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Zhang W, Suyamud B, Lohwacharin J, Yang Y. Large-scale pattern of resistance genes and bacterial community in the tap water along the middle and low reaches of the Yangtze River. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111517. [PMID: 33120256 DOI: 10.1016/j.ecoenv.2020.111517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic and metal resistance genes (ARGs and MRGs) in tap water are of great public health concern. However, very fewer studies focused on the relationship between resistance genes and opportunistic pathogens in tap water. In this study, the diversity and abundance of resistance genes and bacterial community from tap water at a large-scale along the middle and lower reaches of the Yangtze River were investigated. The total relative abundances of ARGs and MRGs were 2.95 × 10-3-1.22 × 10-1 and 1.93 × 10-3-1.20 × 10-1 copies/16S rRNA, respectively. The blaTEM and merP detected were major ARG and MRG subtypes, respectively. Mobile genetic elements (Intl1 and tnpA) showed significant correlations with the abundance of ARGs. Heavy metals also played a vital role in the co-selection of ARGs. Surprisingly, there were still eight opportunistic pathogens in tap water, among which Escherichia coli, Helicobacter pylori, Mycoplasma pneumoniae, and Porphyromonas gingivalis were the potential host of ARGs and MRGs. Escherichia coli had the highest abundance, while Bacillus anthracis had the highest detected frequency (100%), a widespread opportunistic pathogen in tap water.
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Affiliation(s)
- Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Bongkotrat Suyamud
- Department of Environmental Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jenyuk Lohwacharin
- Department of Environmental Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of the Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
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Cutiño-Jiménez AM, Menck CFM, Cambas YT, Díaz-Pérez JC. Protein signatures to identify the different genera within the Xanthomonadaceae family. Braz J Microbiol 2020; 51:1515-1526. [PMID: 32488841 DOI: 10.1007/s42770-020-00304-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/18/2020] [Indexed: 11/26/2022] Open
Abstract
The Xanthomonadaceae family comprises the genera Xanthomonas and Xylella, which include plant pathogenic species that affect economically important crops. The family also includes the plant growth-promoting bacteria Pseudomonas geniculata and Stenotrophomonas rhizophila, and some other species with biotechnological, medical, and environmental relevance. Previous work identified molecular signatures that helped to understand the evolutionary placement of this family within gamma-proteobacteria. In the present study, we investigated whether insertions identified in highly conserved proteins may also be used as molecular markers for taxonomic classification and identification of members within the Xanthomonadaceae family. Four housekeeping proteins (DNA repair and replication-related and protein translation enzymes) were selected. The insertions allowed discriminating phytopathogenic and plant growth-promoting groups within this family, and also amino acid sequences of these insertions allowed distinguishing different genera and, eventually, species as well as pathovars. Moreover, insertions in the proteins MutS and DNA polymerase III (subunit alpha) are conserved in Xylella fastidiosa, but signatures in DNA ligase NAD-dependent and Valyl tRNA synthetase distinguish particular subspecies within the genus. The genus Stenotrophomonas and Pseudomonas geniculata could be distinguishable based on the insertions in MutS, DNA polymerase III (subunit alpha), and Valyl tRNA synthetase, although insertion in DNA ligase NAD-dependent discriminates these bacteria at the species level. All these insertions differentiate species and pathovars within Xanthomonas. Thus, the insertions presented support evolutionary demarcation within Xanthomonadaceae and provide tools for the fast identification in the field of these bacteria with agricultural, environmental, and economic relevance.
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Affiliation(s)
- Ania Margarita Cutiño-Jiménez
- Centre of Studies for Industrial Biotechnology (CEBI), Faculty of Natural and Exact Sciences, University of Oriente, Ave. Patricio Lumumba s/n., Reparto Jiménez, CP 90500, Santiago de Cuba, Cuba.
| | - Carlos Frederico Martins Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo, SP, 05508-000, Brazil
| | - Yusdiel Torres Cambas
- Department of Biology and Geography, Faculty of Natural and Exact Sciences, University of Oriente, Ave. Patricio Lumumba s/n., Reparto Jiménez, CP 90500, Santiago de Cuba, Cuba
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Liu Y, Zhou X, Liu W, Huang J, Liu Q, Sun J, Cai X, Miao W. HpaXpm, a novel harpin of Xanthomonas phaseoli pv. manihotis, acts as an elicitor with high thermal stability, reduces disease, and promotes plant growth. BMC Microbiol 2020; 20:4. [PMID: 31906854 PMCID: PMC6945534 DOI: 10.1186/s12866-019-1691-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 12/24/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Harpins are proteins secreted by the type III secretion system of Gram-negative bacteria during pathogen-plant interactions that can act as elicitors, stimulating defense and plant growth in many types of non-host plants. Harpin-treated plants have higher resistance, quality and yields and, therefore, harpin proteins may potentially have many valuable agricultural applications. Harpins are characterized by high thermal stability at 100 °C. However, it is unknown whether harpins are still active at temperatures above 100 °C or whether different temperatures affect the activity of the harpin protein in different ways. The mechanism responsible for the heat stability of harpins is also unknown. RESULTS We identified a novel harpin, HpaXpm, from the cassava blight bacteria Xanthomonas phaseoli pv. manihotis HNHK. The predicted secondary structure and 3-D structure indicated that the HpaXpm protein has two β-strand domains and two major α-helical domains located at the N- and C-terminal regions, respectively. A phylogenetic tree generated using the maximum likelihood method grouped HpaXpm in clade I of the Hpa1 group along with harpins produced by other Xanthomonas spp. (i.e., HpaG-Xag, HpaG-Xcm, Hpa1-Xac, and Hpa1Xm). Phenotypic assays showed that HpaXpm induced the hypersensitive response (HR), defense responses, and growth promotion in non-host plants more effectively than Hp1Xoo (X. oryzae pv. oryzae). Quantitative real-time PCR analysis indicated that HpaXpm proteins subjected to heat treatments at 100 °C, 150 °C, or 200 °C were still able to stimulate the expression of function-related genes (i.e., the HR marker genes Hin1 and Hsr203J, the defense-related gene NPR1, and the plant growth enhancement-related gene NtEXP6); however, the ability of heat-treated HpaXpm to induce HR was different at different temperatures. CONCLUSIONS These findings add a new member to the harpin family. HpaXpm is heat-stable up to 200 °C and is able to stimulate powerful beneficial biological functions that could potentially be more valuable for agricultural applications than those stimulated by Hpa1Xoo. We hypothesize that the extreme heat resistance of HpaXpm is because the structure of harpin is very stable and, therefore, the HpaXpm structure is less affected by temperature.
