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Bhat SV, Maughan H, Cameron ADS, Yost CK. Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations. Microb Genom 2022; 8:mgen000864. [PMID: 36107145 PMCID: PMC9676026 DOI: 10.1099/mgen.0.000864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/15/2022] [Indexed: 04/01/2024] Open
Abstract
Delftia is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. Delftia spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published Delftia genomes and show that the genus is divided into two well-supported clades: one 'Delftia acidovorans' clade with isolates from soils and plant rhizospheres, and a second 'Delftia lacustris and Delftia tsuruhatensis' clade with isolates from humans and sludge. The pan-genome inferred from 61 Delftia genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of Delftia and supported their role as generalists.
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Affiliation(s)
- Supriya V. Bhat
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | | | - Andrew D. S. Cameron
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
| | - Christopher K. Yost
- Department of Biology, University of Regina, Regina, SK, Canada
- Institute for Microbial Systems and Society, University of Regina, Regina, SK, Canada
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2
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Xu H, Chen Z, Huang R, Cui Y, Li Q, Zhao Y, Wang X, Mao D, Luo Y, Ren H. Antibiotic Resistance Gene-Carrying Plasmid Spreads into the Plant Endophytic Bacteria using Soil Bacteria as Carriers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10462-10470. [PMID: 34114802 DOI: 10.1021/acs.est.1c01615] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Applications of animal manure and treated wastewater could enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the plant microbiome. However, the mechanistic studies of the transmission of ARB and ARGs from the environment to plant endophytic bacteria were few. Herein, a genetically engineered fluorescent Escherichia coli harboring a conjugative RP4 plasmid that carries three ARGs was used to trace its spread into Arabidopsis thaliana interior in a tetracycline-amended hydroponic system in the absence or presence of a simulated soil bacterial community. Confocal microscope observation demonstrated that E. coli was internalized into plant tissues and the carried RP4 plasmid was transferred into plant endophytic bacteria. More importantly, we observed that soil bacteria inhibited the internalization of E. coli but substantially promoted RP4 plasmid spread into the plant microbiome. The altered RP4-carrying bacterial community composition in the plant microbiome and the increased core-shared RP4-carrying bacteria number between plant interior and exterior in the presence of soil bacteria collectively confirmed that soil bacteria, especially Proteobacteria, might capture RP4 from E. coli and then translocate into plant microbiome, resulting in the increased RP4 plasmid spread in the plant endophytes. Overall, our findings provided important insights into the dissemination of ARB and ARGs from the environment to the plant microbiome.
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Affiliation(s)
- Han Xu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yuxiao Cui
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
- Municipal Experimental Teaching Demonstration Center for Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Qiang Li
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, Shandong, China
| | - Yanhui Zhao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
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3
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Cheng C, Zhou W, Dong X, Zhang P, Zhou K, Zhou D, Qian C, Lin X, Li P, Li K, Bao Q, Xu T, Lu J, Ying J. Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance. Front Cell Infect Microbiol 2021; 11:663933. [PMID: 34222039 PMCID: PMC8248536 DOI: 10.3389/fcimb.2021.663933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/31/2021] [Indexed: 12/04/2022] Open
Abstract
Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.
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Affiliation(s)
- Cong Cheng
- Vocational and Technical College, Lishui University, Lishui, China.,Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wangxiao Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xu Dong
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peiyao Zhang
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kexin Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Changrui Qian
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peizhen Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Junwan Lu
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Ying
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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4
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Riley NG, Goller CC, Leggett ZH, Lewis DM, Ciccone K, Dunn RR. Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students. PeerJ 2020; 8:e8925. [PMID: 32322441 PMCID: PMC7164421 DOI: 10.7717/peerj.8925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.
