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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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2
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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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3
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Askari MJ, Kallick JD, McCrory CCL. Selective Reduction of Aqueous Nitrate to Ammonium with an Electropolymerized Chromium Molecular Catalyst. J Am Chem Soc 2024; 146:7439-7455. [PMID: 38465608 DOI: 10.1021/jacs.3c12783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nitrate (NO3-) is a common nitrogen-containing contaminant in agricultural, industrial, and low-level nuclear wastewater that causes significant environmental damage. In this work, we report a bioinspired Cr-based molecular catalyst incorporated into a redox polymer that selectively and efficiently reduces aqueous NO3- to ammonium (NH4+), a desirable value-added fertilizer component and industrial precursor, at rates of ∼0.36 mmol NH4+ mgcat-1 h-1 with >90% Faradaic efficiency for NH4+. The NO3- reduction reaction occurs through a cascade catalysis mechanism involving the stepwise reduction of NO3- to NH4+ via observed NO2- and NH2OH intermediates. To our knowledge, this is one of the first examples of a molecular catalyst, homogeneous or heterogenized, that is reported to reduce aqueous NO3- to NH4+ with rates and Faradaic efficiencies comparable to those of state-of-the-art solid-state electrocatalysts. This work highlights a promising and previously unexplored area of electrocatalyst research using polymer-catalyst composites containing complexes with oxophilic transition metal active sites for electrochemical nitrate remediation with nutrient recovery.
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Affiliation(s)
- Maiko J Askari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeremy D Kallick
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles C L McCrory
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Wang Q, Li N, Jiang S, Li G, Yuan J, Li Y, Chang R, Gong X. Composting of post-consumption food waste enhanced by bioaugmentation with microbial consortium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168107. [PMID: 37884139 DOI: 10.1016/j.scitotenv.2023.168107] [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: 09/01/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
There is escalating interest in composting of post-consumption food waste (PCFW) to recycle nutrients and mitigate pollution by inappropriate disposal. The present study aimed to evaluate the performance of bioaugmentation to composting of PCFW, which is in difficulties caused by high sugar, protein and gross lipid content. Inoculation of the microbial consortium effectively induced rapid temperature and pH rising, which led to OM reduction rate at 25.11 % and maturity at 150 % in terms of Germination Index value. EEMs-FRI showed that humification was accelerated in the thermophilic stage and further improved in the mature stage. Bacterial community analysis revealed that microbial inoculant ameliorated acidification, and expedited temperature and pH rising in the initial stage, which in turn accelerated bacteria community succession. The abundance of Actinobacteria was much higher in the thermophilic and mature stage in T2 treatment than in T1, which might explain rapid organic degradation. High temperature enriched thermophilic genera (Thermobifida, Compostibacillus, Neobacillus), and Pseudonocardia and Actinoplanes were enriched in the mature stage, which correlated to effective degradation of organic matter, humification and maturity. Temperature and pH mainly motivated bacterial succession. The results suggest that bioaugmentation is a favorable approach for efficient composting of PCFW.
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Affiliation(s)
- Qianqi Wang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Na Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Ordos Environmental Protection Investment Co., Ltd, Ordos 017000, China
| | - Sinan Jiang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Yuan
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yanming Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Ruixue Chang
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyan Gong
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China.
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Liu S, Huang X, Mu H, Zheng M, Kuang S, Chen H, Xu Y, Wang D, Liu H, Li X. Biogeography and diversity patterns of functional genes associated with C, N, P, S cycling processes across China classical sea sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167678. [PMID: 37820797 DOI: 10.1016/j.scitotenv.2023.167678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
Microbial activities influence the ecological functions of marine ecosystems and play an essential role in biogeochemical cycling. However, there are more studies on microbial diversity and community structure, and few reports have explored nutrient cycling processes by microbial functional gene abundance and diversity. Given these limitations, in order to investigate the variability of nutrient cycling among different sea areas and its influencing factors, the sediments of the Bohai Sea, Yellow Sea, East China Sea and South China Sea were used in this study. The number of average copies of each functional gene was obtained by the quantitative microbial element cycling (QMEC) smart chip. A total of 65 functional genes related to C, N, P and S cycling were identified, and the results showed that all functional genes decreased in the order of magnitude from the Bohai Sea to the East China Sea, Yellow Sea and South China Sea, and the abundance of functional genes was significantly higher at the sampling sites near the land side, which related to human activities. Additionally, NH4+, organic carbon, total carbon and geographical factor were the main driving factors of functional gene composition changes (p < 0.05), and all functional genes were significantly correlated with total carbon and geographical distance (p < 0.01). These findings further expand the understanding of marine ecosystems and provide robust support for global biogeochemical cycles.
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Affiliation(s)
- Shuai Liu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xin Huang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China; School of Environment Science and Engineering, Shandong University, Qingdao, Shandong Province 266237, China
| | - Hongyu Mu
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Minggang Zheng
- Research Center for Marine Ecology, First Institute of Oceanography, State Oceanic Administration, Qingdao, Shandong 266061, China
| | - Shaoping Kuang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Hui Chen
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China.
| | - Yan Xu
- College of Environmental Sciences and Engineering, Qingdao University, Qingdao 266071, China
| | - Dong Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China; Shandong Mokerui new material Technology Co., LTD, Zibo, China
| | - Huan Liu
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Xuan Li
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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6
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Wang S, Lyu T, Li S, Jiang Z, Dang Z, Zhu X, Hu W, Yue FJ, Ji G. Unignorable enzyme-specific isotope fractionation for nitrate source identification in aquatic ecosystem. CHEMOSPHERE 2024; 348:140771. [PMID: 38000558 DOI: 10.1016/j.chemosphere.2023.140771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023]
Abstract
Nitrate contamination in aquatic systems is a widespread problem across the world. The isotopic composition (δ15N, δ18O) of nitrate and their isotope effect (15ε, 18ε) can facilitate the identification of the source and transformation of nitrate. Although previous researches claimed the isotope fractionations may change the original δ15N/δ18O values and further bias identification of nitrate sources, isotope effect was often ignored due to its complexity. To fill the gap between the understanding and application, it is crucial to develop a deep understanding of isotopic fractionation based on available evidence. In this regard, this study summarized the available methods to determine isotope effects, thereby systematically comparing the magnitude of isotope effects (15ε and 18ε) in nitrification, denitrification and anammox. We found that the enzymatic reaction plays the key role in isotope fractionations, which is significantly affected by the difference in the affinity, substrate channel properties and redox potential of active site. Due to the overlapping of microbial processes and accumulation of uncertainties, the significant isotope effects at small scales inevitably decrease in large-scale ecosystems. However, the proportionality of N and O isotope fractionation (δ18O/δ15N; 18ε/15ε) associated with nitrate reduction generally follows enzyme-specific proportionalities (i.e., Nar, 0.95; Nap, 0.57; eukNR, 0.98) in aquatic ecosystems, providing enzyme-specific constant factors for the identification of nitrate transformation. With these results, this study finally discussed feasible source portioning methods when considering the isotope effect and aimed to improve the accuracy in nitrate source identification.
