1
|
Jiang Z, Liu S, Zhang D, Sha Z. The Diversity and Metabolism of Culturable Nitrate-Reducing Bacteria from the Photic Zone of the Western North Pacific Ocean. MICROBIAL ECOLOGY 2023; 86:2781-2789. [PMID: 37552473 PMCID: PMC10640468 DOI: 10.1007/s00248-023-02284-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
To better understand bacterial communities and metabolism under nitrogen deficiency, 154 seawater samples were obtained from 5 to 200 m at 22 stations in the photic zone of the Western North Pacific Ocean. Total 634 nitrate-utilizing bacteria were isolated using selective media and culture-dependent methods, and 295 of them were positive for nitrate reduction. These nitrate-reducing bacteria belonged to 19 genera and 29 species and among them, Qipengyuania flava, Roseibium aggregatum, Erythrobacter aureus, Vibrio campbellii, and Stappia indica were identified from all tested seawater layers of the photic zone and at almost all stations. Twenty-nine nitrate-reducing strains representing different species were selected for further the study of nitrogen, sulfur, and carbon metabolism. All 29 nitrate-reducing isolates contained genes encoding dissimilatory nitrate reduction or assimilatory nitrate reduction. Six nitrate-reducing isolates can oxidize thiosulfate based on genomic analysis and activity testing, indicating that nitrate-reducing thiosulfate-oxidizing bacteria exist in the photic zone. Five nitrate-reducing isolates obtained near the chlorophyll a-maximum layer contained a dimethylsulfoniopropionate synthesis gene and three of them contained both dimethylsulfoniopropionate synthesis and cleavage genes. This suggests that nitrate-reducing isolates may participate in dimethylsulfoniopropionate synthesis and catabolism in photic seawater. The presence of multiple genes for chitin degradation and extracellular peptidases may indicate that almost all nitrate-reducing isolates (28/29) can use chitin and proteinaceous compounds as important sources of carbon and nitrogen. Collectively, these results reveal culturable nitrate-reducing bacterial diversity and have implications for understanding the role of such strains in the ecology and biogeochemical cycles of nitrogen, sulfur, and carbon in the oligotrophic marine photic zone.
Collapse
Affiliation(s)
- Zhichen Jiang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sizhen Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dechao Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laoshan Laboratory, Qingdao, 266237, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhongli Sha
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laoshan Laboratory, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
2
|
Stanfill SB, Hecht SS, Joerger AC, González PJ, Maia LB, Rivas MG, Moura JJG, Gupta AK, Le Brun NE, Crack JC, Hainaut P, Sparacino-Watkins C, Tyx RE, Pillai SD, Zaatari GS, Henley SJ, Blount BC, Watson CH, Kaina B, Mehrotra R. From cultivation to cancer: formation of N-nitrosamines and other carcinogens in smokeless tobacco and their mutagenic implications. Crit Rev Toxicol 2023; 53:658-701. [PMID: 38050998 DOI: 10.1080/10408444.2023.2264327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/20/2023] [Indexed: 12/07/2023]
Abstract
Tobacco use is a major cause of preventable morbidity and mortality globally. Tobacco products, including smokeless tobacco (ST), generally contain tobacco-specific N-nitrosamines (TSNAs), such as N'-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-butanone (NNK), which are potent carcinogens that cause mutations in critical genes in human DNA. This review covers the series of biochemical and chemical transformations, related to TSNAs, leading from tobacco cultivation to cancer initiation. A key aim of this review is to provide a greater understanding of TSNAs: their precursors, the microbial and chemical mechanisms that contribute to their formation in ST, their mutagenicity leading to cancer due to ST use, and potential means of lowering TSNA levels in tobacco products. TSNAs are not present in harvested tobacco but can form due to nitrosating agents reacting with tobacco alkaloids present in tobacco during certain types of curing. TSNAs can also form during or following ST production when certain microorganisms perform nitrate metabolism, with dissimilatory nitrate reductases converting nitrate to nitrite that is then released into tobacco and reacts chemically with tobacco alkaloids. When ST usage occurs, TSNAs are absorbed and metabolized to reactive compounds that form DNA adducts leading to mutations in critical target genes, including the RAS oncogenes and the p53 tumor suppressor gene. DNA repair mechanisms remove most adducts induced by carcinogens, thus preventing many but not all mutations. Lastly, because TSNAs and other agents cause cancer, previously documented strategies for lowering their levels in ST products are discussed, including using tobacco with lower nornicotine levels, pasteurization and other means of eliminating microorganisms, omitting fermentation and fire-curing, refrigerating ST products, and including nitrite scavenging chemicals as ST ingredients.
