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Giri NC, Mintmier B, Radhakrishnan M, Mielke JW, Wilcoxen J, Basu P. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions. J Biol Inorg Chem 2024; 29:395-405. [PMID: 38782786 DOI: 10.1007/s00775-024-02057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.
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Affiliation(s)
- Nitai C Giri
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Jonathan W Mielke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA.
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Wei M, Zeng X, Han X, Shao Z, Xie Q, Dong C, Wang Y, Qiu Z. Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field. Front Microbiol 2022; 13:930601. [PMID: 36316996 PMCID: PMC9616709 DOI: 10.3389/fmicb.2022.930601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13CVPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.
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Affiliation(s)
- Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiqiu Han
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Xiqiu Han,
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Xie
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanqi Dong
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhongyan Qiu
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
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Wang X, Xie GJ, Tian N, Dang CC, Cai C, Ding J, Liu BF, Xing DF, Ren NQ, Wang Q. Anaerobic microbial manganese oxidation and reduction: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153513. [PMID: 35101498 DOI: 10.1016/j.scitotenv.2022.153513] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Manganese is a vital heavy metal abundant in terrestrial and aquatic environments. Anaerobic manganese redox reactions mediated by microorganisms have been recognized for a long time, which promote elements mobility and bioavailability in the environment. Biological anaerobic redox of manganese serves two reactions, including Mn(II) oxidation and Mn(IV) reduction. This review provides a comprehensive analysis of manganese redox cycles in the environment, closely related to greenhouse gas mitigation, the fate of nutrients, microbial bioremediation, and global biogeochemical cycle, including nitrogen, sulfur, and carbon. The oxidation and reduction of manganese occur cyclically and simultaneously in the environment. Anaerobic reduction of Mn(IV) receives electrons from methane, ammonium and sulfide, while Mn(II) can function as an electron source for manganese-oxidizing microorganisms for autotrophic denitrification and photosynthesis. The anaerobic redox transition between Mn(II) and Mn(IV) promotes a dynamic biogeochemical cycle coupled to microorganisms in water, soil and sediment environments. The discussion of reaction mechanisms, microorganism diversity, environmental influence bioremediation and application identify the research gaps for future investigation, which provides promising opportunities for further development of biotechnological applications to remediate contaminated environments.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Ning Tian
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
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Nielsen TK, Horemans B, Lood C, T'Syen J, van Noort V, Lavigne R, Ellegaard-Jensen L, Hylling O, Aamand J, Springael D, Hansen LH. The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids. Sci Rep 2021; 11:18943. [PMID: 34556718 PMCID: PMC8460812 DOI: 10.1038/s41598-021-98184-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 11/14/2022] Open
Abstract
Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Section for Microbiology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Copenhagen, Denmark
| | - Benjamin Horemans
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium.,Sustainable Materials Unit, BAT Knowledge Centre, Vlaams Instituut voor Technologisch Onderzoek, Mol, Belgium
| | - Cédric Lood
- Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Jeroen T'Syen
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Lea Ellegaard-Jensen
- Section of Environmental Microbiology and Circular Resource Flow, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Ole Hylling
- Section of Environmental Microbiology and Circular Resource Flow, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark
| | - Dirk Springael
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium.
| | - Lars Hestbjerg Hansen
- Section for Microbiology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Copenhagen, Denmark.
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Jackson WA, Brundrett M, Böhlke JK, Hatzinger PB, Mroczkowski SJ, Sturchio NC. Isotopic composition of natural and synthetic chlorate (δ 18O, Δ 17O, δ 37Cl, 36Cl/Cl): Methods and initial results. CHEMOSPHERE 2021; 274:129586. [PMID: 33529957 DOI: 10.1016/j.chemosphere.2021.129586] [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: 11/14/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Natural chlorate (ClO3-) is widely distributed in terrestrial and extraterrestrial environments. To improve understanding of the origins and distribution of ClO3-, we developed and tested methods to determine the multi-dimensional isotopic compositions (δ18O, Δ17O, δ37Cl, 36Cl/Cl) of ClO3- and then applied the methods to samples of natural nitrate-rich caliche-type salt deposits in the Atacama Desert, Chile, and Death Valley, USA. Tests with reagents and artificial mixed samples indicate stable-isotope ratios were minimally affected by the purification processes. Chlorate extracted from Atacama samples had δ18O = +7.0 to +11.1‰, Δ17O = +5.7 to +6.4‰, δ37Cl = -1.4 to +1.3‰, and 36Cl/Cl = 48 × 10-15 to 104 × 10-15. Chlorate from Death Valley samples had δ18O = -6.9 to +1.6‰, Δ17O = +0.4 to +2.6‰, δ37Cl = +0.8 to +1.0‰, and 36Cl/Cl = 14 × 10-15 to 44 × 10-15. Positive Δ17O values of natural ClO3- indicate that its production involved reaction with O3, while its Cl isotopic composition is consistent with a tropospheric or near-surface source of Cl. The Δ17O and δ18O values of natural ClO3- are positively correlated, as are those of ClO4- and NO3- from the same localities, possibly indicating variation in the relative contributions of O3 as a source of O in the formation of the oxyanions. Additional isotopic analyses of ClO3- could provide stronger constraints on its production mechanisms and/or post-formational alterations, with applications for environmental forensics, global biogeochemical cycling of Cl, and the origins of oxyanions detected on Mars.
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Affiliation(s)
| | | | - J K Böhlke
- U. S. Geological Survey, Reston, VA, 20192, USA
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Boes DM, Godoy-Hernandez A, McMillan DGG. Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life. MEMBRANES 2021; 11:346. [PMID: 34066904 PMCID: PMC8151925 DOI: 10.3390/membranes11050346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Membrane proteins can be classified into two main categories-integral and peripheral membrane proteins-depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5'-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.
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Affiliation(s)
- Deborah M. Boes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Albert Godoy-Hernandez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Duncan G. G. McMillan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
- School of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11 222, New Zealand
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Durand S, Guillier M. Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria. Front Mol Biosci 2021; 8:667758. [PMID: 34026838 PMCID: PMC8139620 DOI: 10.3389/fmolb.2021.667758] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022] Open
Abstract
In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.
