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Wasai-Hara S, Itakura M, Fernandes Siqueira A, Takemoto D, Sugawara M, Mitsui H, Sato S, Inagaki N, Yamazaki T, Imaizumi-Anraku H, Shimoda Y, Minamisawa K. Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression. Sci Rep 2023; 13:18862. [PMID: 37914789 PMCID: PMC10620151 DOI: 10.1038/s41598-023-46019-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
N2O is an important greenhouse gas influencing global warming, and agricultural land is the predominant (anthropogenic) source of N2O emissions. Here, we report the high N2O-reducing activity of Bradyrhizobium ottawaense, suggesting the potential for efficiently mitigating N2O emission from agricultural lands. Among the 15 B. ottawaense isolates examined, the N2O-reducing activities of most (13) strains were approximately five-fold higher than that of Bradyrhizobium diazoefficiens USDA110T under anaerobic conditions. This robust N2O-reducing activity of B. ottawaense was confirmed by N2O reductase (NosZ) protein levels and by mitigation of N2O emitted by nodule decomposition in laboratory system. While the NosZ of B. ottawaense and B. diazoefficiens showed high homology, nosZ gene expression in B. ottawaense was over 150-fold higher than that in B. diazoefficiens USDA110T, suggesting the high N2O-reducing activity of B. ottawaense is achieved by high nos expression. Furthermore, we examined the nos operon transcription start sites and found that, unlike B. diazoefficiens, B. ottawaense has two transcription start sites under N2O-respiring conditions, which may contribute to the high nosZ expression. Our study indicates the potential of B. ottawaense for effective N2O reduction and unique regulation of nos gene expression towards the high performance of N2O mitigation in the soil.
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Affiliation(s)
- Sawa Wasai-Hara
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | | | - Daisaku Takemoto
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Masayuki Sugawara
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Haruko Imaizumi-Anraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Yoshikazu Shimoda
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan.
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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] [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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Parejo S, Cabrera JJ, Jiménez-Leiva A, Tomás-Gallardo L, Bedmar EJ, Gates AJ, Mesa S. Fine-Tuning Modulation of Oxidation-Mediated Posttranslational Control of Bradyrhizobium diazoefficiens FixK 2 Transcription Factor. Int J Mol Sci 2022; 23:5117. [PMID: 35563511 PMCID: PMC9104804 DOI: 10.3390/ijms23095117] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
FixK2 is a CRP/FNR-type transcription factor that plays a central role in a sophisticated regulatory network for the anoxic, microoxic and symbiotic lifestyles of the soybean endosymbiont Bradyrhizobium diazoefficiens. Aside from the balanced expression of the fixK2 gene under microoxic conditions (induced by the two-component regulatory system FixLJ and negatively auto-repressed), FixK2 activity is posttranslationally controlled by proteolysis, and by the oxidation of a singular cysteine residue (C183) near its DNA-binding domain. To simulate the permanent oxidation of FixK2, we replaced C183 for aspartic acid. Purified C183D FixK2 protein showed both low DNA binding and in vitro transcriptional activation from the promoter of the fixNOQP operon, required for respiration under symbiosis. However, in a B. diazoefficiens strain coding for C183D FixK2, expression of a fixNOQP'-'lacZ fusion was similar to that in the wild type, when both strains were grown microoxically. The C183D FixK2 encoding strain also showed a wild-type phenotype in symbiosis with soybeans, and increased fixK2 gene expression levels and FixK2 protein abundance in cells. These two latter observations, together with the global transcriptional profile of the microoxically cultured C183D FixK2 encoding strain, suggest the existence of a finely tuned regulatory strategy to counterbalance the oxidation-mediated inactivation of FixK2 in vivo.
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Affiliation(s)
- Sergio Parejo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Juan J. Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Laura Tomás-Gallardo
- Proteomics and Biochemistry Unit, Andalusian Centre for Developmental Biology, CSIC-Pablo de Olavide University, 41013 Seville, Spain;
| | - Eulogio J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
| | - Andrew J. Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain; (S.P.); (J.J.C.); (A.J.-L.); (E.J.B.)
