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Garcia E, Soares F, Rodrigues C, Trovão J, Pothier JF, Camelo A, Santo CE, Dragnev D, Petrova E, Costa J, Bobev S. Expansion of the Host Range of Xanthomonas euroxanthea: First Occurrence in Sunflower in Bulgaria. PLANT DISEASE 2025; 109:810-815. [PMID: 39504143 DOI: 10.1094/pdis-08-24-1691-sc] [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: 11/08/2024]
Abstract
Sunflower is a short-season crop of the Asteraceae family and the Helianthus genus and is the fourth most important oilseed crop in the world. During a field campaign, unusual symptoms (necrosis and longitudinal cracking of the petiole) were observed in a sunflower crop grown in the region of Kavarna (Dobrich district, Bulgaria) and strains of the genus Xanthomonas were isolated. Results based on phylogenetic and phylogenomic analyses showed that they clustered with Xanthomonas euroxanthea CPBF 424T species, a pathogenic strain isolated from walnut buds in Portugal and responsible for causing walnut bacterial blight. The sunflower strain showed five out of eight X. euroxanthea-specific markers (XEA4 to XEA8), a pattern also observed in some strains isolated from Solanum lycopersicum, Phaseolus vulgaris, and rainwater sources, reinforcing the emergence of a recent lineage driven by evolutionary adaptations to new plant hosts. This is the first report of X. euroxanthea in sunflower crops in Bulgaria, which represents a potential threat to production, and its distribution should be monitored.
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Affiliation(s)
- Eva Garcia
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Fabiana Soares
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Cristiana Rodrigues
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - João Trovão
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Alexandra Camelo
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- CATAA-Centro de Apoio Tecnológico Agro-Alimentar 6000-459 Castelo Branco, Portugal
| | - Christophe Espírito Santo
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- CATAA-Centro de Apoio Tecnológico Agro-Alimentar 6000-459 Castelo Branco, Portugal
| | - Dian Dragnev
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
| | - Eli Petrova
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
| | - Joana Costa
- Centre for Functional Ecology - Science for People & the Planet, TERRA Associate Laboratory, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, Coimbra 3030-199, Portugal
| | - Svetoslav Bobev
- Department of Phytopathology, Agricultural University, Plovdiv, Bulgaria
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McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Djordjevic SP, Bogema DR, Chapman TA. Xanthomonas bundabergensis sp. nov., Xanthomonas medicagonis sp. nov. and Xanthomonas tesorieronis sp. nov.: three members of group 1 Xanthomonas. Int J Syst Evol Microbiol 2025; 75:006686. [PMID: 40063667 PMCID: PMC11893732 DOI: 10.1099/ijsem.0.006686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 02/07/2025] [Indexed: 03/14/2025] Open
Abstract
Between 1976 and 2010, four bacterial isolates were collected in New South Wales and Queensland, Australia, and stored as part of routine biosecurity surveillance. Recently, these historic isolates were analysed as part of a larger project to enhance the taxonomic accuracy of our culture collection and improve Australia's biosecurity preparedness. Three isolates were collected from Fragaria × ananassa, initially identified as Xanthomonas sp., and one from Medicago sativa, identified as Xanthomonas axonopodis subsp. alfalfae. In this study, we employed modern phenotypic and genomic techniques to further characterize these isolates. Matrix-assisted laser desorption ionization-time of flight MS biotyping and Biolog GEN III MicroPlates confirmed that they are members of the Xanthomonas genus but did not allow for species-level classification. Genome-relatedness indices and phylogenetic analysis confirmed that they were Xanthomonas and revealed that they represent three novel species. The maximum average nucleotide identity and digital DNA-DNA hybridization values observed when comparing the four isolates to all Xanthomonas type strains and each other were 93.9% and 50.7%, respectively. Pathogenesis assays confirmed that two of the isolates are not pathogenic to Fragaria, the plant from which they were isolated. Based on these findings, we propose the names Xanthomonas bundabergensis sp. nov. (DAR 80977T=ICMP 24943), Xanthomonas medicagonis sp. nov. (DAR 35659T=ICMP 24942) and Xanthomonas tesorieronis sp. nov. (DAR 34887T=ICMP 24940).