Collapse
Affiliation(s)
- Stephen B Stanfill
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andreas C Joerger
- Structural Genomics Consortium (SGC), Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pablo J González
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - Luisa B Maia
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | - Maria G Rivas
- Department of Physics, Universidad Nacional Litoral, and CONICET, Santa Fe, Argentina
| | - José J G Moura
- Department of Chemistry, LAQV, REQUIMTE, NOVA School of Science and Technology (FCT NOVA), Caparica, Portugal
| | | | - Nick E Le Brun
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Jason C Crack
- School of Chemistry, Centre for Molecular and Structural Biochemistry, University of East Anglia, Norwich, UK
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Grenoble Alpes University, Grenoble, France
| | - Courtney Sparacino-Watkins
- University of Pittsburgh, School of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Vascular Medicine Institute, PA, USA
| | - Robert E Tyx
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suresh D Pillai
- Department of Food Science & Technology, National Center for Electron Beam Research, Texas A&M University, College Station, TX, USA
| | - Ghazi S Zaatari
- Department of Pathology and Laboratory Medicine, American University of Beirut, Beirut, Lebanon
| | - S Jane Henley
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin C Blount
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clifford H Watson
- Tobacco and Volatiles Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Kaina
- Institute of Toxicology, University Medical Center, Mainz, Germany
| | - Ravi Mehrotra
- Centre for Health, Innovation and Policy Foundation, Noida, India
| |
Collapse
|
3
|
Qi Z, Gao A, Li L, Li Z, Zhang W, Dong S, Liu X. A novel strategy to improving Rhodobacter azotoformans denitrification efficiency: Insight into the role of a two-component system NtrX/Y in denitrification regulation. BIORESOURCE TECHNOLOGY 2023; 368:128349. [PMID: 36400277 DOI: 10.1016/j.biortech.2022.128349] [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: 09/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Transcription factors (TFs) can manage the coordinated expression of genes clusters or multiple genes. TF was used to improve bacterial denitrification ability in this study. During denitrification, the ntrY of R. azotoformans, which encodes the sensor of NtrX/Y system, was significantly upregulated in transcription. Denitrification of the mutant △ntrY was significantly inhibited, and it was recovered after replenishing this gene to the mutant, which indicates the NtrX/Y system plays an important role in regulating bacterial denitrification. According to additional research, the NtrX/Y system regulates bacterial denitrification by directly promoting the expression of the nitrite reductase. ntrY overexpression appears to accelerate bacterial denitrification, and the introduction of a strong promoter tac in conjunction with iron supply optimization increases the rate by 72% further. This study realizes bacterial denitrification enhancement from the perspective of global transcription regulation, which provides a novel strategy for improving microbial ability to degrade pollutants.
Collapse
Affiliation(s)
- Zhengliang Qi
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China.
| | - Anxin Gao
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Lu Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Zhen Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Wenyue Zhang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Shuhan Dong
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Xinli Liu
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| |
Collapse
|
4
|
Alloul A, Blansaer N, Cabecas Segura P, Wattiez R, Vlaeminck SE, Leroy B. Dehazing redox homeostasis to foster purple bacteria biotechnology. Trends Biotechnol 2023; 41:106-119. [PMID: 35843758 DOI: 10.1016/j.tibtech.2022.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 12/27/2022]
Abstract
Purple non-sulfur bacteria (PNSB) show great potential for environmental and industrial biotechnology, producing microbial protein, biohydrogen, polyhydroxyalkanoates (PHAs), pigments, etc. When grown photoheterotrophically, the carbon source is typically more reduced than the PNSB biomass, which leads to a redox imbalance. To mitigate the excess of electrons, PNSB can exhibit several 'electron sinking' strategies, such as CO2 fixation, N2 fixation, and H2 and PHA production. The lack of a comprehensive (over)view of these redox strategies is hindering the implementation of PNSB for biotechnology applications. This review aims to present the state of the art of redox homeostasis in phototrophically grown PNSB, presenting known and theoretically expected strategies, and discussing them from stoichiometric, thermodynamic, metabolic, and economic points of view.
