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Yang F, Wang Y, Liu Q, Xu B, Chen H, Li Y, Wang K, Liang G, Zhang R, Jiao X, Zhang Y. High Prevalence and Varied Distribution of Antibiotic-Resistant Bacteria in the Rhizosphere and Rhizoplane of Citrus medica. Microorganisms 2022; 10:microorganisms10091708. [PMID: 36144310 PMCID: PMC9501533 DOI: 10.3390/microorganisms10091708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The plant-associated bacteria, including that in the rhizosphere and rhizoplane, play important roles in human exposure to antibiotic-resistant bacteria (ARB). The rhizosphere and rhizoplane represent two distinct environments with different selective pressures for bacterial colonization. However, whether the difference in characteristics between the rhizosphere and rhizoplane can affect the abundance and antibiotic resistance profiles of ARB colonizing, the two environments remain largely unknown. In this study, we obtained 174 bacterial isolates from the rhizosphere (113 isolates) and rhizoplane (61 isolates) of Citrus medica trees grown in a park, where humans could easily and frequently contact the trees. A very high proportion of isolates exhibited resistance to several clinically important antibiotics, including β-lactam class antibiotics and polymyxin, with several known antibiotic-resistant opportunistic pathogens, such as Micrococcus luteus, being identified. The prevalence of ARB in the rhizoplane was higher than that in the rhizosphere. While the prevalence of polymyxin-resistant isolates was higher in the rhizoplane, the prevalence of amphenicol-resistant isolates was significantly higher in the rhizosphere. In summary, our findings suggest that the rhizosphere and rhizoplane are important media for the spread of ARB, and the different characteristics between the two environments can affect the distribution of ARB.
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Affiliation(s)
- Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yaomen Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.J.); (Y.Z.); Tel.: +86-5145-87971136 (X.J.); +86-5145-87971136 (Y.Z.)
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.J.); (Y.Z.); Tel.: +86-5145-87971136 (X.J.); +86-5145-87971136 (Y.Z.)
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Rasskazov D, Chadaeva I, Sharypova E, Zolotareva K, Khandaev B, Ponomarenko P, Podkolodnyy N, Tverdokhleb N, Vishnevsky O, Bogomolov A, Podkolodnaya O, Savinkova L, Zemlyanskaya E, Golubyatnikov V, Kolchanov N, Ponomarenko M. Plant_SNP_TATA_Z-Tester: A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression. Int J Mol Sci 2022; 23:ijms23158684. [PMID: 35955817 PMCID: PMC9369029 DOI: 10.3390/ijms23158684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic targeted optimization of plant promoters is becoming a part of progress in mainstream postgenomic agriculture along with hybridization of cultivated plants with wild congeners, as well as marker-assisted breeding. Therefore, here, for the first time, we compiled all the experimental data—on mutational effects in plant proximal promoters on gene expression—that we could find in PubMed. Some of these datasets cast doubt on both the existence and the uniqueness of the sought solution, which could unequivocally estimate effects of proximal promoter mutation on gene expression when plants are grown under various environmental conditions during their development. This means that the inverse problem under study is ill-posed. Furthermore, we found experimental data on in vitro interchangeability of plant and human TATA-binding proteins allowing the application of Tikhonov’s regularization, making this problem well-posed. Within these frameworks, we created our Web service Plant_SNP_TATA_Z-tester and then determined the limits of its applicability using those data that cast doubt on both the existence and the uniqueness of the sought solution. We confirmed that the effects (of proximal promoter mutations on gene expression) predicted by Plant_SNP_TATA_Z-tester correlate statistically significantly with all the experimental data under study. Lastly, we exemplified an application of Plant_SNP_TATA_Z-tester to agriculturally valuable mutations in plant promoters.
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Affiliation(s)
| | - Irina Chadaeva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | | | - Bato Khandaev
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
- Institute of Computational Mathematics and Mathematical Geophysics, 630090 Novosibirsk, Russia
| | | | - Oleg Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
| | | | | | | | | | | | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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