1
|
Flores-López LF, Olalde-Portugal V, Vidaver AK, Morales-Galván Ó, Hernández-Rosales M, Huerta AI. Unlocking a Mystery: Characterizing the First Appearance of Clavibacter nebraskensis in Mexican Cornfields. PLANT DISEASE 2024:PDIS08231493RE. [PMID: 38105456 DOI: 10.1094/pdis-08-23-1493-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The Goss's wilt and leaf blight is a disease of maize (Zea mays) caused by Clavibacter nebraskensis, which was widespread in the last several years throughout the Midwest in the United States, south in Texas, and north to Canada. The bacterium is included within the high-risk list of quarantine pathogens by many plant protection organizations and countries including Mexico. Severe blight symptoms on maize plants were found in different provinces from Coahuila and Tlaxcala, Mexico, in 2012 and 2021, respectively. Twenty bacterial isolates with morphology similar to C. nebraskensis were obtained from the diseased maize leaves. The isolates were confirmed by phenotypic tests and 16S rRNA and gyrB sequencing. Two strains were tested for pathogenicity tests on seven hybrid sweet corn cultivars available in Mexico, and the most sensitive cultivar was tested for all the strains to fulfill Koch's postulates. The phylogenetic reconstruction based on two single loci reveals a remarkable clustering of Mexican strains to American strains reported approximately 50 years ago. The presence of this pathogen represents a risk and a significant challenge for plant protection strategies in Mexico and maize diversity.
Collapse
Affiliation(s)
- Luis Fernando Flores-López
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados de IPN (CINVESTAV) Unidad Irapuato, Irapuato 368224, México
| | - Anne K Vidaver
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Óscar Morales-Galván
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, México
| | - Maribel Hernández-Rosales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados de IPN (CINVESTAV) Unidad Irapuato, Irapuato 368224, México
| | - Alejandra I Huerta
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Heiden N, Broders KA, Hutin M, Castro MO, Roman-Reyna V, Toth H, Jacobs JM. Bacterial Leaf Streak Diseases of Plants: Symptom Convergence in Monocot Plants by Distant Pathogenic Xanthomonas Species. PHYTOPATHOLOGY 2023; 113:2048-2055. [PMID: 37996392 DOI: 10.1094/phyto-05-23-0155-ia] [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: 11/25/2023]
Abstract
Bacterial leaf streak (BLS) is a disease of monocot plants caused by Xanthomonas translucens on small grains, X. vasicola on maize and sorghum, and X. oryzae on rice. These three pathogens cause remarkably similar symptomology in their host plants. Despite causing similar symptoms, BLS pathogens are dispersed throughout the larger Xanthomonas phylogeny. Each aforementioned species includes strain groups that do not cause BLS and instead cause vascular disease. In this commentary, we hypothesize that strains of X. translucens, X. vasicola, and X. oryzae convergently evolved to cause BLS due to shared evolutionary pressures. We examined the diversity of secreted effectors, which may be important virulence factors for BLS pathogens and their evolution. We discuss evidence that differences in gene regulation and abilities to manipulate plant hormones may also separate BLS pathogens from other Xanthomonas species or pathovars. BLS is becoming an increasing issue across the three pathosystems. Overall, we hope that a better understanding of conserved mechanisms used by BLS pathogens will enable researchers to translate findings across production systems and guide approaches to control this (re)emerging threat.
Collapse
Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kirk A Broders
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, U.S.A
| | - Mathilde Hutin
- Plant Health Institute of Montpellier, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mary Ortiz Castro
- Horticulture and Extension Programs, Colorado State University, Castle Rock, CO 80106, U.S.A
| | - Verónica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases 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 Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| |
Collapse
|
4
|
Kałużna M, Prokić A, Obradović A, Weldon WA, Stockwell VO, Pothier JF. Specific and sensitive detection tools for Xanthomonas arboricola pv. corylina, the causal agent of bacterial blight of hazelnut, developed with comparative genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1254107. [PMID: 37780515 PMCID: PMC10535005 DOI: 10.3389/fpls.2023.1254107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Xanthomonas arboricola pv. corylina (Xac; formerly Xanthomonas campestris pv. corylina) is the causal agent of the bacterial blight of hazelnuts, a devastating disease of trees in plant nurseries and young orchards. Currently, there are no PCR assays to distinguish Xac from all other pathovars of X. arboricola. A comparative genomics approach with publicly available genomes of Xac was used to identify unique sequences, conserved across the genomes of the pathogen. We identified a 2,440 bp genomic region that was unique to Xac and designed identification and detection systems for conventional PCR, qPCR (SYBR® Green and TaqMan™), and loop-mediated isothermal amplification (LAMP). All PCR assays performed on genomic DNA isolated from eight X. arboricola pathovars and closely related bacterial species confirmed the specificity of designed primers. These new multi-platform molecular diagnostic tools may be used by plant clinics and researchers to detect and identify Xac in pure cultures and hazelnut tissues rapidly and accurately.
Collapse
Affiliation(s)
- Monika Kałużna
- The National Institute of Horticultural Research, Skierniewice, Poland
| | - Andjelka Prokić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Aleksa Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Virginia O. Stockwell
- United States Department of Agriculture, Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, United States
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| |
Collapse
|
5
|
Lee MH, Hong SJ, Park DS, Ham H, Kong HG. Genomic Analysis of the Carrot Bacterial Blight Pathogen Xanthomonas hortorum pv. carotae in Korea. THE PLANT PATHOLOGY JOURNAL 2023; 39:409-416. [PMID: 37550986 PMCID: PMC10412968 DOI: 10.5423/ppj.nt.11.2022.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 08/09/2023]
Abstract
Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.
Collapse
Affiliation(s)
- Mi-Hyun Lee
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Sung-Jun Hong
- Organic Agricultural Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Dong Suk Park
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Hyeonheui Ham
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
| | - Hyun Gi Kong
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875,
Korea
- Department of Plant Medicine, College of Agriculture, Life & Environment Sciences, Chungbuk National University, Cheongju 28644,
Korea
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Vicente JG, McHugh J, Bryning A, Carroll S, Harrison J, Studholme D. First identification of Xanthomonas nasturtii as the cause of black rot of watercress in Hawaii. PLANT DISEASE 2023; 107:2511. [PMID: 36867585 DOI: 10.1094/pdis-05-22-1043-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Watercress (Nasturtium officinale) has been in continuous production in Hawaii for over a century and is part of the local diet. Black rot of watercress was first identified as caused by Xanthomonas nasturtii in Florida (Vicente et al., 2017), but symptoms of this disease have also been regularly observed in Hawaii production in all islands, mostly during the rainy season from December to April in areas with poor air circulation (McHugh & Constantinides, 2004). Initially, this disease was attributed to X. campestris due to similar symptoms to black rot of brassicas. Samples of watercress with symptoms that could be attributed to a bacterial disease including yellow spots and lesions on leaves and stunting and deformation of plants in more advanced stages, were collected from a farm in Aiea in the island of Oahu, Hawaii, in October 2017. Isolations were performed at the University of Warwick. Fluid from macerated leaves was streaked into plates of King's B (KB) medium and Yeast Dextrose Calcium Carbonate Agar (YDC). After 48-72 hrs incubation at 28°C, the plates showed a range of mixed colonies. Single cream-yellow mucoid colonies were sub-cultured several times and pure isolates including WHRI 8984 were stored at -76°C as previously described (Vicente et al., 2017). Colony morphology was observed in KB plates and, in contrast to the type strain from Florida (WHRI 8853 = NCPPB 4600), isolate WHRI 8984 did not cause browning of the medium. Pathogenicity was tested on four-week old watercress and Savoy cabbage cv. Wirosa F1 plants by inoculations on leaves as previously described (Vicente et al., 2017). WHRI 8984 did not produce symptoms when inoculated on cabbage but produced typical symptoms on watercress. A re-isolation from a leaf showing a V-shaped lesion, produced isolates with the same morphology, including isolate WHRI 10007A, that was also shown to be pathogenic to watercress therefore completing the Koch's postulates. Fatty acid profiling was performed on WHRI 8984 and 10007A and controls grown on trypticase soy broth agar (TSBA) plates at 28°C for 48 hrs as described by Weller et al. (2000). Profiles were compared with the RTSBA6 v6.21 library; as the database does not include X. nasturtii, the results were only interpreted at the genus level, and both isolates were shown to be Xanthomonas sp. For molecular analysis, DNA was extracted and the gyrB partial gene was amplified and sequenced as described by Parkinson et al. (2007). Comparisons with sequences available in the National Centre for Biotechnology Information (NCBI) databases using the Basic Local Alignment Search Tool (BLAST) showed that partial gyrB of WHRI 8984 and 10007A were identical to the type strain from Florida therefore confirming that they belong to X. nasturtii. For whole genome sequencing, genomic libraries for WHRI 8984 were prepared using Illumina's Nextera XT v2 kit and sequenced on a HiSeq Rapid Run flowcell. The sequences were processed as previously described (Vicente et al., 2017) and the whole genome assembly has been deposited in GenBank (accession QUZM00000000.1); the phylogenetic tree shows that WHRI 8984 is close, but not identical to the type strain. This is the first identification of X. nasturtii in watercress crops in Hawaii. Control of this disease generally involves the use of copper bactericides and minimizing moisture on leaves by reducing overhead irrigation and increasing air circulation (McHugh & Constantinides, 2004); seed testing might help to select batches that are disease free and, in longer term, breeding for disease resistance might produce cultivars that can be part of management strategies.