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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] [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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Bueno E, Mania D, Mesa S, Bedmar EJ, Frostegård Å, Bakken LR, Delgado MJ. Regulation of the Emissions of the Greenhouse Gas Nitrous Oxide by the Soybean Endosymbiont Bradyrhizobium diazoefficiens. Int J Mol Sci 2022; 23:1486. [PMID: 35163408 PMCID: PMC8836242 DOI: 10.3390/ijms23031486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022] Open
Abstract
The greenhouse gas nitrous oxide (N2O) has strong potential to drive climate change. Soils are a major source of N2O, with microbial nitrification and denitrification being the primary processes involved in such emissions. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model microorganism to study denitrification, a process that depends on a set of reductases, encoded by the napEDABC, nirK, norCBQD, and nosRZDYFLX genes, which sequentially reduce nitrate (NO3-) to nitrite (NO2-), nitric oxide (NO), N2O, and dinitrogen (N2). In this bacterium, the regulatory network and environmental cues governing the expression of denitrification genes rely on the FixK2 and NnrR transcriptional regulators. To understand the role of FixK2 and NnrR proteins in N2O turnover, we monitored real-time kinetics of NO3-, NO2-, NO, N2O, N2, and oxygen (O2) in a fixK2 and nnrR mutant using a robotized incubation system. We confirmed that FixK2 and NnrR are regulatory determinants essential for NO3- respiration and N2O reduction. Furthermore, we demonstrated that N2O reduction by B. diazoefficiens is independent of canonical inducers of denitrification, such as the nitrogen oxide NO3-, and it is negatively affected by acidic and alkaline conditions. These findings advance the understanding of how specific environmental conditions and two single regulators modulate N2O turnover in B. diazoefficiens.
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Affiliation(s)
- Emilio Bueno
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Socorro Mesa
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Eulogio J. Bedmar
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway; (D.M.); (Å.F.); (L.R.B.)
| | - María J. Delgado
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain; (S.M.); (E.J.B.)
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Cabrera JJ, Jiménez-Leiva A, Tomás-Gallardo L, Parejo S, Casado S, Torres MJ, Bedmar EJ, Delgado MJ, Mesa S. Dissection of FixK 2 protein-DNA interaction unveils new insights into Bradyrhizobium diazoefficiens lifestyles control. Environ Microbiol 2021; 23:6194-6209. [PMID: 34227211 DOI: 10.1111/1462-2920.15661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/28/2022]
Abstract
The FixK2 protein plays a pivotal role in a complex regulatory network, which controls genes for microoxic, denitrifying, and symbiotic nitrogen-fixing lifestyles in Bradyrhizobium diazoefficiens. Among the microoxic-responsive FixK2 -activated genes are the fixNOQP operon, indispensable for respiration in symbiosis, and the nnrR regulatory gene needed for the nitric-oxide dependent induction of the norCBQD genes encoding the denitrifying nitric oxide reductase. FixK2 is a CRP/FNR-type transcription factor, which recognizes a 14 bp-palindrome (FixK2 box) at the regulated promoters through three residues (L195, E196, and R200) within a C-terminal helix-turn-helix motif. Here, we mapped the determinants for discriminatory FixK2 -mediated regulation. While R200 was essential for DNA binding and activity of FixK2 , L195 was involved in protein-DNA complex stability. Mutation at positions 1, 3, or 11 in the genuine FixK2 box at the fixNOQP promoter impaired transcription activation by FixK2 , which was residual when a second mutation affecting the box palindromy was introduced. The substitution of nucleotide 11 within the NnrR box at the norCBQD promoter allowed FixK2 -mediated activation in response to microoxia. Thus, position 11 within the FixK2 /NnrR boxes constitutes a key element that changes FixK2 targets specificity, and consequently, it might modulate B. diazoefficiens lifestyle as nitrogen fixer or as denitrifier.
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Affiliation(s)
- Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Laura Tomás-Gallardo
- Proteomics and Biochemistry Unit, Andalusian Centre for Developmental Biology, CSIC-Junta de Andalucía-Pablo de Olavide University, Seville, 41013, Spain
| | - Sergio Parejo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Sara Casado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - María J Torres
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
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Salas A, Cabrera JJ, Jiménez-Leiva A, Mesa S, Bedmar EJ, Richardson DJ, Gates AJ, Delgado MJ. Bacterial nitric oxide metabolism: Recent insights in rhizobia. Adv Microb Physiol 2021; 78:259-315. [PMID: 34147187 DOI: 10.1016/bs.ampbs.2021.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N2-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.