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Affiliation(s)
- Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Tao Lyu
- School of Water, Energy and Environment, Cranfield University, College Road, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Shengjie Li
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Zhuo Jiang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Zhengzhu Dang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Fu-Jun Yue
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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7
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De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
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8
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Pan D, Chen P, Yang G, Niu R, Bai Y, Cheng K, Huang G, Liu T, Li X, Li F. Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21156-21167. [PMID: 38064275 DOI: 10.1021/acs.est.3c06337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2- accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4+ to the reduced NO3- were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2--to-NH4+ reduction in the cytoplasm. Dechloromonas dominated the NO2--to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2--to-NH4+ during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4+ production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.
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Affiliation(s)
- Dandan Pan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Pengcheng Chen
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guang Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Rumiao Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yan Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Kuan Cheng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guoyong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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9
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Ryzhmanova YV, Avdeeva LV, Saratovskikh EA, Shcherbakova VA, Golosov EV, Yarullin RN. Microorganisms for the oxidation of nitrated cellulose in its effluents (review). Biophys Rev 2023; 15:1379-1391. [PMID: 37974989 PMCID: PMC10643570 DOI: 10.1007/s12551-023-01159-1] [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: 06/07/2023] [Accepted: 09/25/2023] [Indexed: 11/19/2023] Open
Abstract
The processes of microbiological destruction of toxic and large-tonnage waste are the most attractive processes for protecting the environment. The review considers the results of studies of microbial decomposition of nitrate esters, including hardly decomposable nitrocellulose. The published data show that specific microorganisms are able to degrade nitrated cellulose compounds under both anaerobic and aerobic conditions. The most promising microorganisms in terms of the efficiency of the nitrocellulose degradation process are bacteria belonging to Desulfovibrio genera, fungi Fusarium solani and Sclerotium rolfsii, as well as their co-cultivation. Recently, the first information about the enzymes involved in the process of nitrocellulose degradation, possible mechanisms of reactions carried out by these enzymes, and the effect of electron donors and acceptors adding to the process have been obtained. Contamination of industrial wastewater with nitrocellulose leads to treatment necessity by using cost-effective, harmless methods. A combined aerobic-anaerobic system, including both bacteria and fungi, has shown hopeful results.
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Affiliation(s)
- Yana V. Ryzhmanova
- Institute of the Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center of Biological Research of Russian Academy of Sciences”, pr. Nauki 5, Pushchino, Moscow Region 142292 Russia
| | - Lidia V. Avdeeva
- Federal Research Center of Problems of Chemical Physics and Medical Chemistry of the Russian Academy of Sciences, Academician Semenov avenue 1, Chernogolovka, Moscow region 142432 Russia
| | - Elena A. Saratovskikh
- Federal Research Center of Problems of Chemical Physics and Medical Chemistry of the Russian Academy of Sciences, Academician Semenov avenue 1, Chernogolovka, Moscow region 142432 Russia
| | - Viktoria A. Shcherbakova
- Institute of the Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center of Biological Research of Russian Academy of Sciences”, pr. Nauki 5, Pushchino, Moscow Region 142292 Russia
| | - Evgeniy V. Golosov
- Federal Research Center of Problems of Chemical Physics and Medical Chemistry of the Russian Academy of Sciences, Academician Semenov avenue 1, Chernogolovka, Moscow region 142432 Russia
| | - Rashit N. Yarullin
- Kazan (Volga region) Federal University, Kremlin street 18, Kazan, 420008 Russia
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10
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He W, Chandra S, Quast T, Varhade S, Dieckhöfer S, Junqueira JRC, Gao H, Seisel S, Schuhmann W. Enhanced Nitrate-to-Ammonia Efficiency over Linear Assemblies of Copper-Cobalt Nanophases Stabilized by Redox Polymers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303050. [PMID: 37235856 DOI: 10.1002/adma.202303050] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/13/2023] [Indexed: 05/28/2023]
Abstract
Renewable electricity-powered nitrate (NO3 - ) reduction reaction (NO3 RR) offers a net-zero carbon route to the realization of high ammonia (NH3 ) productivity. However, this route suffers from low energy efficiency (EE, with a half-cell EE commonly <36%), since high overpotentials are required to overcome the weak NO3 - binding affinity and sluggish NO3 RR kinetics. To alleviate this, a rational catalyst design strategy that involves the linear assembly of sub-5 nm Cu/Co nanophases into sub-20 nm thick nanoribbons is suggested. The theoretical and experimental studies show that the Cu-Co nanoribbons, similar to enzymes, enable strong NO3 - adsorption and rapid tandem catalysis of NO3 - to NH3 , owing to their richly exposed binary phase boundaries and adjacent Cu-Co sites at sub-5 nm distance. In situ Raman spectroscopy further reveals that at low applied overpotentials, the Cu/Co nanophases are rapidly activated and subsequently stabilized by a specifically designed redox polymer that in situ scavenges intermediately formed highly oxidative nitrogen dioxide (NO2 ). As a result, a stable NO3 RR with a current density of ≈450 mA cm-2 is achieved, a Faradaic efficiency of >97% for the formation of NH3 , and an unprecedented half-cell EE of ≈42%.
