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Partipilo M, Whittaker JJ, Pontillo N, Coenradij J, Herrmann A, Guskov A, Slotboom DJ. Biochemical and structural insight into the chemical resistance and cofactor specificity of the formate dehydrogenase from Starkeya novella. FEBS J 2023; 290:4238-4255. [PMID: 37213112 DOI: 10.1111/febs.16871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/23/2023]
Abstract
Formate dehydrogenases (Fdhs) mediate the oxidation of formate to carbon dioxide and concomitant reduction of nicotinamide adenine dinucleotide (NAD+ ). The low cost of the substrate formate and importance of the product NADH as a cellular source of reducing power make this reaction attractive for biotechnological applications. However, the majority of Fdhs are sensitive to inactivation by thiol-modifying reagents. In this study, we report a chemically resistant Fdh (FdhSNO ) from the soil bacterium Starkeya novella strictly specific for NAD+ . We present its recombinant overproduction, purification and biochemical characterization. The mechanistic basis of chemical resistance was found to be a valine in position 255 (rather than a cysteine as in other Fdhs) preventing the inactivation by thiol-modifying compounds. To further improve the usefulness of FdhSNO as for generating reducing power, we rationally engineered the protein to reduce the coenzyme nicotinamide adenine dinucleotide phosphate (NADP+ ) with better catalytic efficiency than NAD+ . The single mutation D221Q enabled the reduction of NADP+ with a catalytic efficiency kCAT /KM of 0.4 s-1 ·mm-1 at 200 mm formate, while a quadruple mutant (A198G/D221Q/H379K/S380V) resulted in a fivefold increase in catalytic efficiency for NADP+ compared with the single mutant. We determined the cofactor-bound structure of the quadruple mutant to gain mechanistic evidence behind the improved specificity for NADP+ . Our efforts to unravel the key residues for the chemical resistance and cofactor specificity of FdhSNO may lead to wider use of this enzymatic group in a more sustainable (bio)manufacture of value-added chemicals, as for instance the biosynthesis of chiral compounds.
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Affiliation(s)
- Michele Partipilo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Jacob J Whittaker
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Nicola Pontillo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
| | - Jelmer Coenradij
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Andreas Herrmann
- Polymer Chemistry and Bioengineering, Zernike Institute for Advanced Materials, Groningen, The Netherlands
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Germany
| | - Albert Guskov
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, The Netherlands
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Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter. Antonie Van Leeuwenhoek 2023; 116:153-170. [PMID: 36462112 DOI: 10.1007/s10482-022-01788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/23/2022] [Indexed: 12/04/2022]
Abstract
Three novel facultatively methylotrophic bacteria, strains 3CT, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С18:1ω7c, C19:0ω8c cyclo and C16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4-99.4%). Genomic comparisons of 3CT and its closest relatives, S. novella DSM 506T and S. koreensis Jip08T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA-DNA hybridization values, respectively. The average amino acid identities between the strain 3CT and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6-84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3CT, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3CT (= VKM B-3218T = KCTC 62336T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter.
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Han L, Xu M, Kong X, Liu X, Wang Q, Chen G, Xu K, Nie J. Deciphering the diversity, composition, function, and network complexity of the soil microbial community after repeated exposure to a fungicide boscalid. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120060. [PMID: 36058318 DOI: 10.1016/j.envpol.2022.120060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Boscalid is a novel, highly effective carboximide fungicide that has been substantially and irrationally applied in greenhouses. However, little is known about the residual characteristics of boscalid and its ecological effects in long-term polluted greenhouse soils. Therefore, actual boscalid pollution status in greenhouse soils was simulated by repeatedly introducing boscalid into the soil under laboratory conditions. The degradation characteristics of boscalid, and its effects on the diversity, composition, function, and co-occurrence patterns of the soil microbial community were systematically investigated. Boscalid degraded slowly, with its degradation half-lives ranging from 31.5 days to 180.1 days in the soil. Boscalid degradation was further delayed by repeated treatment and increasing its initial concentration. Boscalid significantly decreased soil microbial diversity, particularly at the recommended dosage. Amplicon sequencing analysis showed that boscalid altered the soil microbial community and further stimulated the phylum Proteobacteria and four potential boscalid-degrading bacterial genera, Sphingomonas, Starkeya, Citrobacter, and Castellaniella. Although the network analysis revealed that boscalid significantly reduced the microbial network complexity, it enhanced the vital roles of Proteobacteria by increasing its proportion and strengthening the relationships among the internal bacteria in the network. The soil microbial function in the boscalid treatment were simulated at the recommended dosage and two-fold recommended dosage but showed an inhibition-recovery-stimulation trend at the five-fold recommended dosage with an increase in treatment frequency. Moreover, the expression of nitrogen cycling functional genes, nifH, AOA amoA, AOB amoA, nirK, and nirS in all boscalid treatments displayed an inhibition-recovery-stimulation trend during the entire experimental period, and the effects were more pronounced at the five-fold recommended dosage. In conclusion, repeated boscalid treatments delayed degradation, reduced soil microbial diversity and network complexity, disturbed soil microbial community, and interfered with soil microbial function.