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Affiliation(s)
- Ana Salas
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Semedo M, Wittorf L, Hallin S, Song B. Differential expression of clade I and II N2O reductase genes in denitrifying Thauera linaloolentis 47LolT under different nitrogen conditions. FEMS Microbiol Lett 2021; 367:6029120. [PMID: 33296469 DOI: 10.1093/femsle/fnaa205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/07/2020] [Indexed: 01/14/2023] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and its reduction to dinitrogen gas by the N2O reductase (encoded by the nosZ gene) is the only known biological N2O sink. Within the nosZ phylogeny there are two major clades (I and II), which seem to have different ecological niches. However, physiological differences of nosZI and nosZII expression that may impact emissions of N2O are not well understood. Here, we evaluated the differential expression of nosZI and nosZII, both present in Thauera linaloolentis strain 47LolT, in response to N2O concentration and the presence of the competing electron acceptor nitrate (NO3-). Different N2O levels had a negligible effect on the expression of both nosZ clades. Interestingly, nosZII expression was strongly upregulated in the absence of NO3-, while nosZI expression remained constant across the conditions tested. Thus, NO3- possibly inhibited nosZII expression, which suggests that N2O mitigation mediated by nosZII can be restricted due to the presence of NO3- in the environment. This is the first study demonstrating differential expression of nosZI and nosZII genes under the same physiological conditions and their implications for N2O emission under varying environmental conditions in terms of NO3- availability.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, USA
| | - Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala, Sweden, Sweden
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, P.O. Box 1346, Gloucester Point, Virginia 23062, USA
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Gao Y, Mania D, Mousavi SA, Lycus P, Arntzen MØ, Woliy K, Lindström K, Shapleigh JP, Bakken LR, Frostegård Å. Competition for electrons favours N 2 O reduction in denitrifying Bradyrhizobium isolates. Environ Microbiol 2021; 23:2244-2259. [PMID: 33463871 DOI: 10.1111/1462-2920.15404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Bradyrhizobia are common members of soil microbiomes and known as N2 -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N2 O. Inoculation with compatible rhizobia is often needed for optimal N2 -fixation, but the choice of inoculant may have consequences for N2 O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N2 O. The N2 O-reducing isolates had strong preference for N2 O- over NO3 - -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO3 - reductase) and Nos (N2 O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO3 - reductase (Nar), reduced N2 O and NO3 - simultaneously. We propose that the control at the metabolic level, favouring N2 O reduction over NO3 - reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.
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Affiliation(s)
- Yuan Gao
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Daniel Mania
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Seyed Abdollah Mousavi
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | - Pawel Lycus
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Kristina Lindström
- Ecosystems and Environment Research programme, Faculty of Biological and Environmental Sciences, and Helsinki Institute of Sustainability Science (HELSUS), University of Helsinki, Finland
| | | | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
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10
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Gaimster H, Alston M, Richardson DJ, Gates AJ, Rowley G. Transcriptional and environmental control of bacterial denitrification and N2O emissions. FEMS Microbiol Lett 2019; 365:4768087. [PMID: 29272423 DOI: 10.1093/femsle/fnx277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/18/2017] [Indexed: 12/18/2022] Open
Abstract
In oxygen-limited environments, denitrifying bacteria can switch from oxygen-dependent respiration to nitrate (NO3-) respiration in which the NO3- is sequentially reduced via nitrite (NO2-), nitric oxide (NO) and nitrous oxide (N2O) to dinitrogen (N2). However, atmospheric N2O continues to rise, a significant proportion of which is microbial in origin. This implies that the enzyme responsible for N2O reduction, nitrous oxide reductase (NosZ), does not always carry out the final step of denitrification either efficiently or in synchrony with the rest of the pathway. Despite a solid understanding of the biochemistry underpinning denitrification, there is a relatively poor understanding of how environmental signals and respective transcriptional regulators control expression of the denitrification apparatus. This minireview describes the current picture for transcriptional regulation of denitrification in the model bacterium, Paracoccus denitrificans, highlighting differences in other denitrifying bacteria where appropriate, as well as gaps in our understanding. Alongside this, the emerging role of small regulatory RNAs in regulation of denitrification is discussed. We conclude by speculating how this information, aside from providing a better understanding of the denitrification process, can be translated into development of novel greenhouse gas mitigation strategies.