Collapse
Affiliation(s)
- Joana G Vicente
- Fera Science Ltd, 16233, York, United Kingdom of Great Britain and Northern Ireland
- University of Warwick, 2707, School of Life Sciences, Coventry, United Kingdom of Great Britain and Northern Ireland;
| | - John McHugh
- Plant Industry Division, Department of Agriculture, Honolulu, Hawaii, United States;
| | - Adam Bryning
- Fera Science Ltd, 16233, York, United Kingdom of Great Britain and Northern Ireland;
| | - Sarah Carroll
- Fera Science Ltd, 16233, York, United Kingdom of Great Britain and Northern Ireland;
| | - James Harrison
- University of Exeter, 3286, College of Life and Environmental Sciences, Exeter, United Kingdom of Great Britain and Northern Ireland;
| | - David Studholme
- University of Exeter, 3286, College of Life and Environmental Sciences, Exeter, United Kingdom of Great Britain and Northern Ireland;
| |
Collapse
|
8
|
Wang LH, Chan JJ, Wang YH, Fang ZQ, Lee S, Chu CC. Bacterial Leaf Blight of Polyscias guilfoylei Caused by a Novel Pathovar of Xanthomonas euvesicatoria. PLANT DISEASE 2023; 107:298-305. [PMID: 35787010 DOI: 10.1094/pdis-03-22-0602-re] [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: 06/15/2023]
Abstract
Polyscias guilfoylei is a popular ornamental belonging to the Araliaceae family. The present study identified and characterized bacterial strains causing leaf lesions on P. guilfoylei in a nursery in Taiwan. Strains Pgu1 to Pgu5 were isolated from infected leaf tissues and Koch's postulates were fulfilled. Observation of Pgu1 under a transmission electron microscope revealed that its cells were single flagellated and rod shaped. Sequencing of Pgu1 to Pgu5's 16S ribosomal DNA showed that they belong to the genus Xanthomonas. The biochemical and physiological traits of these bacteria were determined, and many of them also resemble those of other xanthomonads. However, the strains were unable to produce yellow pigments typically found in most members of the Xanthomonas genus, even when grown on yeast dextrose calcium carbonate (YDC) agar. Physiological assays and phylogenetic analyses based on multiple loci showed that the isolates were closely associated with members of the species Xanthomonas euvesicatoria and phylogenetically distant from X. hortorum pv. hederae, the currently only known xanthomonad capable of inducing diseases on Polyscias spp. Artificial inoculation into different host plants revealed that a representative strain, Pgu1, is specialized to P. guilfoylei and perhaps other members of the Araliaceae family. Based on the results from the phylogenetic and phenotypic analyses, the present work concludes that these strains belong to a novel pathovar of X. euvesicatoria. The pathovar epithet polysciadis is proposed.
Collapse
Affiliation(s)
- Liang-Hsuan Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Jiun-Jie Chan
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Yi-Hsin Wang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Zi-Qing Fang
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Shin Lee
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Ching Chu
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Holeva MC, Glynos PE, Reppa C, Karafla CD, Mylonopoulos IS. First Report of the Occurrence of the Bacterial Spot Disease of Stone Fruits Caused by Xanthomonas arboricola pv. pruni on Almond in Greece. PLANT DISEASE 2022; 107:1620. [PMID: 36281014 DOI: 10.1094/pdis-06-22-1492-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In 2021, two samples of almond (Prunus dulcis (Mill) Webb) shoots with symptoms resembling those caused by Xanthomonas arboricola pv. pruni (Xap), were examined at the Benaki Phytopathological Institute. The first sample was collected in June from a 0.4-ha orchard of fifteen-year-old almond trees (cv. 'Texas') with 40% disease incidence, in the Regional Unit of Serres (Northern Greece). Leaves exhibited, mainly at their tip and margins, small, angular, necrotic spots with chlorotic halo, often coalesced into larger necrotic lesions which fell out leaving leaves with a 'shot-hole' like appearance. Fruits displayed dark brown, sunken, corky, gum oozing lesions and shoots developed dark brown, elongated, slightly sunken lesions. Bacterial streaming from the marginal areas of necrotic lesions was observed microscopically. On the lesions of fruits, leaves and shoots, Xap was detected by immunofluorescence assay (IF) using polyclonal antibodies (Plant Research International, the Netherlands) and two qPCR assays (Garita-Cambronero et al. 2017; Palacio-Bielsa et al. 2011). Eight Xanthomonas-like isolates obtained on the SP agar (Hayward 1960) and Nutrient agar (Schaad et al. 2001) culture media were Gram-negative, oxidase negative, strictly aerobic, sensitive to 0.1% w/v TTC, hydrolysing gelatin and Tween 80 but not starch, and also inducing hypersensitive response in tomato plants, as expected for Xap (Schaad et al. 2001). Isolates' identification was confirmed by the IF and the two qPCR assays cited above, as well as a conventional PCR (Pothier et al., 2011). Infiltration of a suspension (107 cfu/ml) of one isolate into five leaves of a two-year-old almond tree cv. 'Texas', and also into five detached leaves from the same tree (Randhawa and Civerolo 1985), caused necrotic spots on all inoculated leaves (10 inoculation sites/leaf), after a four day incubation period at 25oC under high humidity. The Xap reference strain NCPPB 3877 and sterile water were used as positive and negative controls, respectively. The pathogen was reisolated from necrotic spots of the inoculated leaves and identified by IF and two qPCR assays, as previously. The second sample was collected by a grower in September from a 3.7-ha orchard of five-year-old almond trees (cv. 'Tuono') exhibiting 50% disease incidence, in the Regional Unit of Fthiotida (Central Greece). Leaves and fruits showed symptoms similar to those described for the first sample, except that, lesions on fruits, which were at a stage of advanced mesocarp dehydration, were raised. Five Xap isolates were obtained from symptomatic leaves and fruits, and their pathogenicity on almond was confirmed, as in the first sample. Furthermore, sequences of PCR products using primers targeting the 16S-rDNA (Lane 1991;Lane et al., 1985), gyrB (Parkinson et al. 2007) and ftsX (Pothier et al. 2011) genes of two Xap isolates, one from fruit- and one from leaf-necrotic lesions of the first sample, were searched against the NCBI GenBank database, revealing that the obtained sequences of 16S-rRNA (OP412487; OP412488), gyrB (OP467593; OP467594) and ftsX (OP467595; OP467596) genes were 100% identical to the corresponding genomic regions of the Xap strains IVIA 2626.1 (CP076628.1) and CITA 33 (CP076701.1). This is the first report on the presence of Xap in Greece. As these Xap outbreaks have occurred in regions with extensive almond cultivation, a crop of great economic importance for Greece, measures for its eradication have already been advised.
