hotspots are extensively discussed in anammox-based processes and are related to the dominant ammonia-oxidizing bacteria (AOB) and denitrifying heterotrophs. In contrast, N2O is not produced in the metabolism pathways of AnAOB and DAMO-archaea; Moreover, the actual contribution of N2O production by dissimilatory nitrate reduction to ammonium (DNRA) and DAMO-bacteria in their species remains uncertain. Thus, PD-A and DAMO-A processes would achieve reduction in greenhouse gas production, as well as energy consumption for the reliability of N removal efficiencies. In addition to reaction mechanisms, this review covers the mathematical models for simultaneous anammox, partial nitrification and/or denitrification (i.e., PN-A, PD-A, and SNAD). Promising NO3- reduction technologies by endogenous PD, sulfur-driven autotrophic denitrification, and DNRA by anammox are also discussed. In summary, this review provides a better understanding of sustainable N removal in anammox-mediated systems, thereby encouraging future investigation and exploration of the sustainable N bio-treatment from wastewater.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Xi Lu
- Three Gorges Smart Water Technology Co., Ltd., 65 LinXin Road, ChangNing District, 200335 Shanghai, China
| | - Dominika Grubba
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Joanna Majtacz
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques UMR CNRS 7019, Université de Lorraine, Nancy, France
| | - Jacek Mąkinia
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
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Gong JC, Jin H, Li BH, Tian Y, Liu CY, Li PF, Liu Q, Ingeniero RCO, Yang GP. Emissions of Nitric Oxide from Photochemical and Microbial Processes in Coastal Waters of the Yellow and East China Seas. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4039-4049. [PMID: 36808991 DOI: 10.1021/acs.est.2c08978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nitric oxide (NO) is an atmospheric pollutant and climate forcer as well as a key intermediary in the marine nitrogen cycle, but the ocean's NO contribution and production mechanisms remain unclear. Here, high-resolution NO observations were conducted simultaneously in the surface ocean and the lower atmosphere of the Yellow Sea and the East China Sea; moreover, NO production from photolysis and microbial processes was analyzed. The NO sea-air exchange showed uneven distributions (RSD = 349.1%) with an average flux of 5.3 ± 18.5 × 10-17 mol cm-2 s-1. In coastal waters where nitrite photolysis was the predominant source (89.0%), NO concentrations were remarkably higher (84.7%) than the overall average of the study area. The NO from archaeal nitrification accounted for 52.8% of all microbial production (11.0%). We also examined the relationship between gaseous NO and ozone which helped identify sources of atmospheric NO. The sea-to-air flux of NO in coastal waters was narrowed by contaminated air with elevated NO concentrations. These findings indicate that the emissions of NO from coastal waters, mainly controlled by reactive nitrogen inputs, will increase with the reduced terrestrial NO discharge.
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Affiliation(s)
- Jiang-Chen Gong
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hong Jin
- Shandong Qingdao Ecological Environment Monitoring Center, Qingdao 266003, China
| | - Bing-Han Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Ye Tian
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Chun-Ying Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Pei-Feng Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Qian Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | | | - Gui-Peng Yang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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Lycus P, Einsle O, Zhang L. Structural biology of proteins involved in nitrogen cycling. Curr Opin Chem Biol 2023; 74:102278. [PMID: 36889028 DOI: 10.1016/j.cbpa.2023.102278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 03/08/2023]
Abstract
Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.
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Affiliation(s)
- Pawel Lycus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.