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Affiliation(s)
- Yue Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Xiaoyun Zhou
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Wenbo Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Jiamin Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Qinghuan Liu
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Jianzhang Sun
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Xinfeng Cai
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China
| | - Weiguo Miao
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan Province, China.
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, Hainan Province, China.
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Assis RDAB, Polloni LC, Patané JSL, Thakur S, Felestrino ÉB, Diaz-Caballero J, Digiampietri LA, Goulart LR, Almeida NF, Nascimento R, Dandekar AM, Zaini PA, Setubal JC, Guttman DS, Moreira LM. Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. Sci Rep 2017; 7:16133. [PMID: 29170530 PMCID: PMC5700972 DOI: 10.1038/s41598-017-16325-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023] Open
Abstract
The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria.
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Affiliation(s)
- Renata de A B Assis
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | | | - José S L Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Shalabh Thakur
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | - Érica B Felestrino
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil
| | - Julio Diaz-Caballero
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | | | - Luiz Ricardo Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Nalvo F Almeida
- School of Computing, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, MS, Brazil
| | - Rafael Nascimento
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Paulo A Zaini
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil.,Department of Plant Sciences, University of California, Davis, CA, USA
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, Ontario, M5S 3B2, Canada
| | - Leandro Marcio Moreira
- Center of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil. .,Department of Biological Science, Institute of Exact and Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
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Huang CL, Pu PH, Huang HJ, Sung HM, Liaw HJ, Chen YM, Chen CM, Huang MB, Osada N, Gojobori T, Pai TW, Chen YT, Hwang CC, Chiang TY. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts. BMC Genomics 2015; 16:188. [PMID: 25879893 PMCID: PMC4372319 DOI: 10.1186/s12864-015-1369-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/20/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. RESULTS Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. CONCLUSION Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.
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Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Pei-Hua Pu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hung-Jiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yi-Min Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chien-Ming Chen
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Ming-Ban Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Naoki Osada
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
| | - Takashi Gojobori
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Yu-Tin Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chi-Chuan Hwang
- Department of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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Facincani AP, Moreira LM, Soares MR, Ferreira CB, Ferreira RM, Ferro MIT, Ferro JA, Gozzo FC, de Oliveira JCF. Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri. Funct Integr Genomics 2013; 14:205-17. [PMID: 24676796 DOI: 10.1007/s10142-013-0340-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/18/2013] [Accepted: 09/26/2013] [Indexed: 01/02/2023]
Abstract
The bacteria Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. The disease symptoms are characterized by localized host cell hyperplasia followed by tissue necrosis at the infected area. An arsenal of bacterial pathogenicity- and virulence-related proteins is expressed to ensure a successful infection process. At the post-genomic stage of Xac, we used a proteomic approach to analyze the proteins that are displayed differentially over time when the pathogen attacks the host plant. Protein extracts were prepared from infectious Xac grown in inducing medium (XAM1) for 24 h or from host citrus plants for 3 or 5 days after infection, detached times to evaluate the adaptation and virulence of the pathogen. The protein extracts were proteolyzed, and the peptides derived from tryptic digestion were investigated using liquid chromatography and tandem mass spectrometry. Changes in the protein expression profile were compared with the Xac genome and the proteome recently described under non-infectious conditions. An analysis of the proteome of Xac under infectious conditions revealed proteins directly involved in virulence such as the type III secretion system (T3SS) and effector proteins (T3SS-e), the type IV pilus (Tfp), and xanthan gum biosynthesis. Moreover, four new mutants related to proteins detected in the proteome and with different functions exhibited reduced virulence relative to the wild-type proteins. The results of the proteome analysis of infectious Xac define the processes of adaptation to the host and demonstrate the induction of the virulence factors of Xac involved in plant-pathogen interactions.
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Affiliation(s)
- Agda P Facincani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, Departamento de Tecnologia, UNESP-Universidade Estadual Paulista, São Paulo, SP, Brazil
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Fones H, Preston GM. The impact of transition metals on bacterial plant disease. FEMS Microbiol Rev 2013; 37:495-519. [DOI: 10.1111/1574-6976.12004] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Revised: 09/05/2012] [Accepted: 09/14/2012] [Indexed: 12/24/2022] Open
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