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Affiliation(s)
- Wenhui He
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Shubhadeep Chandra
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Thomas Quast
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Swapnil Varhade
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Stefan Dieckhöfer
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - João R C Junqueira
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Huimin Gao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Sabine Seisel
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, D-44780, Bochum, Germany
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11
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Tejada-Jimenez M, Leon-Miranda E, Llamas A. Chlamydomonas reinhardtii-A Reference Microorganism for Eukaryotic Molybdenum Metabolism. Microorganisms 2023; 11:1671. [PMID: 37512844 PMCID: PMC10385300 DOI: 10.3390/microorganisms11071671] [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: 05/16/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
Molybdenum (Mo) is vital for the activity of a small but essential group of enzymes called molybdoenzymes. So far, specifically five molybdoenzymes have been discovered in eukaryotes: nitrate reductase, sulfite oxidase, xanthine dehydrogenase, aldehyde oxidase, and mARC. In order to become biologically active, Mo must be chelated to a pterin, forming the so-called Mo cofactor (Moco). Deficiency or mutation in any of the genes involved in Moco biosynthesis results in the simultaneous loss of activity of all molybdoenzymes, fully or partially preventing the normal development of the affected organism. To prevent this, the different mechanisms involved in Mo homeostasis must be finely regulated. Chlamydomonas reinhardtii is a unicellular, photosynthetic, eukaryotic microalga that has produced fundamental advances in key steps of Mo homeostasis over the last 30 years, which have been extrapolated to higher organisms, both plants and animals. These advances include the identification of the first two molybdate transporters in eukaryotes (MOT1 and MOT2), the characterization of key genes in Moco biosynthesis, the identification of the first enzyme that protects and transfers Moco (MCP1), the first characterization of mARC in plants, and the discovery of the crucial role of the nitrate reductase-mARC complex in plant nitric oxide production. This review aims to provide a comprehensive summary of the progress achieved in using C. reinhardtii as a model organism in Mo homeostasis and to propose how this microalga can continue improving with the advancements in this field in the future.
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Affiliation(s)
- Manuel Tejada-Jimenez
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Esperanza Leon-Miranda
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
| | - Angel Llamas
- Department of Biochemistry and Molecular Biology, Campus de Rabanales and Campus Internacional de Excelencia Agroalimentario (CeiA3), Edificio Severo Ochoa, University of Córdoba, 14071 Córdoba, Spain
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12
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Wang H, Li Z, Chen H, Jin J, Zhang P, Shen L, Hu S, Liu H. Metabolomic analysis reveals the impact of ketoprofen on carbon and nitrogen metabolism in rice (Oryza sativa L.) seedling leaves. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:21825-21837. [PMID: 36279067 DOI: 10.1007/s11356-022-23716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Pharmacologically active compounds (PACs) are becoming common pollutants in the natural environment, posing potential risks to crop quality; however, the toxic effects and metabolic changes that they cause in agricultural plants remain unclear. Here, we investigated the effects of ketoprofen on respiration rate, ATP synthesis, carbon and nitrogen metabolism, and metabolomics in rice seedling leaves. The results showed that ketoprofen treatment adversely affected the respiration rate, ATP content, H+-ATPase activity and induced changes in the contents of carbon assimilation products (soluble sugar, reducing sugar, sucrose, and starch) and the activities of key enzymes in carbon metabolism (sucrose synthase (SS), sucrose phosphate synthase (SPS), and sucrose invertase (InV)). The contents of nitrate, ammonium, and free amino acids, and the activities of key enzymes involved in nitrogen metabolism (nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH)) were also affected in a concentration-dependent manner. Metabolomics analysis showed that ketoprofen disturbed the type and content of metabolites (amino acids, carbohydrates, and secondary metabolites) to varying degrees and perturbed key metabolic pathways (substance synthesis and energy metabolism), ultimately resulting in the reduction of rice seedling biomass. This study provides important information and a useful reference for the accurate assessment of the environmental risks of PACs.
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Affiliation(s)
- Huan Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
- College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Zhiheng Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
- Instrumental Analysis Center of Zhejiang, Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Hanmei Chen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Jiaojun Jin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Ping Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Luoqin Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Shuhao Hu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China
| | - Huijun Liu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Zhejiang Province, Hangzhou, 310018, China.
- Instrumental Analysis Center of Zhejiang, Gongshang University, Zhejiang Province, Hangzhou, 310018, China.
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13
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Verde C, Giordano D, Bruno S. NO and Heme Proteins: Cross-Talk between Heme and Cysteine Residues. Antioxidants (Basel) 2023; 12:antiox12020321. [PMID: 36829880 PMCID: PMC9952723 DOI: 10.3390/antiox12020321] [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: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Heme proteins are a diverse group that includes several unrelated families. Their biological function is mainly associated with the reactivity of the heme group, which-among several other reactions-can bind to and react with nitric oxide (NO) and other nitrogen compounds for their production, scavenging, and transport. The S-nitrosylation of cysteine residues, which also results from the reaction with NO and other nitrogen compounds, is a post-translational modification regulating protein activity, with direct effects on a variety of signaling pathways. Heme proteins are unique in exhibiting this dual reactivity toward NO, with reported examples of cross-reactivity between the heme and cysteine residues within the same protein. In this work, we review the literature on this interplay, with particular emphasis on heme proteins in which heme-dependent nitrosylation has been reported and those for which both heme nitrosylation and S-nitrosylation have been associated with biological functions.