Collapse
Affiliation(s)
- Abbas Alloul
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium.
| | - Naïm Blansaer
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | | | - Ruddy Wattiez
- Laboratory of Proteomics and Microbiology, University of Mons, Mons, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | - Baptiste Leroy
- Laboratory of Proteomics and Microbiology, University of Mons, Mons, Belgium
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Abstract
Lagoons are fragile marine ecosystems that are considerably affected by anthropogenic pollutants. We performed a spatiotemporal characterization of the microbiome of two Moroccan lagoons, Marchica and Oualidia, both classified as Ramsar sites, the former on the Mediterranean coast and the latter on the Atlantic coast. We investigated their microbial diversity and abundance using 16S rRNA amplicon- and shotgun-based metagenomics approaches during the summers of 2014 and 2015. The bacterial microbiome was composed primarily of Proteobacteria (25–53%, 29–29%), Cyanobacteria (34–12%, 11–0.53%), Bacteroidetes (24–16%, 23–43%), Actinobacteria (7–11%, 13–7%), and Verrucomicrobia (4–1%, 15–14%) in Marchica and Oualidia in 2014 and 2015, respectively. Interestingly, 48 strains were newly reported in lagoon ecosystems, while eight unknown viruses were detected in Mediterranean Marchica only. Statistical analysis showed higher microbial diversity in the Atlantic lagoon than in the Mediterranean lagoon and a robust relationship between alpha diversity and geographic sampling locations. This first-ever metagenomics study on Moroccan aquatic ecosystems enriched the national catalog of marine microorganisms. They will be investigated as candidates for bioindication properties, biomonitoring potential, biotechnology valorization, biodiversity protection, and lagoon health assessment.
Collapse
|
7
|
Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
8
|
Li Z, Li L, Sun H, Wang W, Yang Y, Qi Z, Liu X. Ammonia assimilation: A double-edged sword influencing denitrification of Rhodobacter azotoformans and for nitrogen removal of aquaculture wastewater. BIORESOURCE TECHNOLOGY 2022; 345:126495. [PMID: 34883195 DOI: 10.1016/j.biortech.2021.126495] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
NO3--N and NH4+-N are two prevalent nitrogenous pollutants in aquaculture wastewater posing a significant health risk to aquatic animals. R. azotoformans ATCC17025 can rapidly denitrify to remove NO3--N, assimilating NH4+-N. The study investigated the influence of ammonia assimilation on bacterial denitrification. Results revealed that low concentration of NH4+-N (≤0.3 mM) accelerated denitrification, whereas high concentration inhibited it. RT-qPCR indicated that the inhibition of NO reduction under high concentration of NH4+-N was the primary cause of denitrification depression, whereas low concentration of NH4+-N enhanced the synthesis of practically all enzymes involved in denitrification. Finally, nitrogen-rich aquaculture effluent was effectively treated in lab-scale using a semi-continuous operation that provided an appropriate NH4+-N concentration for denitrification. This semi-continuous operation treated wastewater 2 times faster than the batch operation and the content of nitrogen decreased to effluent standard. The study can provide guidance for nitrogen removal of aquaculture wastewater with bioaugmentation.
