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Kraus A, Spät P, Timm S, Wilson A, Schumann R, Hagemann M, Maček B, Hess WR. Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria. Nat Commun 2024; 15:1911. [PMID: 38429292 PMCID: PMC10907346 DOI: 10.1038/s41467-024-46253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/19/2024] [Indexed: 03/03/2024] Open
Abstract
When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. It has been hypothesized that the excreted nitrite represents excess nitrogen that cannot be further assimilated due to the missing carbon, but the underlying molecular mechanisms are unclear. Here, we identified a protein that interacts with nitrite reductase, regulates nitrogen metabolism and promotes nitrite excretion. The protein, which we named NirP1, is encoded by an unannotated gene that is upregulated under low carbon conditions and controlled by transcription factor NtcA, a central regulator of nitrogen homeostasis. Ectopic overexpression of nirP1 in Synechocystis sp. PCC 6803 resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments indicated that NirP1 interacts with nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite. Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting nitrite reductase.
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Affiliation(s)
- Alexander Kraus
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Philipp Spät
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Stefan Timm
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Amy Wilson
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany
| | - Rhena Schumann
- Biological Station Zingst, University of Rostock, D-18374, Zingst, Germany
| | - Martin Hagemann
- Plant Physiology Department, Institute of Biosciences, University of Rostock, D-18059, Rostock, Germany
| | - Boris Maček
- Department of Quantitative Proteomics, Interfaculty Institute for Cell Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, Freiburg University, D-79104, Freiburg, Germany.
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Nie L, Xiao Y, Zhou T, Feng H, He M, Liang Q, Mu K, Nie H, Huang Q, Chen W. Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida. Nucleic Acids Res 2024; 52:186-203. [PMID: 38000372 PMCID: PMC10783516 DOI: 10.1093/nar/gkad1117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The ubiquitous bacterial second messenger cyclic diguanylate (c-di-GMP) coordinates diverse cellular processes through its downstream receptors. However, whether c-di-GMP participates in regulating nitrate assimilation is unclear. Here, we found that NasT, an antiterminator involved in nitrate assimilation in Pseudomonas putida, specifically bound c-di-GMP. NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation. High-level c-di-GMP inhibited the binding of NasT to the leading RNA of nirBD operon (NalA), thus attenuating the antitermination function of NasT, resulting in decreased nirBD expression and nitrite reductase activity, which in turn led to increased nitrite accumulation in cells and its export. Molecular docking and point mutation assays revealed five residues in NasT (R70, Q72, D123, K127 and R140) involved in c-di-GMP-binding, of which R140 was essential for both c-di-GMP-binding and NalA-binding. Three diguanylate cyclases (c-di-GMP synthetases) were found to interact with NasT and inhibited nirBD expression, including WspR, PP_2557, and PP_4405. Besides, the c-di-GMP-binding ability of NasT was conserved in the other three representative Pseudomonas species, including P. aeruginosa, P. fluorescens and P. syringae. Our findings provide new insights into nitrate assimilation regulation by revealing the mechanism by which c-di-GMP inhibits nitrate assimilation via NasT.
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Affiliation(s)
- Liang Nie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yujie Xiao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tiantian Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoqi Feng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meina He
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingyuan Liang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kexin Mu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailing Nie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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3
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Saghaï A, Pold G, Jones CM, Hallin S. Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Nat Commun 2023; 14:8249. [PMID: 38086813 PMCID: PMC10716430 DOI: 10.1038/s41467-023-44022-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.
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Affiliation(s)
- Aurélien Saghaï
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Grace Pold
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden.
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Zhao R, Le Moine Bauer S, Babbin AR. " Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces. Appl Environ Microbiol 2023; 89:e0080023. [PMID: 37470485 PMCID: PMC10467342 DOI: 10.1128/aem.00800-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.
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Affiliation(s)
- Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sven Le Moine Bauer
- Centre for Deep Sea Research, Department of Earth Science, University of Bergen, Bergen, Norway
| | - Andrew R. Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Ju CJ, Niyazi S, Cao WY, Wang Q, Chen RP, Yu L. Characteristics and comparisons of the aerobic and anaerobic denitrification of a Klebsiella oxytoca strain: Performance, electron transfer pathway, and mechanism. J Environ Manage 2023; 338:117787. [PMID: 36965422 DOI: 10.1016/j.jenvman.2023.117787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
The performance and electron (e-) transfer mechanisms of anaerobic and aerobic denitrification by strain Klebsiella were investigated in this study. The RT-PCR results demonstrated that the membrane bound nitrate reductase gene (narG) and Cu-nitrite reductase gene (nirK) were responsible for both aerobic and anerobic denitrification. The extreme low gene relative abundance of nirK might be responsible for the severe accumulation of NO2--N (nitrogen in the form of NO2- ion) under anaerobic condition. Moreover, the nitrite reductase (Nir) activity was 0.31 μg NO2--N min-1 mg-1 protein under anaerobic conditions, which was lower than that under aerobic conditions (0.38 μg NO2--N min-1 mg-1 protein). By using respiration chain inhibitors, the e- transfer pathways of anaerobic and aerobic denitrification of Klebsiella strain were constructed. Fe-S protein and Complex III were the core components under anaerobic conditions, while Coenzyme Q (CoQ), Complexes I and III played a key role in aerobic denitrification. Nitrogen assimilation was found to be the main way to generate NH4+-N (nitrogen in the form of NH4+ ion) during anaerobic denitrification, and also served as the primary nitrogen removal way under aerobic condition. The results of this study may help to improve the understanding of the core components of strain Klebsiella during aerobic and anaerobic denitrifications, and may suggest potential applications of the strain for nitrogen-containing wastewater.
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Affiliation(s)
- Cheng-Jia Ju
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Shareen Niyazi
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Wen-Yin Cao
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Quan Wang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Rong-Ping Chen
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Lei Yu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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6
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Pacheco PJ, Cabrera JJ, Jiménez-Leiva A, Torres MJ, Gates AJ, Bedmar EJ, Richardson DJ, Mesa S, Tortosa G, Delgado MJ. The copper-responsive regulator CsoR is indirectly involved in Bradyrhizobium diazoefficiens denitrification. FEMS Microbiol Lett 2023; 370:fnad084. [PMID: 37573143 PMCID: PMC10457146 DOI: 10.1093/femsle/fnad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/14/2023] Open
Abstract
The soybean endosymbiont Bradyrhizobium diazoefficiens harbours the complete denitrification pathway that is catalysed by a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a nitrous oxide reductase (Nos), encoded by the napEDABC, nirK, norCBQD, and nosRZDFYLX genes, respectively. Induction of denitrification genes requires low oxygen and nitric oxide, both signals integrated into a complex regulatory network comprised by two interconnected cascades, FixLJ-FixK2-NnrR and RegSR-NifA. Copper is a cofactor of NirK and Nos, but it has also a role in denitrification gene expression and protein synthesis. In fact, Cu limitation triggers a substantial down-regulation of nirK, norCBQD, and nosRZDFYLX gene expression under denitrifying conditions. Bradyrhizobium diazoefficiens genome possesses a gene predicted to encode a Cu-responsive repressor of the CsoR family, which is located adjacent to copA, a gene encoding a putative Cu+-ATPase transporter. To investigate the role of CsoR in the control of denitrification gene expression in response to Cu, a csoR deletion mutant was constructed in this work. Mutation of csoR did not affect the capacity of B. diazoefficiens to grow under denitrifying conditions. However, by using qRT-PCR analyses, we showed that nirK and norCBQD expression was much lower in the csoR mutant compared to wild-type levels under Cu-limiting denitrifying conditions. On the contrary, copA expression was significantly increased in the csoR mutant. The results obtained suggest that CsoR acts as a repressor of copA. Under Cu limitation, CsoR has also an indirect role in the expression of nirK and norCBQD genes.
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Affiliation(s)
- Pedro J Pacheco
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Juan J Cabrera
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Andrea Jiménez-Leiva
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - María J Torres
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
- Department of Biochemistry and Molecular Biology, Campus Universitario de Rabanales, University of Córdoba, Ed. C6, Planta Baja, 14071 Córdoba, Spain
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Eulogio J Bedmar
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Socorro Mesa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - Germán Tortosa
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
| | - María J Delgado
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, C/Profesor Albareda 1, E-18008 Granada, Spain
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Denkhaus L, Siffert F, Einsle O. An unusual active site architecture in cytochrome c nitrite reductase NrfA-1 from Geobacter metallireducens. FEMS Microbiol Lett 2023; 370:fnad068. [PMID: 37460131 DOI: 10.1093/femsle/fnad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/21/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
Dissimilatory nitrate reduction to ammonia (DNRA) is a central pathway in the biogeochemical nitrogen cycle, allowing for the utilization of nitrate or nitrite as terminal electron acceptors. In contrast to the competing denitrification to N2, a major part of the essential nutrient nitrogen in DNRA is retained within the ecosystem and made available as ammonium to serve as a nitrogen source for other organisms. The second step of DNRA is mediated by the pentahaem cytochrome c nitrite reductase NrfA that catalyzes the six-electron reduction of nitrite to ammonium and is widely distributed among bacteria. A recent crystal structure of an NrfA ortholog from Geobacter lovleyi was the first characterized representative of a novel subclass of NrfA enzymes that lacked the canonical Ca2+ ion close to the active site haem 1. Here, we report the structural and functional characterization of NrfA from the closely related G. metallireducens. We established the recombinant production of catalytically active NrfA with its unique, lysine-coordinated active site haem heterologously in Escherichia coli and determined its three-dimensional structure by X-ray crystallography to 1.9 Å resolution. The structure confirmed GmNrfA as a further calcium-independent NrfA protein, and it also shows an altered active site that contained an unprecedented aspartate residue, D80, close to the substrate-binding site. This residue formed part of a loop that also caused a changed arrangement of the conserved substrate/product channel relative to other NrfA proteins and rendered the protein insensitive to the inhibitor sulphate. To elucidate the relevance of D80, we produced and studied the variants D80A and D80N that showed significantly reduced catalytic activity.
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Affiliation(s)
- Lukas Denkhaus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Fanny Siffert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
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8
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Qi Z, Gao A, Li L, Li Z, Zhang W, Dong S, Liu X. A novel strategy to improving Rhodobacter azotoformans denitrification efficiency: Insight into the role of a two-component system NtrX/Y in denitrification regulation. Bioresour Technol 2023; 368:128349. [PMID: 36400277 DOI: 10.1016/j.biortech.2022.128349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Transcription factors (TFs) can manage the coordinated expression of genes clusters or multiple genes. TF was used to improve bacterial denitrification ability in this study. During denitrification, the ntrY of R. azotoformans, which encodes the sensor of NtrX/Y system, was significantly upregulated in transcription. Denitrification of the mutant △ntrY was significantly inhibited, and it was recovered after replenishing this gene to the mutant, which indicates the NtrX/Y system plays an important role in regulating bacterial denitrification. According to additional research, the NtrX/Y system regulates bacterial denitrification by directly promoting the expression of the nitrite reductase. ntrY overexpression appears to accelerate bacterial denitrification, and the introduction of a strong promoter tac in conjunction with iron supply optimization increases the rate by 72% further. This study realizes bacterial denitrification enhancement from the perspective of global transcription regulation, which provides a novel strategy for improving microbial ability to degrade pollutants.