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Affiliation(s)
- Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Napoli, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
- Biopharmanet-TEC, University of Parma, 43124 Parma, Italy
- Correspondence:
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14
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The Contribution of Nitrate Dissimilation to Nitrate Consumption in narG- and napA-Containing Nitrate Reducers with Various Oxygen and Nitrate Supplies. Microbiol Spectr 2022; 10:e0069522. [PMID: 36453888 PMCID: PMC9769761 DOI: 10.1128/spectrum.00695-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Nitrate reducers containing narG or napA play an important role in the nitrogen cycle, but little is known about their functional differentiations in relation to environmental changes. In this study, three types of nitrate reducers in the genus Pseudomonas, including strains containing narG (G type), napA (A type) and both narG and napA (GA type), were selected to explore their functional performances under varied nitrate and oxygen concentrations. Their growth characteristics, nitrate consumption, and dissimilatory nitrate-reducing activity were investigated. Growth and nitrate consumption of all three types of strains were generally promoted with increasing oxygen and nitrate concentrations. However, their dissimilatory nitrate-reducing activities were restricted by oxygen supply. When supplied with 0.25 mM KNO3, A-type strains showed a higher growth rate but lower activity of dissimilatory nitrate reduction (DNR) than G-type strains, regardless of oxygen concentration. However, when nitrate concentration increased to 0.75 mM or 5 mM, G-type strains displayed stronger capability of nitrate consumption and DNR than A-type strains under anaerobic conditions, whereas under oxygenated conditions, A-type strains exhibited higher growth and nitrate consumption but weaker DNR than G-type strains. The GA-type strains appeared similar to G type under anaerobic conditions but performed more similarly to A type in aerobic environments. In summary, the nitrate consumption of narG-containing nitrate reducers is mainly caused by DNR in both anaerobic and aerobic environments, while the large proportion of nitrate consumption in A-type nitrate reducers under the aerobic condition is attributed to the assimilation by cell growth. IMPORTANCE Nitrate reducers containing narG or napA are ubiquitous, but little is known about their functional performance in various environments. Our study provides an important clue that the nitrate consumption of narG-containing strains is mainly caused by dissimilatory reduction in the environments, while that of napA-containing nitrate reducers under anaerobic conditions is ascribed to nitrate dissimilation but under the aerobic condition is attributed to the assimilation by cell growth. This finding broadens the understanding of aerobic nitrate reduction in the nitrogen cycle and highlights the important role of narG-containing bacteria in nitrate reduction under aerobic conditions.
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15
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He W, Zhang J, Dieckhöfer S, Varhade S, Brix AC, Lielpetere A, Seisel S, Junqueira JRC, Schuhmann W. Splicing the active phases of copper/cobalt-based catalysts achieves high-rate tandem electroreduction of nitrate to ammonia. Nat Commun 2022; 13:1129. [PMID: 35236840 PMCID: PMC8891333 DOI: 10.1038/s41467-022-28728-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022] Open
Abstract
Electrocatalytic recycling of waste nitrate (NO3−) to valuable ammonia (NH3) at ambient conditions is a green and appealing alternative to the Haber−Bosch process. However, the reaction requires multi-step electron and proton transfer, making it a grand challenge to drive high-rate NH3 synthesis in an energy-efficient way. Herein, we present a design concept of tandem catalysts, which involves coupling intermediate phases of different transition metals, existing at low applied overpotentials, as cooperative active sites that enable cascade NO3−-to-NH3 conversion, in turn avoiding the generally encountered scaling relations. We implement the concept by electrochemical transformation of Cu−Co binary sulfides into potential-dependent core−shell Cu/CuOx and Co/CoO phases. Electrochemical evaluation, kinetic studies, and in−situ Raman spectra reveal that the inner Cu/CuOx phases preferentially catalyze NO3− reduction to NO2−, which is rapidly reduced to NH3 at the nearby Co/CoO shell. This unique tandem catalyst system leads to a NO3−-to-NH3 Faradaic efficiency of 93.3 ± 2.1% in a wide range of NO3− concentrations at pH 13, a high NH3 yield rate of 1.17 mmol cm−2 h−1 in 0.1 M NO3− at −0.175 V vs. RHE, and a half-cell energy efficiency of ~36%, surpassing most previous reports. Electrocatalytic recycling of waste nitrate to NH3 under ambient conditions maybe an appealing alternative to the Haber−Bosch process. Here the authors report a tandem catalyst system involving cooperative adsorption of reaction intermediate on different transition metal active sites for nitrate electroreduction with high efficiency.
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Affiliation(s)
- Wenhui He
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Jian Zhang
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Stefan Dieckhöfer
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Swapnil Varhade
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Ann Cathrin Brix
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Anna Lielpetere
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Sabine Seisel
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - João R C Junqueira
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Wolfgang Schuhmann
- Analytical Chemistry-Center for Electrochemical Sciences (CES), Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstr. 150, 44780, Bochum, Germany.
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16
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Guo K, Feng X, Sun W, Han S, Wu S, Gao H. NapB Restores cytochrome c biosynthesis in bacterial dsbD-deficient mutants. Commun Biol 2022; 5:87. [PMID: 35064202 PMCID: PMC8782879 DOI: 10.1038/s42003-022-03034-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Cytochromes c (cyts c), essential for respiration and photosynthesis in eukaryotes, confer bacteria respiratory versatility for survival and growth in natural environments. In bacteria having a cyt c maturation (CCM) system, DsbD is required to mediate electron transport from the cytoplasm to CcmG of the Ccm apparatus. Here with cyt c-rich Shewanella oneidensis as the research model, we identify NapB, a cyt c per se, that suppresses the CCM defect of a dsbD mutant during anaerobiosis, when NapB is produced at elevated levels, a result of activation by cAMP-Crp. Data are then presented to suggest that NapB reduces CcmG, leading to the suppression. We further show that NapB proteins capable of rescuing CCM in the dsbD mutant form a small distinct clade. The study sheds light on multifunctionality of cyts c, and more importantly, unravels a self-salvation strategy through which bacteria have evolved to better adjust to the natural world. The DsbD protein is normally required for cytochrome c maturation (Ccm) in bacteria. With cytochrome c-rich Shewanella oneidensis as the research model, NapB, the small subunit of the nitrate reductase which is a cytochrome c per se, was found to suppress the Ccm defect resulting from DsbD loss under anaerobic conditions.
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17
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Ji K, Baek K, Peng W, Alberto KA, Torabifard H, Nielsen SO, Dodani SC. Biophysical and in silico characterization of NrtA: a protein-based host for aqueous nitrate and nitrite recognition. Chem Commun (Camb) 2022; 58:965-968. [PMID: 34937073 PMCID: PMC9197583 DOI: 10.1039/d1cc05879g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nitrate and nitrite are key components of the global nitrogen cycle. As such, Nature has evolved proteins as biological supramolecular hosts for the recognition, translocation, and transformation of both nitrate and nitrite. To understand the supramolecular principles that govern these anion-protein interactions, here, we employ a hybrid biophysical and in silico approach to characterize the thermodynamic properties and protein dynamics of NrtA from the cyanobacterium Synechocystis sp. PCC 6803 for the recognition of nitrate and nitrite.