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Affiliation(s)
- Lingxi Han
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, 266109, China
| | - Min Xu
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, 266109, China
| | - Xiabing Kong
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, 266109, China
| | - Xiaoli Liu
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, 266109, China
| | - Qianwen Wang
- Central Laboratory, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guilan Chen
- Central Laboratory, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kun Xu
- Central Laboratory, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jiyun Nie
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, 266109, China.
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In vitro and in vivo evidence for the mitigation of monocrotophos toxicity using native Trichoderma harzianum isolate. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Singh S, Kumar V, Kanwar R, Wani AB, Gill JPK, Garg VK, Singh J, Ramamurthy PC. Toxicity and detoxification of monocrotophos from ecosystem using different approaches: A review. CHEMOSPHERE 2021; 275:130051. [PMID: 33676273 DOI: 10.1016/j.chemosphere.2021.130051] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Monocrotophos (MCP) is an organophosphate insecticide with broad application in agricultural crops like rice, maize, sugarcane, cotton, soybeans, groundnut and vegetables. MCP solubilize in water readily and thus reduced sorption occurs in soil. This leads to MCP leaching into the groundwater and pose a significant threat of contamination. The MCP's half-life depends on the temperature and pH value and estimated as 17-96 d. But the half-life of technical grade MCP can exceed up to 2500 days if properly stored at 38 °C in a glass or polyethylene container in a stable condition. It causes abnormality, ranging from mild to severe confusion, agitation, hypersalivation, convulsion, pulmonary failure, senescence in mammals and insects. MCP affects humans by inhibiting the activity of the acetylcholine esterase enzyme. MCP is accountable for the catalytic degradation of acetylcholine and affects the neurotransmission between neurons. This review discusses MCP's various aspects and fate on aquatic and terrestrial life forms, quantification methods for monitoring, various degradation processes, and their mechanisms. Different case studies related to its impact on the human population in different parts of the world have been discussed. Efforts have also been made to summarize and present different microbial population's role in its degradation and mineralization.
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Affiliation(s)
- Simranjeet Singh
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, 560012, India
| | - Vijay Kumar
- Department of Chemistry, Regional Ayurveda Research Institute for Drug Development, Gwalior, 474009, India
| | - Ramesh Kanwar
- Department of Agricultural and Biosystems Engineering, Iowa State University, USA
| | - Abdul Basit Wani
- Department of Chemistry, School of Bioengineering and Biosciences, Lovely Professional University, Delhi-Jalandhar Highway, Phagwara, 144411, Punjab, India
| | | | - Vinod Kumar Garg
- Department of Environmental Sciences and Technology, Central University of Punjab, Mansa Road, Bathinda, 151001, Punjab, India.
| | - Joginder Singh
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Delhi-Jalandhar Highway, Phagwara, 144411, Punjab, India.
| | - Praveen C Ramamurthy
- Interdisciplinary Centre for Water Research (ICWaR), Indian Institute of Sciences, Bangalore, 560012, India.
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d’Errico G, Aloj V, Ventorino V, Bottiglieri A, Comite E, Ritieni A, Marra R, Bolletti Censi S, Flematti GR, Pepe O, Vinale F. Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes. PLoS One 2020; 15:e0228936. [PMID: 32084150 PMCID: PMC7034917 DOI: 10.1371/journal.pone.0228936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/27/2020] [Indexed: 11/27/2022] Open
Abstract
A total of fifteen potential methyl t-butyl ether (MtBE)-degrading bacterial strains were isolated from contaminated soil. They have been identified as belonging to the genera Bacillus, Pseudomonas, Kocuria, Janibacter, Starkeya, Bosea, Mycolicibacterium, and Rhodovarius. Bacillus aryabhattai R1B, S. novella R8b, and M. mucogenicum R8i were able to grow using MtBE as carbon source, exhibiting different growth behavior and contaminant degradation ability. Their biocontrol ability was tested against various fungal pathogens. Both S. novella R8b and B. aryabhattai were effective in reducing the development of necrotic areas on leaves within 48 hours from Botritys cinerea and Alternaria alternata inoculation. Whereas, M. mucogenicum effectively controlled B. cinerea after 72 hours. Similar results were achieved using Pythium ultimum, in which the application of isolated bacteria increased seed germination. Only M. mucogenicum elicited tomato plants resistance against B. cinerea. This is the first report describing the occurrence of bioremediation and biocontrol activities in M. mucogenicum, B. aryabhattai and S. novella species. The production of maculosin and its antibiotic activity against Rhizoctonia solani has been reported for first time from S. novella. Our results highlight the importance of multidisciplinary approaches to achieve a consistent selection of bacterial strains useful for plant protection and bioremediation purposes.