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Affiliation(s)
- Zhengliang Qi
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China.
| | - Anxin Gao
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Lu Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Zhen Li
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Wenyue Zhang
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Shuhan Dong
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
| | - Xinli Liu
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China; State Key Laboratory of Bio-based Material and Green Papermaking (LBMP), Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, PR China
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9
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Keller TCS, Lechauve C, Keller AS, Broseghini-Filho GB, Butcher JT, Askew Page HR, Islam A, Tan ZY, DeLalio LJ, Brooks S, Sharma P, Hong K, Xu W, Padilha AS, Ruddiman CA, Best AK, Macal E, Kim-Shapiro DB, Christ G, Yan Z, Cortese-Krott MM, Ricart K, Patel R, Bender TP, Sonkusare SK, Weiss MJ, Ackerman H, Columbus L, Isakson BE. Endothelial alpha globin is a nitrite reductase. Nat Commun 2022; 13:6405. [PMID: 36302779 PMCID: PMC9613979 DOI: 10.1038/s41467-022-34154-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 10/04/2022] [Indexed: 01/29/2023] Open
Abstract
Resistance artery vasodilation in response to hypoxia is essential for matching tissue oxygen and demand. In hypoxia, erythrocytic hemoglobin tetramers produce nitric oxide through nitrite reduction. We hypothesized that the alpha subunit of hemoglobin expressed in endothelium also facilitates nitrite reduction proximal to smooth muscle. Here, we create two mouse strains to test this: an endothelial-specific alpha globin knockout (EC Hba1Δ/Δ) and another with an alpha globin allele mutated to prevent alpha globin's inhibitory interaction with endothelial nitric oxide synthase (Hba1WT/Δ36-39). The EC Hba1Δ/Δ mice had significantly decreased exercise capacity and intracellular nitrite consumption in hypoxic conditions, an effect absent in Hba1WT/Δ36-39 mice. Hypoxia-induced vasodilation is significantly decreased in arteries from EC Hba1Δ/Δ, but not Hba1WT/Δ36-39 mice. Hypoxia also does not lower blood pressure in EC Hba1Δ/Δ mice. We conclude the presence of alpha globin in resistance artery endothelium acts as a nitrite reductase providing local nitric oxide in response to hypoxia.
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Affiliation(s)
- T C Stevenson Keller
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Christophe Lechauve
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alexander S Keller
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Gilson Brás Broseghini-Filho
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Joshua T Butcher
- Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| | - Henry R Askew Page
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Aditi Islam
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhe Yin Tan
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Leon J DeLalio
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Steven Brooks
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Poonam Sharma
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Kwangseok Hong
- Department of Physical Education, College of Education, Chung-Ang University, Seoul, South Korea
| | - Wenhao Xu
- Transgenic Mouse Facility, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | - Claire A Ruddiman
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Angela K Best
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Edgar Macal
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Daniel B Kim-Shapiro
- Department of Physics, Translational Science Center, Wake Forest University, Winston-Salem, NC, USA
| | - George Christ
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Zhen Yan
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Miriam M Cortese-Krott
- Cardiovascular Research Laboratory, Division of Cardiology, Pneumology and Angiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Karina Ricart
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rakesh Patel
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Timothy P Bender
- Department of Microbiology, Immunology and Cancer, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Swapnil K Sonkusare
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hans Ackerman
- Physiology Unit, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Linda Columbus
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Brant E Isakson
- Robert M Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Molecular Physiology and Biophysics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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10
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Pacheco PJ, Cabrera JJ, Jiménez-Leiva A, Bedmar EJ, Mesa S, Tortosa G, Delgado MJ. Effect of Copper on Expression of Functional Genes and Proteins Associated with Bradyrhizobium diazoefficiens Denitrification. Int J Mol Sci 2022; 23:ijms23063386. [PMID: 35328804 PMCID: PMC8951191 DOI: 10.3390/ijms23063386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/16/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas that contributes to climate change. Denitrification is one of the largest sources of N2O in soils. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model for rhizobial denitrification studies since, in addition to fixing N2, it has the ability to grow anaerobically under free-living conditions by reducing nitrate from the medium through the complete denitrification pathway. This bacterium contains a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a Cu-dependent nitrous oxide reductase (Nos) encoded by the napEDABC, nirK, norCBQD and nosRZDFYLX genes, respectively. In this work, an integrated study of the role of Cu in B. diazoefficiens denitrification has been performed. A notable reduction in nirK, nor, and nos gene expression observed under Cu limitation was correlated with a significant decrease in NirK, NorC and NosZ protein levels and activities. Meanwhile, nap expression was not affected by Cu, but a remarkable depletion in Nap activity was found, presumably due to an inhibitory effect of nitrite accumulated under Cu-limiting conditions. Interestingly, a post-transcriptional regulation by increasing Nap and NirK activities, as well as NorC and NosZ protein levels, was observed in response to high Cu. Our results demonstrate, for the first time, the role of Cu in transcriptional and post-transcriptional control of B. diazoefficiens denitrification. Thus, this study will contribute by proposing useful strategies for reducing N2O emissions from agricultural soils.
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11
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Schwartz SL, Momper L, Rangel LT, Magnabosco C, Amend JP, Fournier GP. Novel nitrite reductase domain structure suggests a chimeric denitrification repertoire in the phylum Chloroflexi. Microbiologyopen 2022; 11:e1258. [PMID: 35212484 PMCID: PMC8756737 DOI: 10.1002/mbo3.1258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/09/1999] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
Denitrification plays a central role in the global nitrogen cycle, reducing and removing nitrogen from marine and terrestrial ecosystems. The flux of nitrogen species through this pathway has a widespread impact, affecting ecological carrying capacity, agriculture, and climate. Nitrite reductase (Nir) and nitric oxide reductase (NOR) are the two central enzymes in this pathway. Here we present a previously unreported Nir domain architecture in members of phylum Chloroflexi. Phylogenetic analyses of protein domains within Nir indicate that an ancestral horizontal transfer and fusion event produced this chimeric domain architecture. We also identify an expanded genomic diversity of a rarely reported NOR subtype, eNOR. Together, these results suggest a greater diversity of denitrification enzyme arrangements exist than have been previously reported.
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Affiliation(s)
- Sarah L. Schwartz
- Microbiology Graduate ProgramMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Lily Momper
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Exponent Inc.PasadenaCaliforniaUSA
| | - Luiz Thiberio Rangel
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | | | - Jan P. Amend
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Gregory P. Fournier
- Department of Earth, Atmospheric, and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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12
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Xu Y, Lu J, Huang S, Zhao J. Submerged plants alleviated the impacts of increased ammonium pollution on anammox bacteria and nirS denitrifiers in the rhizosphere. Environ Sci Pollut Res Int 2021; 28:58755-58767. [PMID: 34120278 DOI: 10.1007/s11356-021-14715-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Excess nitrogen input into water bodies can cause eutrophication and affect the community structure and abundance of the nitrogen-transforming microorganisms; thus, it is essential to remove nitrogen from eutrophic water bodies. Aquatic plants can facilitate the growth of rhizosphere microorganisms. This study investigated the impact of ammonium pollution on the anammox and denitrifying bacteria in the rhizosphere of a cultivated submerged macrophyte, Potamogeton crispus (P. crispus) by adding three different concentrations of slow-release urea (0, 400, 600 mg per kg sediment) to the sediment to simulate different levels of nitrogen pollution in the lake. Results showed that the ammonium concentrations in the interstitial water under three pollution treatments were significantly different, but the nitrate concentration remained stable. The abundance of anammox 16S rRNA and nitrite reductase (nirS) gene in rhizosphere sediments exhibited no significant differences under the three pollution conditions. The increase in the nitrogen pollution levels did not significantly affect the growth of anammox bacteria and nirS denitrifying bacteria (denitrifiers). The change trend of the abundance ratio of (anammox 16S rRNA)/nirS in different nitrogen treatment groups on the same sampling date was very close, indicating that this ratio was not affected by ammonium pollution levels when P. crispus existed. The redundancy analysis showed that there was a positive correlation between the abundance of anammox 16S rRNA and nirS gene and that the abundance of these bacteria was significantly affected by the mole ratio of NH4+/NO3-. This study reveals that submerged plants weaken the environmental changes caused by ammonia pollution in the rhizosphere, thereby avoiding strong fluctuation of anammox bacteria and nirS denitrifiers.
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Affiliation(s)
- Yangfan Xu
- Research and Development Center of Transport Industry of Intelligent Manufacturing Technologies of Transport Infrastructure, Wuhan, 430040, China
- Key Laboratory of Large-span Bridge Construction Technology, Wuhan, 430040, China
- CCCC Second Harbor Engineering Company Ltd., Wuhan, 430040, China
| | - Jing Lu
- Australian Rivers Institute, Griffith University, QLD, Nathan, 4111, Australia
| | - Shanshan Huang
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070, Hubei Province, China.
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13
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Chen Q, Fan J, Ming H, Su J, Wang Y, Wang B. Effects of environmental factors on denitrifying bacteria and functional genes in sediments of Bohai Sea, China. Mar Pollut Bull 2020; 160:111621. [PMID: 32919123 DOI: 10.1016/j.marpolbul.2020.111621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
The ability of denitrifying microorganisms to respond to different ecological pressures remains unknown, especially in marine sediments rich in various heavy metals. Here, gene abundance and transcriptional abundance of five functional denitrification genes (narG, nirK, nirS, norB, and nosZ) in Bohai Sea sediments were examined, and high-throughput Illumina sequencing was used to analyze the community structure of nirK and nirS denitrifying bacteria. The nirS- and nirK-type denitrifying bacteria were classified into different genera. The heavy metal content in sediments was negatively correlated with transcriptional abundance of denitrifying genes, and RNA: DNA ratio for each gene was highest in central Bohai Sea. These results indicated the distribution of nitrite reductase denitrifying bacterial communities was affected by depth, total nitrogen, total phosphorus and sediment grain size. Heavy metal contamination in sediment environment may negatively regulate the transcriptional abundance of denitrifying genes and cause geographical differences in the denitrifying bacterial community structure.