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Affiliation(s)
- Ke Ji
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
| | - Kiheon Baek
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
| | - Weicheng Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Kevin A Alberto
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
| | - Hedieh Torabifard
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
| | - Steven O Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA.
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18
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Maiti BK, Maia LB, Moura JJG. Sulfide and transition metals - A partnership for life. J Inorg Biochem 2021; 227:111687. [PMID: 34953313 DOI: 10.1016/j.jinorgbio.2021.111687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/13/2022]
Abstract
Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Department of Chemistry, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India.
| | - Luisa B Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
| | - José J G Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology (FCT NOVA), Universidade NOVA de Lisboa, Campus de Caparica, Portugal.
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19
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Wang Y, Yuan J, Li S, Hui L, Li Y, Chen K, Meng T, Yu C, Leng F, Ma J. Comparative analysis of carbon and nitrogen metabolism, antioxidant indexes, polysaccharides and lobetyolin changes of different tissues from Codonopsis pilosula co-inoculated with Trichoderma. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153546. [PMID: 34736004 DOI: 10.1016/j.jplph.2021.153546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Codonopsis pilosula is a traditional Chinese herbal medicinal plant and contains various bioactive components, such as C. pilosula polysaccharides (CPPs) and lobetyolin (Lob). Hydrogen peroxide (H2O2) and nitric oxide (NO) are gaseous molecule and have been well known for their ability to relieve some adverse influences on plant from abiotic stress. Endophytic fungus is non-pathogenic plant-associated fungus that could play a significant role in improving plant tolerance by signal molecule. In this work, we determined how inoculation of Trichoderma strain RHTA01 with C. pilosula changed the plant's growth, metabolite accumulation, and related enzyme activity. Results demonstrated that application of Trichoderma strain RHTA01 significantly improved the growth of C. pilosula. Moreover, it noticeably decreased antioxidant enzyme superoxide dismutase (SOD) and catalase (CAT) activity in C. pilosula leaves, reduced the content of H2O2 and malondialdehyde (MDA), and weakened the peroxidation of cell membrane lipids, which reduced the damage of abiotic stress to C. pilosula. Research has shown that it had obvious effects on levels of nitrogen and carbon metabolic enzymes. For example, sucrose synthase (SS) and acid invertase (AI) levels in C. pilosula roots were nearly 1.43 and 1.7 times higher, respectively, than those in the control (CK) group. In addition, it was notable that the production of CPPs and Lob, the most significant secondary metabolites in C. pilosula, were influenced by Trichoderma strain RHTA01. The obtained results indicate that inoculating C. pilosula with Trichoderma stimulates the carbon and nitrogen metabolism of the plant, and helps to increase the content of CPPs and Lob in the root of the plant.
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Affiliation(s)
- Yonggang Wang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China.
| | - Jiaping Yuan
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Shaowei Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Hui
- Gansu Shule River Basin Water Resources Bureau, Yumen 735200, China.
| | - Yuanli Li
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Kai Chen
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Tongtong Meng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China; Gansu Academy for water Conservancy, Lanzhou 730030, China
| | - Chengqun Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feifan Leng
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
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20
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Scheffer G, Hubert CRJ, Enning DR, Lahme S, Mand J, de Rezende JR. Metagenomic Investigation of a Low Diversity, High Salinity Offshore Oil Reservoir. Microorganisms 2021; 9:2266. [PMID: 34835392 PMCID: PMC8621343 DOI: 10.3390/microorganisms9112266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Oil reservoirs can represent extreme environments for microbial life due to low water availability, high salinity, high pressure and naturally occurring radionuclides. This study investigated the microbiome of saline formation water samples from a Gulf of Mexico oil reservoir. Metagenomic analysis and associated anaerobic enrichment cultures enabled investigations into metabolic potential for microbial activity and persistence in this environment given its high salinity (4.5%) and low nutrient availability. Preliminary 16S rRNA gene amplicon sequencing revealed very low microbial diversity. Accordingly, deep shotgun sequencing resulted in nine metagenome-assembled genomes (MAGs), including members of novel lineages QPJE01 (genus level) within the Halanaerobiaceae, and BM520 (family level) within the Bacteroidales. Genomes of the nine organisms included respiratory pathways such as nitrate reduction (in Arhodomonas, Flexistipes, Geotoga and Marinobacter MAGs) and thiosulfate reduction (in Arhodomonas, Flexistipes and Geotoga MAGs). Genomic evidence for adaptation to high salinity, withstanding radioactivity, and metal acquisition was also observed in different MAGs, possibly explaining their occurrence in this extreme habitat. Other metabolic features included the potential for quorum sensing and biofilm formation, and genes for forming endospores in some cases. Understanding the microbiomes of deep biosphere environments sheds light on the capabilities of uncultivated subsurface microorganisms and their potential roles in subsurface settings, including during oil recovery operations.
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Affiliation(s)
- Gabrielle Scheffer
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada;
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
| | - Dennis R. Enning
- Faculty of Life Sciences and Technology, Berlin University of Applied Sciences and Technology, D-13347 Berlin, Germany;
| | - Sven Lahme
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Jaspreet Mand
- Exxon Mobil Upstream Research Company, Spring, TX 77389, USA;
| | - Júlia R. de Rezende
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; (S.L.); (J.R.d.R.)
- The Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AS, UK
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21
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Gomaa OM, Abd El Kareem H, Selim N. Nitrate modulation of Bacillus sp. biofilm components: a proposed model for sustainable bioremediation. Biotechnol Lett 2021; 43:2185-2197. [PMID: 34510307 DOI: 10.1007/s10529-021-03185-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
The presence of different pollutants in wastewater hinder microbial growth, compromise enzymatic activity or compete for electrons required for bioremediation pathway. Therefore, there is a need to use a single microorganism that is capable of tolerating different toxic compounds and can perform simultaneous bioremediation. In the present study, nitrate reducing bacteria capable of decolorizing azo dye was identified as Bacillus subtillis sp. DN using protein profiling, morphological and biochemical tests X-ray diffraction pattern, Raman spectroscopy and cyclic voltammetry confirm that the bacterium under study possesses membrane-bound nitrate reductase and that is capable of direct electron transfer. The addition of nitrate concentrations (0-50 mM) resulted in increased biofilm formation with variable exopolysaccharides, protein, and eDNA. Fourier Transform Infrared spectrum revealed the presence of a biopolymer at high nitrate concentrations. Effective capacitance and conductivity of the cells grown in different nitrate concentrations suggest changes in the relative position of polar groups, their relative orientation and permeability of cell membrane as detected by dielectric spectroscopy. The increase in biofilm shifted the removal of the azo dye from biodegradation to bioadsorption. Our results indicate that nitrate modulates biofilm components. Bacillus sp. DN granular biofilm can be used for simultaneous nitrate and azo dye removal from wastewater.