Collapse
Affiliation(s)
- Zhen Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Lu Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Haoyu Sun
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Wenjuan Wang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Yuying Yang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Zhengliang Qi
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China.
| | - Xinli Liu
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| |
Collapse
|
9
|
Eltarahony M, Ibrahim A, El-shall H, Ibrahim E, Althobaiti F, Fayad E. Antibacterial, Antifungal and Antibiofilm Activities of Silver Nanoparticles Supported by Crude Bioactive Metabolites of Bionanofactories Isolated from Lake Mariout. Molecules 2021; 26:3027. [PMID: 34069487 PMCID: PMC8161313 DOI: 10.3390/molecules26103027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Lake Mariout is one of the polluted coastal marine ecosystems in Egypt which is considered to be a reservoir of serious effluents from different anthropogenic activities. Such selective pressure enforces indigenous microbial populations to acquire new advantageous themes. Thus, in this study, two Streptomyces strains were screened, from Lake Mariout's sediment for bioreduction of 5 mM AgNO3. Both strains were identified molecularly; their biochemical and physiological characterization revealed their ability to secrete bioactive metabolites with antagonistic activity. The cultural and incubation conditions influencing AgNPs productivity were evaluated. Subsequently, the physicochemical properties of the biofabricated AgNPs were pursued. UV-Vis spectroscopy detected surface plasmon resonance at range 458-422 nm. XRD indicated crystalline, pure, face-centered cubic AgNPs; EDX demonstrated strong silver signal at 3.5 keV. Besides, FT-IR and TGA analysis unveiled self-stabilization and functionalization of AgNPs by bioorganic molecules. However, electron microscopy micrographs depicted numerous uniform spherical AgNPs (1.17-13.3 nm). Potent bactericidal and fungicide activity were recorded by zone of inhibition assay at 50 μg/mL. Further, the antibiofilm activity was exerted in a dose-dependent manner. Moreover, the conjugation of AgNPs with the crude bioactive metabolites of both bionanofactories ameliorated the antimicrobial potency, reflecting a synergistic efficiency versus examined pathogens (free-living and biofilm).
Collapse
Affiliation(s)
- Marwa Eltarahony
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Amany Ibrahim
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Hadeel El-shall
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Eman Ibrahim
- Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City 21934, Alexandria, Egypt; (H.E.-s.); (E.I.)
| | - Fayez Althobaiti
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
| | - Eman Fayad
- Department of Biotechnology, College of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.)
| |
Collapse
|
10
|
Ren J, Wei C, Ma H, Dai M, Fan J, Liu Y, Wu Y, Han R. The Nitrogen-Removal Efficiency of a Novel High-Efficiency Salt-Tolerant Aerobic Denitrifier, Halomonas Alkaliphile HRL-9, Isolated from a Seawater Biofilter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16224451. [PMID: 31766146 PMCID: PMC6888400 DOI: 10.3390/ijerph16224451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/16/2022]
Abstract
Aerobic denitrification microbes have great potential to solve the problem of NO3--N accumulation in industrialized recirculating aquaculture systems (RASs). A novel salt-tolerant aerobic denitrifier was isolated from a marine recirculating aquaculture system (RAS) and identified as Halomonas alkaliphile HRL-9. Its aerobic denitrification performance in different dissolved oxygen concentrations, temperatures, and C/N ratios was studied. Investigations into nitrogen balance and nitrate reductase genes (napA and narG) were also carried out. The results showed that the optimal conditions for nitrate removal were temperature of 30 °C, a shaking speed of 150 rpm, and a C/N ratio of 10. For nitrate nitrogen (NO3--N) (initial concentration 101.8 mg·L-1), the sole nitrogen source of the growth of HRL-9, the maximum NO3--N removal efficiency reached 98.0% after 24 h and the maximum total nitrogen removal efficiency was 77.3% after 48 h. Nitrogen balance analysis showed that 21.7% of NO3--N was converted into intracellular nitrogen, 3.3% of NO3--N was converted into other nitrification products (i.e., nitrous nitrogen, ammonium nitrogen, and organic nitrogen), and 74.5% of NO3--N might be converted to gaseous products. The identification of functional genes confirmed the existence of the napA gene in strain HRL-9, but no narG gene was found. These results confirm that the aerobic denitrification strain, Halomonas alkaliphile HRL-9, which has excellent aerobic denitrification abilities, can also help us understand the microbiological mechanism and transformation pathway of aerobic denitrification in RASs.