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Affiliation(s)
- Quanrui Chen
- National Marine Environmental Monitoring Center, Dalian 116023, China; Xiamen University, Xiamen 361000, China
| | - Jingfeng Fan
- National Marine Environmental Monitoring Center, Dalian 116023, China.
| | - Hongxia Ming
- National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Jie Su
- National Marine Environmental Monitoring Center, Dalian 116023, China
| | - Yantao Wang
- National Marine Environmental Monitoring Center, Dalian 116023, China; Dalian Ocean University, Dalian 116000, China
| | - Bin Wang
- Dalian Ocean University, Dalian 116000, China
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14
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Costa-Broseta Á, Castillo M, León J. Nitrite Reductase 1 Is a Target of Nitric Oxide-Mediated Post-Translational Modifications and Controls Nitrogen Flux and Growth in Arabidopsis. Int J Mol Sci 2020; 21:ijms21197270. [PMID: 33019636 PMCID: PMC7582248 DOI: 10.3390/ijms21197270] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/16/2022] Open
Abstract
Plant growth is the result of the coordinated photosynthesis-mediated assimilation of oxidized forms of C, N and S. Nitrate is the predominant N source in soils and its reductive assimilation requires the successive activities of soluble cytosolic NADH-nitrate reductases (NR) and plastid stroma ferredoxin-nitrite reductases (NiR) allowing the conversion of nitrate to nitrite and then to ammonium. However, nitrite, instead of being reduced to ammonium in plastids, can be reduced to nitric oxide (NO) in mitochondria, through a process that is relevant under hypoxic conditions, or in the cytoplasm, through a side-reaction catalyzed by NRs. We use a loss-of-function approach, based on CRISPR/Cas9-mediated genetic edition, and gain-of-function, using transgenic overexpressing HA-tagged Arabidopsis NiR1 to characterize the role of this enzyme in controlling plant growth, and to propose that the NO-related post-translational modifications, by S-nitrosylation of key C residues, might inactivate NiR1 under stress conditions. NiR1 seems to be a key target in regulating nitrogen assimilation and NO homeostasis, being relevant to the control of both plant growth and performance under stress conditions. Because most higher plants including crops have a single NiR, the modulation of its function might represent a relevant target for agrobiotechnological purposes.
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Affiliation(s)
| | | | - José León
- Correspondence: ; Tel.: +34-963877882
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15
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Liu RR, Tian Y, Zhou EM, Xiong MJ, Xiao M, Li WJ. Distinct Expression of the Two NO-Forming Nitrite Reductases in Thermus antranikianii DSM 12462 T Improved Environmental Adaptability. Microb Ecol 2020; 80:614-626. [PMID: 32474659 DOI: 10.1007/s00248-020-01528-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/14/2020] [Indexed: 05/21/2023]
Abstract
Hot spring ecosystems are analogous to some thermal environments on the early Earth and represent ideal models to understand life forms and element cycling on the early Earth. Denitrification, an important component of biogeochemical nitrogen cycle, is highly active in hot springs. Nitrite (NO2-) reduction to nitric oxide (NO) is the significant and rate-limiting pathway in denitrification and is catalyzed by two types of nitrite reductases, encoded by nirS and nirK genes. NirS and NirK were originally considered incompatible in most denitrifying organisms, although a few strains have been reported to possess both genes. Herein, we report the functional division of nirS and nirK in Thermus, a thermophilic genus widespread in thermal ecosystems. Transcriptional levels of nirS and nirK coexisting in Thermus antranikianii DSM 12462T were measured to assess the effects of nitrite, oxygen, and stimulation time. Thirty-nine Thermus strains were used to analyze the phylogeny and distribution of nirS and nirK; six representative strains were used to assess the denitrification phenotype. The results showed that both genes were actively transcribed and expressed independently in T. antranikianii DSM 12462T. Strains with both nirS and nirK had a wider range of nitrite adaptation and revealed nir-related physiological adaptations in Thermus: nirK facilitated adaptation to rapid changes and extended the adaptation range of nitrite under oxygen-limited conditions, while nirS expression was higher under oxic and relatively stable conditions.
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Affiliation(s)
- Rui-Rui Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - En-Min Zhou
- School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming, 650091, People's Republic of China
| | - Meng-Jie Xiong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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16
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Fujimura R, Azegami Y, Wei W, Kakuta H, Shiratori Y, Ohte N, Senoo K, Otsuka S, Isobe K. Distinct Community Composition of Previously Uncharacterized Denitrifying Bacteria and Fungi across Different Land-Use Types. Microbes Environ 2020; 35:ME19064. [PMID: 31996500 PMCID: PMC7104279 DOI: 10.1264/jsme2.me19064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022] Open
Abstract
Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite reductase gene (nirK and nirS) sequences. These genes can be phylogenetically grouped into several clusters. We used cluster-specific PCR primers to amplify nirK and nirS belonging to each cluster because the most widely used primers only amplify genes belonging to a single cluster. We found that the dominant taxa as well as overall community composition of denitrifying bacteria and fungi, regardless of the cluster they belonged to, differed according to the land-use type. We also identified distinguishing taxa based on individual land-use types, the distribution of which has not previously been characterized, such as denitrifying bacteria or fungi dominant in forest soils, Rhodanobacter having nirK, Penicillium having nirK, and Bradyrhizobium having nirS. These results suggest that land-use management affects the ecological constraints and consequences of denitrification in terrestrial environments through the assembly of distinct communities of denitrifiers.
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Affiliation(s)
- Reiko Fujimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
| | - Yoichi Azegami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
| | - Wei Wei
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
- Jiangsu University, Jiangsu 212013, China
| | - Hiroko Kakuta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata 940–0826, Japan
| | - Nobuhito Ohte
- Graduate School of Informatics, Kyoto University, Kyoto 606–8501, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113–8657, Japan
| | - Shigeto Otsuka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113–8657, Japan
| | - Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113–8657, Japan
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17
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Yamada T, Tsuji H, Daimon H. Nitrate removal performance and diversity of active denitrifying bacteria in denitrification reactors using poly(L-lactic acid) with enhanced chemical hydrolyzability. Environ Sci Pollut Res Int 2019; 26:36236-36247. [PMID: 31713134 DOI: 10.1007/s11356-019-06722-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Poly(L-lactic acid) (PLLA) can be used as an external electron donor in denitrification reactors to treat drinking water, aquaculture water, and industrial wastewater with an imbalanced carbon/nitrogen ratio. However, for PLLA to function in these applications, its chemical hydrolyzability requires improvement. Although the adjustment of the crystallinity (Xc) is effective in improving the hydrolyzability of PLLA, the condition for the Xc of PLLA, in which a sufficient amount of lactic acid is released for denitrification, must be clarified. Therefore, this study investigated the effective Xc range and optimal PLLA content as an electron donor for continuous nitrate removal in denitrification reactors. This study also explored the abundance, succession, and diversity of active denitrifying bacteria in denitrification reactors. The nitrate removal activity of activated sludge using the highly crystalline PLLA (Xc = 39.4%) was 1.8 mg NO3- -N g MLSS-1 h-1, which is 2.4 times higher than that using the nearly amorphous PLLA (Xc = 0.9%). During the 57 days of operation, the denitrification reactor with 3% (w/v) highly crystalline PLLA continued to completely remove nitrate, with a maximum nitrate removal activity of 22.8 mg NO3- -N g MLSS-1 h-1. The 16S rRNA amplicon sequencing and clone library analyses are using transcripts of two nitrite reductase genes, encoding cytochrome cd1 nitrite reductase, and copper-containing nitrite reductase revealed that bacteria belonging to the families Comamonadaceae, Rhodocyclaceae, and Alcaligenaceae were active denitrifying bacteria in the denitrification reactor using PLLA.
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Affiliation(s)
- Takeshi Yamada
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan.
| | - Hideto Tsuji
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
| | - Hiroyuki Daimon
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
- Core for Global Network Innovation in Technology Education, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580, Japan
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18
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Zhou G, Peng H, Wang YS, Li CL, Shen PF, Huang XM, Xie XB, Shi QS. Biological functions of nirS in Pseudomonas aeruginosa ATCC 9027 under aerobic conditions. J Ind Microbiol Biotechnol 2019; 46:1757-1768. [PMID: 31512096 DOI: 10.1007/s10295-019-02232-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/23/2019] [Indexed: 01/10/2023]
Abstract
Through our previous study, we found an up-regulation in the expression of nitrite reductase (nirS) in the isothiazolone-resistant strain of Pseudomonas aeruginosa. However, the definitive molecular role of nirS in ascribing the resistance remained elusive. In the present study, the nirS gene was deleted from the chromosome of P. aeruginosa ATCC 9027 and the resulting phenotypic changes of ΔnirS were studied alongside the wild-type (WT) strain under aerobic conditions. The results demonstrated a decline in the formations of biofilms but not planktonic growth by ΔnirS as compared to WT, especially in the presence of benzisothiazolinone (BIT). Meanwhile, the deletion of nirS impaired swimming motility of P. aeruginosa under the stress of BIT. To assess the influence of nirS on the transcriptome of P. aeruginosa, RNA-seq experiments comparing the ΔnirS with WT were also performed. A total of 694 genes were found to be differentially expressed in ΔnirS, of which 192 were up-regulated, while 502 were down-regulated. In addition, these differently expressed genes were noted to significantly enrich the carbon metabolism along with glyoxylate and dicarboxylate metabolisms. Meanwhile, results from RT-PCR suggested the contribution of mexEF-oprN to the development of BIT resistance by ΔnirS. Further, c-di-GMP was less in ΔnirS than in WT, as revealed by HPLC. Taken together, our results confirm that nirS of P. aeruginosa ATCC 9027 plays a role in BIT resistance along with biofilm formation and further affects several metabolic patterns under aerobic conditions.
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Affiliation(s)
- Gang Zhou
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Hong Peng
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Ying-Si Wang
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Cai-Ling Li
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Peng-Fei Shen
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Xiao-Mo Huang
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China
| | - Xiao-Bao Xie
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China.
| | - Qing-Shan Shi
- Guangdong Open Laboratory of Applied Microbiology, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, Guangdong, People's Republic of China.
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19
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Wang M, Xiong W, Zou Y, Lin M, Zhou Q, Xie X, Sun Y. Evaluating the net effect of sulfadimidine on nitrogen removal in an aquatic microcosm environment. Environ Pollut 2019; 248:1010-1019. [PMID: 31091633 DOI: 10.1016/j.envpol.2019.02.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/22/2019] [Accepted: 02/15/2019] [Indexed: 06/09/2023]
Abstract
Antibiotics enter into aquatic pond sediments by wastewater and could make detrimental effects on microbial communities. In this study, we examined the effects of sulfadimidine on nitrogen removal when added to experimental pond sediments. We found that sulfadimidine increased the number of sulfadimidine resistant bacteria and significantly increased the abundance of sul2 at the end of the incubation time (ANOVA test at Tukey HSD, P < 0.05). In addition, sulfadimidine decreased the N2O reduction rate as well as the amount of nitrate reduction. Pearson correlation analysis revealed that the N2O reduction rate was significantly and negatively correlated with narG (r = -0.679, P < 0.05). In contrast, we found a significant positive correlation between the amount of nitrate reduction and the abundance of narG (r = 0.609, P < 0.05) and nirK (r = 0.611, P < 0.05). High-throughput sequencing demonstrated that Actinobacteria, Euryarchaeota, Gemmatimonadetes, Nitrospirae, Burkholderiaceae (a family of Proteobacteria), and Thermoanaerobaculaceae (a family of Firmicutes) decreased with sulfadimidine exposure. In sediments, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonbacteraeota, Euryarchaeota, Firmicutes, Gemmatimonadetes, and Spirochaetesat may play key roles in nitrogen transformation. Overall, the study exhibited a net effect of antibiotic exposure regarding nitrogen removal in an aquatic microcosm environment through a combination of biochemical pathways and molecular pathways, and draws attention to controlling antibiotic pollution in aquatic ecosystems.