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Affiliation(s)
- Daniel J. E. McKnight
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- University of Technology Sydney, 15 Broadway, Ultimo, NSW, Australia
| | - Johanna Wong-Bajracharya
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Efenaide B. Okoh
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- Western Sydney University, Penrith, NSW, Australia
| | - Fridtjof Snijders
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Fiona Lidbetter
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - John Webster
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | - Mathew Haughton
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
| | | | - Daniel R. Bogema
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- University of Technology Sydney, 15 Broadway, Ultimo, NSW, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries and Regional Development, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle, NSW, Australia
- University of Technology Sydney, 15 Broadway, Ultimo, NSW, Australia
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Jaiswal G, Rana R, Nayak PK, Chouhan R, Gandhi SG, Patel HK, Patil PB. Luteibacter sahnii sp. nov., A Novel Yellow-Colored Xanthomonadin Pigment Producing Probiotic Bacterium from Healthy Rice Seed Microbiome. Curr Microbiol 2024; 81:424. [PMID: 39446145 DOI: 10.1007/s00284-024-03950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
Abstract
To explore the rice seed microbiome, our objective was to isolate novel strains of Xanthomonas, a plant-associated bacterium with diverse lifestyles. Four isolates, anticipated to be Xanthomonas based on morphological features of yellow colonies, were obtained from healthy rice seeds. Phylo-taxono-genomic analysis revealed that these isolates formed monophyletic lineages belonging to a novel species within the genus Luteibacter. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization confirmed their distinct species status. We propose Luteibacter sahnii sp. nov. as a novel species, with PPL193T = MTCC 13290T = ICMP 24807T = CFBP 9144T as the type strain and PPL201, PPL552, and PPL554 as other constituent members. The fatty acid profile of the type strain is dominated by branched fatty acids like Iso-C15:0, consistent with other members of the genus. The novel species displays non-pathogenic attributes and exhibits plant probiotic properties, protecting rice plants from the leaf blight pathogen X. oryzae pv. oryzae. Production of Indole-3-Acetic Acid (IAA) and genomic regions encoding anti-microbial peptides emphasize its potential contributions to plant hosts. This study underscores the importance of employing a combination of phenotypic and genotypic methods in culturomics to enhance our understanding of rice seed microbiome diversity.
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Affiliation(s)
- Gagandeep Jaiswal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Praveen Kumar Nayak
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rekha Chouhan
- CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Sumit G Gandhi
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Hitendra K Patel
- The Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
- The Academy of Scientific and Innovative Research, Ghaziabad, India.
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Rana R, Nayak PK, Madhavan VN, Sonti RV, Patel HK, Patil PB. Comparative genomics-based insights into Xanthomonas indica, a non-pathogenic species of healthy rice microbiome with bioprotection function. Appl Environ Microbiol 2024; 90:e0084824. [PMID: 39158313 PMCID: PMC11409687 DOI: 10.1128/aem.00848-24] [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: 05/01/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Xanthomonas species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic Xanthomonas (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly Xanthomonas indica, a newly discovered NPX species from rice. The study establishes the relationship of X. indica strains within clade I of Xanthomonads with another NPX species, X. sontii, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic Xanthomonas indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of X. indica and X. sontii were found to protect rice from bacterial leaf blight pathogen, X. oryzae pv. oryzae (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocin-encoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies.IMPORTANCEThe Xanthomonas group of bacteria is known for its characteristic lifestyle as a phytopathogen. However, the discovery of non-pathogenic Xanthomonas (NPX) species is a major shift in understanding this group of bacteria. Multi-strain, in-depth genomic, evolutionary and functional studies on each of these NPX species are still lacking. This study on diverse non-pathogenic strains provides novel insights into genome diversity, dynamics, and evolutionary trends of NPX species from rice microbiome apart from its relationship with other relatives that form a sub-clade. Interestingly, we also uncovered that NPX species protect rice from pathogenic Xanthomonas species. The plant protection property shows their importance as a part of a healthy plant microbiome. Furthermore, finding an open pan-genome and large-scale variation at lipopolysaccharide biosynthetic locus indicates a significant role of the NPX community in host adaptation. The findings and high-quality genomic resources of NPX species and the strains will allow further systematic molecular and host-associated microbial community studies for plant health.