Collapse
Affiliation(s)
- Jilong Ren
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Chenzheng Wei
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Hongjing Ma
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Mingyun Dai
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Jize Fan
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Ying Liu
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
| | - Yinghai Wu
- College of Marine and Civil Engineering, Dalian Ocean University, Dalian 116023, China;
- South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, China
| | - Rui Han
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China; (J.R.); (C.W.); (H.M.); (M.D.); (J.F.); (Y.L.)
- Key Laboratory of Environment Controlled Aquaculture, Ministry of Education, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, China
- Correspondence:
| |
Collapse
|
11
|
Wu YW, Yang SH, Hwangbo M, Chu KH. Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system. PLoS One 2019; 14:e0222143. [PMID: 31513626 PMCID: PMC6742469 DOI: 10.1371/journal.pone.0222143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/22/2019] [Indexed: 01/25/2023] Open
Abstract
Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.
Collapse
Affiliation(s)
- Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Shih-Hung Yang
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
12
|
Samad MS, Johns C, Richards KG, Lanigan GJ, de Klein CAM, Clough TJ, Morales SE. Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria. Mol Ecol 2017; 26:5500-5514. [DOI: 10.1111/mec.14275] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Md Sainur Samad
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
| | - Charlotte Johns
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | | | | | | | - Timothy J. Clough
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | - Sergio E. Morales
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
| |
Collapse
|
13
|
Bueno E, Robles EF, Torres MJ, Krell T, Bedmar EJ, Delgado MJ, Mesa S. Disparate response to microoxia and nitrogen oxides of the Bradyrhizobium japonicum napEDABC, nirK and norCBQD denitrification genes. Nitric Oxide 2017; 68:137-149. [DOI: 10.1016/j.niox.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/27/2017] [Accepted: 02/02/2017] [Indexed: 01/25/2023]
|
14
|
Mauffrey F, Martineau C, Villemur R. Importance of the Two Dissimilatory (Nar) Nitrate Reductases in the Growth and Nitrate Reduction of the Methylotrophic Marine Bacterium Methylophaga nitratireducenticrescens JAM1. Front Microbiol 2015; 6:1475. [PMID: 26733997 PMCID: PMC4689864 DOI: 10.3389/fmicb.2015.01475] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/08/2015] [Indexed: 02/04/2023] Open
Abstract
Methylophaga nitratireducenticrescens JAM1 is the only reported Methylophaga species capable of growing under anaerobic conditions with nitrate as electron acceptor. Its genome encodes a truncated denitrification pathway, which includes two nitrate reductases, Nar1 and Nar2; two nitric oxide reductases, Nor1 and Nor2; and one nitrous oxide reductase, Nos; but no nitrite reductase (NirK or NirS). The transcriptome of strain JAM1 cultivated with nitrate and methanol under anaerobic conditions showed the genes for these enzymes were all expressed. We investigated the importance of Nar1 and Nar2 by knocking out narG1, narG2 or both genes. Measurement of the specific growth rate and the specific nitrate reduction rate of the knockout mutants JAM1ΔnarG1 (Nar1) and JAM1ΔnarG2 (Nar2) clearly demonstrated that both Nar systems contributed to the growth of strain JAM1 under anaerobic conditions, but at different levels. The JAM1ΔnarG1 mutant exhibited an important decrease in the nitrate reduction rate that consequently impaired its growth under anaerobic conditions. In JAM1ΔnarG2, the mutation induced a 20-h lag period before nitrate reduction occurred at specific rate similar to that of strain JAM1. The disruption of narG1 did not affect the expression of narG2. However, the expression of the Nar1 system was highly downregulated in the presence of oxygen with the JAM1ΔnarG2 mutant. These results indicated that Nar1 is the major nitrate reductase in strain JAM1 but Nar2 appears to regulate the expression of Nar1.