Collapse
Affiliation(s)
- Maria C Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, P.C. 14561 Kifissia, Greece;
| | - Paraskevas E Glynos
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, P.C. 14561 Kifissia, Greece;
| | - Chrysavgi Reppa
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, P.C. 14561 Kifissia, Greece;
| | - Charikleia D Karafla
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, P.C. 14561 Kifissia, Greece;
| | - Ioannis S Mylonopoulos
- Region of Central Macedonia, Directorate of Agricultural Economy and Veterinary of Serres, Department of Quality and Plant Health Control, End of Omonias Street, P.C. 62125, Serres , Greece;
| |
Collapse
|
11
|
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: 1.0] [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.
Collapse
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
| |
Collapse
|
12
|
Popović T, Menković J, Pantelić M, Obradović A. First Report of Xanthomonas euvesicatoria Causing Bacterial Leaf Spot of Pepper ( Capsicum annuum) in Montenegro. PLANT DISEASE 2022; 106:1514. [PMID: 34689587 DOI: 10.1094/pdis-08-21-1655-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- T Popović
- Administration of Food Safety, Veterinary and Phytosanitary Affairs, Podgorica, Montenegro
| | - J Menković
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - M Pantelić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - A Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| |
Collapse
|
13
|
Dia NC, Morinière L, Cottyn B, Bernal E, Jacobs J, Koebnik R, Osdaghi E, Potnis N, Pothier J. Xanthomonas hortorum - beyond gardens: Current taxonomy, genomics, and virulence repertoires. MOLECULAR PLANT PATHOLOGY 2022; 23:597-621. [PMID: 35068051 PMCID: PMC8995068 DOI: 10.1111/mpp.13185] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 05/02/2023]
Abstract
TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Lysobacterales (earlier synonym of Xanthomonadales); Family Lysobacteraceae (earlier synonym of Xanthomonadaceae); Genus Xanthomonas; Species X. hortorum; Pathovars: pv. carotae, pv. vitians, pv. hederae, pv. pelargonii, pv. taraxaci, pv. cynarae, and pv. gardneri. HOST RANGE Xanthomonas hortorum affects agricultural crops, and horticultural and wild plants. Tomato, carrot, artichoke, lettuce, pelargonium, ivy, and dandelion were originally described as the main natural hosts of the seven separate pathovars. Artificial inoculation experiments also revealed other hosts. The natural and experimental host ranges are expected to be broader than initially assumed. Additionally, several strains, yet to be assigned to a pathovar within X. hortorum, cause diseases on several other plant species such as peony, sweet wormwood, lavender, and oak-leaf hydrangea. EPIDEMIOLOGY AND CONTROL X. hortorum pathovars are mainly disseminated by infected seeds (e.g., X. hortorum pvs carotae and vitians) or cuttings (e.g., X. hortorum pv. pelargonii) and can be further dispersed by wind and rain, or mechanically transferred during planting and cultivation. Global trade of plants, seeds, and other propagating material constitutes a major pathway for their introduction and spread into new geographical areas. The propagules of some pathovars (e.g., X. horturum pv. pelargonii) are spread by insect vectors, while those of others can survive in crop residues and soils, and overwinter until the following growing season (e.g., X. hortorum pvs vitians and carotae). Control measures against X. hortorum pathovars are varied and include exclusion strategies (i.e., by using certification programmes and quarantine regulations) to multiple agricultural practices such as the application of phytosanitary products. Copper-based compounds against X. hortorum are used, but the emergence of copper-tolerant strains represents a major threat for their effective management. With the current lack of efficient chemical or biological disease management strategies, host resistance appears promising, but is not without challenges. The intrastrain genetic variability within the same pathovar poses a challenge for breeding cultivars with durable resistance. USEFUL WEBSITES https://gd.eppo.int/taxon/XANTGA, https://gd.eppo.int/taxon/XANTCR, https://gd.eppo.int/taxon/XANTPE, https://www.euroxanth.eu, http://www.xanthomonas.org, http://www.xanthomonas.org/dokuwiki.
Collapse
Affiliation(s)
- Nay C. Dia
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
- Molecular Plant BreedingInstitute of Agricultural SciencesETH ZurichZurichSwitzerland
| | - Lucas Morinière
- University of LyonUniversité Claude Bernard Lyon 1CNRSINRAEUMR Ecologie MicrobienneVilleurbanneFrance
| | - Bart Cottyn
- Plant Sciences UnitFlanders Research Institute for Agriculture, Fisheries and FoodMerelbekeBelgium
| | - Eduardo Bernal
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
| | - Jonathan M. Jacobs
- Department of Plant PathologyThe Ohio State UniversityColumbusOhioUSA
- Infectious Diseases InstituteThe Ohio State UniversityColumbusOhioUSA
| | - Ralf Koebnik
- Plant Health Institute of MontpellierUniversity of Montpellier, CIRAD, INRAe, Institut Agro, IRDMontpellierFrance
| | - Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Neha Potnis
- Department of Entomology and Plant PathologyAuburn UniversityAlabamaUSA
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research GroupInstitute for Natural Resource SciencesZurich University of Applied SciencesWädenswilSwitzerland
| |
Collapse
|
14
|
Prokić A, Marković T, Menković J, Ivanović M, Obradović A. First Report of Xanthomonas campestris pv. campestris Causing Marginal Leaf Necrosis of Arugula ( Eruca vesicaria subsp. sativa) in Serbia. PLANT DISEASE 2022; 106:1056. [PMID: 34524866 DOI: 10.1094/pdis-04-21-0740-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- A Prokić
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - T Marković
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - J Menković
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - M Ivanović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - A Obradović
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| |
Collapse
|
15
|
Holtappels D, Fortuna KJ, Moons L, Broeckaert N, Bäcker LE, Venneman S, Rombouts S, Lippens L, Baeyen S, Pollet S, Noben JP, Oechslin F, Vallino M, Aertsen A, Maes M, Van Vaerenbergh J, Lavigne R, Wagemans J. The potential of bacteriophages to control Xanthomonas campestris pv. campestris at different stages of disease development. Microb Biotechnol 2022; 15:1762-1782. [PMID: 35084112 PMCID: PMC9151335 DOI: 10.1111/1751-7915.14004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas campestris pv. campestris (Xcc) is a vascular pathogen that invades the xylem of Brassica crops. Current chemical and antibiotics‐based control measures for this bacterium are unsustainable and inefficient. After establishing a representative collection of Xcc strains, we isolated and characterized bacteriophages from two clades of phages to assess their potential in phage‐based biocontrol. The most promising phages, FoX2 and FoX6, specifically recognize (lipo) polysaccharides, associated with the wxc gene cluster, on the surface of the bacterial cell wall. Next, we determined and optimized the applicability of FoX2 and FoX6 in an array of complementary bioassays, ranging from seed decontamination to irrigation‐ and spray‐based applications. Here, an irrigation‐based application showed promising results. In a final proof‐of‐concept, a CaCl2‐formulated phage cocktail was shown to control the outbreak of Xcc in the open field. This comprehensive approach illustrates the potential of phage biocontrol of black rot disease in Brassica and serves as a reference for the broader implementation of phage biocontrol in integrated pest management strategies.