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Affiliation(s)
- Mei Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yong Zou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Manxia Lin
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Xiying Xie
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
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20
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Zhang H, Feng J, Chen S, Zhao Z, Li B, Wang Y, Jia J, Li S, Wang Y, Yan M, Lu K, Hao H. Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants. Microb Ecol 2019; 77:304-316. [PMID: 30046860 DOI: 10.1007/s00248-018-1236-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/17/2018] [Indexed: 05/10/2023]
Abstract
Denitrifying bacteria is a driver of nitrogen removal process in wastewater treatment ecosystem. However, the geographical characteristics of denitrifying bacterial communities associated with activated sludge from diverse wastewater treatment plants (WWTPs) are still unclear. Here, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs. The results showed that the nirS abundance ranged from 4.6 × 102 to 2.4 × 103 copies per ng DNA, while nirS-type denitrifying bacterial populations were diverse and distinct from activated sludge communities. Among WWTPs, total nitrogen removal efficiencies varied from 25.8 to 84%, which was positively correlated with diversity indices, whereas abundance-based coverage estimator index decreased with an increase in latitude. The dominant phyla across all samples were proteobacteria, accounting for 46.23% (ranging from 17.98 to 87.07%) of the sequences. Eight of the 22 genera detected were dominant: Thauera sp., Alicycliphilus sp., and Pseudomonas sp., etc. Based on network analysis, the coexistence and interaction between dominant genera may be vital for regulating the nitrogen and carbon removal behaviors. Multivariate statistical analysis revealed that both geographic location and wastewater factors concurrently govern the distribution patterns of nirS-type denitrifying bacterial community harbored in WWTPs. Taking together, these results from the present study provide novel insights into the nirS gene abundance and nirS-type denitrifying bacterial community composition in geographically distributed WWTPs. Moreover, the knowledge gained will improve the operation and management of WWTPs for nitrogen removal.
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Affiliation(s)
- Haihan Zhang
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
| | - Ji Feng
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Shengnan Chen
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Zhenfang Zhao
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science and Technology, Guangzhou, 510650, Guangdong Province, People's Republic of China
| | - Yue Wang
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Jingyu Jia
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Sulin Li
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Yan Wang
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Miaomiao Yan
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Kuanyu Lu
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Huiyan Hao
- Key Laboratory of Northwest Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
- Institute of Environmental Microbial Technology, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
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21
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Jang J, Sakai Y, Senoo K, Ishii S. Potentially Mobile Denitrification Genes Identified in Azospirillum sp. Strain TSH58. Appl Environ Microbiol 2019; 85:e02474-18. [PMID: 30413471 PMCID: PMC6328785 DOI: 10.1128/aem.02474-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Denitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifying Azospirillum sp. strains and searched for mobile genetic elements that contain denitrification genes. All Azospirillum sp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase gene nirK was located on large replicons (549 to 941 kbp). Genome sequencing showed that Azospirillum strains that had similar nirK sequences also shared similar nir-nor gene arrangements, especially between the TSH58, Sp7T, and Sp245 strains. In addition to the high similarity between nir-nor gene clusters among the three Azospirillum strains, a composite transposon structure was identified in the genome of strain TSH58, which contains the nir-nor gene cluster and the novel IS6 family insertion sequences (ISAz581 and ISAz582). The nirK gene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing the nir-nor gene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely related Azospirillum sp. denitrifiers.IMPORTANCE The evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses of Azospirillum sp. denitrifiers, we identified denitrification genes, including nirK and norCBQD, located on a mobile genetic element in the genome of Azospirillum sp. strain TSH58. The nirK was actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.
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Affiliation(s)
- Jeonghwan Jang
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Yoriko Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, USA
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22
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Woehle C, Roy AS, Glock N, Wein T, Weissenbach J, Rosenstiel P, Hiebenthal C, Michels J, Schönfeld J, Dagan T. A Novel Eukaryotic Denitrification Pathway in Foraminifera. Curr Biol 2018; 28:2536-2543.e5. [PMID: 30078568 PMCID: PMC6783311 DOI: 10.1016/j.cub.2018.06.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/22/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022]
Abstract
Benthic foraminifera are unicellular eukaryotes inhabiting sediments of aquatic environments. Several species were shown to store and use nitrate for complete denitrification, a unique energy metabolism among eukaryotes. The population of benthic foraminifera reaches high densities in oxygen-depleted marine habitats, where they play a key role in the marine nitrogen cycle. However, the mechanisms of denitrification in foraminifera are still unknown, and the possibility of a contribution of associated bacteria is debated. Here, we present evidence for a novel eukaryotic denitrification pathway that is encoded in foraminiferal genomes. Large-scale genome and transcriptomes analyses reveal the presence of a denitrification pathway in foraminifera species of the genus Globobulimina. This includes the enzymes nitrite reductase (NirK) and nitric oxide reductase (Nor) as well as a wide range of nitrate transporters (Nrt). A phylogenetic reconstruction of the enzymes' evolutionary history uncovers evidence for an ancient acquisition of the foraminiferal denitrification pathway from prokaryotes. We propose a model for denitrification in foraminifera, where a common electron transport chain is used for anaerobic and aerobic respiration. The evolution of hybrid respiration in foraminifera likely contributed to their ecological success, which is well documented in palaeontological records since the Cambrian period.
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Affiliation(s)
- Christian Woehle
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany.
| | - Alexandra-Sophie Roy
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany.
| | - Nicolaas Glock
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Tanita Wein
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Julia Weissenbach
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
| | - Claas Hiebenthal
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Jan Michels
- Institute of Zoology, Kiel University, Am Botanischen Garten 1-9, Kiel 24118, Germany
| | - Joachim Schönfeld
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstrasse, Kiel 24148, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Am Botanischen Garten 11, Kiel 24118, Germany
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23
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Nikolova D, Heilmann C, Hawat S, Gäbelein P, Hippler M. Absolute quantification of selected photosynthetic electron transfer proteins in Chlamydomonas reinhardtii in the presence and absence of oxygen. Photosynth Res 2018; 137:281-293. [PMID: 29594952 DOI: 10.1007/s11120-018-0502-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/22/2018] [Indexed: 05/10/2023]
Abstract
The absolute amount of plastocyanin (PC), ferredoxin-NADP+-oxidoreductase (FNR), hydrogenase (HYDA1), and ferredoxin 5 (FDX5) were quantified in aerobic and anaerobic Chlamydomonas reinhardtii whole cells using purified (recombinant) proteins as internal standards in a mass spectrometric approach. Quantified protein amounts were related to the estimated amount of PSI. The ratios of PC to FNR to HYDA1 to FDX5 in aerobic cells were determined to be 1.4:1.2:0.003:0. In anaerobic cells, the ratios changed to 1.1:1.3:0.019:0.027 (PC:FNR:HYDA1:FDX5). Employing sodium dithionite and methyl viologen as electron donors, the specific activity of hydrogenase in whole cells was calculated to be 382 ± 96.5 μmolH2 min-1 mg-1. Importantly, these data reveal an about 70-fold lower abundance of HYDA1 compared to FNR. Despite this great disproportion between both proteins, which might further enhance the competition for electrons, the alga is capable of hydrogen production under anaerobic conditions, thus pointing to an efficient channeling mechanism of electrons from FDX1 to the HYDA1.
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Affiliation(s)
- Denitsa Nikolova
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Claudia Heilmann
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Susan Hawat
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Philipp Gäbelein
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Michael Hippler
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, 48143, Münster, Germany.
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24
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Liu LX, Li QQ, Zhang YZ, Hu Y, Jiao J, Guo HJ, Zhang XX, Zhang B, Chen WX, Tian CF. The nitrate-reduction gene cluster components exert lineage-dependent contributions to optimization of Sinorhizobium symbiosis with soybeans. Environ Microbiol 2017; 19:4926-4938. [PMID: 28967174 DOI: 10.1111/1462-2920.13948] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/02/2017] [Accepted: 09/26/2017] [Indexed: 11/28/2022]
Abstract
Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate-reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S. sp. III. In S. fredii, the deletion mutation of the nap (nitrate reductase), instead of nir (nitrite reductase) and nor (nitric oxide reductase), led to defects in nitrogen-fixation (Fix- ). By contrast, none of these core nitrate-reduction genes were required for the symbiosis of S. sp. III. However, within the same gene cluster, the deletion of hemN1 (encoding oxygen-independent coproporphyrinogen III oxidase) in both S. fredii and S. sp. III led to the formation of nitrogen-fixing (Fix+ ) but ineffective (Eff- ) nodules. These Fix+ /Eff- nodules were characterized by significantly lower enzyme activity of glutamine synthetase indicating rhizobial modulation of nitrogen-assimilation by plants. A distant homologue of HemN1 from S. sojae can complement this defect in S. fredii and S. sp. III, but exhibited a more pleotropic role in symbiosis establishment. These findings highlighted the lineage-dependent optimization of symbiotic functions in different rhizobial species associated with the same host.
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Affiliation(s)
- Li Xue Liu
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qin Qin Li
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yue Hu
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hui Juan Guo
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xing Xing Zhang
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, Ministry of Agriculture Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
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25
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Lisa JA, Jayakumar A, Ward BB, Song B. nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary. Environ Microbiol Rep 2017; 9:766-778. [PMID: 28914491 DOI: 10.1111/1758-2229.12594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2 S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.
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Affiliation(s)
- Jessica A Lisa
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & May, Gloucester Point, VA, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & May, Gloucester Point, VA, USA
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26
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Ma KC, Unemo M, Jeverica S, Kirkcaldy RD, Takahashi H, Ohnishi M, Grad YH. Genomic Characterization of Urethritis-Associated Neisseria meningitidis Shows that a Wide Range of N. meningitidis Strains Can Cause Urethritis. J Clin Microbiol 2017; 55:3374-3383. [PMID: 28904187 PMCID: PMC5703804 DOI: 10.1128/jcm.01018-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022] Open
Abstract
Neisseria meningitidis, typically a resident of the oro- or nasopharynx and the causative agent of meningococcal meningitis and meningococcemia, is capable of invading and colonizing the urogenital tract. This can result in urethritis, akin to the syndrome caused by its sister species, N. gonorrhoeae, the etiologic agent of gonorrhea. Recently, meningococcal strains associated with outbreaks of urethritis were reported to share genetic characteristics with the gonococcus, raising the question of the extent to which these strains contain features that promote adaptation to the genitourinary niche, making them gonococcus-like and distinguishing them from other N. meningitidis strains. Here, we analyzed the genomes of 39 diverse N. meningitidis isolates associated with urethritis, collected independently over a decade and across three continents. In particular, we characterized the diversity of the nitrite reductase gene (aniA), the factor H-binding protein gene (fHbp), and the capsule biosynthetic locus, all of which are loci previously suggested to be associated with urogenital colonization. We observed notable diversity, including frameshift variants, in aniA and fHbp and the presence of intact, disrupted, and absent capsule biosynthetic genes, indicating that urogenital colonization and urethritis caused by N. meningitidis are possible across a range of meningococcal genotypes. Previously identified allelic patterns in urethritis-associated N. meningitidis strains may reflect genetic diversity in the underlying meningococcal population rather than novel adaptation to the urogenital tract.