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Affiliation(s)
- Sylvain Durand
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Maude Guillier
- CNRS, UMR 8261, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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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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Vos SJ, Wijnker JJ, Overgaauw PAM. A Pilot Study on the Contamination of Assistance Dogs' Paws and Their Users' Shoe Soles in Relation to Admittance to Hospitals and (In)Visible Disability. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:E513. [PMID: 33435167 PMCID: PMC7827110 DOI: 10.3390/ijerph18020513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: People with disabilities may benefit from an assistance dog (AD). Despite regulations that prohibit the denial of ADs to public places, this still occurs on a regular basis. The main argument for denial of access is that dogs compromise hygiene with their presence, which could cause a health hazard. Meanwhile, people are allowed to walk into and out of public places freely. (2) Objective: As a pilot study, to investigate the number of Enterobacteriaceae and the presence of Clostridium difficile bacteria on the paws of ADs and pet dogs (PDs) as well as the shoe soles of their users and owners. With the results, an assessment can be made as to whether measures are required to reduce environmental contamination (e.g., in hospitals). (3) Methods: In total, 25 ADs, 25 PDs, and their 50 users/owners participated in the study. Each participant walked their dog for 15-30 min prior to the sampling of the front paws. Each PD owner or AD user filled out a general questionnaire about the care of their dogs, and AD users were asked to fill out an additional questionnaire on their experiences regarding the admittance of their ADs to public places (in particular, hospitals). Dutch hospitals were questioned on their protocols regarding the admittance of ADs and their visitor numbers, including the percentage of AD users, to put these numbers into perspective. (4) Results: Dog paws were more often negative for Enterobacteriaceae compared to shoe soles (72% and 42%, respectively) and also had significantly lower bacterial counts (mean of 3.54log10 and 5.03log10 colony-forming units (CFUs), respectively; p < 0.05). This was most distinct in the comparison between PDs and their owners (3.75log10 and 5.25log10 CFUs; p < 0.05); the numbers were similar between ADs and their users (3.09log10 and 4.58log10 CFUs; p = 0.2). C. difficile was found on one (4%) AD user's shoe soles. Moreover, 81% of AD users had been denied access with their current AD once or several times, the main reason being hygiene. The results of the visibly and invisibly disabled were significantly different. The number of AD users as opposed to the total number of hospital visitors was 0.03% in one hospital and is estimated to be 0.02% in the Netherlands. (5) Conclusions: The general hygiene of dogs' paws is far better than that of shoe soles, mostly demonstrated by the better general hygiene of PD paws compared with their owners' shoe soles; ADs and their users had comparable levels of general hygiene. In addition, the number of AD users amongst the total number of hospital visitors in the Netherlands is very limited. Thus, hygiene measures to reduce any contamination due to dog paws do not seem necessary.
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Affiliation(s)
| | - Joris J. Wijnker
- Department of Population Health Sciences, Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, P.O. Box 80178, 3508 TD Utrecht, The Netherlands; (S.J.V.)
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Preferential Use of the Perchlorate over the Nitrate in the Respiratory Processes Mediated by the Bacterium Azospira sp. OGA 24. WATER 2020. [DOI: 10.3390/w12082220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here we report the results obtained for a strain isolated from a polluted site and classified as Azospira sp. OGA 24. The capability of OGA 24 to utilize perchlorate and nitrate and the regulation of pathways were investigated by growth kinetic studies and analysis of messenger RNA (mRNA) expression of the genes of perchlorate reductase alpha subunit (pcrA), chlorite dismutase (cld), and periplasmic nitrate reductase large subunit (napA). In aerobic conditions and in a minimal medium containing 10 mM acetate as carbon source, 5.6 ± 0.34 mmol L−1 perchlorate or 9.7 ± 0.22 mmol L−1 nitrate were efficiently reduced during the growth with 10 mM of either perchlorate or nitrate. In anaerobiosis, napA was completely inhibited in the presence of perchlorate as the only electron acceptor, pcrA was barely detectable in nitrate-reducing conditions. The cell growth kinetics were in accordance with expression data, indicating a separation of nitrate and perchlorate respiration pathways. In the presence of both compounds, anaerobic nitrate consumption was reduced to 50% (4.9 ± 0.4 vs. 9.8 ± 0.15 mmol L−1 without perchlorate), while that of perchlorate was not affected (7.2 ± 0.5 vs. 6.9 ± 0.6 mmol L−1 without nitrate). Expression analysis confirmed the negative effect of perchlorate on nitrate respiration. Based on sequence analysis of the considered genes and 16S ribosomal gene (rDNA), the taxonomic position of Azospira sp. OGA 24 in the perchlorate respiring bacteria (PRB) group was further defined by classifying it in the oryzae species. The respiratory characteristics of OGA 24 strain make it very attractive in terms of potential applications in the bioremediation of environments exposed to perchlorate salts.
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Mintmier B, McGarry JM, Sparacino-Watkins CE, Sallmen J, Fischer-Schrader K, Magalon A, McCormick JR, Stolz JF, Schwarz G, Bain DJ, Basu P. Molecular cloning, expression and biochemical characterization of periplasmic nitrate reductase from Campylobacter jejuni. FEMS Microbiol Lett 2019; 365:5040225. [PMID: 29931366 DOI: 10.1093/femsle/fny151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/17/2018] [Indexed: 02/07/2023] Open
Abstract
Campylobacter jejuni, a human gastrointestinal pathogen, uses nitrate for growth under microaerophilic conditions using periplasmic nitrate reductase (Nap). The catalytic subunit, NapA, contains two prosthetic groups, an iron sulfur cluster and a molybdenum cofactor. Here we describe the cloning, expression, purification, and Michaelis-Menten kinetics (kcat of 5.91 ± 0.18 s-1 and a KM (nitrate) of 3.40 ± 0.44 μM) in solution using methyl viologen as an electron donor. The data suggest that the high affinity of NapA for nitrate could support growth of C. jejuni on nitrate in the gastrointestinal tract. Site-directed mutagenesis was used and the codon for the molybdenum coordinating cysteine residue has been exchanged for serine. The resulting variant NapA is 4-fold less active than the native enzyme confirming the importance of this residue. The properties of the C. jejuni enzyme reported here represent the first isolation and characterization of an epsilonproteobacterial NapA. Therefore, the fundamental knowledge of Nap has been expanded.