Collapse
Affiliation(s)
| | | | - Lauren Moons
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | | - Léon E Bäcker
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | - Sofie Venneman
- Proefstation voor de groenteteelt, Sint-Katelijne-Waver, Belgium
| | - Sofie Rombouts
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium.,Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | - Louis Lippens
- Provinciaal Proefcentrum voor de Groenteteelt Oost-Vlaanderen, Kruishoutem, Belgium
| | - Steve Baeyen
- Flanders Research Institute for Agriculture, Fisheries and Food, Ghent, Belgium
| | | | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Counsil of Italy, Turin, Italy
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | | | | | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | | |
Collapse
|
16
|
Dia NC, Van Vaerenbergh J, Van Malderghem C, Blom J, Smits THM, Cottyn B, Pothier JF. Xanthomonas hydrangeae sp. nov., a novel plant pathogen isolated from Hydrangea arborescens. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913859 DOI: 10.1099/ijsem.0.005163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This paper describes a novel species isolated in 2011 and 2012 from nursery-grown Hydrangea arborescens cultivars in Flanders, Belgium. After 4 days at 28 °C, the strains yielded yellow, round, convex and mucoid colonies. Pathogenicity of the strains was confirmed on its isolation host, as well as on Hydrangea quercifolia. Analysis using MALDI-TOF MS identified the Hydrangea strains as belonging to the genus Xanthomonas but excluded them from the species Xanthomonas hortorum. A phylogenetic tree based on gyrB confirmed the close relation to X. hortorum. Three fatty acids were dominant in the Hydrangea isolates: anteiso-C15 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Unlike X. hortorum pathovars, the Hydrangea strains were unable to grow in the presence of lithium chloride and could only weakly utilize d-fructose-6-PO4 and glucuronamide. Phylogenetic characterization based on multilocus sequence analysis and phylogenomic characterization revealed that the strains are close to, yet distinct from, X. hortorum. The genome sequences of the strains had average nucleotide identity values ranging from 94.35-95.19 % and in silico DNA-DNA hybridization values ranging from 55.70 to 59.40 % to genomes of the X. hortorum pathovars. A genomics-based loop-mediated isothermal amplification assay was developed which was specific to the Hydrangea strains for its early detection. A novel species, Xanthomonas hydrangeae sp. nov., is proposed with strain LMG 31884T (=CCOS 1956T) as the type strain.
Collapse
Affiliation(s)
- Nay C Dia
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Johan Van Vaerenbergh
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Cinzia Van Malderghem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| |
Collapse
|
17
|
Hu M, Li C, Zhou X, Xue Y, Wang S, Hu A, Chen S, Mo X, Zhou J. Microbial Diversity Analysis and Genome Sequencing Identify Xanthomonas perforans as the Pathogen of Bacterial Leaf Canker of Water Spinach ( Ipomoea aquatic). Front Microbiol 2021; 12:752760. [PMID: 34777306 PMCID: PMC8579042 DOI: 10.3389/fmicb.2021.752760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Ipomoea aquatica is a leafy vegetable widely cultivated in tropical Asia, Africa, and Oceania. Bacterial leaf canker disease has been attacking the planting fields and seriously affecting the quality of I. aquatica in epidemic areas in China. This study examined the microbial composition of I. aquatica leaves with classical symptoms of spot disease. The results showed that Xanthomonas was overwhelmingly dominant in all four diseased leaf samples but rarely present in rhizospheric soil or irrigation water samples. In addition, Pantoea was also detected in two of the diseased leaf samples. Pathogen isolation, identification, and inoculation revealed that both Xanthomonas sp. TC2-1 and P. ananatis were pathogenic to the leaves of I. aquatic, causing crater-shaped ulcerative spots and yellowing with big brown rot lesions on leaves, respectively. We further sequenced the whole genome of strain TC2-1 and showed that it is a member of X. perforans. Overall, this study identified X. perforans as the causal pathogen of I. aquatica bacterial leaf canker, and P. ananatis as a companion pathogen causing yellowing and brown rot on leaves. The correct identification of the pathogens will provide important basis for future efforts to formulate targeted application strategy for bacterial disease control.
Collapse
Affiliation(s)
- Ming Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chuhao Li
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yang Xue
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Si Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Anqun Hu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Shanshan Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xiuwen Mo
- Agricultural Technology Service Centre of Daojiao Town, Dongguan, China
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| |
Collapse
|
18
|
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: 3] [Impact Index Per Article: 1.0] [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.
Collapse
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.
| |
Collapse
|
19
|
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
Collapse
Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| |
Collapse
|
20
|
Koebnik R, Burokiene D, Bragard C, Chang C, Saux MFL, Kölliker R, Lang JM, Leach JE, Luna EK, Portier P, Sagia A, Ziegle J, Cohen SP, Jacobs JM. The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads. PHYTOPATHOLOGY 2021; 111:611-616. [PMID: 32997607 DOI: 10.1094/phyto-07-20-0273-sc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here, we release a high-quality complete genome sequence for the X. theicola type strain, CFBP 4691T. Single-molecule real-time sequencing with a mean coverage of 264× revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.
Collapse
Affiliation(s)
- Ralf Koebnik
- IRD, Cirad, Université Montpellier, IPME, Montpellier, France
| | - Daiva Burokiene
- Nature Research Centre, Institute of Botany, Laboratory of Plant Pathology, Akademijos g. 2, Vilnius, Lithuania
| | - Claude Bragard
- Earth & Life Institute, Université Catholique Louvain-la-Neuve, Louvain-la-Neuve, Belgium
| | | | - Marion Fischer-Le Saux
- IRHS-UMR 1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, CIRM-CFBP, Beaucouzé, France
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Jillian M Lang
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Jan E Leach
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Emily K Luna
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Perrine Portier
- IRHS-UMR 1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, CIRM-CFBP, Beaucouzé, France
| | - Angeliki Sagia
- IRD, Cirad, Université Montpellier, IPME, Montpellier, France
- Department of Biology, University of Crete, Heraklion, Greece
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA 94025, U.S.A
| | - Stephen P Cohen
- Department of Plant Pathology, 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
| |
Collapse
|
21
|
Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R. Molecular Epidemiology of Xanthomonas euvesicatoria Strains from the Balkan Peninsula Revealed by a New Multiple-Locus Variable-Number Tandem-Repeat Analysis Scheme. Microorganisms 2021; 9:microorganisms9030536. [PMID: 33807692 PMCID: PMC8002079 DOI: 10.3390/microorganisms9030536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.
Collapse
Affiliation(s)
- Taca Vancheva
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Nevena Bogatzevska
- Institute of Soil Science, Agrotechnologies and Plant Protection ‘Nikola Pushkarov’, Sofia, Bulgaria;
| | - Penka Moncheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Sasa Mitrev
- Department for Plant and Environment Protection, Faculty of Agriculture, Goce Delchev University, Štip, North Macedonia;
| | - Christian Vernière
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
| | - Ralf Koebnik
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
- Correspondence: ; Tel.: +33-467-416-228
| |
Collapse
|
22
|
Popović T, Menković J, Prokić A, Obradoviċ A. First Report of Xanthomonas arboricola pv. pruni Causing Leaf and Fruit Spot on Apricot (Prunus armeniaca L.) in Montenegro. PLANT DISEASE 2021; 105:2712. [PMID: 33576687 DOI: 10.1094/pdis-01-21-0161-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In July 2020, symptoms of leaf and fruit spot were observed on two-year old apricot plants (Prunus armeniaca L.), cultivar Rubista in plantation covering approximately 0,5 ha near Podgorica, central Montenegro. The intensity of infection on leaves was more than 70%. Initially, leaf spots were mainly circular, 2 to 5 mm in diameter, water-soaked, surrounded by a weak chlorotic halo, but later became light to dark brown and necrotic. Eventually, the spots merged and necrotic tissue dropped out, leaving a "shot-hole" leaf appearance. On apricot fruits small, dark brown, mainly circular superficial lesions were observed. The lesions merged and formed large necrotic areas reducing the quality of fruits. Symptoms were not observed on woody parts, such as twigs or stem. A total of 10 bacterial strains, forming yellow, convex, and mucoid colonies on yeast extract-dextrose-CaCO3 (YDC) medium, were isolated from symptomatic leaf and fruit tissue. All strains induced hypersensitive reaction in tobacco leaves. They were Gram-negative, strictly aerobic, oxidase negative, catalase positive, hydrolyzed gelatine and esculin but not starch, and did not grow at 37°C, showing similar biochemical properties as a reference strain Xanthomonas arboricola pv. pruni (Xap) (NCPPB 416) used in all tests as a positive control. Strains were further identified by PCR analysis, using primer pair XapY17-F/XapY17-R (Pagani 2004; Pothier et al. 2011), resulting in a single band of 943 bp, characteristic for Xap. Additionally, BOX-PCR with the BOX A1R primer (Schaad et al. 2001) showed 100% homology in genetic profiles of all tested strains and control strain. Amplification and partial sequencing of the gyrB gene of four representative strains was performed using set of primers described by Parkinson et al. (2007). Obtained DNA sequences showed that analysed strains (GenBank nos. MW473770, MW473771, MW473772, and MW473773) share 99.44 to 99.57% of gyrB sequence identity with Xap pathotype strain ICMP51. Pathogenicity of all strains was confirmed by spraying young apricot shoots using a hand-held sprayer, and by infiltration of apricot leaves (cv. Roksana) from the abaxial surface using a syringe without needle, with the bacterial suspension (107 CFU/ml in sterile distilled water), in three replicates. Sterile distilled water and reference Xap strain (NCPPB 416), were used as negative and positive controls, respectively. The inoculated shoots and leaves were maintained at approx. 25°C and high humidity conditions. Tissue necrosis appeared on all inoculated shoots 5 to 11 days and leaves 5 to 9 days after inoculation. Koch's postulates were completed by re-isolation of the pathogen from inoculated tissue and identification by PCR using XapY17-F/XapY17-R primers. Based on pathogenic, biochemical and molecular characteristics, the strains isolated from apricot leaves and fruits in Montenegro were identified as Xap - causal agent of bacterial leaf spot and canker of stone fruits. This quarantine pathogen was previously reported on almond (Panić et al. 1998) and on peach (Popović et al. 2020) in Montenegro. This is the first report of Xap affecting apricot in this country. Therefore, strict phytosanitary measures have to be implemented to prevent spread of the pathogen in other areas and other susceptible hosts.