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Affiliation(s)
- Hannah Gaimster
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Mark Alston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew J Gates
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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11
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Sánchez C, Minamisawa K. Nitrogen Cycling in Soybean Rhizosphere: Sources and Sinks of Nitrous Oxide (N 2O). Front Microbiol 2019; 10:1943. [PMID: 31497007 PMCID: PMC6712156 DOI: 10.3389/fmicb.2019.01943] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Nitrous oxide (N2O) is the third most important greenhouse gas after carbon dioxide and methane, and a prominent ozone-depleting substance. Agricultural soils are the primary anthropogenic source of N2O because of the constant increase in the use of industrial nitrogen (N) fertilizers. The soybean crop is grown on 6% of the world's arable land, and its production is expected to increase rapidly in the future. In this review, we summarize the current knowledge on N-cycle in the rhizosphere of soybean plants, particularly sources and sinks of N2O. Soybean root nodules are the host of dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Nodule decomposition is the main source of N2O in soybean rhizosphere, where soil organisms mediate the nitrogen transformations that produce N2O. This N2O is either emitted into the atmosphere or further reduced to N2 by the bradyrhizobial N2O reductase (N2OR), encoded by the nos gene cluster. The dominance of nos - indigenous populations of soybean bradyrhizobia results in the emission of N2O into the atmosphere. Hence, inoculation with nos + or nos ++ (mutants with enhanced N2OR activity) bradyrhizobia has proved to be promising strategies to reduce N2O emission in the field. We discussed these strategies, the molecular mechanisms underlying them, and the future perspectives to develop better options for global mitigation of N2O emission from soils.
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Affiliation(s)
- Cristina Sánchez
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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12
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Jiménez-Leiva A, Cabrera JJ, Bueno E, Torres MJ, Salazar S, Bedmar EJ, Delgado MJ, Mesa S. Expanding the Regulon of the Bradyrhizobium diazoefficiens NnrR Transcription Factor: New Insights Into the Denitrification Pathway. Front Microbiol 2019; 10:1926. [PMID: 31481951 PMCID: PMC6710368 DOI: 10.3389/fmicb.2019.01926] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/05/2019] [Indexed: 12/02/2022] Open
Abstract
Denitrification in the soybean endosymbiont Bradyrhizobium diazoefficiens is controlled by a complex regulatory network composed of two hierarchical cascades, FixLJ-FixK2-NnrR and RegSR-NifA. In the former cascade, the CRP/FNR-type transcription factors FixK2 and NnrR exert disparate control on expression of core denitrifying systems encoded by napEDABC, nirK, norCBQD, and nosRZDFYLX genes in response to microoxia and nitrogen oxides, respectively. To identify additional genes controlled by NnrR and involved in the denitrification process in B. diazoefficiens, we compared the transcriptional profile of an nnrR mutant with that of the wild type, both grown under anoxic denitrifying conditions. This approach revealed more than 170 genes were simultaneously induced in the wild type and under the positive control of NnrR. Among them, we found the cycA gene which codes for the c550 soluble cytochrome (CycA), previously identified as an intermediate electron donor between the bc1 complex and the denitrifying nitrite reductase NirK. Here, we demonstrated that CycA is also required for nitrous oxide reductase activity. However, mutation in cycA neither affected nosZ gene expression nor NosZ protein steady-state levels. Furthermore, cycA, nnrR and its proximal divergently oriented nnrS gene, are direct targets for FixK2 as determined by in vitro transcription activation assays. The dependence of cycA expression on FixK2 and NnrR in anoxic denitrifying conditions was validated at transcriptional level, determined by quantitative reverse transcription PCR, and at the level of protein by performing heme c-staining of soluble cytochromes. Thus, this study expands the regulon of NnrR and demonstrates the role of CycA in the activity of the nitrous oxide reductase, the key enzyme for nitrous oxide mitigation.