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Affiliation(s)
- Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Jennifer M McGarry
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | | | - Joseph Sallmen
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | | | - Axel Magalon
- Aix Marseille Université, CNRS, Laboratoire de Chimie Bactérienne (UMR7283), IMM, 13402 Marseille, France
| | - Joseph R McCormick
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Günter Schwarz
- Institute for Biochemistry, University of Cologne, Cologne 50674, Germany
| | - Daniel J Bain
- Department of Geology and Environmental Science, University of Pittsburgh, PA 15260, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University, Indianapolis, IN 46202, USA
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12
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Rubio-Rincón FJ, Weissbrodt DG, Lopez-Vazquez CM, Welles L, Abbas B, Albertsen M, Nielsen PH, van Loosdrecht MCM, Brdjanovic D. "Candidatus Accumulibacter delftensis": A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate. WATER RESEARCH 2019; 161:136-151. [PMID: 31189123 DOI: 10.1016/j.watres.2019.03.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/18/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Populations of "Candidatus Accumulibacter", a known polyphosphate-accumulating organism, within clade IC have been proposed to perform anoxic P-uptake activity in enhanced biological phosphorus removal (EBPR) systems using nitrate as electron acceptor. However, no consensus has been reached on the ability of "Ca. Accumulibacter" members of clade IC to reduce nitrate to nitrite. Discrepancies might relate to the diverse operational conditions which could trigger the expression of the Nap and/or Nar enzyme and/or to the accuracy in clade classification. This study aimed to assess whether and how certain operational conditions could lead to the enrichment and enhance the denitrification capacity of "Ca. Accumulibacter" within clade IC. To study the potential induction of the denitrifying enzyme, an EBPR culture was enriched under anaerobic-anoxic-oxic (A2O) conditions that, based on fluorescence in situ hybridization and ppk gene sequencing, was composed of around 97% (on a biovolume basis) of affiliates of "Ca. Accumulibacter" clade IC. The influence of the medium composition, sludge retention time (SRT), polyphosphate content of the biomass (poly-P), nitrate dosing approach, and minimal aerobic SRT on potential nitrate reduction were studied. Despite the different studied conditions applied, only a negligible anoxic P-uptake rate was observed, equivalent to maximum 13% of the aerobic P-uptake rate. An increase in the anoxic SRT at the expenses of the aerobic SRT resulted in deterioration of P-removal with limited aerobic P-uptake and insufficient acetate uptake in the anaerobic phase. A near-complete genome (completeness = 100%, contamination = 0.187%) was extracted from the metagenome of the EBPR biomass for the here-proposed "Ca. Accumulibacter delftensis" clade IC. According to full-genome-based phylogenetic analysis, this lineage was distant from the canonical "Ca. Accumulibacter phosphatis", with closest neighbor "Ca. Accumulibacter sp. UW-LDO-IC" within clade IC. This was cross-validated with taxonomic classification of the ppk1 gene sequences. The genome-centric metagenomic analysis highlighted the presence of genes for assimilatory nitrate reductase (nas) and periplasmic nitrate reductase (nap) but no gene for respiratory nitrate reductases (nar). This suggests that "Ca. Accumulibacter delftensis" clade IC was not capable to generate the required energy (ATP) from nitrate under strict anaerobic-anoxic conditions to support an anoxic EBPR metabolism. Definitely, this study stresses the incongruence in denitrification abilities of "Ca. Accumulibacter" clades and reflects the true intra-clade diversity, which requires a thorough investigation within this lineage.
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Affiliation(s)
- F J Rubio-Rincón
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - D G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - C M Lopez-Vazquez
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands.
| | - L Welles
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands.
| | - B Abbas
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - M Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - P H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - M C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - D Brdjanovic
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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13
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Hilgarth M, Lehner E, Behr J, Vogel R. Diversity and anaerobic growth ofPseudomonasspp. isolated from modified atmosphere packaged minced beef. J Appl Microbiol 2019; 127:159-174. [DOI: 10.1111/jam.14249] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/29/2022]
Affiliation(s)
- M. Hilgarth
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - E.M. Lehner
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - J. Behr
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
| | - R.F. Vogel
- Lehrstuhl für Technische Mikrobiologie Technische Universität München Freising Germany
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Zhang Y, Hua ZS, Lu H, Oehmen A, Guo J. Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics. WATER RESEARCH 2019; 148:219-230. [PMID: 30388523 DOI: 10.1016/j.watres.2018.10.061] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/11/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1-4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1-4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.
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Affiliation(s)
- Yan Zhang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; School of Environmental and Chemical Engineering, Foshan University, Foshan, 528000, PR China
| | - Zheng-Shuang Hua
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, 510275, PR China.
| | - Adrian Oehmen
- School of Chemical Engineering, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Queensland, 4072, Australia.
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15
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Effect of zero-valent iron/starch nanoparticle on nitrate removal using MD simulation. Int J Biol Macromol 2019; 121:727-733. [DOI: 10.1016/j.ijbiomac.2018.09.183] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 08/28/2018] [Accepted: 09/28/2018] [Indexed: 01/09/2023]
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Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8110399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.
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17
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D'Amico K, Filiatrault MJ. The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000. FEMS Microbiol Lett 2018; 364:fnx004. [PMID: 28073812 DOI: 10.1093/femsle/fnx004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/09/2017] [Indexed: 11/13/2022] Open
Abstract
The plant pathogen Pseudomonas syringae accounts for substantial crop losses and is considered an important agricultural issue. To better manage disease in the field, it is important to have an understanding of the underlying genetic mechanisms that mediate virulence. There are a substantial number of genes in sequenced bacterial genomes, including P. syringae, that encode for conserved hypothetical proteins; some of these have been functionally characterized in other Pseudomonads and have been demonstrated to play important roles in disease. PSPTO_3957 encodes a conserved hypothetical protein of unknown function. To evaluate the role of PSPTO_3957 in P. syringae pv. tomato DC3000, a PSPTO_3957 deletion mutant was constructed. Here, we show that PSPTO_3957 does not influence growth on rich media, motility or biofilm formation but is necessary for nitrate assimilation and full virulence in P. syringae. Our results have revealed an important role for PSPTO_3957 in the biology of P. syringae. Given the conservation of this protein among many bacteria, this protein might serve as an attractive target for disease management of this and other bacterial plant pathogens.
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Affiliation(s)
- Katherine D'Amico
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853, USA
| | - Melanie J Filiatrault
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, US Department of Agriculture, Ithaca, NY 14853, USA
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Torres M, Simon J, Rowley G, Bedmar E, Richardson D, Gates A, Delgado M. Nitrous Oxide Metabolism in Nitrate-Reducing Bacteria: Physiology and Regulatory Mechanisms. Adv Microb Physiol 2016; 68:353-432. [PMID: 27134026 DOI: 10.1016/bs.ampbs.2016.02.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nitrous oxide (N2O) is an important greenhouse gas (GHG) with substantial global warming potential and also contributes to ozone depletion through photochemical nitric oxide (NO) production in the stratosphere. The negative effects of N2O on climate and stratospheric ozone make N2O mitigation an international challenge. More than 60% of global N2O emissions are emitted from agricultural soils mainly due to the application of synthetic nitrogen-containing fertilizers. Thus, mitigation strategies must be developed which increase (or at least do not negatively impact) on agricultural efficiency whilst decrease the levels of N2O released. This aim is particularly important in the context of the ever expanding population and subsequent increased burden on the food chain. More than two-thirds of N2O emissions from soils can be attributed to bacterial and fungal denitrification and nitrification processes. In ammonia-oxidizing bacteria, N2O is formed through the oxidation of hydroxylamine to nitrite. In denitrifiers, nitrate is reduced to N2 via nitrite, NO and N2O production. In addition to denitrification, respiratory nitrate ammonification (also termed dissimilatory nitrate reduction to ammonium) is another important nitrate-reducing mechanism in soil, responsible for the loss of nitrate and production of N2O from reduction of NO that is formed as a by-product of the reduction process. This review will synthesize our current understanding of the environmental, regulatory and biochemical control of N2O emissions by nitrate-reducing bacteria and point to new solutions for agricultural GHG mitigation.