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Affiliation(s)
- Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Samo Jeverica
- Institute for Microbiology and Immunology, Medical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Robert D Kirkcaldy
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, CDC, Atlanta, Georgia, USA
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Tolar BB, Herrmann J, Bargar JR, van den Bedem H, Wakatsuki S, Francis CA. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea. Environ Microbiol Rep 2017; 9:484-491. [PMID: 28677304 DOI: 10.1111/1758-2229.12567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/01/2017] [Accepted: 06/25/2017] [Indexed: 06/07/2023]
Abstract
Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK).
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Affiliation(s)
- Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - John R Bargar
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Henry van den Bedem
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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Xin Y, Zhao T, Qu X. [Distribution, structure and sequence alignment, and metagenomics analysis of two nitrite reductases with NO forming]. Wei Sheng Wu Xue Bao 2017; 57:597-608. [PMID: 29756742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To reflect the importance of nitrite reductase (NIR) in the environment, we studied its distribution. METHODS The sequences of NIR were searched in the sequenced genome database at NCBI based on previous reported NIR sequences. The sequence similarity was done by multiple sequence alignment, and phylogenetic relationship was evaluated via constructing the phylogenetic tree. Furthermore, their distribution in the marine metagenome was studied by metagenomics. RESULTS The homologues of these two enzymes were 397 and 812 strains in sequenced genome, and the proportion was 8 and 15.7 percent, respectively. Almost all of archaea containing type II NIR. They have high identity by multiple sequence alignment analysis. The cofactor, the substrate and the cooper binding sites in type II were high conserved, suggesting that these enzymes had the specific function in denitrification. Phylogenetic analysis showed the two enzymes may have the common ancestor. In marine metagenome analysis, type I and II have 6 and 35 reads per 100000 reads, respectively, the two types of NIRs have the biggest proportion at the tropical south pacific area. CONCLUSION Collectively, we suggested NIR, especially type II, play a key role in bioremediation of nitrogen contamination.
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López MF, Cabrera JJ, Salas A, Delgado MJ, López-García SL. Dissecting the role of NtrC and RpoN in the expression of assimilatory nitrate and nitrite reductases in Bradyrhizobium diazoefficiens. Antonie Van Leeuwenhoek 2017; 110:531-542. [PMID: 28040856 DOI: 10.1007/s10482-016-0821-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/19/2016] [Indexed: 11/28/2022]
Abstract
Bradyrhizobium diazoefficiens, a nitrogen-fixing endosymbiont of soybeans, is a model strain for studying rhizobial denitrification. This bacterium can also use nitrate as the sole nitrogen (N) source during aerobic growth by inducing an assimilatory nitrate reductase encoded by nasC located within the narK-bjgb-flp-nasC operon along with a nitrite reductase encoded by nirA at a different chromosomal locus. The global nitrogen two-component regulatory system NtrBC has been reported to coordinate the expression of key enzymes in nitrogen metabolism in several bacteria. In this study, we demonstrate that disruption of ntrC caused a growth defect in B. diazoefficiens cells in the presence of nitrate or nitrite as the sole N source and a decreased activity of the nitrate and nitrite reductase enzymes. Furthermore, the expression of narK-lacZ or nirA-lacZ transcriptional fusions was significantly reduced in the ntrC mutant after incubation under nitrate assimilation conditions. A B. diazoefficiens rpoN 1/2 mutant, lacking both copies of the gene encoding the alternative sigma factor σ54, was also defective in aerobic growth with nitrate as the N source as well as in nitrate and nitrite reductase expression. These results demonstrate that the NtrC regulator is required for expression of the B. diazoefficiens nasC and nirA genes and that the sigma factor RpoN is also involved in this regulation.
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Affiliation(s)
- María F López
- Instituto de Biotecnología y Biología Molecular (IBBM), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT La Plata-CONICET, Calles 47 y 115, B1900AJL, La Plata, Argentina
| | - Juan J Cabrera
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain
| | - Ana Salas
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain
| | - María J Delgado
- Estación Experimental del Zaidín, CSIC, PO Box 419, 18080, Granada, Spain.
| | - Silvina L López-García
- Instituto de Biotecnología y Biología Molecular (IBBM), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata y CCT La Plata-CONICET, Calles 47 y 115, B1900AJL, La Plata, Argentina.
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Gao M, Liu J, Qiao Y, Zhao M, Zhang XH. Diversity and Abundance of the Denitrifying Microbiota in the Sediment of Eastern China Marginal Seas and the Impact of Environmental Factors. Microb Ecol 2017; 73:602-615. [PMID: 27924403 DOI: 10.1007/s00248-016-0906-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
Investigating the environmental influence on the community composition and abundance of denitrifiers in marine sediment ecosystem is essential for understanding of the ecosystem-level controls on the biogeochemical process of denitrification. In the present study, nirK-harboring denitrifying communities in different mud deposit zones of eastern China marginal seas (ECMS) were investigated via clone library analysis. The abundance of three functional genes affiliated with denitrification (narG, nirK, nosZ) was assessed by fluorescent quantitative PCR. The nirK-harboring microbiota were dominated by a few operational taxonomic units (OTUs), which were widely distributed in different sites with each site harboring their unique phylotypes. The mean abundance of nirK was significantly higher than that of narG and nosZ genes, and the abundance of narG was higher than that of nosZ. The inconsistent abundance profile of different functional genes along the process of denitrification might indicate that nitrite reduction occurred independently of denitrification in the mud deposit zones of ECMS, and sedimentary denitrification was accomplished by cooperation of different denitrifying species rather than a single species. Such important information would be missed when targeting only a single denitrifying functional gene. Analysis of correlation between abundance ratios and environmental factors revealed that the response of denitrifiers to environmental factors was not invariable in different mud deposit zones. Our results suggested that a comprehensive analysis of different denitrifying functional genes may gain more information about the dynamics of denitrifying microbiota in marine sediments.
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Affiliation(s)
- Minghong Gao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yanlu Qiao
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Meixun Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Li Y, Zhuang S, Wu Y, Ren H, Chen F, Lin X, Wang K, Beardall J, Gao K. Ocean acidification modulates expression of genes and physiological performance of a marine diatom. PLoS One 2017; 12:e0170970. [PMID: 28192486 PMCID: PMC5305191 DOI: 10.1371/journal.pone.0170970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/13/2017] [Indexed: 12/03/2022] Open
Abstract
Ocean Acidification (OA) is known to affect various aspects of physiological performances of diatoms, but little is known about the underlining molecular mechanisms involved. Here, we show that in the model diatom Phaeodactylum tricornutum, the expression of key genes associated with photosynthetic light harvesting as well as those encoding Rubisco, carbonic anhydrase, NADH dehydrogenase and nitrite reductase, are modulated by OA (1000 μatm, pHnbs 7.83). Growth and photosynthetic carbon fixation were enhanced by elevated CO2. OA treatment decreased the expression of β-carbonic anhydrase (β-ca), which functions in balancing intracellular carbonate chemistry and the CO2 concentrating mechanism (CCM). The expression of the genes encoding fucoxanthin chlorophyll a/c protein (lhcf type (fcp)), mitochondrial ATP synthase (mtATP), ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene (rbcl) and NADH dehydrogenase subunit 2 (ndh2), were down-regulated during the first four days (< 8 generations) after the cells were transferred from LC (cells grown under ambient air condition; 390 μatm; pHnbs 8.19) to OA conditions, with no significant difference between LC and HC treatments with the time elapsed. The expression of nitrite reductase (nir) was up-regulated by the OA treatment. Additionally, the genes for these proteins (NiR, FCP, mtATP synthase, β-CA) showed diel expression patterns. It appeared that the enhanced photosynthetic and growth rates under OA could be attributed to stimulated nitrogen assimilation, increased CO2 availability or saved energy from down-regulation of the CCM and consequently lowered cost of protein synthesis versus that of non-nitrogenous cell components.
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Affiliation(s)
- Yahe Li
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shufang Zhuang
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yaping Wu
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Honglin Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Fangyi Chen
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kunshan Gao
- State Key Laboratory of Marine Environmental Science (Xiamen University), College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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Lee JA, Francis CA. Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance. Microb Ecol 2017; 73:271-284. [PMID: 27709247 DOI: 10.1007/s00248-016-0865-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/16/2016] [Indexed: 06/06/2023]
Abstract
Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.
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Affiliation(s)
- Jessica A Lee
- Department of Earth System Science, Stanford University, Stanford, CA, USA
- Present address: Department of Biological Sciences, University of Idaho, Moscow, ID, USA
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Gusakova SV, Smagliy LV, Birulina YG, Kovalev IV, Nosarev V, Petrova IV, Reutov VP. [Molecular Mechanisms of Action of Gas Transmitters NO, CO and H2S in Smooth Muscle Cells and Effect of NO-generating Compounds (Nitrates and Nitrites) on Average Life Expectancy]. Usp Fiziol Nauk 2017; 48:24-52. [PMID: 29283238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Gaseous signaling molecules (gas transmitters) take an especial position among the numerous signaling molecules involved in the regulation of both intracellular processes that occur in different types of cells and cell-cell interactions. At present time, gas transmitters include three molecules whose enzymatic systems of synthesis and degradation, physiological action and intracellular effectors, the change of which under the action of gas transmitters may result in physiological and/or pathophysiological effects are well- determined. These molecules include nitrogen oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S). They are involved in the regulation of functions of various organs and systems of the human body, including the circulatory system. Interaction of NO, CO and H2S with various enzymatic and structural components of endothelial and, especially, smooth muscle cells has a significant impact on vascular tone and blood pressure. Furthermore, the crossing of NO-, CO- and H2S-mediated signaling pathways at common effectors and interaction with each other can determine the end, resulting functional response of the cell. The knowledge of the molecular targets of gas transmitters' action, the structure of the binding centers for gas transmitters and their interaction with each other may be essential in the development of methods of regulation of these signaling systems by targeted, directed action. This review summarizes the molecular mechanisms of the NO, CO and H2S interaction with the main targets, which carry out their regulatory effect on vascular smooth muscle cells. Also we describe here different ways of cross-regulation of NO-, CO- and H2S-dependent signaling pathways. We analyzed NO-synthase and nitrite reductase systems of nitric oxide cycle and discuss the nitrate-nitrite background of the existence of modern man, which can substantially modify the signaling system, the metabolism of virtually all cell ultrastructure of neurons, neuron-neuron and neuron-glial interactions and exerts its influence on socially significant diseases that can affect the quality and the average life expectancy.