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38
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Zhao ZC, Fan SQ, Lu Y, Dang CC, Wang X, Liu BF, Xing DF, Ma J, Ren NQ, Wang Q, Xie GJ. Reactivated biofilm coupling n-DAMO with anammox achieved high-rate nitrogen removal in membrane aerated moving bed biofilm reactor. ENVIRONMENTAL RESEARCH 2023; 220:115184. [PMID: 36586714 DOI: 10.1016/j.envres.2022.115184] [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: 11/13/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
As a promising technology, the combination of nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) with Anammox offers a solution to achieve effective and sustainable wastewater treatment. However, this sustainable process faces challenges to accumulate sufficient biomass for reaching practical nitrogen removal performance. This study developed an innovative membrane aerated moving bed biofilm reactor (MAMBBR), which supported sufficient methane supply and excellent biofilm attachment, for cultivating biofilms coupling n-DAMO with Anammox. Biofilms were developed rapidly on the polyurethane foam with the supply of ammonium and nitrate, achieving the bioreactor performance of 275 g N m-3 d-1 within 102 days. After the preservation at -20 °C for 8 months, the biofilm was successfully reactivated and achieved 315 g N m-3 d-1 after 188 days. After reactivation, MAMBBR was applied to treat synthetic sidestream wastewater. Up to 99.9% of total nitrogen was removed with the bioreactor performance of 4.0 kg N m-3 d-1. Microbial community analysis and mass balance calculation demonstrated that n-DAMO microorganisms and Anammox bacteria collectively contributed to nitrogen removal in MAMBBR. The MAMBBR developed in this study provides an ideal system of integrating n-DAMO with Anammox for sustainable wastewater treatment.
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Affiliation(s)
- Zhi-Cheng Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Sheng-Qiang Fan
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xuan Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jun Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
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Kong Z, Wang H, Yan G, Yan Q, Kim JR. Limited dissolved oxygen facilitated nitrogen removal at biocathode during the hydrogenotrophic denitrification process using bioelectrochemical system. BIORESOURCE TECHNOLOGY 2023; 372:128662. [PMID: 36693505 DOI: 10.1016/j.biortech.2023.128662] [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: 12/26/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Effects of limited dissolved oxygen (DO) on hydrogenotrophic denitrification at biocathode was investigated using bioelectrochemical system. It was found that total nitrogen removal increased by 5.9%, as DO reached about 0.24 mg/L with the cathodic chamber unplugged (group R_Exposure). With the presence of limited DO, not only the nitrogen metabolic pathway was influenced, but the composition of microbial communities of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were enriched accordingly. After metagenomic analysis, enriched genes in R_Exposure were found to be associated with nearly each of nitrogen removal steps as denitrification, nitrification, DNRA, nitrate assimilation and even nitrogen fixation. Moreover, genes encoding both Complexes III and IV constituted the electron transfer chain were significantly enriched, indicating that more electrons would be orientated to the reduction of NO2--N, NO-N and oxygen. Therefore, enhanced nitrogen removal could be attained through the co-respiration of nitrate and oxygen by means of NH4+-N oxidation.
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Affiliation(s)
- Ziang Kong
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Han Wang
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Guoliang Yan
- College of Food Science and Nutritional Engineering, China Agricultural University, 17 East Tsinghua Rd, Beijing 100083, China
| | - Qun Yan
- School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215011, China.
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
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40
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Su Q, Huang S, Zhang H, Wei Z, Ng HY. Abiotic transformations of sulfamethoxazole by hydroxylamine, nitrite and nitric oxide during wastewater treatment: Kinetics, mechanisms and pH effects. JOURNAL OF HAZARDOUS MATERIALS 2023; 444:130328. [PMID: 36402107 DOI: 10.1016/j.jhazmat.2022.130328] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/10/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Hydroxylamine (NH2OH), nitrite (NO2-) and nitric oxide (NO), intermediates enzymatically formed during biological nitrogen removal processes, can engage in chemical (abiotic) transformations of antibiotics. This study determined the kinetics, mechanisms and pathways of abiotic transformations of the antibiotic sulfamethoxazole (SMX) by NH2OH, NO2- and NO in a series of batch tests under different pH and oxygen conditions. While NH2OH was not able to directly transform SMX, NO2- (with HNO2 as the actual reactant) and NO can chemically transform SMX primarily through hydroxylation, nitration, deamination, nitrosation, cleavage of S-N, N-C and C-S bonds, and coupling reactions. There were substantial overlaps in transformation product formations during abiotic transformations by HNO2- and NO. The second order rate constants of SMX with NO2- and NO were determined in the range of 1.5 × 10-1 - 4.8 × 103 M-1 s-1 and 1.0 × 102 - 3.1 × 104 M-1 s-1, respectively, under varying pH (4 - 9) and anoxic or oxic conditions. Acidic pH significantly enhanced abiotic transformation kinetics, and facilitated nitration, nitrosation, and cleavage of S-N and N-C bonds. The findings advance our understanding of the fate of antibiotics during biological nitrogen removal, and highlight the role of enzymatically formed reactive nitrogen species in the antibiotic degradation.