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Praveen Kumar Nayak
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Ramesh V. Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Hitendra K. Patel
- Academy of Scientific and Innovative Research, Ghaziabad, India
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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Rana R, Patil PB. Xanthomonas sontii, and Not X. sacchari, Is the Predominant Vertically Transmitted Core Rice Seed Endophyte. PHYTOPATHOLOGY 2024; 114:2017-2023. [PMID: 38916954 DOI: 10.1094/phyto-04-24-0141-sc] [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: 06/27/2024]
Abstract
Seed endophytes, particularly the abundant, core, and vertically transmitted species, are major areas of focus in host microbiome studies. Apart from being the first members to colonize, they accompany the plant throughout its development stages and to the next generation. Recently published studies have reported the keystone species to be Xanthomonas sacchari, a core endophyte that is vertically transmitted in rice with probiotic properties. Furthermore, the Xanthomonas species was reported to be involved in the assembly of beneficial bacteria after early inoculation in rice seeds. However, the strains discussed in these studies were misclassified as X. sacchari, a well-known pathogen of sugarcane. By including nonpathogenic Xanthomonas species with plant-protective functions reported from rice seeds, we have correctly established the phylogenetic and taxonomic identity of the keystone species as X. sontii. This will enable researchers to use the correct reference or lab strain of X. sontii for further systematic and in-depth studies as a model endophyte in plant-microbe interactions apart from its exploitation in seed health.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
- The Academy of Scientific and Innovative Research, Ghaziabad, India
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Chuang SC, Dobhal S, Pal K, Amore TD, Alvarez AM, Arif M. Xanthomonas Strains Isolated from Hosts in the Family Araceae Reveal Diverse Phylogenetic Relationships and Origins. PHYTOPATHOLOGY 2024; 114:1963-1974. [PMID: 38568984 DOI: 10.1094/phyto-08-23-0265-r] [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: 04/05/2024]
Abstract
The family Araceae, comprising ornamentals including Anthurium, Dieffenbachia, Philodendron, Colocasia, and Zantedeschia, is susceptible to Xanthomonas pathogens. Previous analyses have established heterogeneity in aroid strains, yet unresolved taxonomic positions and dynamics between Xanthomonas and frequently associated Stenotrophomonas in aroids necessitate in-depth genetic investigation to resolve these complex relationships. This study utilized multilocus sequence analysis of housekeeping genes atpD, dnaA, dnaK, gltA, and gyrB to investigate 59 aroid strains, selected based on hosts, time, and geographical origins. After adding sequences from additional strains from NCBI GenBank, analysis of 161 concatenated sequences indicated that all aroid strains fell within Xanthomonas and Stenotrophomonas. Thirty-six strains isolated from Anthurium grouped under X. phaseoli, with outliers including one strain each in X. arboricola and X. sacchari and two in Stenotrophomonas. Six strains from Caladium, Dieffenbachia, and Philodendron formed host-specific subgroups within X. euvesicatoria. One strain from Dieffenbachia aligned with X. campestris, whereas strains from Colocasia, Aglaonema, and Spathiphyllum clustered with X. sacchari. Apart from the zantedeschia strain described as X. arboricola pv. zantedeschiae, two colocasia, one epipremnum, and one anthurium strain joined the X. arboricola group. Overall, this study revealed significant heterogeneity among aroid strains, with anthurium strains clustering closely despite distant geographical origins. The analysis underscores the complexity of host-pathogen specificity within Xanthomonas and emphasizes the need for further taxonomic clarification through whole-genome analysis of representative strains. The findings of this research will facilitate strain selection for inclusivity and exclusivity panels in developing diagnostic assays for X. phaseoli and xanthomonads affecting aroids.