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Affiliation(s)
- Giada d’Errico
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Veronica Aloj
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Valeria Ventorino
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Assunta Bottiglieri
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Ernesto Comite
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Alberto Ritieni
- University of Naples Federico II, Department of Pharmacy, Naples, Italy
| | - Roberta Marra
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | | | - Gavin R. Flematti
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Olimpia Pepe
- University of Naples Federico II, Department of Agricultural Sciences, Portici (NA), Italy
| | - Francesco Vinale
- University of Naples Federico II, Department of Veterinary Medicine and Animal Production, Naples, Italy
- National Research Council, Institute for Sustainable Plant Protection, Portici (NA), Italy
- * E-mail:
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Balasubramanian J, Ponnaiah SK, Periakaruppan P, Kamaraj D. Accelerated photodeterioration of class I toxic monocrotophos in the presence of one-pot constructed Ag 3PO 4/polyaniline@g-C 3N 4 nanocomposite: efficacy in light harvesting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:2328-2339. [PMID: 31782097 DOI: 10.1007/s11356-019-06811-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Water and soil contamination has become unavoidable due to the enormous usage of pesticides in agriculture. Among the pesticides, monocrotophos (MCP), a popular and largely used pesticide, is extremely toxic to birds and humans, which is easily leached into the environment. Therefore, establishment of a green tactic to clean the environment from such hazard is very essential. Herein, we have developed a novel ternary nanocomposite, Ag3PO4/polyaniline@g-C3N4 with enhanced electron-hole separation efficiency, a condition which is very much required for any photocatalyst. The nanocomposite was one-pot synthesized by a simple and economical hydrothermal method. The strategically modulated band gaps of the nanocomposite help harvest the sunlight efficaciously for the robust degradation of MCP (99.6%). It has been found that the active species involved in the photo-cleaning process are OH· and O2·-. A suitable reaction mechanism has been proposed and discussed. Analytical techniques, which include energy-dispersive X-ray spectroscopy (EDX), field emission scanning electron microscopy (FE-SEM), elemental mapping analysis, high-resolution transmission electron microscopy (HR-TEM), Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible diffuse reflectance spectroscopy (UV-DRS), and X-ray diffraction (XRD), were used to characterize the synthesized nanocomposite. This nano-photocatalyst, which is simple, stable, and reusable, certainly has potential applications in soil contamination remediation, sewage treatments, and other environment decontaminations. Also, a study of this kind offers more strategic plans for the production of clean energy (hydrogen) by solar-driven water splitting.
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Affiliation(s)
| | | | | | - Dhivya Kamaraj
- Department of Civil Engineering, Sethu Institute of Technology, Virudhunagar, Tamil Nadu, 626115, India
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Sun L, Gao X, Chen W, Huang K, Bai N, Lyu W, Liu H. Characterization of the Propham Biodegradation Pathway in Starkeya sp. Strain YW6 and Cloning of a Novel Amidase Gene mmH. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:4193-4199. [PMID: 30864436 DOI: 10.1021/acs.jafc.8b06928] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 μM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.
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Affiliation(s)
- Lina Sun
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
| | - Xinhua Gao
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Wei Chen
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Key Laboratory of Horticultural Technology , Shanghai 201403 , People's Republic of China
| | - Kaihua Huang
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Environmental Protection Monitoring Station of Shanghai , Shanghai 201403 , People's Republic of China
| | - Naling Bai
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Weiguang Lyu
- Eco-Environmental Protection Research Institute , Shanghai Academy of Agricultural Sciences , Shanghai 201403 , People's Republic of China
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA) , Shanghai 201403 , People's Republic of China
- Shanghai Agricultural Environment and Farmland Conservation Experiment Station of Ministry of Agriculture , Shanghai 201403 , People's Republic of China
| | - Hongming Liu
- Institute of Molecular Biology and Biotechnology , Anhui Normal University , Wuhu , Anhui 241000 , People's Republic of China
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