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Lu T, Lei C, Gao M, Lv L, Zhang C, Qian H, Tang T. A risk entropy approach for linking pesticides and soil bacterial communities. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133970. [PMID: 38457974 DOI: 10.1016/j.jhazmat.2024.133970] [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: 12/29/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Pesticides play a vital role in ensuring modern agricultural production, but also adversely affecting soil health. Microorganisms are the cornerstone of soil ecology, however, to date, there are few unified standards to measure the risk of soil pesticide residues to soil microbial community. To compensate for this gap, we collected soil samples from 55 orchards and monitored and risk-assessed 165 pesticides to microbial community in the soil. Results showed that a total of 137 pesticides were detected in all samples. Pesticide residues significantly influenced the microbial diversity and community structure in orchard soils, particularly fungicides and herbicides. The risk entropy of each pesticide was calculated in all samples and it was found that 60% of the samples had a "pesticide risk" (Risk quotient > 0.01), where the relative abundance significantly increased in 43 genera and significantly decreased in 111 genera (p < 0.05). Through multiple screens, we finally identified Bacillus and Sphingomonas as the most abundant sensitive genera under pesticide perturbation. The results showed that despite the complexity of the effects of pesticide residues on soils health, we could reveal them by identifying changes in soil bacterial, especially by the differences of microbial biomarkers abundance. The present study could provide new insights into the research strategy for pesticide pollution on soil microbial communities. ENVIRONMENTAL IMPLICATION: The risk of pesticide residues in soil needs to be quantified and standardized. We believe that microorganisms can be used as a marker to indicate soil pesticide residue risk. For this end, we investigated the residues of 165 pesticides in 55 orchard soil samples, calculated pesticide risk entropy and their effects on the soil microbial community. Through multiple analyzing and screening, we ultimately identified that, out of the 154 detected biomarkers, Bacillus and Sphingomonas were the most abundant sensitive genera under pesticide perturbation, which have the potential to be used as key biomarkers of soil microbiomes induced by pesticide perturbation.
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Affiliation(s)
- Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingyu Gao
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lu Lv
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Chunrong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory for Pesticide Residue Detection of Ministry of Agriculture and Rural Affairs, Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Liu Q, Jia J, Hu H, Li X, Zhao Y, Wu C. Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133786. [PMID: 38367442 DOI: 10.1016/j.jhazmat.2024.133786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/26/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jia Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Hongjuan Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yanhui Zhao
- Ecology and Environment Monitoring and Scientific Research Center, Yangtze Basin Ecology and Environment Administration, Ministry of Ecological and Environment, Wuhan 430010, China
| | - Chenxi Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Zhang Z, Zhang Q, Yang H, Cui L, Qian H. Mining strategies for isolating plastic-degrading microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123572. [PMID: 38369095 DOI: 10.1016/j.envpol.2024.123572] [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: 12/27/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.
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Affiliation(s)
- Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huihui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Yang Y, Xu N, Zhang Z, Lei C, Chen B, Qin G, Qiu D, Lu T, Qian H. Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5659-5670. [PMID: 38442360 DOI: 10.1021/acs.jafc.3c09160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.
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Affiliation(s)
- Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, P. R. China
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Jin MK, Zhang Q, Xu N, Zhang Z, Guo HQ, Li J, Ding K, Sun X, Yang XR, Zhu D, Su X, Qian H, Zhu YG. Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4476-4486. [PMID: 38382547 DOI: 10.1021/acs.est.3c05741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.
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Affiliation(s)
- Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Hong-Qin Guo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xin Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiaoxuan Su
- Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400715, China
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Yu Y, Zhang Q, Kang J, Xu N, Zhang Z, Deng Y, Gillings M, Lu T, Qian H. Effects of organic fertilizers on plant growth and the rhizosphere microbiome. Appl Environ Microbiol 2024; 90:e0171923. [PMID: 38193672 PMCID: PMC10880660 DOI: 10.1128/aem.01719-23] [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: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/10/2024] Open
Abstract
Application of organic fertilizers is an important strategy for sustainable agriculture. The biological source of organic fertilizers determines their specific functional characteristics, but few studies have systematically examined these functions or assessed their health risk to soil ecology. To fill this gap, we analyzed 16S rRNA gene amplicon sequencing data from 637 soil samples amended with plant- and animal-derived organic fertilizers (hereafter plant fertilizers and animal fertilizers). Results showed that animal fertilizers increased the diversity of soil microbiome, while plant fertilizers maintained the stability of soil microbial community. Microcosm experiments verified that plant fertilizers were beneficial to plant root development and increased carbon cycle pathways, while animal fertilizers enriched nitrogen cycle pathways. Compared with animal fertilizers, plant fertilizers harbored a lower abundance of risk factors such as antibiotic resistance genes and viruses. Consequently, plant fertilizers might be more suitable for long-term application in agriculture. This work provides a guide for organic fertilizer selection from the perspective of soil microecology and promotes sustainable development of organic agriculture.IMPORTANCEThis study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jian Kang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yu Deng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, New South Wales, Australia
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, China
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7
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Zhang Q, Lei C, Jin M, Qin G, Yu Y, Qiu D, Wang Y, Zhang Z, Zhang Z, Lu T, Peijnenburg WJGM, Gillings M, Yao Z, Qian H. Glyphosate Disorders Soil Enchytraeid Gut Microbiota and Increases Its Antibiotic Resistance Risk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2089-2099. [PMID: 38235689 DOI: 10.1021/acs.jafc.3c05436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Pesticides promote the stable development of intensive global agriculture. Nevertheless, their residues in the soil can cause ecological and human health risks. Glyphosate is a popular herbicide and is generally thought to be ecologically safe and nontoxic, but this conclusion has been questioned. Herein, we investigated the interaction among soil fauna (Enchytraeus crypticus) exposed to glyphosate and found that glyphosate induced oxidative stress and detoxification responses in E. crypticus and disturbed their lipid metabolism and digestive systems. We further demonstrated that glyphosate disordered the gut microbiota of E. crypticus and increased the abundance of resistance determinants with significant human health risks. Empirical tests and structural equation models were then used to confirm that glyphosate could cause E. crypticus to generate reactive oxygen species, indirectly interfering with their gut microbiota. Our study provides important implications for deciphering the mechanisms of the ecotoxicity of pesticides under the challenge of worldwide pesticide contamination.
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Affiliation(s)
- Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Mingkang Jin
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA Leiden 2300, The Netherlands
- Center for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), P.O. Box 1, Bilthoven 3720 BA, The Netherlands
| | - Michael Gillings
- ARC Centre of Excellence in Synthetic Biology, Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales 2109, Australia
| | - Ziang Yao
- College of Life Science, Dalian Minzu University, Dalian, Liaoning 116600, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, P. R. China
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