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Affiliation(s)
- Shu-Cheng Chuang
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Kanak Pal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Teresita D Amore
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822-2243
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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024; 114:1433-1446. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [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: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Chuang SC, Dobhal S, Alvarez AM, Arif M. Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from the Araceae family. Front Microbiol 2024; 15:1356025. [PMID: 38655077 PMCID: PMC11035887 DOI: 10.3389/fmicb.2024.1356025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Xanthomonas and Stenotrophomonas are closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium and other aroids were reclassified as X. phaseoli and other Xanthomonas species. However, two strains isolated from Spathiphyllum and Colocasia were phylogenetically distant from other strains in the Xanthomonas clade and two strains isolated from Anthurium clustered within the Stenotrophomonas clade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with the type strain of X. sacchari from sugarcane and the latter strains with the type strain of S. bentonitica from bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70 and 95%, respectively. Hence, three new species are proposed: S. aracearum sp. nov. and S. oahuensis sp. nov. for two strains from anthurium and X. hawaiiensis sp. nov. for the strains from spathiphyllum and colocasia, respectively. The genome size of X. hawaiiensis sp. nov. is ~4.88 Mbp and higher than S. aracearum sp. nov. (4.33 Mbp) and S. oahuensis sp. nov. (4.68 Mbp). Gene content analysis revealed 425 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes in Stenotrophomonas spp. was higher than in Xanthomonas spp., implying higher genetic diversity in Stenotrophomonas.
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Affiliation(s)
| | | | | | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
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Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N. Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biol Evol 2024; 16:evae074. [PMID: 38648506 PMCID: PMC11032200 DOI: 10.1093/gbe/evae074] [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] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.
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Affiliation(s)
- Michelle M Pena
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
- Present address: Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kylie Weis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Marie-Agnès Jacques
- Institut Agro, INRAE, IRHS, SFR QUASAV, University of Angers, Angers F-49000, France
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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McKnight DJE, Wong-Bajracharya J, Okoh EB, Snijders F, Lidbetter F, Webster J, Haughton M, Darling AE, Djordjevic SP, Bogema DR, Chapman TA. Xanthomonas rydalmerensis sp. nov., a non-pathogenic member of Group 1 Xanthomonas. Int J Syst Evol Microbiol 2024; 74:006294. [PMID: 38536071 PMCID: PMC10995728 DOI: 10.1099/ijsem.0.006294] [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: 11/06/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024] Open
Abstract
Five bacterial isolates were isolated from Fragaria × ananassa in 1976 in Rydalmere, Australia, during routine biosecurity surveillance. Initially, the results of biochemical characterisation indicated that these isolates represented members of the genus Xanthomonas. To determine their species, further analysis was conducted using both phenotypic and genotypic approaches. Phenotypic analysis involved using MALDI-TOF MS and BIOLOG GEN III microplates, which confirmed that the isolates represented members of the genus Xanthomonas but did not allow them to be classified with respect to species. Genome relatedness indices and the results of extensive phylogenetic analysis confirmed that the isolates were members of the genus Xanthomonas and represented a novel species. On the basis the minimal presence of virulence-associated factors typically found in genomes of members of the genus Xanthomonas, we suggest that these isolates are non-pathogenic. This conclusion was supported by the results of a pathogenicity assay. On the basis of these findings, we propose the name Xanthomonas rydalmerensis, with DAR 34855T = ICMP 24941 as the type strain.
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Affiliation(s)
- Daniel J. E. McKnight
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Johanna Wong-Bajracharya
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Efenaide B. Okoh
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- Western Sydney University, Penrith, NSW, Australia
| | - Fridtjof Snijders
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Fiona Lidbetter
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - John Webster
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Mathew Haughton
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
| | - Aaron E. Darling
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | | | - Daniel R. Bogema
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW 2568, Australia
- University of Technology Sydney, 15 Broadway, Ultimo NSW 2007, Australia
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11
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Rana R, Sharma A, Madhavan VN, Korpole S, Sonti RV, Patel HK, Patil PB. Xanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen. FEMS Microbiol Lett 2024; 371:fnae093. [PMID: 39500549 DOI: 10.1093/femsle/fnae093] [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: 05/07/2024] [Revised: 10/28/2024] [Accepted: 11/01/2024] [Indexed: 11/28/2024] Open
Abstract
Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species.