Collapse
Affiliation(s)
- Florian Mauffrey
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval QC, Canada
| | - Christine Martineau
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval QC, Canada
| | - Richard Villemur
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Laval QC, Canada
| |
Collapse
|
15
|
|
16
|
Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii. Appl Environ Microbiol 2015; 81:5003-14. [PMID: 25979892 DOI: 10.1128/aem.00848-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/12/2015] [Indexed: 12/22/2022] Open
Abstract
Hyphomicrobium spp. are commonly identified as major players in denitrification systems supplied with methanol as a carbon source. However, denitrifying Hyphomicrobium species are poorly characterized, and very few studies have provided information on the genetic and physiological aspects of denitrification in pure cultures of these bacteria. This is a comparative study of three denitrifying Hyphomicrobium species, H. denitrificans ATCC 51888, H. zavarzinii ZV622, and a newly described species, H. nitrativorans NL23, which was isolated from a denitrification system treating seawater. Whole-genome sequence analyses revealed that although they share numerous orthologous genes, these three species differ greatly in their nitrate reductases, with gene clusters encoding a periplasmic nitrate reductase (Nap) in H. nitrativorans, a membrane-bound nitrate reductase (Nar) in H. denitrificans, and one Nap and two Nar enzymes in H. zavarzinii. Concurrently with these differences observed at the genetic level, important differences in the denitrification capacities of these Hyphomicrobium species were determined. H. nitrativorans grew and denitrified at higher nitrate and NaCl concentrations than did the two other species, without significant nitrite accumulation. Significant increases in the relative gene expression levels of the nitrate (napA) and nitrite (nirK) reductase genes were also noted for H. nitrativorans at higher nitrate and NaCl concentrations. Oxygen was also found to be a strong regulator of denitrification gene expression in both H. nitrativorans and H. zavarzinii, although individual genes responded differently in these two species. Taken together, the results presented in this study highlight the potential of H. nitrativorans as an efficient and adaptable bacterium that is able to perform complete denitrification under various conditions.
Collapse
|
17
|
Nitrogen removal characteristics of heterotrophic nitrification-aerobic denitrification by Alcaligenes faecalis C16. Chin J Chem Eng 2015. [DOI: 10.1016/j.cjche.2014.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
18
|
Duan J, Fang H, Su B, Chen J, Lin J. Characterization of a halophilic heterotrophic nitrification-aerobic denitrification bacterium and its application on treatment of saline wastewater. BIORESOURCE TECHNOLOGY 2015; 179:421-428. [PMID: 25557251 DOI: 10.1016/j.biortech.2014.12.057] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 05/03/2023]
Abstract
A novel halophilic bacterium capable of heterotrophic nitrification-aerobic denitrification was isolated from marine sediments and identified as Vibrio diabolicus SF16. It had ability to remove 91.82% of NH4(+)-N (119.77 mg/L) and 99.71% of NO3(-)-N (136.43 mg/L). The nitrogen balance showed that 35.83% of initial NH4(+)-N (119.77 mg/L) was changed to intracellular nitrogen, and 53.98% of the initial NH4(+)-N was converted to gaseous denitrification products. The existence of napA gene further proved the aerobic denitrification ability of strain SF16. The optimum culture conditions were salinity 1-5%, sodium acetate as carbon source, C/N 10, and pH 7.5-9.5. When an aerated biological filter system inoculated with strain SF16 was employed to treat saline wastewater, the average removal efficiency of NH4(+)-N and TN reached 97.14% and 73.92%, respectively, indicating great potential of strain SF16 for future full-scale applications.