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Frey C, Hietanen S, Jürgens K, Labrenz M, Voss M. N and O isotope fractionation in nitrate during chemolithoautotrophic denitrification by Sulfurimonas gotlandica. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13229-13237. [PMID: 25347214 DOI: 10.1021/es503456g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chemolithoautotrophic denitrification is an important mechanism of nitrogen loss in the water column of euxinic basins, but its isotope fractionation factor is not known. Sulfurimonas gotlandica GD1(T), a recently isolated bacterial key player in Baltic Sea pelagic redoxcline processes, was used to determine the isotope fractionation of nitrogen and oxygen in nitrate during denitrification. Under anoxic conditions, nitrate reduction was accompanied by nitrogen and oxygen isotope fractionation of 23.8 ± 2.5‰ and 11.7 ± 1.1‰, respectively. The isotope effect for nitrogen was in the range determined for heterotrophic denitrification, with only the absence of stirring resulting in a significant decrease of the fractionation factor. The relative increase in δ(18)ONO3 to δ(15)NNO3 did not follow the 1:1 relationship characteristic of heterotrophic, marine denitrification. Instead, δ(18)ONO3 increased slower than δ(15)NNO3, with a conserved ratio of 0.5:1. This result suggests that the periplasmic nitrate reductase (Nap) of S. gotlandica strain GD1(T) fractionates the N and O in nitrate differently than the membrane-bound nitrate reductase (Nar), which is generally prevalent among heterotrophic denitrifiers and is considered as the dominant driver for the observed isotope fractionation. Hence in the Baltic Sea redoxcline, other, as yet-unidentified factors likely explain the low apparent fractionation.
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Affiliation(s)
- Claudia Frey
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW) , Seestrasse 15, 18119 Rostock, Germany
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Zhou S, Borjigin S, Riya S, Terada A, Hosomi M. The relationship between anammox and denitrification in the sediment of an inland river. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 490:1029-1036. [PMID: 24914531 DOI: 10.1016/j.scitotenv.2014.05.096] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/12/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
This study measured the microbial processes of anaerobic ammonium oxidation (anammox) and denitrification in sediment sampled from two sites in the estuary of an inland river (Koisegawa River, Ibaragi prefecture, Japan) using a nitrogen isotope pairing technique (IPT). The responses of anammox and denitrification activities to temperature and nitrate concentration were also evaluated. Further, to elucidate the correlation between anammox and denitrification processes, an inhibition experiment was conducted, using chlorate to inhibit the first step of denitrification. Denitrification activity was much higher than anammox activity, and it reached a maximum at the surface layer in February 2012. Denitrification activity decreased as sediment depth increased, and a similar phenomenon was observed for anammox activity in the sediment of site A, where aquatic plants were absent from the surroundings. The activities of both denitrification and anammox were temperature-dependent, but they responded differently to changes in incubation temperature. Compared to a linear increase in denitrification as temperature rose to 35 °C, the optimal temperature for anammox was 25 °C, after which the activity decreased sharply. At the same time, both anammox and denitrification activities increased with NO3(-) concentration. The Michaelis-Menten kinetic constants (Vmax and Km) of denitrification were significantly higher than those of the anammox process. Furthermore, anammox activity decreased accordingly when the first step of denitrification was inhibited, which probably reduced the amount of the intermediate NO2(-). Our study provides the first direct exploration of the denitrification-dependent correlation of anammox activity in the sediment of inland river.
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Affiliation(s)
- Sheng Zhou
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, No. 1000 Jinqi Road, Shanghai 201403, China; Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | - Sodbilig Borjigin
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shohei Riya
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Akihiko Terada
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaaki Hosomi
- Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Torres MJ, Rubia MI, de la Peña TC, Pueyo JJ, Bedmar EJ, Delgado MJ. Genetic basis for denitrification in Ensifer meliloti. BMC Microbiol 2014; 14:142. [PMID: 24888981 PMCID: PMC4064527 DOI: 10.1186/1471-2180-14-142] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/28/2014] [Indexed: 11/20/2022] Open
Abstract
Background Denitrification is defined as the dissimilatory reduction of nitrate or nitrite to nitric oxide (NO), nitrous oxide (N2O), or dinitrogen gas (N2). N2O is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Legume crops might contribute to N2O production by providing nitrogen-rich residues for decomposition or by associating with rhizobia that are able to denitrify under free-living and symbiotic conditions. However, there are limited direct empirical data concerning N2O production by endosymbiotic bacteria associated with legume crops. Analysis of the Ensifer meliloti 1021 genome sequence revealed the presence of the napEFDABC, nirK, norECBQD and nosRZDFYLX denitrification genes. It was recently reported that this bacterium is able to grow using nitrate respiration when cells are incubated with an initial O2 concentration of 2%; however, these cells were unable to use nitrate respiration when initially incubated anoxically. The involvement of the nap, nirK, nor and nos genes in E. meliloti denitrification has not been reported. Results E. meliloti nap, nirK and norC mutant strains exhibited defects in their ability to grow using nitrate as a respiratory substrate. However, E meliloti nosZ was not essential for growth under these conditions. The E. meliloti napA, nirK, norC and nosZ genes encode corresponding nitrate, nitrite, nitric oxide and nitrous oxide reductases, respectively. The NorC component of the E. meliloti nitric oxide reductase has been identified as a c-type cytochrome that is 16 kDa in size. Herein, we also show that maximal expression of the E. meliloti napA, nirK, norC and nosZ genes occurred when cells were initially incubated anoxically with nitrate. Conclusion The E. meliloti napA, nirK, norC and nosZ genes are involved in nitrate respiration and in the expression of denitrification enzymes in this bacterium. Our findings expand the short list of rhizobia for which denitrification gene function has been demonstrated. The inability of E. meliloti to grow when cells are initially subjected to anoxic conditions is not attributable to defects in the expression of the napA, nirK, norC and nosZ denitrification genes.
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Affiliation(s)
| | | | | | | | | | - María J Delgado
- Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), P,O, Box 419, 18080 Granada, Spain.
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Oosterkamp MJ, Veuskens T, Talarico Saia F, Weelink SAB, Goodwin LA, Daligault HE, Bruce DC, Detter JC, Tapia R, Han CS, Land ML, Hauser LJ, Langenhoff AAM, Gerritse J, van Berkel WJH, Pieper DH, Junca H, Smidt H, Schraa G, Davids M, Schaap PJ, Plugge CM, Stams AJM. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.). PLoS One 2013; 8:e66971. [PMID: 23825601 PMCID: PMC3692508 DOI: 10.1371/journal.pone.0066971] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/14/2013] [Indexed: 12/04/2022] Open
Abstract
The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.