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Affiliation(s)
- Rekha Rana
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Anushika Sharma
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | | | - Suresh Korpole
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Ramesh V Sonti
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Prabhu B Patil
- Bacterial Genetic, Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- The Academy of Scientific and Innovative Research, Ghaziabad 201002, India
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12
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Liu X, Liu X, Deng Z, He X, Jiang Y. Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material. Antonie Van Leeuwenhoek 2024; 117:17. [PMID: 38189878 DOI: 10.1007/s10482-023-01904-2] [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: 09/03/2023] [Accepted: 10/27/2023] [Indexed: 01/09/2024]
Abstract
A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan'an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.
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Affiliation(s)
- Xiaodong Liu
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xin Liu
- Research and Development Department, Shandong Xianglong Pharmaceutical Research Institute Co., Ltd, Yantai, 264003, China
| | - Zhenshan Deng
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Xiaolong He
- College of Life Sciences, Yan'an University, Yan'an, 716000, China
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China
| | - Yingying Jiang
- College of Life Sciences, Yan'an University, Yan'an, 716000, China.
- Shaanxi Key Laboratory of Chinese Jujube, Yan'an University, Yan'an, 716000, Shaanxi, China.
- Shaanxi Engineering and Technological Research Center for Conversation and Utilization of Regional Biological Resources, Yan'an University, Yan'an, 716000, China.
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13
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Wang X, He SW, He Q, Ju ZC, Ma YN, Wang Z, Han JC, Zhang XX. Early inoculation of an endophyte alters the assembly of bacterial communities across rice plant growth stages. Microbiol Spectr 2023; 11:e0497822. [PMID: 37655928 PMCID: PMC10580921 DOI: 10.1128/spectrum.04978-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/07/2023] [Indexed: 09/02/2023] Open
Abstract
The core endophytes of plants are regarded as promising resources in future agroecosystems. How they affect the assembly of rice-related bacterial communities after early inoculation remains unclear. Here, we examined bacterial communities across 148 samples, including bulk and rhizosphere soils, sterilized roots, stems, and seeds at the seedling, tillering, booting, and maturity stages. Tissue cultured rice seedlings were inoculated with Xathomonas sacchari JR3-14, a core endophytic bacterium of rice seeds, before transplanting. The results revealed that α-diversity indices were significantly enhanced in the root and stem endosphere at the seedling stage. β-diversity was altered at most plant developmental stages, except for the root and stem at the booting stage. Network complexity consequently increased in the root and stem across rice growth stages, other than the stem endosphere at the booting stage. Four abundant beneficial bacterial taxa, Bacillus, Azospira, Azospirillum, and Arthrobacter, were co-enriched during the early growth stage. Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis revealed a higher relative contribution of drift and other eco-evolutionary processes mainly in root compartments across all growth stages, but the opposite pattern was observed in stem compartments. IMPORTANCE Endophytic bacteria are regarded as promising environmentally friendly resources to promote plant growth and plant health. Some of microbes from the seed are able to be carried over to next generation, and contribute to the plant's ability to adapt to new environments. However, the effects of early inoculation with core microbes on the assembly of the plant microbiome are still unclear. In our study, we demonstrate that early inoculation of the rice seed core endophytic bacterium Xanthomonas sacchari could alter community diversity, enhance complexity degree of network structure at most the growth stages, and enrich beneficial bacteria at the seedling stage of rice. We further analyzed the evolutionary processes caused by the early inoculation. Our results highlight the new possibilities for research and application of sustainable agriculture by considering the contribution of seed endophytes in crop production and breeding.