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Yao YH, Wang MX, Zuo XH, Li ZL, Luo F, Zhou ZF. [Effects of PAHs Pollution on the Community Structure of Denitrifiers in a Typical Oilfield]. Huan Jing Ke Xue 2016; 37:4750-4759. [PMID: 29965317 DOI: 10.13227/j.hjkx.201606071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agricultural soils in the oilfields have the potential risk of PAHs (polycyclic aromatic hydrocarbons) pollution, and the denitrification process with nitrate as the terminal electron acceptor might be important for soil PAHs elimination under anaerobic condition. In this study, 9 soil samples listed as JH-1 to JH-9 were collected from the JiangHan oilfield with a history of more than 50 years. Using the functional genes (nirK: Cu-nitrite reductase gene; nirS: cd1-nitrite reductase gene) involved in denitrification as biomarkers, the community structure of soil denitrifiers was investigated by quantitative-PCR and T-RFLP (terminal-restriction fragment length polymorphism) combined with clone library, and the relationship between soil properties and community structure of soil denitrifers was discussed. The result indicated that the copy numbers of nirK were higher than those of nirS in all soil samples, and the lowest copy numbers of nirK and nirS were both detected in the JH-4 with the highest PAHs content. Meanwhile, the correlation analysis also showed a negative correlation between the copy numbers of those functional genes and soil PAHs content (nirK: R2=0.54, P<0.05; nirS: R2=0.58, P<0.05). Furthermore, the result of T-RFLP indicated that the nirK community structures in different soil samples varied significantly, which was obviously unique in the sample (JH-4) with the highest PAHs content. The subsequent RDA (redundancy analysis) also demonstrated that soil PAHs content as well as the available nitrogen and phosphorus belonged to the most important factors affecting the nirK community structure in this oilfield soil. Compared with nirK, little variation was shown about the nirS community structure among the soil samples. However, the abundance of nirS-harboring pseudomonas had a remarkably positive relation with the soil PAHs content, which indicated that pseudomonas, a well known bacterial genus with strong ability to degrade organic pollutants, might be an essential driver for PAHs degradation via denitrification process in this oilfield soil.
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Affiliation(s)
- Yan-Hong Yao
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ming-Xia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Xiao-Hu Zuo
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhen-Lun Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Feng Luo
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhi-Feng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China
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Vaishnav A, Kumari S, Jain S, Varma A, Tuteja N, Choudhary DK. PGPR-mediated expression of salt tolerance gene in soybean through volatiles under sodium nitroprusside. J Basic Microbiol 2016; 56:1274-1288. [PMID: 27439917 DOI: 10.1002/jobm.201600188] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/06/2016] [Indexed: 12/27/2022]
Abstract
Increasing evidence shows that nitric oxide (NO), a typical signaling molecule plays important role in development of plant and in bacteria-plant interaction. In the present study, we tested the effect of sodium nitroprusside (SNP)-a nitric oxide donor, on bacterial metabolism and its role in establishment of PGPR-plant interaction under salinity condition. In the present study, we adopted methods namely, biofilm formation assay, GC-MS analysis of bacterial volatiles, chemotaxis assay of root exudates (REs), measurement of electrolyte leakage and lipid peroxidation, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) for gene expression. GC-MS analysis revealed that three new volatile organic compounds (VOCs) were expressed after treatment with SNP. Two VOCs namely, 4-nitroguaiacol and quinoline were found to promote soybean seed germination under 100 mM NaCl stress. Chemotaxis assay revealed that SNP treatment, altered root exudates profiling (SS-RE), found more attracted to Pseudomonas simiae bacterial cells as compared to non-treated root exudates (S-RE) under salt stress. Expression of Peroxidase (POX), catalase (CAT), vegetative storage protein (VSP), and nitrite reductase (NR) genes were up-regulated in T6 treatment seedlings, whereas, high affinity K+ transporter (HKT1), lipoxygenase (LOX), polyphenol oxidase (PPO), and pyrroline-5-carboxylate synthase (P5CS) genes were down-regulated under salt stress. The findings suggest that NO improves the efficiency and establishment of PGPR strain in the plant environment during salt condition. This strategy may be applied on soybean plants to increase their growth during salinity stress.
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Affiliation(s)
- Anukool Vaishnav
- Department of Biological Science, College of Arts, Science and Humanities (CASH), Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
| | - Sarita Kumari
- Department of Biological Science, College of Arts, Science and Humanities (CASH), Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
| | - Shekhar Jain
- Department of Biological Science, College of Arts, Science and Humanities (CASH), Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
| | - Ajit Varma
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
| | - Narendra Tuteja
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
| | - Devendra Kumar Choudhary
- Department of Biological Science, College of Arts, Science and Humanities (CASH), Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
- Amity Institute of Microbial Technology (AIMT), Amity University Campus, Gautam Buddha Nagar, Noida, Uttar Pradesh, India
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Floryszak-Wieczorek J, Arasimowicz-Jelonek M, Izbiańska K. The combined nitrate reductase and nitrite-dependent route of NO synthesis in potato immunity to Phytophthora infestans. Plant Physiol Biochem 2016; 108:468-477. [PMID: 27588710 DOI: 10.1016/j.plaphy.2016.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 05/10/2023]
Abstract
In contrast to the in-depth knowledge concerning nitric oxide (NO) function, our understanding of NO synthesis in plants is still very limited. In view of the above, this paper provides a step by step presentation of the reductive pathway for endogenous NO generation involving nitrate reductase (NR) activity and nitrite implication in potato defense to Phytophthora infestans. A biphasic character of NO emission, peaking mainly at 3 and then at 24 hpi, was detected during the hypersensitive response (HR). In avr P. infestans potato leaves enhanced NR gene and protein expression was tuned with the depletion of nitrate contents and the increase in nitrite supply at 3 hpi. In the same time period a temporary down-regulation of nitrite reductase (NiR) and activity was found. The study for the link between NO signaling and HR revealed an up-regulation of used markers of effective defense, i.e. Nonexpressor of PR genes (NPR1), thioredoxins (Thx) and PR1, at early time-points (1-3 hpi) upon inoculation. In contrast to the resistant response, in the susceptible one a late overexpression (24-48 hpi) of NPR1 and PR1 mRNA levels was observed. Presented data confirmed the importance of nitrite processed by NR in NO generation in inoculated potato leaves. However, based on the pharmacological approach the potential formation of NO from nitrite bypassing the NR activity during HR response to P. infestans has also been discussed.
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Affiliation(s)
| | | | - Karolina Izbiańska
- Department of Plant Ecophysiology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
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Fan Z, Han RM, Ma J, Wang GX. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China. Environ Sci Pollut Res Int 2016; 23:14102-14114. [PMID: 27048324 DOI: 10.1007/s11356-016-6390-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.
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Affiliation(s)
- Zhou Fan
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Rui-Ming Han
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ma
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Guo-Xiang Wang
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China.
- Nanjing Normal University, School of Geography Science, Wenyuan Road 1, Nanjing, 210023, China.
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Taha MK, Claus H, Lappann M, Veyrier FJ, Otto A, Becher D, Deghmane AE, Frosch M, Hellenbrand W, Hong E, Parent du Châtelet I, Prior K, Harmsen D, Vogel U. Evolutionary Events Associated with an Outbreak of Meningococcal Disease in Men Who Have Sex with Men. PLoS One 2016; 11:e0154047. [PMID: 27167067 PMCID: PMC4864352 DOI: 10.1371/journal.pone.0154047] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022] Open
Abstract
Meningococci spread via respiratory droplets, whereas the closely related gonococci are transmitted sexually. Several outbreaks of invasive meningococcal disease have been reported in Europe and the United States among men who have sex with men (MSM). We recently identified an outbreak of serogroup C meningococcal disease among MSM in Germany and France. In this study, genomic and proteomic techniques were used to analyze the outbreak isolates. In addition, genetically identical urethritis isolates were recovered from France and Germany and included in the analysis. Genome sequencing revealed that the isolates from the outbreak among MSM and from urethritis cases belonged to a clade within clonal complex 11. Proteome analysis showed they expressed nitrite reductase, enabling anaerobic growth as previously described for gonococci. Invasive isolates from MSM, but not urethritis isolates, further expressed functional human factor H binding protein associated with enhanced survival in a newly developed transgenic mouse model expressing human factor H, a complement regulatory protein. In conclusion, our data suggest that urethritis and outbreak isolates followed a joint adaptation route including adaption to the urogenital tract.
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MESH Headings
- Animals
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Complement Factor H/antagonists & inhibitors
- Complement Factor H/genetics
- Complement Factor H/metabolism
- Disease Outbreaks
- Evolution, Molecular
- France/epidemiology
- Gene Expression
- Germany/epidemiology
- Homosexuality, Male
- Host-Pathogen Interactions
- Humans
- Male
- Meningitis, Meningococcal/diagnosis
- Meningitis, Meningococcal/epidemiology
- Meningitis, Meningococcal/microbiology
- Meningitis, Meningococcal/pathology
- Mice
- Mice, Transgenic
- Neisseria meningitidis/classification
- Neisseria meningitidis/genetics
- Neisseria meningitidis/isolation & purification
- Neisseria meningitidis/pathogenicity
- Neisseria meningitidis, Serogroup C/classification
- Neisseria meningitidis, Serogroup C/genetics
- Neisseria meningitidis, Serogroup C/isolation & purification
- Neisseria meningitidis, Serogroup C/pathogenicity
- Nitrite Reductases/genetics
- Nitrite Reductases/metabolism
- Phylogeny
- Proteome/genetics
- Proteome/metabolism
- Urethritis/diagnosis
- Urethritis/epidemiology
- Urethritis/microbiology
- Urethritis/pathology
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Affiliation(s)
- Muhamed-Kheir Taha
- Institut Pasteur, Invasive Bacterial Infections Unit and National Reference Center for meningococci, Paris, France
- * E-mail: (MKT); (UV)
| | - Heike Claus
- University of Würzburg, Institute for Hygiene and Microbiology, Reference laboratory for meningococci and Haemophilus influenzae, Würzburg, Germany
| | - Martin Lappann
- University of Würzburg, Institute for Hygiene and Microbiology, Reference laboratory for meningococci and Haemophilus influenzae, Würzburg, Germany
| | - Frédéric J. Veyrier
- Institut Pasteur, Invasive Bacterial Infections Unit and National Reference Center for meningococci, Paris, France
| | - Andreas Otto
- Ernst-Moritz-Arndt-University, Department of Microbial Proteomics and Mass Spectrometry, Greifswald, Germany
| | - Dörte Becher
- Ernst-Moritz-Arndt-University, Department of Microbial Proteomics and Mass Spectrometry, Greifswald, Germany
| | - Ala-Eddine Deghmane
- Institut Pasteur, Invasive Bacterial Infections Unit and National Reference Center for meningococci, Paris, France
| | - Matthias Frosch
- University of Würzburg, Institute for Hygiene and Microbiology, Reference laboratory for meningococci and Haemophilus influenzae, Würzburg, Germany
| | | | - Eva Hong
- Institut Pasteur, Invasive Bacterial Infections Unit and National Reference Center for meningococci, Paris, France
| | | | - Karola Prior
- University of Münster, Department of Periodontology, Münster, Germany
| | - Dag Harmsen
- University of Münster, Department of Periodontology, Münster, Germany
| | - Ulrich Vogel
- University of Würzburg, Institute for Hygiene and Microbiology, Reference laboratory for meningococci and Haemophilus influenzae, Würzburg, Germany
- * E-mail: (MKT); (UV)
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Cheng JH, Dou ZY, Sun QY. [Distribution Characteristics of Nitrifiers and Denitrifiers in the River Sediments of Tongling City]. Huan Jing Ke Xue 2016; 37:1362-1370. [PMID: 27548957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Rivers in mining areas were influenced by contaminants such as nitrogen, phosphorus and organic matter due to domestic and agricultural wastewater discharge in addition to pollutants caused by mining activities. In this study, surface sediment samples of rivers in Tongling city were collected to address the effect of season and pollution type on the abundance of nitrifiers and denitrifiers using quantitative polymerase chain reaction (QPCR) technique targeting at the ammonia monooxygenase (amoA) and nitrite reductase (nir) genes. The results showed that the average ahundance of ammonia oxidizing archaea (AGA) (ranging from 1.74 x 10⁵ to 1.45 x 10⁸ copies · g⁻¹) was 4.39 times that of ammonia oxidizing hacteria (AGH) (ranging from 1.39 x 10⁵ to 3.39 x 10⁷ copies · g⁻¹); and the average abundance of nirK gene (ranging from 4.45 x 10⁶ to 1.51 x 10⁸ copies · g) was almost a thirtieth part of nirS gene (ranging from 1.69 x 10⁷ to 8.55 x 10⁹ copies · g⁻¹). The abundance of AOA was higher in spring and autumn, and lower in summer and winter. And sediment AOB abundance was higher in spring and winter than in summer and autumn. Meanwhile, the abundance of nir genes was in the order of spring (nirS )/autumn (nirK) > summer > winter > autumn (nirS )/spring (nirK). Moreover, the abundance of bacterial and archaeal arnoA and nirS genes in sediments influenced by mine pollution was generally higher than that in sediments influenced by agricultural non-point pollution, whereas the abundance of nirK gene showed an opposite trend.
