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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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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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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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Hu ZT, Ntambo MS, Zhao JY, Javed T, Shi Y, Fu HY, Huang MT, Gao SJ. Genetic Divergence and Population Structure of Xanthomonas albilineans Strains Infecting Saccharum spp. Hybrid and Saccharum officinarum. PLANTS (BASEL, SWITZERLAND) 2023; 12:1937. [PMID: 37653854 PMCID: PMC10222335 DOI: 10.3390/plants12101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/02/2023] [Accepted: 05/06/2023] [Indexed: 06/28/2023]
Abstract
Leaf scald caused by Xanthomonas albilineans (Xa) is a major bacterial disease in sugarcane that represents a threat to the global sugar industry. Little is known about the population structure and genetic evolution of this pathogen. In this study, 39 Xa strains were collected from 6 provinces in China. Of these strains, 15 and 24 were isolated from Saccharum spp. hybrid and S. officinarum plants, respectively. Based on multilocus sequence analysis (MLSA), with five housekeeping genes, these strains were clustered into two distinct phylogenetic groups (I and II). Group I included 26 strains from 2 host plants, Saccharum spp. hybrid and S. officinarum collected from 6 provinces, while Group II consisted of 13 strains from S. officinarum plants in the Zhejiang province. Among the 39 Xa strains, nucleotide sequence identities from 5 housekeeping genes were: ABC (99.6-100%), gyrB (99.3-100%), rpoD (98.4-100%), atpD (97.0-100%), and glnA (97.6-100%). These strains were clustered into six groups (A-F), based on the rep-PCR fingerprinting, using primers for ERIC2, BOX A1R, and (GTG)5. UPGMA and PCoA analyses revealed that group A had the most strains (24), followed by group C with 11 strains, while there was 1 strain each in groups B and D-F. Neutral tests showed that the Xa population in S. officinarum had a trend toward population expansion. Selection pressure analysis showed purification selection on five concatenated housekeeping genes from all tested strains. Significant genetic differentiation and infrequent gene flow were found between two Xa populations hosted in Saccharum spp. hybrids and S. officinarum. Altogether, these results provide evidence of obvious genetic divergence and population structures among Xa strains from China.
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Affiliation(s)
- Zhong-Ting Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - Mbuya Sylvain Ntambo
- Université de Lubumbashi, Faculté des Sciences Agronomiques, Département de Phytotechnie, Laboratoire de Recherche en Biofortification, Défense et Valorisation des Cultures (BioDeV), Lubumbashi 7010, Congo;
| | - Jian-Ying Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - Talha Javed
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - Yang Shi
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - Hua-Ying Fu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - Mei-Ting Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Z.-T.H.); (J.-Y.Z.); (T.J.); (Y.S.); (H.-Y.F.); (M.-T.H.)
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Zhao JY, Chen J, Shi Y, Fu HY, Huang MT, Rott PC, Gao SJ. Sugarcane responses to two strains of Xanthomonas albilineans differing in pathogenicity through a differential modulation of salicylic acid and reactive oxygen species. FRONTIERS IN PLANT SCIENCE 2022; 13:1087525. [PMID: 36589125 PMCID: PMC9798216 DOI: 10.3389/fpls.2022.1087525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Leaf scald caused by Xanthomonas albilineans is one of the major bacterial diseases of sugarcane that threaten the sugar industry worldwide. Pathogenic divergence among strains of X. albilineans and interactions with the sugarcane host remain largely unexplored. In this study, 40 strains of X. albilineans from China were distributed into three distinct evolutionary groups based on multilocus sequence analysis and simple sequence repeats loci markers. In pathogenicity assays, the 40 strains of X. albilineans from China were divided into three pathogenicity groups (low, medium, and high). Twenty-four hours post inoculation (hpi) of leaf scald susceptible variety GT58, leaf populations of X. albilineans strain XaCN51 (high pathogenicity group) determined by qPCR were 3-fold higher than those of strain XaCN24 (low pathogenicity group). Inoculated sugarcane plants modulated the reactive oxygen species (ROS) homoeostasis by enhancing respiratory burst oxidase homolog (ScRBOH) expression and superoxide dismutase (SOD) activity and by decreasing catalase (CAT) activity, especially after infection by X. albilineans XaCN51. Furthermore, at 24 hpi, plants infected with XaCN51 maintained a lower content of endogenous salicylic acid (SA) and a lower expression level of SA-mediated genes (ScNPR3, ScTGA4, ScPR1, and ScPR5) as compared to plants infected with XaCN24. Altogether, these data revealed that the ROS production-scavenging system and activation of the SA pathway were involved in the sugarcane defense response to an attack by X. albilineans.
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Affiliation(s)
- Jian-Ying Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Juan Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yang Shi
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Hua-Ying Fu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Mei-Ting Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Philippe C. Rott
- CIRAD, UMR PHIM, Montpellier, France, and PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Ke M, Xu N, Zhang Z, Qiu D, Kang J, Lu T, Wang T, Peijnenburg WJGM, Sun L, Hu B, Qian H. Development of a machine‐learning model to identify the impacts of pesticides characteristics on soil microbial communities from high‐throughput sequencing data. Environ Microbiol 2022; 24:5561-5573. [DOI: 10.1111/1462-2920.16175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022]
Affiliation(s)
- Mingjing Ke
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Nuohan Xu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Zhenyan Zhang
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Danyan Qiu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Jian Kang
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Tao Lu
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Tingzhang Wang
- Key laboratory of microbial technology and bioinformatics of Zhejiang Province Hangzhou P.R. of China
| | - W. J. G. M. Peijnenburg
- Institute of Environmental Sciences (CML) Leiden University RA Leiden the Netherlands
- National Institute of Public Health and the Environment (RIVM) , Center for Safety of Substances and Products, P.O. Box 1 Bilthoven the Netherlands
| | - Liwei Sun
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
| | - Baolan Hu
- Department of Environmental Science Zhejiang University Hangzhou P.R. of China
| | - Haifeng Qian
- College of Environment Zhejiang University of Technology Hangzhou P.R. of China
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7
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Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. Sci Rep 2022; 12:10857. [PMID: 35760985 PMCID: PMC9237127 DOI: 10.1038/s41598-022-14913-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/15/2022] [Indexed: 12/30/2022] Open
Abstract
The rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between beneficial and pathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here we used the Genome properties (GP) common biological pathways annotation system and Machine Learning (ML) to establish the relationship between the genome wide GP composition and the plant-associated lifestyle of 91 Pseudomonas strains isolated from the rhizosphere and the phyllosphere representing both plant-associated phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A test set of 75 new strains confirmed the importance of the selected features for classification. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated lifestyle.
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