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Affiliation(s)
- Xing Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Wen He
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Zhi-Cheng Ju
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yi-Nan Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhe Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia-Cheng Han
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Harrison J, Hussain RMF, Greer SF, Ntoukakis V, Aspin A, Vicente JG, Grant M, Studholme DJ. Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiol 2023; 5:acmi000532.v3. [PMID: 37601434 PMCID: PMC10436009 DOI: 10.1099/acmi.0.000532.v3] [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: 11/23/2022] [Accepted: 06/25/2023] [Indexed: 08/22/2023] Open
Abstract
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis, X. campestris pv. cannae, X. campestris pv. esculenti, X. campestris pv. nigromaculans, X. campestris pv. parthenii, X. campestris pv. phormiicola, X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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Affiliation(s)
| | - Rana Muhammad Fraz Hussain
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Shannon F. Greer
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Vardis Ntoukakis
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew Aspin
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Joana G. Vicente
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Murray Grant
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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15
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Peduzzi C, Sagia A, Burokienė D, Nagy IK, Fischer-Le Saux M, Portier P, Dereeper A, Cunnac S, Roman-Reyna V, Jacobs JM, Bragard C, Koebnik R. Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas. PHYTOPATHOLOGY 2023; 113:1185-1191. [PMID: 36611232 DOI: 10.1094/phyto-10-22-0373-sc] [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: 06/17/2023]
Abstract
Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
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Affiliation(s)
- Chloé Peduzzi
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Angeliki Sagia
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Daiva Burokienė
- Nature Research Centre, Institute of Botany, Laboratory of Plant Pathology, Vilnius, Lithuania
| | | | | | - Perrine Portier
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Alexis Dereeper
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Claude Bragard
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
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16
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Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Gram-negative bacterial genus Xanthomonas includes numerous infra-specific taxa known as pathovars, which are defined primarily on host range and disease symptoms. With the advent of molecular sequence data, many pathovars have been transferred from X. campestris into other Xanthomonas species to better harmonise taxonomy and phylogeny. We performed whole-genome shotgun sequencing on pathotype strains of the following X. campestris pathovars: blepharidis, carissae, clerodendri, convolvuli, coriandri, daturae, euphorbiae, fici, heliotropii, ionidii, lawsoniae, mirabilis, obscurae, paulliniae, pennamericanum, spermacoces, uppalii, vernoniae, viegasii and zingibericola. These genomes showed more than 98% average nucleotide identity with the type-strain of X. euvesicatoria and less than 88% with the type-strain of X. campestris. We propose the transfer of these pathovars into X. euvesicatoria and present an emended species description for X. euvesicatoria.
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17
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Rana R, Madhavan VN, Saroha T, Bansal K, Kaur A, Sonti RV, Patel HK, Patil PB. Xanthomonas indica sp. nov., a Novel Member of Non-Pathogenic Xanthomonas Community from Healthy Rice Seeds. Curr Microbiol 2022; 79:304. [PMID: 36064810 DOI: 10.1007/s00284-022-03001-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/16/2022] [Indexed: 11/03/2022]
Abstract
Xanthomonas is a major group of pathogenic bacteria infecting staple food crops like rice. Increasingly it is being recognized that non-pathogenic Xanthomonas (NPX) are also important members of a healthy plant microbiome. However, the vast majority of the species described in this genus are of pathogenic nature, and only a few NPX species have been reported till now. Genomic and taxonogenomic analysis of NPX is needed for the management of this important group of bacteria. In this study, two yellow-pigmented bacterial isolates were obtained from healthy rice seeds in Punjab, India. The isolates designated PPL560T and PPL568 were identified as members of the genus Xanthomonas based on biochemical tests and 16S rRNA gene sequence analysis retrieved from the whole-genome sequences. Isolates formed a distinct monophyletic lineage with Xanthomonas sontii and Xanthomonas sacchari as the closest relatives in the phylogenetic tree based on core gene content shared by the representative species of the genus Xanthomonas. Pairwise ortho Average Nucleotide Identity and digital DNA-DNA hybridization values calculated against other species of Xanthomonas were below their respective cut-offs. In planta studies revealed that PPL560T and PPL568 are non-pathogenic to rice plants upon leaf clip inoculation. The absence of type III secretion system-related genes and effectors further supported their non-pathogenic status. Herein, we propose Xanthomonas indica sp. nov. as novel species of the genus Xanthomonas with PPL560T = MTCC 13185 = CFBP 9039 = ICMP 24394 as its type strain and PPL568 as another constituent member.