Collapse
Affiliation(s)
- Jinming Duan
- Research Center of Water Treatment Engineering, Jimei University, Xiamen 361021, PR China; School of Food and Biological Engineering, Jimei University, Xiamen 361021, PR China.
| | - Hongda Fang
- Research Center of Water Treatment Engineering, Jimei University, Xiamen 361021, PR China; School of Food and Biological Engineering, Jimei University, Xiamen 361021, PR China
| | - Bing Su
- School of Food and Biological Engineering, Jimei University, Xiamen 361021, PR China
| | - Jinfang Chen
- Research Center of Water Treatment Engineering, Jimei University, Xiamen 361021, PR China; School of Food and Biological Engineering, Jimei University, Xiamen 361021, PR China
| | - Jinmei Lin
- Research Center of Water Treatment Engineering, Jimei University, Xiamen 361021, PR China; School of Food and Biological Engineering, Jimei University, Xiamen 361021, PR China
| |
Collapse
|
19
|
Sparacino-Watkins C, Stolz JF, Basu P. Nitrate and periplasmic nitrate reductases. Chem Soc Rev 2014; 43:676-706. [PMID: 24141308 DOI: 10.1039/c3cs60249d] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.
Collapse
|
20
|
Role of norEF in denitrification, elucidated by physiological experiments with Rhodobacter sphaeroides. J Bacteriol 2014; 196:2190-200. [PMID: 24706737 DOI: 10.1128/jb.00003-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many denitrifying organisms contain the norEF gene cluster, which codes for two proteins that are thought to be involved in denitrification because they are expressed during the reduction of nitrite and nitric oxide. The products of both genes are predicted to be membrane associated, and the norE product is a member of the cytochrome c oxidase subunit III family. However, the specific role of norEF is unknown. The denitrification phenotypes of Rhodobacter sphaeroides strains with and without norEF genes were studied, and it was found that loss of norEF lowered the rate of denitrification from nitrate and resulted in accumulation of micromolar concentrations of nitric oxide during denitrification from nitrite. norEF appears to have no direct role in the reduction of nitric oxide; however, since deletion of norEF in the wild-type 2.4.3 strain had essentially no influence on the kinetics of potential nitric oxide reduction (Vmax and Ks), as measured by monitoring the depletion of a bolus of nitric oxide injected into anoxic cultures without any other electron acceptors. However, norEF-deficient cells that had undergone a more chronic exposure to micromolar concentrations of nitric oxide showed an ∼50% reduction in Vmax but no change in apparent Ks. These results can explain the occurrence of norEF in the 2.4.3 strain of R. sphaeroides, which can reduce nitrate to nitrous oxide, and their absence from strains such as 2.4.1, which likely use nitric oxide reductase to mitigate stress due to episodic exposure to nitric oxide from exogenous sources.
Collapse
|
21
|
Huang X, Li W, Zhang D, Qin W. Ammonium removal by a novel oligotrophic Acinetobacter sp. Y16 capable of heterotrophic nitrification-aerobic denitrification at low temperature. BIORESOURCE TECHNOLOGY 2013; 146:44-50. [PMID: 23911816 DOI: 10.1016/j.biortech.2013.07.046] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 06/02/2023]
Abstract
Ammonium removal from source water is usually inhibited by insufficient carbon sources and low temperature in Northeastern China. A strain Y16 was isolated from oligotrophic niche and was identified as Acinetobacter sp. Y16. It demonstrated excellent capability for ammonium removal at 2 °C, and simultaneously produced nitrogen gas as the end product. About 66% of ammonium was removed after 36 h of incubation. Only trace accumulation of nitrate was observed during the process. The utilization of nitrite and nitrate as well as the existence of napA gene further proved the aerobic denitrification ability of strain Y16. Sodium acetate was the most favorable carbon source for ammonium oxidation by strain Y16. High rotation speed was beneficial for ammonium oxidation. Furthermore, strain Y16 could efficiently remove ammonium at low C/N ratio and low temperature conditions, which was advantageous for nitrogen removal from source water under cold temperatures.