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Affiliation(s)
- Ola M Gomaa
- Radiation Microbiology Department, National Center for Radiation Research and Tecnology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt.
| | - Hussein Abd El Kareem
- Radiation Microbiology Department, National Center for Radiation Research and Tecnology (NCRRT), Egyptian Atomic Energy Authority, Cairo, Egypt
| | - Nabila Selim
- Physics Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
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22
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Asamoto CK, Rempfert KR, Luu VH, Younkin AD, Kopf SH. Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5537-5546. [PMID: 33687201 DOI: 10.1021/acs.est.0c07816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (14N, 15N) and oxygen (16O, 18O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (18ε/15ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the 18ε/15ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of 18ε/15ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an 18ε/15ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in 18ε/15ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar 18ε/15ε signatures.
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Affiliation(s)
- Ciara K Asamoto
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Kaitlin R Rempfert
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Victoria H Luu
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
| | - Adam D Younkin
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Sebastian H Kopf
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
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23
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Yang J, Feng L, Pi S, Cui D, Ma F, Zhao HP, Li A. A critical review of aerobic denitrification: Insights into the intracellular electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139080. [PMID: 32417477 DOI: 10.1016/j.scitotenv.2020.139080] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/04/2020] [Accepted: 04/26/2020] [Indexed: 05/23/2023]
Abstract
Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.
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Affiliation(s)
- Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Di Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China; Engineering Research Center for Medicine, College of Pharmacy, Harbin University of Commerce, Harbin 150076, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
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24
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Vo CDT, Michaud J, Elsen S, Faivre B, Bouveret E, Barras F, Fontecave M, Pierrel F, Lombard M, Pelosi L. The O 2-independent pathway of ubiquinone biosynthesis is essential for denitrification in Pseudomonas aeruginosa. J Biol Chem 2020; 295:9021-9032. [PMID: 32409583 PMCID: PMC7335794 DOI: 10.1074/jbc.ra120.013748] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/10/2020] [Indexed: 01/05/2023] Open
Abstract
Many proteobacteria, such as Escherichia coli, contain two main types of quinones: benzoquinones, represented by ubiquinone (UQ) and naphthoquinones, such as menaquinone (MK), and dimethyl-menaquinone (DMK). MK and DMK function predominantly in anaerobic respiratory chains, whereas UQ is the major electron carrier in the reduction of dioxygen. However, this division of labor is probably not very strict. Indeed, a pathway that produces UQ under anaerobic conditions in an UbiU-, UbiV-, and UbiT-dependent manner has been discovered recently in E. coli Its physiological relevance is not yet understood, because MK and DMK are also present in E. coli Here, we established that UQ9 is the major quinone of Pseudomonas aeruginosa and is required for growth under anaerobic respiration (i.e. denitrification). We demonstrate that the ORFs PA3911, PA3912, and PA3913, which are homologs of the E. coli ubiT, ubiV, and ubiU genes, respectively, are essential for UQ9 biosynthesis and, thus, for denitrification in P. aeruginosa These three genes here are called ubiTPa , ubiVPa , and ubiUPa We show that UbiVPa accommodates an iron-sulfur [4Fe-4S] cluster. Moreover, we report that UbiUPa and UbiTPa can bind UQ and that the isoprenoid tail of UQ is the structural determinant required for recognition by these two Ubi proteins. Since the denitrification metabolism of P. aeruginosa is believed to be important for the pathogenicity of this bacterium in individuals with cystic fibrosis, our results highlight that the O2-independent UQ biosynthetic pathway may represent a target for antibiotics development to manage P. aeruginosa infections.
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Affiliation(s)
- Chau-Duy-Tam Vo
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Julie Michaud
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Sylvie Elsen
- Biology of Cancer and Infection, U1036 INSERM, CEA, Université Grenoble Alpes, ERL5261 CNRS, Grenoble, France
| | - Bruno Faivre
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Emmanuelle Bouveret
- SAMe Unit, Department of Microbiology, Institut Pasteur, Paris, France; IMM-UMR 2001 CNRS-Institut Pasteur, Paris, France
| | - Frédéric Barras
- SAMe Unit, Department of Microbiology, Institut Pasteur, Paris, France; IMM-UMR 2001 CNRS-Institut Pasteur, Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France
| | - Fabien Pierrel
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France
| | - Murielle Lombard
- Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS UMR 8229, PSL Research University, Sorbonne Université, Paris, France.
| | - Ludovic Pelosi
- CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, Université Grenoble Alpes, Grenoble, France.
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25
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Salah ZB, Charles CJ, Humphreys PN, Laws AP, Rout SP. Genomic Insights Into A Novel, Alkalitolerant Nitrogen Fixing Bacteria, Azonexus sp. Strain ZS02. J Genomics 2019; 7:1-6. [PMID: 30662569 PMCID: PMC6328298 DOI: 10.7150/jgen.28153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/09/2018] [Indexed: 02/03/2023] Open
Abstract
Alkaline environments represent a significant challenge to the growth of micro-organisms. Despite this, there are a number of alkaline environments which contain active microbial communities. Here we describe the genome of a diazotrophic, alkalitolerant strain of Azonexus, which was isolated from a microcosm seeded with hyperalkaline soils resulting from lime depositions. The isolate has a genome size 3.60 Mb with 3431 protein coding genes. The proteome indicated the presence of genes associated with the cycling of nitrogen, in particular the fixation of atmospheric nitrogen. Although closely related to Azonexus hydrophilus strain d8-1 by both 16S (97.9%) and in silico gDNA (84.1%) relatedness, the isolate demonstrates a pH tolerance above that reported for this strain. The proteome contained genes for the complete Na+/H+ antiporter (subunits A to G) for cytoplasmic pH regulation; this may account for the phenotypic characteristics of this strain which exhibited optimal growth conditions of pH 9 and 30°C.