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40
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Barrett M, Khalil MI, Jahangir MMR, Lee C, Cardenas LM, Collins G, Richards KG, O'Flaherty V. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils. Environ Sci Pollut Res Int 2016; 23:7899-910. [PMID: 26762934 DOI: 10.1007/s11356-015-6030-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 12/28/2015] [Indexed: 05/22/2023]
Abstract
The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P < 0.03). Denitrifier gene copy concentrations per gram of soil (GCC) varied in response to carbon type amendment (P < 0.01). Denitrifier GCCs were high (ca. 10(7)) and the bac:nirK, bac:nirS, bac:nir (T) , and bac:nosZ ratios were low (ca. 10(-1)/10) in horizon A in all three respective treatments. Glucose-C amendment favored partial denitrification, resulting in higher nir abundance and higher N2O fluxes compared to the control. DOC amendment, by contrast, resulted in relatively higher nosZ abundance and N2 emissions, thus favoring complete denitrification. We also noted soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.
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Affiliation(s)
- M Barrett
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
| | - M I Khalil
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - M M R Jahangir
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - C Lee
- School of Civil & Environmental Engineering Nanyang Technological University, Singapore, 639798, Singapore
| | - L M Cardenas
- Rothamsted Research, North Wyke, Okehampton, Devon, EX20 2SB, UK
| | - G Collins
- Microbial EcoEngineering Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
- Environmental Engineering Laboratory, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - K G Richards
- Crops, Environment and Land-Use Department, Teagasc, Johnstown Castle, Co., Wexford, Ireland
| | - V O'Flaherty
- Microbial Ecology Laboratory, Microbiology, School of Natural Sciences & Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland.
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41
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Davenport S, Le Lay P, Sanchez-Tamburrrino JP. Nitrate metabolism in tobacco leaves overexpressing Arabidopsis nitrite reductase. Plant Physiol Biochem 2015; 97:96-107. [PMID: 26447683 DOI: 10.1016/j.plaphy.2015.09.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 05/07/2023]
Abstract
Primary nitrogen assimilation in plants includes the reduction of nitrite to ammonium in the chloroplasts by the enzyme nitrite reductase (NiR EC:1.7.7.1) or in the plastids of non-photosynthetic organs. Here we report on a study overexpressing the Arabidopsis thaliana NiR (AtNiR) gene in tobacco plants under the control of a constitutive promoter (CERV - Carnation Etched Ring Virus). The aim was to overexpress AtNiR in an attempt to alter the level of residual nitrite in the leaf which can act as precursor to the formation of nitrosamines. The impact of increasing the activity of AtNiR produced an increase in leaf protein and a stay-green phenotype in the primary transformed AtNiR population. Investigation of the T1 homozygous population demonstrated elevated nitrate reductase (NR) activity, reductions in leaf nitrite and nitrate and the amino acids proline, glutamine and glutamate. Chlorophyl content of the transgenic lines was increased, as evidenced by the stay-green phenotype. This reveals the importance of NiR in primary nitrogen assimilation and how modification of this key enzyme affects both the nitrogen and carbon metabolism of tobacco plants.
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Affiliation(s)
- Susie Davenport
- British American Tobacco, R&D Cambridge, 210 The Science Park, Cambridge, CB4 0WA, UK.
| | - Pascaline Le Lay
- British American Tobacco, R&D Cambridge, 210 The Science Park, Cambridge, CB4 0WA, UK
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42
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Li X, Zhang M, Liu F, Li Y, He Y, Zhang S, Wu J. Abundance and distribution of microorganisms involved in denitrification in sediments of a Myriophyllum elatinoides purification system for treating swine wastewater. Environ Sci Pollut Res Int 2015; 22:17906-17916. [PMID: 26165997 DOI: 10.1007/s11356-015-5041-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/05/2015] [Indexed: 06/04/2023]
Abstract
Environmental pollution from livestock production, particularly swine production, is often managed by the use of constructed wetlands, which incorporate plants such as Myriophyllum elatinoides as a means of treating wastewater. The M. elatinoides purification system has been shown to effectively remove, via nitrification and denitrification, more than 90% of the total nitrogen (TN) and 84% of the NH4 (+)-N produced in swine wastewater. However, the mechanisms of variation in aquatic environmental factors and how the interaction of these factors affects denitrification by microorganisms in sediments remain poorly understood. In this study, the impacts of dissolved oxygen (DO), TN, NH4(+)-N, and NO3(-)-N on the abundance, diversity, and community distribution of denitrifiers in the sediments from different concentrations and types of wastewater including tap water (CK), two strengths of synthetic wastewater: 200 mg NH4(+)-N L(-1) (T1) and 400 mg NH4(+)-N L(-1) (T2), swine wastewater diluted 50% (T3), and swine wastewater (T4) were investigated in a microcosm experiment. A significant improvement was observed in the abundance of denitrification genes (nirK and nirS) in response to increased NO3(-)-N and DO in the swine wastewater sediments. The abundance of these denitrification genes was highest in the T4 sediments compared with other treatments. Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that the DO, TN, and NH4(+)-N positively impacted the richness index (S) of the nirK denitrifiers in T1, whereas the NO3(-)-N negatively affected the Simpson diversity index (D) of nirK and nirS denitrifiers in T3 and T4. However, the NO3(-)-N positively affected the nirK and nirS denitrifier community distribution, whereas the DO negatively affected the nirK and nirS denitrifier distribution in T3 and T4. These findings will be helpful in that they allow us to recognize the effects of environmental factors on the formation of the denitrifiers in the sediments in a M. elatinoides purification system.
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Affiliation(s)
- Xi Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Miaomiao Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
| | - Yong Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
| | - Yang He
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Shunan Zhang
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
- Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, People's Republic of China.
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Turowski VR, Aknin C, Maliandi MV, Buchensky C, Leaden L, Peralta DA, Busi MV, Araya A, Gomez-Casati DF. Frataxin Is Localized to Both the Chloroplast and Mitochondrion and Is Involved in Chloroplast Fe-S Protein Function in Arabidopsis. PLoS One 2015; 10:e0141443. [PMID: 26517126 PMCID: PMC4636843 DOI: 10.1371/journal.pone.0141443] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/07/2015] [Indexed: 11/19/2022] Open
Abstract
Frataxin plays a key role in eukaryotic cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (Fe-S) cluster biosynthesis. However, its precise role has yet to be elucidated. In this work, we studied the subcellular localization of Arabidopsis frataxin, AtFH, using confocal microscopy, and found a novel dual localization for this protein. We demonstrate that plant frataxin is targeted to both the mitochondria and the chloroplast, where it may play a role in Fe-S cluster metabolism as suggested by functional studies on nitrite reductase (NIR) and ferredoxin (Fd), two Fe-S containing chloroplast proteins, in AtFH deficient plants. Our results indicate that frataxin deficiency alters the normal functioning of chloroplasts by affecting the levels of Fe, chlorophyll, and the photosynthetic electron transport chain in this organelle.
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Affiliation(s)
- Valeria R. Turowski
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Cindy Aknin
- UMR5234 Microbiologie Fondamentale et Pathogénicité, Centre National de la Recherche Scientifique and Université Bordeaux-Segalen, 146 rue Léo Saignat, 33076, Bordeaux cedex, France
| | - Maria V. Maliandi
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH) CONICET/UNSAM, Camino de Circunvaación Km 6, 7130, Chascomús, Argentina
| | - Celeste Buchensky
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Laura Leaden
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Diego A. Peralta
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Maria V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Alejandro Araya
- Centre National de la Recherche Scientifique & UMR 1332 –Biologie du Fruit et Pathologie, Institute National de la Recherche Agronomique (INRA) Bordeaux Aquitaine, 71 avenue Edouard Bourlaux, 33882, Villenave D’Ornon, France
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
- * E-mail:
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Guan X, Xie Y, Wang J, Wang J, Liu F. Electron donors and co-contaminants affect microbial community composition and activity in perchlorate degradation. Environ Sci Pollut Res Int 2015; 22:6057-6067. [PMID: 25382499 DOI: 10.1007/s11356-014-3792-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Although microbial reduction of perchlorate (ClO4(-)) is a promising and effective method, our knowledge on the changes in microbial communities during ClO4(-) degradation is limited, especially when different electron donors are supplied and/or other contaminants are present. Here, we examined the effects of acetate and hydrogen as electron donors and nitrate and ammonium as co-contaminants on ClO4(-) degradation by anaerobic microcosms using six treatments. The process of degradation was divided into the lag stage (SI) and the accelerated stage (SII). Quantitative PCR was used to quantify four genes: pcrA (encoding perchlorate reductase), cld (encoding chlorite dismutase), nirS (encoding copper and cytochrome cd1 nitrite reductase), and 16S rRNA. While the degradation of ClO4(-) with acetate, nitrate, and ammonia system (PNA) was the fastest with the highest abundance of the four genes, it was the slowest in the autotrophic system (HYP). The pcrA gene accumulated in SI and played a key role in initiating the accelerated degradation of ClO4(-) when its abundance reached a peak. Degradation in SII was primarily maintained by the cld gene. Acetate inhibited the growth of perchlorate-reducing bacteria (PRB), but its effect was weakened by nitrate (NO3(-)), which promoted the growth of PRB in SI, and therefore, accelerated the ClO4(-) degradation rate. In addition, ammonia (NH4(+)), as nitrogen sources, accelerated the growth of PRB. The bacterial communities' structure and diversity were significantly affected by electron donors and co-contaminants. Under heterotrophic conditions, both ammonia and nitrate promoted Azospira as the most dominant genera, a fact that might significantly influence the rate of ClO4(-) natural attenuation by degradation.