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Affiliation(s)
| | - Teun Veuskens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Hajnalka E. Daligault
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - David C. Bruce
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - John C. Detter
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Roxanne Tapia
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Cliff S. Han
- Los Alamos National Laboratory, Joint Genome Institute, Los Alamos, New Mexico, United States of America
| | - Miriam L. Land
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Loren J. Hauser
- BioEnergy Science Center and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | | | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholz Centre for Infection Research, Braunschweig, Germany
| | - Howard Junca
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Bogotá, Colombia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Gosse Schraa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Mark Davids
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
- * E-mail:
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Zhao B, An Q, He YL, Guo JS. N2O and N2 production during heterotrophic nitrification by Alcaligenes faecalis strain NR. BIORESOURCE TECHNOLOGY 2012; 116:379-385. [PMID: 22534373 DOI: 10.1016/j.biortech.2012.03.113] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/28/2012] [Accepted: 03/29/2012] [Indexed: 05/27/2023]
Abstract
A heterotrophic nitrifier, strain NR, was isolated from a membrane bioreactor. Strain NR was identified as Alcaligenes faecalis by Auto-Microbic system and 16S rRNA gene sequence analysis. A. faecalis strain NR shows a capability of heterotrophic nitrification and N(2)O and N(2) production as well under the aerobic condition. Further tests demonstrated that neither nitrite nor nitrate could be denitrified aerobically by strain NR. However, when hydroxylamine was used as the sole nitrogen source, nitrogenous gases were detected. With an enzyme assay, a 0.063 U activity of hydroxylamine oxidase was observed, while nitrate reductase and nitrite reductase were undetectable. Thus, nitrogenous gas was speculated to be produced via hydroxylamine. Therefore, two different metabolic pathways might exist in A. faecalis NR. One is heterotrophic nitrification by oxidizing ammonium to nitrite and nitrate. The other is oxidizing ammonium to nitrogenous gas directly via hydroxylamine.
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Affiliation(s)
- Bin Zhao
- The Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Chongqing University, Chongqing 400045, PR China.
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Romeo A, Sonnleitner E, Sorger-Domenigg T, Nakano M, Eisenhaber B, Bläsi U. Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD–PA1779–cobA operon. Microbiology (Reading) 2012; 158:1543-1552. [DOI: 10.1099/mic.0.053850-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alessandra Romeo
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Elisabeth Sonnleitner
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Theresa Sorger-Domenigg
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Masayuki Nakano
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671 Singapore
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Dr. Bohrgasse 9/4, 1030 Vienna, Austria
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Bueno E, Mesa S, Bedmar EJ, Richardson DJ, Delgado MJ. Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control. Antioxid Redox Signal 2012; 16:819-52. [PMID: 22098259 PMCID: PMC3283443 DOI: 10.1089/ars.2011.4051] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, CSIC, Granada, Spain
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Rauschenbach I, Bini E, Häggblom MM, Yee N. Physiological response of Desulfurispirillum indicum S5 to arsenate and nitrate as terminal electron acceptors. FEMS Microbiol Ecol 2012; 81:156-62. [DOI: 10.1111/j.1574-6941.2012.01351.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ines Rauschenbach
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Max M. Häggblom
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Nathan Yee
- Department of Environmental Sciences; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
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Liu H, Guo J, Qu J, Lian J, Jefferson W, Yang J, Li H. Catalyzing denitrification of Paracoccus versutus by immobilized 1,5-dichloroanthraquinone. Biodegradation 2011; 23:399-405. [PMID: 22086549 DOI: 10.1007/s10532-011-9518-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 11/06/2011] [Indexed: 11/25/2022]
Abstract
The accelerating effect of non-dissolved redox mediator (1,5-dichloroanthraquinone) on the biological denitrification was investigated in this paper using 1,5-dichloroanthraquinone immobilized by calcium alginate (CA) and a heterotrophic denitrification bacterium of Paracoccus versutus (GU111570). The results suggested that the denitrification rate was enhanced 2.1 fold by 25 mmol l(-1) 1,5-dichloroanthraquinone of this study, and a positive correlation was found for the denitrification rate and 1,5-dichloroanthraquinone concentrations from 0 to 25 mmol l(-1). According to the change characteristic of NO(3) (-) and NO(2) (-) during the denitrification process, the tentative accelerating mechanism of the denitrification by redox mediators was put forward, and redox mediator might play the role of reduced cofactors like NADH, N(A)DH and SDH, or the similar ubiquinol/ubiquinone (Q/QH(2)) role during the denitrification process.
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Affiliation(s)
- Huijuan Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration – Genes, enzymes and environmental distribution. J Biotechnol 2011; 155:104-17. [DOI: 10.1016/j.jbiotec.2010.12.025] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 12/07/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023]
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Four PCR primers necessary for the detection of periplasmic nitrate reductase genes in all groups of Proteobacteria and in environmental DNA. Biochem Soc Trans 2011; 39:321-6. [PMID: 21265796 PMCID: PMC3064403 DOI: 10.1042/bst0390321] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Generic primers are available for detecting bacterial genes required for almost every reaction of the biological nitrogen cycle, the one notable exception being napA (gene for the molybdoprotein of the periplasmic nitrate reductase) encoding periplasmic nitrate reductases. Using an iterative approach, we report the first successful design of three forward oligonucleotide primers and one reverse primer that, in three separate PCRs, can amplify napA DNA from all five groups of Proteobacteria. All 140 napA sequences currently listed in the NCBI (National Center for Biotechnology Information) database are predicted to be amplified by one or more of these primer pairs. We demonstrate that two pairs of these primers also amplify PCR products of the predicted sizes from DNA isolated from human faeces, confirming their ability to direct the amplification of napA fragments from mixed populations. Analysis of the resulting amplicons by high-throughput sequencing will enable a good estimate to be made of both the range and relative abundance of nitrate-reducing bacteria in any community, subject only to any unavoidable bias inherent in a PCR approach to molecular characterization of a highly diverse target.
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32
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Nitrate and (per)chlorate reduction pathways in (per)chlorate-reducing bacteria. Biochem Soc Trans 2011; 39:230-5. [DOI: 10.1042/bst0390230] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reduction of (per)chlorate and nitrate in (per)chlorate-reducing bacteria shows similarities and differences. (Per)chlorate reductase and nitrate reductase both belong to the type II DMSO family of enzymes and have a common bis(molybdopterin guanine dinucleotide)molybdenum cofactor. There are two types of dissimilatory nitrate reductases. With respect to their localization, (per)chlorate reductase is more similar to the dissimilatory periplasmic nitrate reductase. However, the periplasmic, unlike the membrane-bound, respiratory nitrate reductase, is not able to use chlorate. Structurally, (per)chlorate reductase is more similar to respiratory nitrate reductase, since these reductases have analogous subunits encoded by analogous genes. Both periplasmic (per)chlorate reductase and membrane-bound nitrate reductase activities are induced under anoxic conditions in the presence of (per)chlorate and nitrate respectively. During microbial (per)chlorate reduction, molecular oxygen is generated. This is not the case for nitrate reduction, although an atypical reaction in nitrite reduction linked to oxygen formation has been described recently. Microbial oxygen production during reduction of oxyanions may enhance biodegradation of pollutants under anoxic conditions.