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Affiliation(s)
- Rekha Rana
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,The Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Tanu Saroha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,The Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, India
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
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18
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Singh A, Bansal K, Kumar S, Patil PB. Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane. Appl Environ Microbiol 2022; 88:e0055022. [PMID: 35916503 PMCID: PMC9397109 DOI: 10.1128/aem.00550-22] [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: 03/29/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.
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Affiliation(s)
- Anu Singh
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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19
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Mafakheri H, Taghavi SM, Zarei S, Portier P, Dimkić I, Koebnik R, Kuzmanović N, Osdaghi E. Xanthomonas bonasiae sp. nov. and Xanthomonas youngii sp. nov., isolated from crown gall tissues. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005418] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus
Xanthomonas
contains a set of diverse bacterial strains, most of which are known for their pathogenicity on annual crops and fruit trees causing economically important plant diseases. Recently, five
Xanthomonas
strains were isolated from
Agrobacterium
-induced crown gall tissues of amaranth (Amaranthus sp.) and weeping fig (Ficus benjamina) plants in Iran. Phenotypic characteristics (i.e. biochemical tests and pathogenicity features) and whole genome sequence-based core-genome phylogeny followed by average nucleotide identity and digital DNA–DNA hybridization calculations suggested that these gall-associated strains belong to two new species within the genus
Xanthomonas
. In this study, we provide a formal species description for these new species where Xanthomonas bonasiae sp. nov. is proposed for the strains isolated from weeping fig with FX4T (=CFBP 8703T=DSM 112530T) as type strain. The name Xanthomonas youngii sp. nov. is proposed for the strains isolated from amaranth with AmX2T (=CFBP 8902T=DSM 112529T) as type strain.
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Affiliation(s)
- Hamzeh Mafakheri
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - S. Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Sadegh Zarei
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Ivica Dimkić
- University of Belgrade - Faculty of Biology, Chair of Biochemistry and Molecular Biology, Studentski trg 16, 11158 Belgrade, Serbia
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nemanja Kuzmanović
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute for Plant Protection in Horticulture and Forests, Messeweg 11-12, 38104, Braunschweig, Germany
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Bansal K, Kumar S, Patil PB. Phylo-Taxonogenomics Supports Revision of Taxonomic Status of 20 Xanthomonas Pathovars to Xanthomonas citri. PHYTOPATHOLOGY 2022; 112:1201-1207. [PMID: 34844415 DOI: 10.1094/phyto-08-21-0342-sc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Based on phylo-taxonogenomics criteria, we present amended descriptions for 20 pathovars to Xanthomonas citri. Incidentally, 18 were first reported from India. Seven out of twenty are classified as X. axonopodis, 12 out of 20 as X. campestris, and one as X. cissicola. In this study, we have generated genome sequence data of four pathovars, and the genomes of the remaining 16 were used from the published data. Comprehensive genome-based phylogenomic and taxonogenomic analyses reveal that all these pathovars belong to X. citri and need to reconcile their taxonomic status. This proposal will aid in systematic studies of a major species and its constitutent members that infect economically important plants.
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Affiliation(s)
- Kanika Bansal
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Sanjeet Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Prabhu B Patil
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, 160036, India
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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22
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Te Molder D, Poncheewin W, Schaap PJ, Koehorst JJ. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. BMC Genomics 2021; 22:848. [PMID: 34814827 PMCID: PMC8612006 DOI: 10.1186/s12864-021-08093-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.
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Affiliation(s)
- Dennie Te Molder
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Wasin Poncheewin
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- UNLOCK, Wageningen University, Wageningen, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands.
- UNLOCK, Wageningen University, Wageningen, the Netherlands.
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Bansal K, Kumar S, Kaur A, Singh A, Patil PB. Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics 2021; 113:3989-4003. [PMID: 34610367 DOI: 10.1016/j.ygeno.2021.09.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. SIGNIFICANCE STATEMENT: Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.
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Affiliation(s)
- Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anu Singh
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
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