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Affiliation(s)
- Qingxian Su
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411, Singapore; Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Shujuan Huang
- School of Environmental and Municipal Engineering, Qingdao University of Technology, 11 Fushun Road, Qingdao 266033, China
| | - Hui Zhang
- College of Resources and Environment, Chengdu University of Information Technology, Chengdu, Sichuan 610225, China
| | - Zongsu Wei
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Universitetsbyen 36, 8000 Aarhus C, Denmark
| | - How Yong Ng
- National University of Singapore Environmental Research Institute, 5A Engineering Drive 1, 117411, Singapore; Center for Water Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, 519087, China.
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41
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Tang M, Guo Z, Xu X, Sun L, Wang X, Yang Y, Chen J. Performance and microbial mechanism of eletrotrophic bio-cathode denitrification under low temperature. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 328:116960. [PMID: 36493545 DOI: 10.1016/j.jenvman.2022.116960] [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: 10/05/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Insufficient amount of carbon in wastewater and low temperatures hinder the use of biological nitrogen removal for purification of wastewaters. Nitrogen removal using cold-tolerant electrotrophic cathodic microbes is a novel and unique autotrophic denitrification technique in which electrical current, not chemicals, is used as a source of electrons. In this study, integrated MFC (RW) and open-circuit MFC (RO) were cultured and acclimatized in stages at a low temperature (10 °C) to impart cold tolerance to electrotrophic cathodic microbes, investigate the effectiveness of simultaneous nitrification and denitrification (SND) process, and address the possible mechanism of microbial action. The results showed that (i) microbial communities in the RW system were successfully enriched with the cold-tolerant electrotrophic cathodic microbes after five stages, and (ii) the degree of NH4+-N removal and SND were 75.50% and 81.91%, respectively, but the respective values in the RO system were only 40.47% and 54.01%. The desirable SND efficiency was obtained in RW at a DO of ∼0.6 mg/L, a current of ∼20 mA, and pH ∼7.0. In RW, Thauera, Pesudomonas, and Hydrogenophaga were the main electrotrophic cathodic denitrifying bacteria with cold tolerance capable of degrading ammonia, nitrate, and nitrite through autotrophic denitrification and cathodic-driven bio-electrochemical denitrification. Besides, for RW, results from high throughput sequencing analysis revealed that the abundance of genes related to energy production and conversion, amino acid transport, and metabolism, signal transduction, environmental adaptation, and enzymatic activity (AMO, HAO, NAR, NIR, NOR, and NOS) were significantly higher than the corresponding parameters of the RO system. This may explain the reason behind RW having excellent ammonia and TN removal performance at low temperatures.
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Affiliation(s)
- Meizhen Tang
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China.