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Falk S, Liu B, Braker G. Isolation, genetic and functional characterization of novel soil nirK-type denitrifiers. Syst Appl Microbiol 2010; 33:337-47. [DOI: 10.1016/j.syapm.2010.06.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 06/03/2010] [Accepted: 06/08/2010] [Indexed: 10/19/2022]
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Romanowska I, Kwapisz E, Mitka M, Bielecki S. Isolation and preliminary characterization of a respiratory nitrate reductase from hydrocarbon-degrading bacterium Gordonia alkanivorans S7. J Ind Microbiol Biotechnol 2010; 37:625-9. [PMID: 20379760 DOI: 10.1007/s10295-010-0717-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 03/26/2010] [Indexed: 10/19/2022]
Abstract
Gordonia alkanivorans S7 is an efficient degrader of fuel oil hydrocarbons that can simultaneously utilize oxygen and nitrate as electron acceptors. The respiratory nitrate reductase (Nar) from this organism has been isolated using ion exchange chromatography and gel filtration, and then preliminarily characterized. PAGE, SDS-PAGE and gel filtration chromatography revealed that Nar consisted of three subunits of 103, 53 and 25 kDa. The enzyme was optimally active at pH 7.9 and 40 degrees C. K(m) values for NO(3)(-) (110 microM) and for ClO(3)(-) (138 microM) were determined for a reduced viologen as an electron donor. The purified Nar did not use NADH as the electron donor to reduce nitrate or chlorate. Azide was a strong inhibitor of its activity. Our results imply that enzyme isolated from G. alkanivorans S7 is a respiratory membrane-bound nitrate reductase. This is the first report of purification of a nitrate reductase from Gordonia species.
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Affiliation(s)
- Irena Romanowska
- Department of Biotechnology and Food Sciences, Institute of Technical Biochemistry, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland.
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35
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Zhao B, He YL, Huang J, Taylor S, Hughes J. Heterotrophic nitrogen removal by Providencia rettgeri strain YL. J Ind Microbiol Biotechnol 2010; 37:609-16. [DOI: 10.1007/s10295-010-0708-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 03/03/2010] [Indexed: 12/01/2022]
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Novel denitrifying bacterium Ochrobactrum anthropi YD50.2 tolerates high levels of reactive nitrogen oxides. Appl Environ Microbiol 2009; 75:5186-94. [PMID: 19542343 DOI: 10.1128/aem.00604-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most studies of bacterial denitrification have used nitrate (NO3-) as the first electron acceptor, whereas relatively less is understood about nitrite (NO2-) denitrification. We isolated novel bacteria that proliferated in the presence of high levels of NO2- (72 mM). Strain YD50.2, among several isolates, was taxonomically positioned within the alpha subclass of Proteobacteria and identified as Ochrobactrum anthropi YD50.2. This strain denitrified NO2-, as well as NO3-. The gene clusters for denitrification (nar, nir, nor, and nos) were cloned from O. anthropi YD50.2, in which the nir and nor operons were linked. We confirmed that nirK in the nir-nor operon produced a functional NO2- reductase containing copper that was involved in bacterial NO2- reduction. The strain denitrified up to 40 mM NO2- to dinitrogen under anaerobic conditions in which other denitrifiers or NO3- reducers such as Pseudomonas aeruginosa and Ralstonia eutropha and nitrate-respiring Escherichia coli neither proliferated nor reduced NO2-. Under nondenitrifying aerobic conditions, O. anthropi YD50.2 and its type strain ATCC 49188(T) proliferated even in the presence of higher levels of NO2- (100 mM), and both were considerably more resistant to acidic NO2- than were the other strains noted above. These results indicated that O. anthropi YD50.2 is a novel denitrifier that has evolved reactive nitrogen oxide tolerance mechanisms.
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37
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Microbial denitrification by immobilized bacteria Pseudomonas denitrificans stimulated by constant electric field. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2008.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Durvasula K, Jantama K, Fischer K, Vega A, Koopman B, Svoronos SA. Effect of periplasmic nitrate reductase on diauxic lag of Paracoccus pantotrophus. Biotechnol Prog 2009; 25:973-9. [PMID: 19399903 DOI: 10.1002/btpr.176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Paracoccus pantotrophus expresses two nitrate reductases-membrane bound nitrate reductase (Nar) and periplasmic nitrate reductase (Nap). In growth experiments with two denitrifying species (Paracoccus pantotrophus and Alcaligenes eutrophus) that have both Nap and Nar and two species (Pseudomonas denitrificans and Pseudomonas fluorescens) with Nar only, it was found that diauxic lag is shorter for bacteria that express Nap. In P. pantotrophus, napEDABC encodes the periplasmic nitrate reductase. To analyze the effect of Nap on diauxic lag, the nap operon was deleted from P. pantotrophus. The growth experiments with nap(-) mutant resulted in increased diauxic lag when switched from aerobic to anoxic respiration, suggesting Nap is responsible for shorter lags and helps in adaptation to anoxic metabolism after transition from aerobic conditions.
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Affiliation(s)
- Kiranmai Durvasula
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
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39
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Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico). Extremophiles 2008; 13:169-78. [DOI: 10.1007/s00792-008-0207-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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40
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Nde CW, Jang HJ, Toghrol F, Bentley WE. Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol. BMC Genomics 2008; 9:473. [PMID: 18847467 PMCID: PMC2577666 DOI: 10.1186/1471-2164-9-473] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 10/10/2008] [Indexed: 11/13/2022] Open
Abstract
Background Pseudomonas aeruginosa (P. aeruginosa) is the most common opportunistic pathogen implicated in nosocomial infections and in chronic lung infections in cystic fibrosis patients. Ortho-phenylphenol (OPP) is an antimicrobial agent used as an active ingredient in several EPA registered disinfectants. Despite its widespread use, there is a paucity of information on its target molecular pathways and the cellular responses that it elucidates in bacteria in general and in P. aeruginosa in particular. An understanding of the OPP-driven gene regulation and cellular response it elicits will facilitate more effective utilization of this antimicrobial and possibly lead to the development of more effective disinfectant treatments. Results Herein, we performed a genome-wide transcriptome analysis of the cellular responses of P. aeruginosa exposed to 0.82 mM OPP for 20 and 60 minutes. Our data indicated that OPP upregulated the transcription of genes encoding ribosomal, virulence and membrane transport proteins after both treatment times. After 20 minutes of exposure to 0.82 mM OPP, genes involved in the exhibition of swarming motility and anaerobic respiration were upregulated. After 60 minutes of OPP treatment, the transcription of genes involved in amino acid and lipopolysaccharide biosynthesis were upregulated. Further, the transcription of the ribosome modulation factor (rmf) and an alternative sigma factor (rpoS) of RNA polymerase were downregulated after both treatment times. Conclusion Results from this study indicate that after 20 minutes of exposure to OPP, genes that have been linked to the exhibition of anaerobic respiration and swarming motility were upregulated. This study also suggests that the downregulation of the rmf and rpoS genes may be indicative of the mechanism by which OPP causes decreases in cell viability in P. aeruginosa. Consequently, a protective response involving the upregulation of translation leading to the increased synthesis of membrane related proteins and virulence proteins is possibly induced after both treatment times. In addition, cell wall modification may occur due to the increased synthesis of lipopolysaccharide after 60 minutes exposure to OPP. This gene expression profile can now be utilized for a better understanding of the target cellular pathways of OPP in P. aeruginosa and how this organism develops resistance to OPP.
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Affiliation(s)
- Chantal W Nde
- Center for Biosystems Research, University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA.