Collapse
Affiliation(s)
- Tamara Popović
- Administration of Food Safety, Veterinary and Phytosanitary Affairs, Serdara Jola Piletica 26, Podgorica, Montenegro, 81000;
| | - Jelena Menković
- University of Belgrade, Faculty of Agriculture, Institute of Phytomedicine, Plant Pathology, Belgrade, Serbia;
| | - Andjelka Prokić
- University of Belgrade, Faculty of Agriculture, Institute of Phytomedicine, Plant Pathology Dept., Nemanjina 6, Belgrade, Serbia, 11000;
| | - Aleksa Obradoviċ
- University of Belgrade, Faculty of Agriculture, Institute of Phytomedicine, Plant Pathology, Nemanjina 6, Belgrade, Serbia, 11080;
| |
Collapse
|
23
|
Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 2020; 8:microorganisms8091301. [PMID: 32858943 PMCID: PMC7563391 DOI: 10.3390/microorganisms8091301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023] Open
Abstract
Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/μL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.
Collapse
|
24
|
Stulberg MJ, Santillana G, Studholme DJ, Kasiborski B, Ortiz-Castro M, Broders K, Arias S, Block C, Munkvold G, Rascoe J. Genomics-Informed Molecular Detection of Xanthomonas vasicola pv. vasculorum Strains Causing Severe Bacterial Leaf Streak of Corn. PHYTOPATHOLOGY 2020; 110:1174-1179. [PMID: 31107148 DOI: 10.1094/phyto-12-18-0453-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xanthomonas vasicola pv. vasculorum (syn. X. campestris pv. vasculorum) was initially identified as the causal agent of bacterial leaf streak of corn in South Africa. The pathovar vasculorum causes disease on sugarcane and corn, but a subset of these strains was noted for its increased disease severity in corn. This subset was reclassified as X. campestris pv. zeae in the early 1990s and was found to have slightly different biochemical and genetic properties than isolates from sugarcane. There has been an emergence of X. campestris pv. zeae-like strains of X. vasicola pv. vasculorum in both the United States and Argentina since 2010. We performed whole genome sequencing on U.S. isolates to confirm their identity. Informed by comparative genomics, we then developed specific TaqMan qPCR and loop-mediated isothermal amplification (LAMP) assays for the detection of this specific subset of X. vasicola pv. vasculorum strains. The qPCR 4909 assay was tested against 27 xanthomonads (diverse representation), 32 DNA extractions from corn leaves confirmed as positive or negative for the bacterium, 41 X. vasicola pv. vasculorum isolates from corn in the United States and Argentina, and 31 additional bacteria associated with corn, sugarcane, or sorghum. In all cases the assay was shown to be specific for the X. vasicola pv. vasculorum isolates that cause more severe disease on corn. We then tested the LAMP 166 assay against the 27 xanthomonads and 32 corn leaf DNA samples, and we found this assay was also specific for this subset of X. vasicola pv. vasculorum isolates. We also developed a live/dead cells distinction protocol using propidium monoazide prior to DNA extraction for analyzing seed washes using these assays. These two detection assays can be useful for both diagnosticians and researchers to specifically identify the X. vasicola pv. vasculorum isolates that cause more severe symptoms on corn.
Collapse
Affiliation(s)
- Michael J Stulberg
- Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD, U.S.A
| | - Gem Santillana
- Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD, U.S.A
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, U.S.A
| | | | - Beth Kasiborski
- Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD, U.S.A
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, U.S.A
| | - Mary Ortiz-Castro
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, U.S.A
| | - Silvina Arias
- Seed Science Center, Iowa State University, Ames, IA, U.S.A
| | - Charles Block
- Seed Science Center, Iowa State University, Ames, IA, U.S.A
| | - Gary Munkvold
- Seed Science Center, Iowa State University, Ames, IA, U.S.A
| | - John Rascoe
- Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD, U.S.A
| |
Collapse
|
25
|
Studholme DJ, Wicker E, Abrare SM, Aspin A, Bogdanove A, Broders K, Dubrow Z, Grant M, Jones JB, Karamura G, Lang J, Leach J, Mahuku G, Nakato GV, Coutinho T, Smith J, Bull CT. Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov. PHYTOPATHOLOGY 2020; 110:1153-1160. [PMID: 31922946 DOI: 10.1094/phyto-03-19-0098-le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
| | - Emmanuel Wicker
- IPME, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Sadik Muzemil Abrare
- Southern Agricultural Research Institute (SARI), Areka Agricultural Research Center, Areka, Ethiopia
| | | | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Zoe Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Murray Grant
- School of Life Sciences, Gibbet Hill, University of Warwick, Coventry, CV4 7AL, U.K
| | - Jeffrey B Jones
- University of Florida, Plant Pathology Department, 1453 Fifield Hall, Gainesville, FL 32611, U.S.A
| | | | - Jillian Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Jan Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - George Mahuku
- International Institute of Tropical Agiculture (IITA), East Africa Hub, IITA-Tanzania, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Gloria Valentine Nakato
- International Institute of Tropical Agriculture (IITA), Plot 15B, Naguru East Road, Upper Naguru, P.O. Box 7878, Kampala, Uganda
| | - Teresa Coutinho
- Department of Microbiology and Plant Pathology, Centre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X28, Pretoria 0028, South Africa
| | | | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, PA, U.S.A
| |
Collapse
|
26
|
Lee YA, Yang PY, Huang SC. Characterization, Phylogeny, and Genome Analyses of Nonpathogenic Xanthomonas campestris Strains Isolated from Brassica Seeds. PHYTOPATHOLOGY 2020; 110:981-988. [PMID: 32167850 DOI: 10.1094/phyto-08-19-0319-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonads were detected by using the Xan-D(CCF) medium from the brassica seeds, and their pathogenicity was determined by plant inoculation tests. It was found that some seed lots were infested with Xanthomonas campestris pv. campestris, some with X. campestris pv. raphani, and some with nonpathogenic xanthomonads. The nonpathogenic xanthomonad strains were identified as X. campestris, and the multilocus sequence analysis showed that the nonpathogenic X. campestris strains were grouped together with pathogenic X. campestris, but not with nonpathogenic strains of X. arboricola. In addition, all isolated X. campestris pv. campestris and X. campestris pv. raphani strains were positive in the hrpF-PCR, but the nonpathogenic strains were negative. It was further found that nonpathogenic X. campestris strain nE1 does not contain the entire pathogenicity island (hrp gene cluster; type III secretion system) and all type III effector protein genes based on the whole genome sequence analyses. The nonpathogenic X. campestris strain nE1 could acquire the entire pathogenicity island from the endemic X. campestris pv. campestris and X. campestris pv. raphani strains by conjugation, but type III effector genes were not cotransferred. The studies showed that the nonpathogenic X. campestris strains indeed exist on the brassica seeds, but it could be differentiated by the PCR assays on the hrp and type III effector genes. Nevertheless, the nonpathogenic X. campestris strains cannot be ignored because they may be potential gene resources to increase genetic diversity in the endemic pathogenic X. campestris pv. campestris and X. campestris pv. raphani strains.