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Affiliation(s)
- Noah G Riley
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Carlos C Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Biotechnology Program (BIT), North Carolina State University, Raleigh, NC, USA
| | - Zakiya H Leggett
- Department of Forestry and Environmental Resources (FER), North Carolina State University, Raleigh, NC, USA
| | - Danica M Lewis
- North Carolina State University Libraries, North Carolina State University, Raleigh, NC, USA
| | - Karen Ciccone
- North Carolina State University Libraries, North Carolina State University, Raleigh, NC, USA
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA.,University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
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5
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Khalifa AY, AlMalki M. Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa. Saudi J Biol Sci 2019; 26:1262-1267. [PMID: 31516356 PMCID: PMC6733694 DOI: 10.1016/j.sjbs.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 11/25/2022] Open
Abstract
In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C16:1ω7c/C16:1ω6c) and C16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.
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Affiliation(s)
- Ashraf Y.Z. Khalifa
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - M. AlMalki
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
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6
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Frazão DF, Raimundo JR, Domingues JL, Quintela-Sabarís C, Gonçalves JC, Delgado F. Cistus ladanifer (Cistaceae): a natural resource in Mediterranean-type ecosystems. PLANTA 2018; 247:289-300. [PMID: 29218421 DOI: 10.1007/s00425-017-2825-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/27/2017] [Indexed: 06/07/2023]
Abstract
Cistus ladanifer has a well-defined taxonomic identity. 2,2,6-trimethylcyclohexanone may be an authenticity and taxonomic marker. Its traits and applications make it a possible economic resource fitted for Mediterranean areas. Cistus ladanifer is a dominant shrub species endemic to the western Mediterranean region. Due to its dominant nature and its potential ecological, aromatic or pharmacological applications, C. ladanifer has been the object of numerous studies. In this review current knowledge on different aspects of this species is summarized, from its taxonomy to its chemical characterisation or its competitive traits. There are no doubts about the taxonomic entity of C. ladanifer, although the recognition of infraspecific taxa deserves more attention. Given that the fragrant exudate of C. ladanifer holds a very specific composition, one species specific carotenoid, 2,2,6-trimethylcyclohexanone, derivative is proposed as an authenticity marker for uses of C. ladanifer in pharmacological or aromatic industries. Evidence is also gathered on the extreme adaptation of C. ladanifer to stressful conditions in the Mediterranean region, such as the ability to survive in low hydric and high solar exposition conditions, presistence in poor and contaminated soils, and growth inhibition of several other plants through the release of allelochemicals. Thus, the finding of potential applications for this plant may contribute to enhance the economic dimension of derelict lands, such as mine tailings or poor agricultural Mediterranean areas.
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Affiliation(s)
- David F Frazão
- CBPBI, Centro de Biotecnologia de Plantas da Beira Interior, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal
| | - Joana R Raimundo
- CBPBI, Centro de Biotecnologia de Plantas da Beira Interior, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal
| | - Joana L Domingues
- CBPBI, Centro de Biotecnologia de Plantas da Beira Interior, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal
| | - Celestino Quintela-Sabarís
- Laboratoire Sols et Environnement (UMR 1120, INRA-Univ. Lorraine), ENSAIA, 2 Av. de la Forêt de Haye, TSA 40602, 54518, Vandoeuvre-lès-Nancy, France
| | - José C Gonçalves
- CBPBI, Centro de Biotecnologia de Plantas da Beira Interior, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal
- IPCB-ESA, Escola Superior Agrária, Instituto Politécnico de Castelo Branco, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal
- CERNAS/IPCB, Centro de Estudos de Recursos Naturais, Ambiente e Sociedade/Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Fernanda Delgado
- CBPBI, Centro de Biotecnologia de Plantas da Beira Interior, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal.
- IPCB-ESA, Escola Superior Agrária, Instituto Politécnico de Castelo Branco, Quinta da Senhora de Mércules, Apartado 119, 6001-909, Castelo Branco, Portugal.
- CERNAS/IPCB, Centro de Estudos de Recursos Naturais, Ambiente e Sociedade/Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal.
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