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Affiliation(s)
- Andrea Jiménez-Leiva
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Emilio Bueno
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María J Torres
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sergio Salazar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María J Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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13
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Mania D, Woliy K, Degefu T, Frostegård Å. A common mechanism for efficient N2O reduction in diverse isolates of nodule‐forming bradyrhizobia. Environ Microbiol 2019; 22:17-31. [DOI: 10.1111/1462-2920.14731] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Mania
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Science ås Norway
| | - Kedir Woliy
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Science ås Norway
| | - Tulu Degefu
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Science ås Norway
- International Crops Research Institute for the Semi‐Arid Tropics Addis Ababa Ethiopia
| | - åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life Science ås Norway
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14
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Fernández N, Cabrera JJ, Varadarajan AR, Lutz S, Ledermann R, Roschitzki B, Eberl L, Bedmar EJ, Fischer HM, Pessi G, Ahrens CH, Mesa S. An Integrated Systems Approach Unveils New Aspects of Microoxia-Mediated Regulation in Bradyrhizobium diazoefficiens. Front Microbiol 2019; 10:924. [PMID: 31134003 PMCID: PMC6515984 DOI: 10.3389/fmicb.2019.00924] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 01/31/2023] Open
Abstract
The adaptation of rhizobia from the free-living state in soil to the endosymbiotic state comprises several physiological changes in order to cope with the extremely low oxygen availability (microoxia) within nodules. To uncover cellular functions required for bacterial adaptation to microoxia directly at the protein level, we applied a systems biology approach on the key rhizobial model and soybean endosymbiont Bradyrhizobium diazoefficiens USDA 110 (formerly B. japonicum USDA 110). As a first step, the complete genome of B. diazoefficiens 110spc4, the model strain used in most prior functional genomics studies, was sequenced revealing a deletion of a ~202 kb fragment harboring 223 genes and several additional differences, compared to strain USDA 110. Importantly, the deletion strain showed no significantly different phenotype during symbiosis with several host plants, reinforcing the value of previous OMICS studies. We next performed shotgun proteomics and detected 2,900 and 2,826 proteins in oxically and microoxically grown cells, respectively, largely expanding our knowledge about the inventory of rhizobial proteins expressed in microoxia. A set of 62 proteins was significantly induced under microoxic conditions, including the two nitrogenase subunits NifDK, the nitrogenase reductase NifH, and several subunits of the high-affinity terminal cbb3 oxidase (FixNOQP) required for bacterial respiration inside nodules. Integration with the previously defined microoxia-induced transcriptome uncovered a set of 639 genes or proteins uniquely expressed in microoxia. Finally, besides providing proteogenomic evidence for novelties, we also identified proteins with a regulation similar to that of FixK2: transcript levels of these protein-coding genes were significantly induced, while the corresponding protein abundance remained unchanged or was down-regulated. This suggested that, apart from fixK2, additional B. diazoefficiens genes might be under microoxia-specific post-transcriptional control. This hypothesis was indeed confirmed for several targets (HemA, HemB, and ClpA) by immunoblot analysis.
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Affiliation(s)
- Noemí Fernández
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan J Cabrera
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland.,Department of Health Sciences and Technology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Lutz
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | | | - Bernd Roschitzki
- Functional Genomics Center Zurich, ETH & UZH Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics and Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Socorro Mesa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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15
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Wang Y, Wang Z, Duo Y, Wang X, Chen J, Chen J. Gene cloning, expression, and reducing property enhancement of nitrous oxide reductase from Alcaligenes denitrificans strain TB. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:43-52. [PMID: 29649759 DOI: 10.1016/j.envpol.2018.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/14/2018] [Accepted: 04/01/2018] [Indexed: 06/08/2023]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and tends to accumulate as an intermediate in the process of bacteria denitrification. To achieve complete reduction of nitrogen oxide (NOx) in bacteria denitrification, the structural gene nosZ encoding nitrous oxide reductase (N2OR) was cloned from Alcaligenes denitrificans strain TB (GenBank JQ044686). The recombinant plasmid containing the nosZ gene was built, and the expression of nosZ gene in Escherichia coli was determined. Results show that the nosZ gene consisting of 1917 nucleotides achieves heterologous expression successfully by codon optimization strategy under optimal conditions (pre-induction inoculum OD600 of 0.67, final IPTG concentration of 0.5 mM, inducing time of 6 h, and inducing temperature of 28 °C). Determination result of gas chromatography confirms that N2O degradation efficiency of recombinant E. coli is strengthened by at least 1.92 times compared with that of original strain TB when treated with N2O as substrate. Moreover, N2OR activity in recombinant strain is 2.09 times higher than that in wild strain TB, which validates the aforementioned result and implies that the recombinant E. coli BL21 (DE3)-pET28b-nosZ is a potential candidate to control N2O accumulation and alleviate greenhouse effect. In addition, the N2OR structure and the possible N2O binding site in Alcaligenes sp. TB are predicted, which open an avenue for further research on the relationship between N2OR activity and its structure.
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Affiliation(s)
- Yu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zeyu Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yankai Duo
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xiaoping Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jianmeng Chen
- Engineering Research Center of the Ministry of Education for Bioconversion and Biopurification, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jun Chen
- Engineering Research Center of the Ministry of Education for Bioconversion and Biopurification, Zhejiang University of Technology, Hangzhou 310014, PR China.
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