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Affiliation(s)
- Xiangyu Guan
- Beijing Key Laboratory of Water Resources and Environmental Engineering, China University of Geosciences, Beijing, 100083, China
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Saarenheimo J, Rissanen AJ, Arvola L, Nykänen H, Lehmann MF, Tiirola M. Genetic and environmental controls on nitrous oxide accumulation in lakes. PLoS One 2015; 10:e0121201. [PMID: 25756328 PMCID: PMC4355481 DOI: 10.1371/journal.pone.0121201] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/28/2015] [Indexed: 11/19/2022] Open
Abstract
We studied potential links between environmental factors, nitrous oxide (N2O) accumulation, and genetic indicators of nitrite and N2O reducing bacteria in 12 boreal lakes. Denitrifying bacteria were investigated by quantifying genes encoding nitrite and N2O reductases (nirS/nirK and nosZ, respectively, including the two phylogenetically distinct clades nosZI and nosZII) in lake sediments. Summertime N2O accumulation and hypolimnetic nitrate concentrations were positively correlated both at the inter-lake scale and within a depth transect of an individual lake (Lake Vanajavesi). The variability in the individual nirS, nirK, nosZI, and nosZII gene abundances was high (up to tenfold) among the lakes, which allowed us to study the expected links between the ecosystem's nir-vs-nos gene inventories and N2O accumulation. Inter-lake variation in N2O accumulation was indeed connected to the relative abundance of nitrite versus N2O reductase genes, i.e. the (nirS+nirK)/nosZI gene ratio. In addition, the ratios of (nirS+nirK)/nosZI at the inter-lake scale and (nirS+nirK)/nosZI+II within Lake Vanajavesi correlated positively with nitrate availability. The results suggest that ambient nitrate concentration can be an important modulator of the N2O accumulation in lake ecosystems, either directly by increasing the overall rate of denitrification or indirectly by controlling the balance of nitrite versus N2O reductase carrying organisms.
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Affiliation(s)
- Jatta Saarenheimo
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
- * E-mail:
| | - Antti J. Rissanen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Lauri Arvola
- Lammi Biological Station, University of Helsinki, 16900, Lammi, Finland
| | - Hannu Nykänen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Moritz F. Lehmann
- Department for Environmental Science, University of Basel, CH-4058, Basel, Switzerland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
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Huang X, Luo J, Zhao D, Lin W. [Diversity of thaumarchaeal nitrite reductase (nirK) -like genes in environments]. Wei Sheng Wu Xue Bao 2015; 55:351-357. [PMID: 26065277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE Nitrite reductase encoded by nirK is a key enzyme to denitrification, and is found in ammonia-oxidizing archaea (AOA). Based on the diversity of nirK, it was good to study the functions of nitrite reductase to AOA on denitrification. METHODS We constructed nirK gene clone libraries based on the nirK gene PCR products of water, sediment and soil, screened the positive clones by restriction fragment length polymorphism ( RFLP), and sequenced the representative fragments from positive clones. RESULTS RFLP analysis of the clone libraries shows that there were 10 OTUs in fresh water and sediment, 8 in vegetable soil and its nearby water. Phylogenetic analysis indicated that the amino acid sequences of these nirK were most closely related to the Candidatus Nitrosopumilus koreensis AR1 and Nitrosopumilus maritimus SCM1 with similarities ranging from 53% to 68%. Diversity index of clone libraries shows there were many different types of nirK genes in all samples. Diversity and evenness index of nirK gene of water samples was higher than soil samples whreas vegetable field samples were the richest. CONCLUSION Thaumarchaeote nirK gene had high diversity in soil and freshwater environments which were very different from ocean sample. The nirK gene encoding nitrite reductase might be important for thaumarchaeote denitrification.
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Qin L, Wang M, Chen L, Liang X, Wu Z, Lin Z, Zuo J, Feng X, Zhao J, Liao H, Ye H. Soybean Fe-S cluster biosynthesis regulated by external iron or phosphate fluctuation. Plant Cell Rep 2015; 34:411-24. [PMID: 25515083 DOI: 10.1007/s00299-014-1718-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/23/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
KEY MESSAGE Iron and phosphorus are essential for soybean nodulation. Our results suggested that the deficiency of Fe or P impairs nodulation by affecting the assembly of functional iron-sulfur cluster via different mechanisms. Iron (Fe) and phosphorus (P) are important mineral nutrients for soybean and are indispensable for nodulation. However, it remains elusive how the pathways of Fe metabolism respond to the fluctuation of external Fe or P. Iron is required for the iron-sulfur (Fe-S) cluster assembly in higher plant. Here, we investigated the expression pattern of Fe-S cluster biosynthesis genes in the nodulated soybean. Soybean genome encodes 42 putative Fe-S cluster biosynthesis genes, which were expressed differently in shoots and roots, suggesting of physiological relevance. Nodules initiated from roots of soybean after rhizobia inoculation. In comparison with that in shoots, iron concentration was three times higher in nodules. The Fe-S cluster biosynthesis genes were activated and several Fe-S protein activities were increased in nodules, indicating that a more effective Fe-S cluster biosynthesis is accompanied by nodulation. Fe-S cluster biosynthesis genes were massively repressed and some Fe-S protein activities were decreased in nodules by Fe deficiency, leading to tiny nodules. Notably, P deficiency induced a similar Fe-deficiency response in nodules, i.e, certain Fe-S enzyme activity loss and tiny nodules. However, distinct from Fe-deficient nodules, higher iron concentration was accumulated and the Fe-S cluster biosynthesis genes were not suppressed in the P-deficiency-treated nodules. Taken together, our results showed that both Fe deficiency and P deficiency impair nodulation, but they affect the assembly of Fe-S cluster maybe via different mechanisms. The data also suggested that Fe-S cluster biosynthesis likely links Fe metabolism and P metabolism in root and nodule cells of soybean.
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Affiliation(s)
- Lu Qin
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Zhong L, Chen D, Min D, Li W, Xu Z, Zhou Y, Li L, Chen M, Ma Y. AtTGA4, a bZIP transcription factor, confers drought resistance by enhancing nitrate transport and assimilation in Arabidopsis thaliana. Biochem Biophys Res Commun 2015. [PMID: 25596127 DOI: 10.106/j.bbrc.2015.01.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
To cope with environmental stress caused by global climate change and excessive nitrogen application, it is important to improve water and nitrogen use efficiencies in crop plants. It has been reported that higher nitrogen uptake could alleviate the damaging impact of drought stress. However, there is scant evidence to explain how nitrogen uptake affects drought resistance. In this study we observed that bZIP transcription factor AtTGA4 (TGACG motif-binding factor 4) was induced by both drought and low nitrogen stresses, and that overexpression of AtTGA4 simultaneously improved drought resistance and reduced nitrogen starvation in Arabidopsis. Following drought stress there were higher nitrogen and proline contents in transgenic AtTGA4 plants than in wild type controls, and activity of the key enzyme nitrite reductase (NIR) involved in nitrate assimilation processes was also higher. Expressions of the high-affinity nitrate transporter genes NRT2.1 and NRT2.2 and nitrate reductase genes NIA1 and NIA2 in transgenic plants were all higher than in wild type indicating that higher levels of nitrate transport and assimilation activity contributed to enhanced drought resistance of AtTGA4 transgenic plants. Thus genetic transformation with AtTGA4 may provide a new approach to simultaneously improve crop tolerance to drought and low nitrogen stresses.
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Affiliation(s)
- Li Zhong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550006, China
| | - Dandan Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Donghong Min
- College of Life Sciences, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Weiwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaoshi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongbin Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liancheng Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ming Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Youzhi Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Kuroki M, Igarashi Y, Ishii M, Arai H. Fine-tuned regulation of the dissimilatory nitrite reductase gene by oxygen and nitric oxide in Pseudomonas aeruginosa. Environ Microbiol Rep 2014; 6:792-801. [PMID: 25186017 DOI: 10.1111/1758-2229.12212] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/21/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
Nitrite reductase (NIR) catalyses the reduction of nitrite to nitric oxide (NO) in the denitrification pathway. In Pseudomonas aeruginosa, expression of the gene encoding NIR (nirS) is induced by NO and is under control of the NO-sensing regulator DNR (dissimilatory nitrate respiration regulator). Because DNR is under control of the oxygen-sensing regulator ANR (anaerobic regulator of arginine deiminase and nitrate reductase), nirS is expressed only under low oxygen and anaerobic conditions. Both ANR and DNR are FNR (fumarate and nitrate reductase regulator)-type regulators and recognize the consensus FNR-binding motif. The motif of the nirS promoter is thought to be recognized only by DNR, and not by ANR. Here, mutant strains expressing either ANR or DNR were constructed and used to analyse the role of ANR and DNR in the activation of nirS expression. Analysis of transcriptional activity by microarray and quantitative reverse transcription polymerase chain reaction revealed that nirS is transcribed under low oxygen conditions in an ANR-dependent manner, although the expression level was 10-fold lower than that of the DNR-dependent expression. An artificial promoter containing the FNR-binding motif of the nirS promoter was also twofold upregulated by ANR. These results indicate that low-level expression of NIR in the presence of nitrite may provide NO as a trigger for the full expression of denitrification genes when oxygen is depleted.
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Affiliation(s)
- Miho Kuroki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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Wang L, Zheng B, Nan B, Hu P. Diversity of bacterial community and detection of nirS- and nirK-encoding denitrifying bacteria in sandy intertidal sediments along Laizhou Bay of Bohai Sea, China. Mar Pollut Bull 2014; 88:215-223. [PMID: 25256298 DOI: 10.1016/j.marpolbul.2014.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 08/29/2014] [Accepted: 09/06/2014] [Indexed: 06/03/2023]
Abstract
The microbial community and the nirS- and nirK-encoding denitrifiers in the intertidal sediments along Laizhou Bay in China were studied using pyrosequencing and real-time quantitative PCR (qPCR), respectively. There were three primary intertidal zones: Laizhou (La), Weifang Harbor (We), and Dongying (Do). Significant differences in composition and abundances at the different taxonomic levels were observed among the three bacterial communities. The qPCR results indicated that the nirS gene abundance varied from 8.67 × 10(5) to 5.68 × 10(6)copies/gwet weight (ww), whereas the nirK gene abundance varied from 1.26 × 10(5) to 1.89 × 10(6)copies/gww. The canonical correlation analysis (CCA) indicated that the sand percentage was the most important factor in shaping the bacterial community followed by silt percentage, NO2(-), TOC, DO, pH, and clay percentage, whereas the clay percentage, pH, NO3(-), DO, NO2(-), TOC, silt percentage, and sand percentage were the most important factors associated with regulating the abundance of nirS- and nirK-encoding denitrifiers.
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Affiliation(s)
- Liping Wang
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Binghui Zheng
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Bingxu Nan
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Peilong Hu
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
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