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Affiliation(s)
- Zohier B Salah
- Department of Biological and Geographical Sciences, University of Huddersfield, Queensgate Campus, Huddersfield, United Kingdom, HD1 3DH
| | - Christopher J Charles
- Department of Biological and Geographical Sciences, University of Huddersfield, Queensgate Campus, Huddersfield, United Kingdom, HD1 3DH
| | - Paul N Humphreys
- Department of Biological and Geographical Sciences, University of Huddersfield, Queensgate Campus, Huddersfield, United Kingdom, HD1 3DH
| | - Andrew P Laws
- Department of Chemical Sciences, University of Huddersfield, Queensgate Campus, Huddersfield, United Kingdom, HD1 3DH
| | - Simon P Rout
- Department of Biological and Geographical Sciences, University of Huddersfield, Queensgate Campus, Huddersfield, United Kingdom, HD1 3DH
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26
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Mabey T, Andrea Cristaldi D, Oyston P, Lymer KP, Stulz E, Wilks S, William Keevil C, Zhang X. Bacteria and nanosilver: the quest for optimal production. Crit Rev Biotechnol 2019; 39:272-287. [DOI: 10.1080/07388551.2018.1555130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas Mabey
- School of Engineering & Institute for Life Sciences, University of Southampton, Southampton, UK
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Domenico Andrea Cristaldi
- School of Engineering & Institute for Life Sciences, University of Southampton, Southampton, UK
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Petra Oyston
- Chemical, Biological and Radiological Division, Dstl Porton Down, Salisbury, UK
| | - Karl P. Lymer
- Platform Systems Division, Dstl Porton Down, Salisbury, UK
| | - Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Sandra Wilks
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Charles William Keevil
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Xunli Zhang
- School of Engineering & Institute for Life Sciences, University of Southampton, Southampton, UK
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27
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Muras V, Toulouse C, Fritz G, Steuber J. Respiratory Membrane Protein Complexes Convert Chemical Energy. Subcell Biochem 2019; 92:301-335. [PMID: 31214991 DOI: 10.1007/978-3-030-18768-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.
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Affiliation(s)
- Valentin Muras
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Charlotte Toulouse
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Günter Fritz
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Julia Steuber
- Institute of Microbiology, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
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28
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Guo Z, Cui K, Zeng G, Wang J, Guo X. Silver nanomaterials in the natural environment: An overview of their biosynthesis and kinetic behavior. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1325-1336. [PMID: 30189549 DOI: 10.1016/j.scitotenv.2018.06.302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/21/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Silver nanomaterials (Ag NMs) are fabricated by many biological components in our environment. Recently, research on their biosynthesis and reactions has become a focus of attention. Due to the complexity of biological systems and samples, specific processes and mechanisms involving Ag NMs are difficult to identify and elucidate on the molecular and chemical-bond level. The microorganisms and composite components of plant extracts are of great interest in many biological syntheses. Although potential biomolecules have been shown to play essential roles in biological systems in Ag NM biosynthesis, the detailed mechanism of the electron transfer process and crucial molecules that control this reaction have only recently come into focus. The reactive behavior of the Ag NMs is of great significance for understanding their overall behavior and toxicity. Additionally, only limited knowledge is available about their kinetics. All reactions involve chemical bond formation, electron transfer, or electrostatic interactions. An overview is presented of the biosynthesis of Ag NMs based on molecular supports including a nitrate reductase/NADH oxidase-involved electron transfer reaction and their mechanisms in Ag+ reduction: quinol-mediated mechanism and superoxide-dependent mechanism, and molecular supports in plant extracts, is presented. The environmental reaction kinetics and mechanisms of the interactions of Ag NMs with substances are introduced based on the formation and classification of chemical bonds. The particle-particle reaction kinetics of Ag NMs in the environment are discussed to directly explain their stability and aggregation behavior. The toxicity of Ag NMs is also presented. In addition, future prospects are summarized. This review is the first to provide an insight into the mediating molecules and chemical bonds involved in the biosynthesis, kinetics, and mechanisms of action of Ag NMs.
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Affiliation(s)
- Zhi Guo
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China.
| | - Kangping Cui
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Jiajia Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xingpan Guo
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
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29
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Kuang S, Fan X, Peng R. Quantitative proteomic analysis ofRhodococcus ruberresponsive to organic solvents. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1533432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sufang Kuang
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
| | - Xin Fan
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
| | - Ren Peng
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
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30
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Zanello P. Structure and electrochemistry of proteins harboring iron-sulfur clusters of different nuclearities. Part II. [4Fe-4S] and [3Fe-4S] iron-sulfur proteins. J Struct Biol 2018; 202:250-263. [DOI: 10.1016/j.jsb.2018.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/11/2018] [Accepted: 01/29/2018] [Indexed: 01/27/2023]
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31
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Nitrate Reductases Are Relocalized to the Nucleus by AtSIZ1 and Their Levels Are Negatively Regulated by COP1 and Ammonium. Int J Mol Sci 2018; 19:ijms19041202. [PMID: 29662028 PMCID: PMC5979280 DOI: 10.3390/ijms19041202] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 01/18/2023] Open
Abstract
Nitrate reductases (NRs) catalyze the first step in the reduction of nitrate to ammonium. NR activity is regulated by sumoylation through the E3 ligase activity of AtSIZ1. However, it is not clear how NRs interact with AtSIZ1 in the cell, or how nitrogen sources affect NR levels and their cellular localization. Here, we show that the subcellular localization of NRs is modulated by the E3 SUMO (Small ubiquitin-related modifier) ligase AtSIZ1 and that NR protein levels are regulated by nitrogen sources. Transient expression analysis of GFP fusion proteins in onion epidermal cells showed that the NRs NIA1 and NIA2 localize to the cytoplasmic membrane, and that AtSIZ1 localizes to the nucleoplasm, including nuclear bodies, when expressed separately, whereas NRs and AtSIZ1 localize to the nucleus when co-expressed. Nitrate did not affect the subcellular localization of the NRs, but it caused AtSIZ1 to move from the nucleus to the cytoplasm. NRs were not detected in ammonium-treated cells, whereas the localization of AtSIZ1 was not altered by ammonium treatment. NR protein levels increased in response to nitrate but decreased in response to ammonium. In addition, NR protein levels increased in response to a 26S proteasome inhibitor and in cop1-4 and DN-COP1-overexpressing transgenic plants. NR protein degradation occurred later in cop1-4 than in the wild-type, although the NR proteins did not interact with COP1. Therefore, AtSIZ1 controls nuclear localization of NR proteins, and ammonium negatively regulates their levels. The function and stability of NR proteins might be post-translationally modulated by ubiquitination.