Collapse
Affiliation(s)
- Yung-An Lee
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
| | - Pei-Yu Yang
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
| | - Shau-Chang Huang
- Department of Life Science, Fu Jen Catholic University, Xin-Zhuang District, New Taipei City, Taiwan, Republic of China
| |
Collapse
|
27
|
Dhakal U, Dobhal S, Alvarez AM, Arif M. Phylogenetic Analyses of Xanthomonads Causing Bacterial Leaf Spot of Tomato and Pepper: Xanthomonas euvesicatoria Revealed Homologous Populations Despite Distant Geographical Distribution. Microorganisms 2019; 7:microorganisms7100462. [PMID: 31623235 PMCID: PMC6843189 DOI: 10.3390/microorganisms7100462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/28/2022] Open
Abstract
Bacterial leaf spot of tomato and pepper (BLS), an economically important bacterial disease caused by four species of Xanthomonas (X. euvesicatoria (Xe), X. vesicatoria (Xv), X. gardneri (Xg), and X. perforans (Xp)), is a global problem and can cause over 50% crop loss under unfavorable conditions. Among the four species, Xe and Xv are prevalent worldwide. Characterization of the pathogens is crucial for disease management and regulatory purposes. In this study, we performed a multilocus sequence analysis (MLSA) with six genes (hrcN, dnaA gyrB, gapA, pdg, and hmbs) on BLS strains. Other Xanthomonas species were included to determine phylogenetic relationships within and among the tested strains. Four BLS species comprising 76 strains from different serological groups and diverse geographical locations were resolved into three major clades. BLS xanthomonads formed distinct clusters in the phylogenetic analyses. Three other xanthomonads, including X. albilineans, X. sacchari, and X. translucens pv. undolusa revealed less than 85%, 88%, and 89% average nucleotide identity (ANI), respectively, with the other species of Xanthomonas included in this study. Both antibody and MLSA data showed that Xv was clearly separated from Xe and that the latter strains were remarkably clonal, even though they originated from distant geographical locations. The Xe strains formed two separate phylogenetic groups; Xe group A1 consisted only of tomato strains, whereas Xe group A2 included strains from pepper and tomato. In contrast, the Xv group showed greater heterogeneity. Some Xv strains from South America were closely related to strains from California, while others grouped closer to a strain from Indiana and more distantly to a strain from Hawaii. Using this information molecular tests can now be devised to track distribution of clonal populations that may be introduced into new geographic areas through seeds and other infected plant materials.
Collapse
Affiliation(s)
- Upasana Dhakal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| |
Collapse
|
28
|
Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran. Appl Environ Microbiol 2019; 85:AEM.01518-19. [PMID: 31420337 DOI: 10.1128/aem.01518-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022] Open
Abstract
This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding's grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding's grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen.IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads-namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens-have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.
Collapse
|
29
|
Shah SMA, Haq F, Ma W, Xu X, Wang S, Xu Z, Zou L, Zhu B, Chen G. Tal1 NXtc01 in Xanthomonas translucens pv. cerealis Contributes to Virulence in Bacterial Leaf Streak of Wheat. Front Microbiol 2019; 10:2040. [PMID: 31551976 PMCID: PMC6737349 DOI: 10.3389/fmicb.2019.02040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Xanthomonas translucens pv. cerealis (Xtc) causes bacterial leaf streak (BLS) of important cereal crops, including wheat (Triticum aestivum) and barley (Hordeum vulgare). Transcription activator-like effectors (TALEs) play vital roles in many plant diseases caused by Xanthomonas spp., however, TALEs have not been previously characterized in Xtc. In this study, the whole genome of NXtc01, a virulent strain of Xtc from Xinjiang, China, was sequenced and compared with genomes of other Xanthomonas spp. Xtc NXtc01 consists of a single 4,622,298 bp chromosome that encodes 4,004 genes. Alignment of the NXtc01 sequence with the draft genome of Xtc strain CFBP 2541 (United States) revealed a single giant inversion and differences in the location of two tal genes, which were designated tal1 and tal2. In NXtc01, both tal genes are located on the chromosome, whereas tal2 is plasmid-encoded in CFBP 2541. The repeat variable diresidues (RVDs) at the 12th and 13th sites within Tal2 repeat units were identical in both strains, whereas Tal1 showed differences in the third RVD. Xtc NXtc01 and CFBP 2541 encoded 35 and 33 non-TALE type III effectors (T3Es), respectively. tal1, tal2, and tal-free deletion mutants of Xtc NXtc01 were constructed and evaluated for virulence. The tal1 and tal-free deletion mutants were impaired with respect to symptom development and growth in wheat, suggesting that tal1 is a virulence factor in NXtc01. This was confirmed in gain-of-function experiments that showed the introduction of tal1, but not tal2, restored virulence to the tal-free mutant. Furthermore, we generated a hrcC deletion mutant of NXtc01; the hrcC mutant was non-pathogenic on wheat and unable to elicit a hypersensitive response in the non-host Nicotiana benthamiana. Our data provide a platform for exploring the roles of both TALEs and non-TALEs in promoting BLS on wheat.
Collapse
Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
30
|
Garita-Cambronero J, Sena-Vélez M, Ferragud E, Sabuquillo P, Redondo C, Cubero J. Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants. PLoS One 2019; 14:e0219797. [PMID: 31318915 PMCID: PMC6639005 DOI: 10.1371/journal.pone.0219797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/01/2019] [Indexed: 01/06/2023] Open
Abstract
Comparative studies in Xanthomonas have provided a vast amount of data that enabled to deepen in the knowledge of those factors associated with virulence and Xanthomonas plant interaction. The species of this genus present a wide range of host plants and a large number of studies have been focused to elucidate which mechanism are involved in this characteristic. In this study, comparative genomic and phenotypic analysis were performed between X. citri subsp. citri (Xcc), one of the most studied pathogens within Xanthomonas, and X. arboricola pv. pruni (Xap), a pathogen which has aroused great interest in recent time. The work was aimed to find those elements that contribute to their host divergence despite the convergence in the symptoms that each species cause on Citrus spp. and Prunus spp., respectively. This study reveals a set of genes that could be putatively associated with the adaptation of these pathogens to their hosts, being the most remarkable those involved in environmental sensing systems such as the case of the TonB-dependent transporters, the sensors of the two-component system and the methyl accepting chemotaxis proteins. Other important variants were found in processes related to the decomposition of the cell wall as could be appreciated by their dissimilar set of cell-wall degrading enzymes. Type three effectors, as one of the most important factors in delineating the host specificity in Xanthomonas, also showed a different array when comparing both species, being some of them unique to each pathogen. On the other hand, only small variations could be connected to other features such as the motility appendages and surface adhesion proteins, but these differences were accompanied by a dissimilar capacity to attach on host and non-host leaf surface. The molecular factors found in this work provide the basis to perform a more in-depth functional analyses that unveil those actual factors associated with pathogenesis and host specificity in Xcc and Xap.
Collapse
Affiliation(s)
- Jerson Garita-Cambronero
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain.,Centro de Investigación de Biocombustibles y Bioproductos, Instituto Tecnológico Agrario de Castilla y León (ITACyL), Villarejo de Órbigo, Leon, Spain
| | - Marta Sena-Vélez
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain.,Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Elisa Ferragud
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Pilar Sabuquillo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Cristina Redondo
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| | - Jaime Cubero
- Departamento de Protección Vegetal, Laboratorio Bacteriología, Instituto Nacional de Investigación y Tecnología Agraria (INIA), Madrid, Spain
| |
Collapse
|
31
|
Liu F, McDonald M, Schwessinger B, Joe A, Pruitt R, Erickson T, Zhao X, Stewart V, Ronald PC. Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:656-672. [PMID: 30773771 PMCID: PMC6637879 DOI: 10.1111/mpp.12783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.