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Morozkina EV, Zvyagilskaya RA. Nitrate reductases: structure, functions, and effect of stress factors. BIOCHEMISTRY (MOSCOW) 2008; 72:1151-60. [PMID: 18021072 DOI: 10.1134/s0006297907100124] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural and functional peculiarities of four types of nitrate reductases are considered: assimilatory nitrate reductase of eukaryotes, as well as cytoplasmic assimilatory, membrane-bound respiratory, and periplasmic dissimilatory bacterial nitrate reductases. Arguments are presented showing that eukaryotic organisms are capable of nitrate dissimilation. Data concerning new classes of extremophil nitrate reductases, whose active center does not contain molybdocofactor, are summarized.
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Affiliation(s)
- E V Morozkina
- Bach Institute of Biochemistry, Russian Academy of Sciences, 119071 Moscow, Russia.
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Khardenavis AA, Kapley A, Purohit HJ. Simultaneous nitrification and denitrification by diverse Diaphorobacter sp. Appl Microbiol Biotechnol 2007; 77:403-9. [PMID: 17876578 DOI: 10.1007/s00253-007-1176-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 08/17/2007] [Accepted: 08/19/2007] [Indexed: 11/25/2022]
Abstract
Eight bacterial isolates closely related to Diaphorobacter sp. were isolated from activated biomass surviving on wastewater laden with dyes and nitro-substituted chemicals and were identified by 16S rDNA sequence analysis. The isolates showed sequence similarity of 99-100% to other Diaphorobacter strains such as ZY 2006b, F2, NA5, PCA039, D. nitroreducens KSP4, and KSP3 and 98-99% sequence homology to D. nitroreducens NA10B (type strain JCM 11421). Neighbor-joining tree revealed that all the eight strains formed tight cluster together and also showed close clustering with other Diaphorobacter strains. Isolates demonstrated the ability to perform simultaneous nitrification and denitrification under aerobic conditions. Strains HPC 805, 815, 821, and 856 gave highest chemical oxygen demand removal (85-93%) and ammonia removal (92-96%), which correlated well with higher growth rates of the cultures. Simultaneously, complete removal of nitrate supplied in the medium in presence of ammonium and acetate (electron donor) was observed in addition to aerobic nitrite release from ammonium. Thus, the above strains showed ability to perform partial nitrification followed by further aerobic removal of common intermediate nitrite, which indicated their potential application in treatment systems for treatment of high-nitrogen-containing wastewaters.
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Affiliation(s)
- Anshuman A Khardenavis
- Environmental Genomics Unit, National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 440 020, India
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Bru D, Sarr A, Philippot L. Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments. Appl Environ Microbiol 2007; 73:5971-4. [PMID: 17630306 PMCID: PMC2074903 DOI: 10.1128/aem.00643-07] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dissimilatory nitrate reduction is catalyzed by a membrane-bound and a periplasmic nitrate reductase. We set up a real-time PCR assay to quantify these two enzymes, using the narG and napA genes, encoding the catalytic subunits of the two types of nitrate reductases, as molecular markers. The narG and napA gene copy numbers in DNA extracted from 18 different environments showed high variations, with most numbers ranging from 2 x 10(2) to 6.8 x 10(4) copies per ng of DNA. This study provides evidence that, in soil samples, the number of proteobacteria carrying the napA gene is often as high as that of proteobacteria carrying the narG gene. The high correlation observed between narG and napA gene copy numbers in soils suggests that the ecological roles of the corresponding enzymes might be linked.
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Affiliation(s)
- D Bru
- INRA, University of Burgundy, Soil and Environmental Microbiology, CMSE, 17 rue Sully, BP 86510, 21065 Dijon Cedex, France
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44
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Palmer KL, Brown SA, Whiteley M. Membrane-bound nitrate reductase is required for anaerobic growth in cystic fibrosis sputum. J Bacteriol 2007; 189:4449-55. [PMID: 17400735 PMCID: PMC1913347 DOI: 10.1128/jb.00162-07] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Accepted: 03/22/2007] [Indexed: 11/20/2022] Open
Abstract
The autosomal recessive disorder cystic fibrosis (CF) affects approximately 70,000 people worldwide and is characterized by chronic bacterial lung infections with the opportunistic pathogen Pseudomonas aeruginosa. To form a chronic CF lung infection, P. aeruginosa must grow and proliferate within the CF lung, and the highly viscous sputum within the CF lung provides a likely growth substrate. Recent evidence indicates that anaerobic microenvironments may be present in the CF lung sputum layer. Since anaerobic growth significantly enhances P. aeruginosa biofilm formation and antibiotic resistance, it is important to examine P. aeruginosa physiology and metabolism in anaerobic environments. Measurement of nitrate levels revealed that CF sputum contains sufficient nitrate to support significant P. aeruginosa growth anaerobically, and mutational analysis revealed that the membrane-bound nitrate reductase is essential for P. aeruginosa anaerobic growth in an in vitro CF sputum medium. In addition, expression of genes coding for the membrane-bound nitrate reductase complex is responsive to CF sputum nitrate levels. These findings suggest that the membrane-bound nitrate reductase is critical for P. aeruginosa anaerobic growth with nitrate in the CF lung.
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Affiliation(s)
- Kelli L Palmer
- Section of Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX 78712, USA
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Rediers H, Vanderleyden J, De Mot R. Nitrate respiration in Pseudomonas stutzeri A15 and its involvement in rice and wheat root colonization. Microbiol Res 2007; 164:461-8. [PMID: 17467964 DOI: 10.1016/j.micres.2007.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 01/22/2007] [Accepted: 03/05/2007] [Indexed: 11/28/2022]
Abstract
Unlike most bacteria, the nitrogen-fixing rice-associated Pseudomonas stutzeri A15 disposes of three different nitrate reductases that enable conversion of nitrate to nitrite through three physiologically distinct processes, called nitrate assimilation, nitrate respiration and nitrate dissimilation. To study the role of nitrate respiration in rhizosphere fitness, a Pseudomonas stutzeri narG mutant was constructed and characterized by assessing its growth characteristics and whole-cell nitrate reductase activity in different oxygen tensions. Unexpectedly, the Pseudomonas stutzeri A15 narG mutant appeared to be a better root colonizer, outcompeting the wild type strain in a wheat and rice hydroponic system.
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Affiliation(s)
- Hans Rediers
- Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
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Perrine-Walker FM, Gartner E, Hocart CH, Becker A, Rolfe BG. Rhizobium-initiated rice growth inhibition caused by nitric oxide accumulation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:283-92. [PMID: 17378431 DOI: 10.1094/mpmi-20-3-0283] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Isolates of Rhizobium leguminosarum bv. trifolii (the clover root-nodule endosymbiont) from the Nile River delta have been found to infect rice roots and colonize the intercellular spaces of the rice roots. Some of these isolates inhibit rice seedling growth but one in particular, R4, has been found in rice roots which develop and grow normally. We present evidence that the induced growth inhibition is due to a toxic accumulation of nitric oxide (NO), from the reduction of nitrate, and suggest that the reason that R4 does not inhibit rice root growth is because it is capable of completing the reduction of NO through to nitrogen gas. Thus, strain R4 is a candidate for engineering into a future biological nitrogen fixation system within these roots.