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32
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Tsai CL, Tainer JA. Robust Production, Crystallization, Structure Determination, and Analysis of [Fe-S] Proteins: Uncovering Control of Electron Shuttling and Gating in the Respiratory Metabolism of Molybdopterin Guanine Dinucleotide Enzymes. Methods Enzymol 2017; 599:157-196. [PMID: 29746239 DOI: 10.1016/bs.mie.2017.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Fe-S] clusters are essential cofactors in all domains of life. They play many biological roles due to their unique abilities for electron transfer and conformational control. Yet, producing and analyzing Fe-S proteins can be difficult and even misleading if not done anaerobically. Due to unique redox properties of [Fe-S] clusters and their oxygen sensitivity, they pose multiple challenges and can lose enzymatic activity or cause their component proteins to be structurally disordered due to [Fe-S] cluster oxidation and loss in air. Here we highlight tested protocols and strategies enabling efficient and stable [Fe-S] protein production, purification, crystallization, X-ray diffraction data collection, and structure determination. From multiple high-resolution anaerobic crystal structures, we furthermore analyze exemplary data defining [Fe-S] clusters, substrate entry, and product exit for the functional oxidation states of type II molybdo-bis(molybdopterin guanine dinucleotide) (Mo-bisMGD) enzymes. Notably, these enzymes perform electron shuttling between quinone pools and specific substrates to catalyze respiratory metabolism. The identified structure-activity relationships for this enzyme class have broad implications germane to perchlorate environments on Earth and Mars extending to an alternative mechanism underlying metabolic origins for the evolution of the oxygen atmosphere. Integrated structural analyses of type II Mo-bisMGD enzymes unveil novel distinctive shared molecular mechanisms for dynamic control of substrate entry and product release gated by hydrophobic residues. Collective findings support a prototypic model for type II Mo-bisMGD enzymes including insights for a fundamental molecular mechanistic understanding of selectivity and regulation by a conformationally gated channel with general implications for [Fe-S] cluster respiratory enzymes.
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Affiliation(s)
- Chi-Lin Tsai
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - John A Tainer
- The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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33
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Ferrari E, Walter MC, Huptas C, Scherer S, Müller-Herbst S. Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698. Front Microbiol 2017; 8:1672. [PMID: 28919887 PMCID: PMC5585140 DOI: 10.3389/fmicb.2017.01672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/17/2017] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to analyze the adaptation of the environmental Listeria weihenstephanensis DSM 24698 to anaerobiosis. The complete circular genome sequence of this species is reported and the adaptation of L. weihenstephanensis DSM 24698 to oxygen availability was investigated by global transcriptional analyses via RNAseq at 18 and 34°C. A list of operons was created based on the transcriptional data. Forty-two genes were upregulated anaerobically and 62 genes were downregulated anaerobically. The oxygen dependent gene expression of selected genes was further validated via qPCR. Many of the differentially regulated genes encode metabolic enzymes indicating broad metabolic adaptations with respect to oxygen availability. Genes showing the strongest oxygen-dependent adaption encoded nitrate (narGHJI) and nitrite (nirBD) reductases. Together with the observation that nitrate supported anaerobic growth, these data indicate that L. weihenstephanensis DSM 24698 performs anaerobic nitrate respiration. The wide overlap between the oxygen-dependent transcriptional regulation at 18 and 34°C suggest that temperature does not play a key role in the oxygen-dependent transcriptional regulation of L. weihenstephanensis DSM 24698.
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Affiliation(s)
- Elena Ferrari
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Mathias C. Walter
- Department of Genome-Oriented Bioinformatics, Technische Universität MünchenFreising, Germany
| | - Christopher Huptas
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Siegfried Scherer
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
| | - Stefanie Müller-Herbst
- Chair of Microbial Ecology, Technische Universität MünchenFreising, Germany
- ZIEL—Institute for Food & Health, Technische Universität MünchenFreising, Germany
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Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process. Appl Microbiol Biotechnol 2017; 101:3895-3906. [DOI: 10.1007/s00253-017-8163-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022]
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NapB in excess inhibits growth of Shewanella oneidensis by dissipating electrons of the quinol pool. Sci Rep 2016; 6:37456. [PMID: 27857202 PMCID: PMC5114592 DOI: 10.1038/srep37456] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023] Open
Abstract
Shewanella, a group of ubiquitous bacteria renowned for respiratory versatility, thrive in environments where various electron acceptors (EAs) of different chemical and physiological characteristics coexist. Despite being extensively studied, we still know surprisingly little about strategies by which multiple EAs and their interaction define ecophysiology of these bacteria. Previously, we showed that nitrite inhibits growth of the genus representative Shewanella oneidensis on fumarate and presumably some other CymA (quinol dehydrogenase)-dependent EAs by reducing cAMP production, which in turn leads to lowered expression of nitrite and fumarate reductases. In this study, we demonstrated that inhibition of fumarate growth by nitrite is also attributable to overproduction of NapB, the cytochrome c subunit of nitrate reductase. Further investigations revealed that excessive NapB per se inhibits growth on all EAs tested, including oxygen. When overproduced, NapB acts as an electron shuttle to dissipate electrons of the quinol pool, likely to extracellullar EAs, because the Mtr system, the major electron transport pathway for extracellular electron transport, is implicated. The study not only sheds light on mechanisms by which certain EAs, especially toxic ones, impact the bacterial ecophysiology, but also provides new insights into how electron shuttle c-type cytochromes regulate multi-branched respiratory networks.
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