Collapse
Affiliation(s)
- Xiaofei Huang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Weiguang Li
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, PR China.
| | - Duoying Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| | - Wen Qin
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
| |
Collapse
|
22
|
Li Y, Katzmann E, Borg S, Schüler D. The periplasmic nitrate reductase nap is required for anaerobic growth and involved in redox control of magnetite biomineralization in Magnetospirillum gryphiswaldense. J Bacteriol 2012; 194:4847-56. [PMID: 22730130 PMCID: PMC3430331 DOI: 10.1128/jb.00903-12] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/18/2012] [Indexed: 11/20/2022] Open
Abstract
The magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. However, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. Here, we show that in the alphaproteobacterium Magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. A complete denitrification pathway, including gene functions for nitrate (nap), nitrite (nir), nitric oxide (nor), and nitrous oxide reduction (nos), was identified. Transcriptional gusA fusions as reporters revealed that except for nap, the highest expression of the denitrification genes coincided with conditions permitting maximum magnetite synthesis. Whereas microaerobic denitrification overlapped with oxygen respiration, nitrate was the only electron acceptor supporting growth in the entire absence of oxygen, and only the deletion of nap genes, encoding a periplasmic nitrate reductase, and not deletion of nor or nos genes, abolished anaerobic growth and also delayed aerobic growth in both nitrate and ammonium media. While loss of nosZ or norCB had no or relatively weak effects on magnetosome synthesis, deletion of nap severely impaired magnetite biomineralization and resulted in fewer, smaller, and irregular crystals during denitrification and also microaerobic respiration, probably by disturbing the proper redox balance required for magnetite synthesis. In contrast to the case for the wild type, biomineralization in Δnap cells was independent of the oxidation state of carbon substrates. Altogether, our data demonstrate that in addition to its essential role in anaerobic respiration, the periplasmic nitrate reductase Nap has a further key function by participating in redox reactions required for magnetite biomineralization.
Collapse
Affiliation(s)
- Yingjie Li
- Ludwig-Maximilians-Universität München, Department Biologie I, Mikrobiologie, Planegg-Martinsried, Germany
| | | | | | | |
Collapse
|
23
|
Kalvelage T, Jensen MM, Contreras S, Revsbech NP, Lam P, Günter M, LaRoche J, Lavik G, Kuypers MMM. Oxygen sensitivity of anammox and coupled N-cycle processes in oxygen minimum zones. PLoS One 2011; 6:e29299. [PMID: 22216239 PMCID: PMC3247244 DOI: 10.1371/journal.pone.0029299] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/23/2011] [Indexed: 01/16/2023] Open
Abstract
Nutrient measurements indicate that 30-50% of the total nitrogen (N) loss in the ocean occurs in oxygen minimum zones (OMZs). This pelagic N-removal takes place within only ~0.1% of the ocean volume, hence moderate variations in the extent of OMZs due to global warming may have a large impact on the global N-cycle. We examined the effect of oxygen (O(2)) on anammox, NH(3) oxidation and NO(3)(-) reduction in (15)N-labeling experiments with varying O(2) concentrations (0-25 µmol L(-1)) in the Namibian and Peruvian OMZs. Our results show that O(2) is a major controlling factor for anammox activity in OMZ waters. Based on our O(2) assays we estimate the upper limit for anammox to be ~20 µmol L(-1). In contrast, NH(3) oxidation to NO(2)(-) and NO(3)(-) reduction to NO(2)(-) as the main NH(4)(+) and NO(2)(-) sources for anammox were only moderately affected by changing O(2) concentrations. Intriguingly, aerobic NH(3) oxidation was active at non-detectable concentrations of O(2), while anaerobic NO(3)(-) reduction was fully active up to at least 25 µmol L(-1) O(2). Hence, aerobic and anaerobic N-cycle pathways in OMZs can co-occur over a larger range of O(2) concentrations than previously assumed. The zone where N-loss can occur is primarily controlled by the O(2)-sensitivity of anammox itself, and not by any effects of O(2) on the tightly coupled pathways of aerobic NH(3) oxidation and NO(3)(-) reduction. With anammox bacteria in the marine environment being active at O(2) levels ~20 times higher than those known to inhibit their cultured counterparts, the oceanic volume potentially acting as a N-sink increases tenfold. The predicted expansion of OMZs may enlarge this volume even further. Our study provides the first robust estimates of O(2) sensitivities for processes directly and indirectly connected with N-loss. These are essential to assess the effects of ocean de-oxygenation on oceanic N-cycling.
Collapse
Affiliation(s)
- Tim Kalvelage
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|