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Affiliation(s)
- Francine M Perrine-Walker
- ARC Centre of Excellence for Integrative Legume Research, Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia
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Casasús AI, Lee DU, Hamilton RK, Svoronos SA, Koopman B. Effect of carbon substrate on electron acceptor diauxic lag and anoxic maximum specific growth rate in species with and without periplasmic enzyme. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2007; 42:103-8. [PMID: 17129955 DOI: 10.1080/10934520601015917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The effect of oxidation state of carbon substrate on the diauxic lag of facultative anaerobic denitrifying bacteria growing aerobically upon switching to anoxic growth was studied. Also studied was the effect on the anoxic maximum specific growth rate. Two pure bacteria cultures were used, Paracoccus pantotrophus, denitrifying bacteria containing a periplasmic nitrate reductase (Nap), and Pseudomonas denitrificans, denitrifying bacteria lacking the periplasmic nitrate reductase. The anoxic maximum specific growth rate of both cultures following a period of aerobic growth with identical dilution up to steady-state was indeed affected by the oxidation state of the carbon, with the most oxidized substrate yielding the highest anoxic maximum specific growth rate. The diauxic lags for Paracoccus pantotrophus were considerably shorter than those for Pseudomonas denitrificans, something expected due to the presence of Nap, an enzyme not affected by aerobiosis. Since the activity of Nap in Paracoccus pantotrophus under aerobic conditions has been shown to increase with the extent of reduction of the carbon substrate, it was also expected that the diauxic lag length for these bacteria would decrease as the reduction state of the carbon substrate increased. This could not be demonstrated, as no significant lags were observed for this species. Pseudomonas denitrificans exhibited a shorter diauxic lag with the more oxidized carbon source.
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Affiliation(s)
- Anna I Casasús
- Mazyck Technology Solutions, Gainesville, FL 32608, USA.
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Williams HD, Zlosnik JEA, Ryall B. Oxygen, cyanide and energy generation in the cystic fibrosis pathogen Pseudomonas aeruginosa. Adv Microb Physiol 2006; 52:1-71. [PMID: 17027370 DOI: 10.1016/s0065-2911(06)52001-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pseudomonas aeruginosa is a gram-negative, rod-shaped bacterium that belongs to the gamma-proteobacteria. This clinically challenging, opportunistic pathogen occupies a wide range of niches from an almost ubiquitous environmental presence to causing infections in a wide range of animals and plants. P. aeruginosa is the single most important pathogen of the cystic fibrosis (CF) lung. It causes serious chronic infections following its colonisation of the dehydrated mucus of the CF lung, leading to it being the most important cause of morbidity and mortality in CF sufferers. The recent finding that steep O2 gradients exist across the mucus of the CF-lung indicates that P. aeruginosa will have to show metabolic adaptability to modify its energy metabolism as it moves from a high O2 to low O2 and on to anaerobic environments within the CF lung. Therefore, the starting point of this review is that an understanding of the diverse modes of energy metabolism available to P. aeruginosa and their regulation is important to understanding both its fundamental physiology and the factors significant in its pathogenicity. The main aim of this review is to appraise the current state of knowledge of the energy generating pathways of P. aeruginosa. We first look at the organisation of the aerobic respiratory chains of P. aeruginosa, focusing on the multiple primary dehydrogenases and terminal oxidases that make up the highly branched pathways. Next, we will discuss the denitrification pathways used during anaerobic respiration as well as considering the ability of P. aeruginosa to carry out aerobic denitrification. Attention is then directed to the limited fermentative capacity of P. aeruginosa with discussion of the arginine deiminase pathway and the role of pyruvate fermentation. In the final part of the review, we consider other aspects of the biology of P. aeruginosa that are linked to energy metabolism or affected by oxygen availability. These include cyanide synthesis, which is oxygen-regulated and can affect the operation of aerobic respiratory pathways, and alginate production leading to a mucoid phenotype, which is regulated by oxygen and energy availability, as well as having a role in the protection of P. aeruginosa against reactive oxygen species. Finally, we consider a possible link between cyanide synthesis and the mucoid switch that operates in P. aeruginosa during chronic CF lung infection.
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Affiliation(s)
- Huw D Williams
- Division of Biology, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK
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González PJ, Rivas MG, Brondino CD, Bursakov SA, Moura I, Moura JJG. EPR and redox properties of periplasmic nitrate reductase from Desulfovibrio desulfuricans ATCC 27774. J Biol Inorg Chem 2006; 11:609-16. [PMID: 16791644 DOI: 10.1007/s00775-006-0110-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 04/13/2006] [Indexed: 11/30/2022]
Abstract
Nitrate reductases are enzymes that catalyze the conversion of nitrate to nitrite. We report here electron paramagnetic resonance (EPR) studies in the periplasmic nitrate reductase isolated from the sulfate-reducing bacteria Desulfovibrio desulfuricans ATCC 27774. This protein, belonging to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes, comprises a single 80-kDa subunit and contains a Mo bis(molybdopterin guanosine dinucleotide) cofactor and a [4Fe-4S] cluster. EPR-monitored redox titrations, carried out with and without nitrate in the potential range from 200 to -500 mV, and EPR studies of the enzyme, in both catalytic and inhibited conditions, reveal distinct types of Mo(V) EPR-active species, which indicates that the Mo site presents high coordination flexibility. These studies show that nitrate modulates the redox properties of the Mo active site, but not those of the [4Fe-4S] center. The possible structures and the role in catalysis of the distinct Mo(V) species detected by EPR are discussed.
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Affiliation(s)
- Pablo J González
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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Monza J, Irisarri P, Díaz P, Delgado MJ, Mesa S, Bedmar EJ. Denitrification ability of rhizobial strains isolated from Lotus sp. Antonie van Leeuwenhoek 2006; 89:479-84. [PMID: 16779640 DOI: 10.1007/s10482-005-9046-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/21/2005] [Indexed: 10/24/2022]
Abstract
Ten rhizobial strains isolated from Lotus sp. have been characterized by their ability to denitrify. Out of the 10 strains, the five slow-growing isolates grew well under oxygen-limiting conditions with nitrate as a sole nitrogen source, and accumulated nitrous oxide in the growth medium when acetylene was used to inhibit nitrous oxide reductase activity. All five strains contained DNA homologous to the Bradyrhizobium japonicum nirK, norBDQ and nosZ genes. In contrast, fast-growing lotus rhizobia were incapable of growing under nitrate-respiring conditions, and did not accumulate nitrous oxide in the growth medium. DNA from each of the five fast-growing strains showed a hybridization band with the B. japonicum nirK gene but not with norBDQ and nosZ genes. Partial 16S rDNA gene sequencing revealed that fast-growing strains could be identified as Mesorhizobium loti species and the slow-growers as Bradyrhizobium sp.
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Affiliation(s)
- Jorge Monza
- Laboratorio de Bioquímica, Facultad de Agronomía, Universidad de la República, Avenida Garzón 780, 12900, Montevideo, Uruguay.
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