| | - Zhina Guo
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China
| | - Xiaoyan Xu
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China
| | - Lianglun Sun
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China
| | - Xiaoning Wang
- Shandong Deli Environmental Protection Engineering Co. Ltd, PR China
| | - Yuewei Yang
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China
| | - Junfeng Chen
- School of Life Sciences, Qufu Normal University, No.57 Jingxuan West Road, Qufu, 273165, PR China
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42
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Zhang H, Zhang X, Wei D, Wen X, Zhou S, Li Y, Dong Y, Gong Y. Establishment of anammox coupled with sulfide-depending autotrophic denitrification process and its efficient pollutants removal performance. CHEMOSPHERE 2023; 313:137468. [PMID: 36481169 DOI: 10.1016/j.chemosphere.2022.137468] [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: 06/01/2022] [Revised: 11/26/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Nitrogen and sulfur pollutants coexist in many industrial wastewaters, which may cause serious water pollution issues. In this study, Anammox coupled with sulfide-depending autotrophic denitrification process (coupling process) was established by adding sulfide to an Anammox system in a membrane bioreactor. Variations in nitrogen and sulfur removal performance, extracellular polymeric substances (EPS), key enzyme activities, and microbial components were analyzed. The sulfide in 25.0 mg L-1 successfully induced denitrification, and then helped establish the coupling process. This process achieved 96.1% TN removal and complete sulfide removal when the sulfide was increased to 100.0 mg L-1. The protein and polysaccharide in EPS gradually increased to 2.0 and 4.9 mg g-1 SS, respectively. The hydroxylamine oxidoreductase activity, Heme-c content, nitrite reductase activity, and nitrate reductase activity slightly decreased to 19.1 EU g-1 SS, 0.001 mmol g-1 SS, 0.002 μg min-1 mg-1 protein, and 0.005 μg min-1 mg-1 protein, respectively, indicating the slight suppression of sulfide in high concentration on the coupling process. However, after acclimatization, the Anammox and denitrifying bacteria interacted and cooperatively contributed to the simultaneous nitrogen and sulfur removal, with relative abundances of Thiobacillus-denitrifying bacteria and Candidatus Kuenenia-Anammox bacteria of 31.7% and 9.0%, respectively. The establishing strategy was proposed and then verified in another Anammox system, in which the coupling process was also established, with TN removal increasing from 73.4% to 82.5%.
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Affiliation(s)
- Hongli Zhang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Xiaojing Zhang
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China.
| | - Denghui Wei
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Xiaoyu Wen
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Shijie Zhou
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Yuqi Li
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Yongen Dong
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
| | - Yaoyao Gong
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Restoration, College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450001, China
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43
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Oudova-Rivera B, Wright CL, Crombie AT, Murrell JC, Lehtovirta-Morley LE. The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. Environ Microbiol 2023; 25:948-961. [PMID: 36598494 DOI: 10.1111/1462-2920.16316] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023]
Abstract
The ammonia monooxygenase (AMO) is a key enzyme in ammonia-oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia-oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one-carbon (C1) compounds in ammonia-oxidizing archaea.
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Affiliation(s)
| | - Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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Ohbayashi T, Wang Y, Aoyagi LN, Hara S, Tago K, Hayatsu M. Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils. Microbes Environ 2023; 38:ME23068. [PMID: 38092410 PMCID: PMC10728637 DOI: 10.1264/jsme2.me23068] [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: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.
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Affiliation(s)
- Tsubasa Ohbayashi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Yong Wang
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Luciano Nobuhiro Aoyagi
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Shintaro Hara
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), 305–8604, Tsukuba, Japan
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45
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Xu L, Chen Y, Wang Z, Zhang Y, He Y, Zhang A, Chen H, Xue G. Discovering dominant ammonia assimilation: Implication for high-strength nitrogen removal in full scale biological treatment of landfill leachate. CHEMOSPHERE 2023; 312:137256. [PMID: 36395888 DOI: 10.1016/j.chemosphere.2022.137256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Landfill leachate containing high-strength nitrogen is generated in domestic waste landfilling. The integration of anoxic and aerobic process (AO) based on nitrification and denitrification, has been a mainstream process of biological nitrogen removal (BNR). But the high-strength organics as well as aerobic effluent reflux might change the biochemical environment designed and operated as AO. In view of the nitrogen balance in a full scale landfill leachate treatment plant with two-stage AO, we found that approximately 90% removal of total nitrogen (TN) and ammonia (NH4+-N) focused on primary anoxic and aerobic stage. Meanwhile, the less nitrate and nitrite in the aerobic effluent were incapable of sustaining denitrification or anaerobic ammonia oxidation (anammox). The high reflux flow from aerobic to anoxic process enabled the similar microbial community and functional genes in anoxic and aerobic process units. However, the functional genes involving ammonia assimilation in all process units showcased the highest abundance compared to those correlated with other BNR pathways, including nitrification and denitrification, assimilatory and dissimilatory nitrate reduction, nitrogen fixation and anammox. The ammonia assimilation dominated the removals of TN and NH4+-N, rather than other BNR mechanism. The insight of dominant ammonia assimilation is favorable for illustrating the authentic BNR mechanism of landfill leachate in AO, thereby guiding the optimization of engineering design and operation.