Collapse
Affiliation(s)
- Furong Liu
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Megan McDonald
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Anna Joe
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Teresa Erickson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Valley Stewart
- Department of Microbiology & Molecular GeneticsUniversity of CaliforniaDavisCA95616USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| |
Collapse
|
32
|
Kim H, Joe A, Lee M, Yang S, Ma X, Ronald PC, Lee I. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. Mol Cells 2019; 42:166-174. [PMID: 30759970 PMCID: PMC6399010 DOI: 10.14348/molcells.2018.0403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/09/2018] [Accepted: 12/19/2018] [Indexed: 01/24/2023] Open
Abstract
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
Collapse
Affiliation(s)
- Hanhae Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
- Bio and Basic Science R&D Coordination Division, Korea Institute of S&T Evaluation and Planning, Seoul,
Korea
| | - Anna Joe
- Department of Plant Pathology and the Genome Center, University of California, CA 95616,
USA
- Feedstocks Division, Joint Bioenergy Institute, CA 94608,
USA
| | - Muyoung Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
| | - Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou,
China
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, CA 95616,
USA
- Feedstocks Division, Joint Bioenergy Institute, CA 94608,
USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
| |
Collapse
|
33
|
Effector Gene xopAE of Xanthomonas euvesicatoria 85-10 Is Part of an Operon and Encodes an E3 Ubiquitin Ligase. J Bacteriol 2018; 200:JB.00104-18. [PMID: 29784884 DOI: 10.1128/jb.00104-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/13/2018] [Indexed: 01/08/2023] Open
Abstract
The type III effector XopAE from the Xanthomonas euvesicatoria strain 85-10 was previously shown to inhibit plant immunity and enhance pathogen-induced disease symptoms. Evolutionary analysis of 60 xopAE alleles (AEal) revealed that the xopAE locus is conserved in multiple Xanthomonas species. The majority of xopAE alleles (55 out of 60) comprise a single open reading frame (ORF) (xopAE), while in 5 alleles, including AEal 37 of the X. euvesicatoria 85-10 strain, a frameshift splits the locus into two ORFs (hpaF and a truncated xopAE). To test whether the second ORF of AEal 37 (xopAE85-10 ) is translated, we examined expression of yellow fluorescent protein (YFP) fused downstream to truncated or mutant forms of the locus in Xanthomonas bacteria. YFP fluorescence was detected at maximal levels when the reporter was in proximity to an internal ribosome binding site upstream of a rare ATT start codon in the xopAE85-10 ORF but was severely reduced when these elements were abolished. In agreement with the notion that xopAE85-10 is a functional gene, its protein product was translocated into plant cells by the type III secretion system, and translocation was dependent on its upstream ORF, hpaF Homology modeling predicted that XopAE85-10 contains an E3 ligase XL box domain at the C terminus, and in vitro assays demonstrated that this domain displays monoubiquitination activity. Remarkably, the XL box was essential for XopAE85-10 to inhibit pathogen-associated molecular pattern (PAMP)-induced gene expression in Arabidopsis protoplasts. Together, these results indicate that the xopAE85-10 gene resides in a functional operon, which utilizes the alternative start codon ATT and encodes a novel XL box E3 ligase.IMPORTANCEXanthomonas bacteria utilize a type III secretion system to cause disease in many crops. This study provides insights into the evolution, translocation, and biochemical function of the XopAE type III secreted effector, contributing to the understanding of Xanthomonas-host interactions. We establish XopAE as a core effector of seven Xanthomonas species and elucidate the evolution of the Xanthomonas euvesicatoriaxopAE locus, which contains an operon encoding a truncated effector. Our findings indicate that this operon evolved from the split of a multidomain gene into two ORFs that conserved the original domain function. Analysis of xopAE85-10 translation provides the first evidence for translation initiation from an ATT codon in Xanthomonas Our data demonstrate that XopAE85-10 is an XL box E3 ubiquitin ligase and provide insights into the structure and function of this effector family.
Collapse
|
34
|
Draft Genome Assemblages of 10 Xanthomonas vasicola pv. zeae Strains, Pathogens Causing Leaf Streak Disease of Maize in South Africa. GENOME ANNOUNCEMENTS 2018; 6:6/26/e00532-18. [PMID: 29954890 PMCID: PMC6025950 DOI: 10.1128/genomea.00532-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Maize bacterial leaf streak disease has spread across maize crops in South Africa and therefore potentially poses a threat to maize production and food security. Until recently, this pathogen was identified as a Xanthomonas campestris pathovar, whereas our South African genomes seem to be more divergent and create their own subclade.
Collapse
|
35
|
Lang JM, DuCharme E, Ibarra Caballero J, Luna E, Hartman T, Ortiz-Castro M, Korus K, Rascoe J, Jackson-Ziems TA, Broders K, Leach JE. Detection and Characterization of Xanthomonas vasicola pv. vasculorum (Cobb 1894) comb. nov. Causing Bacterial Leaf Streak of Corn in the United States. PHYTOPATHOLOGY 2017; 107:1312-1321. [PMID: 28677478 DOI: 10.1094/phyto-05-17-0168-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak of corn (Zea mays) recently reached epidemic levels in three corn-growing states, and has been detected in another six states in the central United States. Xanthomonas vasicola was identified as the causal agent of this disease. A multilocus sequence alignment of six housekeeping genes and comparison of average nucleotide identity from draft genome sequence were used to confirm phylogenetic relationships and classification of this bacteria relative to other X. vasicola strains. X. vasicola isolates from Nebraska and South Africa were highly virulent on corn and sugarcane and less virulent on sorghum but caused water-soaking symptoms that are typical of X. vasicola infection on the leaves of all three hosts. Based on host range and phylogenetic comparison, we propose the taxonomic designation of this organism to X. vasicola pv. vasculorum ( Cobb 1894 ) comb. nov. Polymerase chain reaction-based diagnostic assays were developed that distinguish X. vasicola pv. vasculorum and X. vasicola pv. holcicola from each other and from other Xanthomonas spp.
Collapse
Affiliation(s)
- J M Lang
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E DuCharme
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Ibarra Caballero
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E Luna
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T Hartman
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - M Ortiz-Castro
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Korus
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Rascoe
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T A Jackson-Ziems
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Broders
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J E Leach
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| |
Collapse
|
36
|
Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017; 67:3645-3654. [PMID: 28840805 DOI: 10.1099/ijsem.0.002189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
Collapse
Affiliation(s)
- Joana G Vicente
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Steve Rothwell
- Vitacress Ltd, Lower Link Farm, St. Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Eric B Holub
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | | |
Collapse
|
37
|
Pesce C, Jacobs JM, Berthelot E, Perret M, Vancheva T, Bragard C, Koebnik R. Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF. Front Microbiol 2017; 8:1177. [PMID: 28694803 PMCID: PMC5483457 DOI: 10.3389/fmicb.2017.01177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023] Open
Abstract
Xanthomonas translucens is the causal agent of bacterial leaf streak, the most common bacterial disease of wheat and barley. To cause disease, most xanthomonads depend on a highly conserved type III secretion system, which translocates type III effectors into host plant cells. Mutagenesis of the conserved type III secretion gene hrcT confirmed that the X. translucens type III secretion system is required to cause disease on the host plant barley and to trigger a non-host hypersensitive response (HR) in pepper leaves. Type III effectors are delivered to the host cell by a surface appendage, the Hrp pilus, and a translocon protein complex that inserts into the plant cell plasma membrane. Homologs of the Xanthomonas HrpF protein, including PopF from Ralstonia solanacearum and NolX from rhizobia, are thought to act as a translocon protein. Comparative genomics revealed that X. translucens strains harbor a noncanonical hrp gene cluster, which rather shares features with type III secretion systems from Ralstonia solanacearum, Paraburkholderia andropogonis, Collimonas fungivorans, and Uliginosibacterium gangwonense than other Xanthomonas spp. Surprisingly, none of these bacteria, except R. solanacearum, encode a homolog of the HrpF translocon. Here, we aimed at identifying a candidate translocon from X. translucens. Notably, genomes from strains that lacked hrpF/popF/nolX instead encode another gene, called hpaT, adjacent to and co-regulated with the type III secretion system gene cluster. An insertional mutant in the X. translucens hpaT gene, which is the first gene of a two-gene operon, hpaT-hpaH, was non-pathogenic on barley and did not cause the HR or programmed cell death in non-host pepper similar to the hrcT mutant. The hpaT mutant phenotypes were partially complemented by either hpaT or the downstream gene, hpaH, which has been described as a facilitator of translocation in Xanthomonas oryzae. Interestingly, the hpaT mutant was also complemented by the hrpF gene from Xanthomonas euvesicatoria. These findings reveal that both HpaT and HpaH contribute to the injection of type III effectors into plant cells.