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Affiliation(s)
- Lei Xu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yuting Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Zheng Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yu Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yueling He
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Ai Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200000, China.
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46
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Melcher M, Hodgskiss LH, Mardini MA, Schleper C, Rittmann SKMR. Analysis of biomass productivity and physiology of Nitrososphaera viennensis grown in continuous culture. Front Microbiol 2023; 14:1076342. [PMID: 36876066 PMCID: PMC9978112 DOI: 10.3389/fmicb.2023.1076342] [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: 10/21/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microbial ammonia oxidation is the first and usually rate limiting step in nitrification and is therefore an important step in the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) play an important role in nitrification. Here, we report a comprehensive analysis of biomass productivity and the physiological response of Nitrososphaera viennensis to different ammonium and carbon dioxide (CO2) concentrations aiming to understand the interplay between ammonia oxidation and CO2 fixation of N. viennensis. The experiments were performed in closed batch in serum bottles as well as in batch, fed-batch, and continuous culture in bioreactors. A reduced specific growth rate (μ) of N. viennensis was observed in batch systems in bioreactors. By increasing CO2 gassing μ could be increased to rates comparable to that of closed batch systems. Furthermore, at a high dilution rate (D) in continuous culture (≥ 0.7 of μmax) the biomass to ammonium yield (Y(X/NH3)) increased up to 81.7% compared to batch cultures. In continuous culture, biofilm formation at higher D prevented the determination of D crit. Due to changes in Y(X/NH3) and due to biofilm, nitrite concentration becomes an unreliable proxy for the cell number in continuous cultures at D towards μmax. Furthermore, the obscure nature of the archaeal ammonia oxidation prevents an interpretation in the context of Monod kinetics and thus the determination of K S. Our findings indicate that the physiological response of N. viennensis might be regulated with different enzymatic make-ups, according to the ammonium catalysis rate. We reveal novel insights into the physiology of N. viennensis that are important for biomass production and the biomass yield of AOA. Moreover, our study has implications to the field of archaea biology and microbial ecology by showing that bioprocess technology and quantitative analysis can be applied to decipher environmental factors affecting the physiology and productivity of AOA.
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Affiliation(s)
- Michael Melcher
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Logan H Hodgskiss
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Mohammad Anas Mardini
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Arkeon GmbH, Tulln a.d. Donau, Austria.,Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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47
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Gong X, Del Río ÁR, Xu L, Chen Z, Langwig MV, Su L, Sun M, Huerta-Cepas J, De Anda V, Baker BJ. New globally distributed bacterial phyla within the FCB superphylum. Nat Commun 2022; 13:7516. [PMID: 36473838 PMCID: PMC9727166 DOI: 10.1038/s41467-022-34388-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Mingxue Sun
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA.
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48
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Al-Hazmi HE, Hassan GK, Maktabifard M, Grubba D, Majtacz J, Mąkinia J. Integrating conventional nitrogen removal with anammox in wastewater treatment systems: Microbial metabolism, sustainability and challenges. ENVIRONMENTAL RESEARCH 2022; 215:114432. [PMID: 36167115 DOI: 10.1016/j.envres.2022.114432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The various forms of nitrogen (N), including ammonium (NH4+), nitrite (NO2-), and nitrate (NO3-), present in wastewaters can create critical biotic stress and can lead to hazardous phenomena that cause imbalances in biological diversity. Thus, biological nitrogen removal (BNR) from wastewaters is considered to be imperatively urgent. Therefore, anammox-based systems, i.e. partial nitrification and anaerobic ammonium oxidation (PN/anammox) and partial denitrification and anammox (PD/anammox) have been universally acknowledged to consider as alternatives, promising and cost-effective technologies for sustainable N removal from wastewaters compared to nitrification-denitrification processes. This review comprehensively presents and discusses the latest advances in BNR technologies, including traditional nitrification-denitrification and anammox-based systems. To a deep understanding of a better-controlled combining anammox with traditional processes, the microbial community diversity and metabolism, as well as, biomass morphological characteristics were clearly reviewed in the anammox-based systems. Explaining simultaneous microbial competition and control of crucial operation parameters in single-stage anammox-based processes in terms of optimization and economic benefits makes this contribution a different vision from available review papers. The most important sustainability indicators, including global warming potential (GWP), carbon footprint (CF) and energy behaviours were explored to evaluate the sustainability of BNR processes in wastewater treatment. Additionally, the challenges and solutions for BNR processes are extensively discussed. In summary, this review helps facilitate a critical understanding of N removal technologies. It is confirmed that sustainability and saving energy would be achieved by anammox-based systems, thereby could be encouraged future outcomes for a sustainable N removal economy.
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Affiliation(s)
- Hussein E Al-Hazmi
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland.
| | - Gamal K Hassan
- Water Pollution Research Department, National Research Centre, 33 Bohouth St, Giza, Dokki, P.O. Box 12622, Egypt
| | - Mojtaba Maktabifard
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Dominika Grubba
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Joanna Majtacz
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
| | - Jacek Mąkinia
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdańsk University of Technology, Ul. Narutowicza 11/12, Gdańsk, 80-233, Poland
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49
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Dong X, Huang Z, Peng X, Jia X. Advanced simultaneous nitrogen and phosphorus removal for non-sterile wastewater through a novel coupled yeast-sludge system: Performance, microbial interaction, and mechanism. CHEMOSPHERE 2022; 309:136645. [PMID: 36183892 DOI: 10.1016/j.chemosphere.2022.136645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/17/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
A novel coupled yeast-sludge system (CYSS) was constructed by the yeast Candida sp. PNY integrated with activated sludge to treat non-sterile mainstream wastewater. After 240-day cultivation, compared with single activated sludge, simultaneous removal efficiency of total organic carbon (TOC), nitrogen and phosphorus increased by 19.5% (176.34 mg TOC g-1 d-1), 21.3% (11.25 mg TN g-1 d-1) and 15.0% (6.95 mg TP g-1 d-1), respectively, while the amount of sludge reduced by 50%. Amplicon sequencing analysis showed that the abundance of Nitrosomonas, Nitrospira, Zoogloea, Dechloromonas, and Candidatus Accumulibacter significantly decreased to 0% on Day 200. Abundance of nirS and nirK for denitrification significantly decreased in CYSS by quantitative PCR (qPCR), and the copies of nirS and nirK were 3.37-fold and 1.71-fold decrease from Day 0 to Day 240, respectively. The results of Fluorescence in situ hybridization and co-occurrence network showed that Candida sp. PNY predominated its distribution in CYSS, and strongly connected with environmental variables based on network analysis. Furthermore, this study reconstructed the carbon, nitrogen and phosphorus metabolic pathways of the CYSS based on metagenomics.
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Affiliation(s)
- Xiaoqi Dong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zidan Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingxing Peng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Xiaoshan Jia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China
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Palomo A, Dechesne A, Pedersen AG, Smets BF. Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira. MICROBIOME 2022; 10:204. [PMID: 36451244 PMCID: PMC9714041 DOI: 10.1186/s40168-022-01411-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete. RESULTS In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification. CONCLUSIONS Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.
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Affiliation(s)
- Alejandro Palomo
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Arnaud Dechesne
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Anders G. Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs Lyngby, Denmark
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