Collapse
Affiliation(s)
- Céline Pesce
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Jonathan M. Jacobs
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Edwige Berthelot
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Marion Perret
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Taca Vancheva
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Claude Bragard
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Ralf Koebnik
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| |
Collapse
|
38
|
PM 7/129 (1) DNA barcoding as an identification tool for a number of regulated pests. ACTA ACUST UNITED AC 2016. [DOI: 10.1111/epp.12344] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
39
|
Tian Q, Zhao W, Lu S, Zhu S, Li S. DNA Barcoding for Efficient Species- and Pathovar-Level Identification of the Quarantine Plant Pathogen Xanthomonas. PLoS One 2016; 11:e0165995. [PMID: 27861494 PMCID: PMC5115671 DOI: 10.1371/journal.pone.0165995] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/23/2016] [Indexed: 11/29/2022] Open
Abstract
Genus Xanthomonas comprises many economically important plant pathogens that affect a wide range of hosts. Indeed, fourteen Xanthomonas species/pathovars have been regarded as official quarantine bacteria for imports in China. To date, however, a rapid and accurate method capable of identifying all of the quarantine species/pathovars has yet to be developed. In this study, we therefore evaluated the capacity of DNA barcoding as a digital identification method for discriminating quarantine species/pathovars of Xanthomonas. For these analyses, 327 isolates, representing 45 Xanthomonas species/pathovars, as well as five additional species/pathovars from GenBank (50 species/pathovars total), were utilized to test the efficacy of four DNA barcode candidate genes (16S rRNA gene, cpn60, gyrB, and avrBs2). Of these candidate genes, cpn60 displayed the highest rate of PCR amplification and sequencing success. The tree-building (Neighbor-joining), ‘best close match’, and barcode gap methods were subsequently employed to assess the species- and pathovar-level resolution of each gene. Notably, all isolates of each quarantine species/pathovars formed a monophyletic group in the neighbor-joining tree constructed using the cpn60 sequences. Moreover, cpn60 also demonstrated the most satisfactory results in both barcoding gap analysis and the ‘best close match’ test. Thus, compared with the other markers tested, cpn60 proved to be a powerful DNA barcode, providing a reliable and effective means for the species- and pathovar-level identification of the quarantine plant pathogen Xanthomonas.
Collapse
Affiliation(s)
- Qian Tian
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Wenjun Zhao
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing, China
- * E-mail: (SLi); (WZ)
| | - Songyu Lu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Shuifang Zhu
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Shidong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (SLi); (WZ)
| |
Collapse
|
40
|
Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses. Stand Genomic Sci 2016; 11:50. [PMID: 27536340 PMCID: PMC4988018 DOI: 10.1186/s40793-016-0170-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 08/03/2016] [Indexed: 01/24/2023] Open
Abstract
As causal agents of bacterial wilt in pastures and meadows, bacteria of the species Xanthomonas translucens are a serious issue in forage grass production. So far, only little is known about host-pathogen interactions at the molecular level and the lack of comprehensive genome data impeded targeted breeding strategies towards resistant forage grass cultivars. Here we announce the draft genome sequences of three grass-pathogenic Xanthomonas translucens pathotype strains, i.e. pv. arrhenatheri LMG 727, pv. poae LMG 728 and pv. phlei LMG 730 isolated from Arrhenatherum elatius (L.) P. Beauv. ex J. Presl & C. Presl (Switzerland), Poa trivialis L. (Switzerland) and Phleum pratense L. (Norway), respectively. The genomes of all three strains revealed a non-canonical type III secretion system and a set of 22 type III effectors as common virulence-related traits. Distinct inter-pathovar differences were observed for the lipopolysaccharide biosynthesis gene cluster and the presence of nonribosomal peptide synthetases.
Collapse
|
41
|
Fischer-Le Saux M, Bonneau S, Essakhi S, Manceau C, Jacques MA. Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing. Appl Environ Microbiol 2015; 81:4651-68. [PMID: 25934623 PMCID: PMC4551192 DOI: 10.1128/aem.00050-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/25/2015] [Indexed: 12/11/2022] Open
Abstract
Deep and comprehensive knowledge of the genetic structure of pathogenic species is the cornerstone on which the design of precise molecular diagnostic tools is built. Xanthomonas arboricola is divided into pathovars, some of which are classified as quarantine organisms in many countries and are responsible for diseases on nut and stone fruit trees that have emerged worldwide. Recent taxonomic studies of the genus Xanthomonas showed that strains isolated from other hosts should be classified in X. arboricola, extending the host range of the species. To investigate the genetic structure of X. arboricola and the genetic relationships between highly pathogenic strains and strains apparently not relevant to plant health, we conducted multilocus sequence analyses on a collection of strains representative of the known diversity of the species. Most of the pathovars were clustered in separate monophyletic groups. The pathovars pruni, corylina, and juglandis, responsible for pandemics in specific hosts, were highly phylogenetically related and clustered in three distinct clonal complexes. In contrast, strains with no or uncertain pathogenicity were represented by numerous unrelated singletons scattered in the phylogenic tree. Depending on the pathovar, intra- and interspecies recombination played contrasting roles in generating nucleotide polymorphism. This work provides a population genetics framework for molecular epidemiological surveys of emerging plant pathogens within X. arboricola. Based on our results, we propose to reclassify three former pathovars of Xanthomonas campestris as X. arboricola pv. arracaciae comb. nov., X. arboricola pv. guizotiae comb. nov., and X. arboricola pv. zantedeschiae comb. nov. An emended description of X. arboricola Vauterin et al. 1995 is provided.
Collapse
Affiliation(s)
- Marion Fischer-Le Saux
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sophie Bonneau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Salwa Essakhi
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Charles Manceau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| |
Collapse
|
42
|
Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 DOI: 10.3389/fpls.2015.00431.ecollection2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/24/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
Collapse
Affiliation(s)
- Jonathan M Jacobs
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France ; Department of Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain Louvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical Saint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
| |
Collapse
|
43
|
Characterization of a novel clade of Xanthomonas isolated from rice leaves in Mali and proposal of Xanthomonas maliensis sp. nov. Antonie Van Leeuwenhoek 2015; 107:869-81. [PMID: 25588569 DOI: 10.1007/s10482-015-0379-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
Four bacterial strains, designated M89, M92, M97(T), and M106, were isolated in a previous study from surface-sterilized leaves of rice (Oryza sativa) or murainagrass (Ischaemum rugosum) at three sites in Mali, Africa. Here they were examined by a polyphasic taxonomic approach and analysis of a whole-genome sequence. Phylogenetic analyses based on 16S rRNA sequence and multilocus sequence analysis of seven genes showed that these four strains formed a distinct lineage representing a novel species within the genus Xanthomonas. This was supported by whole-genome average nucleotide identity values calculated from comparisons of strain M97(T) with established Xanthomonas species. The strains can be differentiated from the known Xanthomonas species on the basis of their fatty acid and carbohydrate utilization profiles. Population growth studies on rice confirmed that these bacteria multiply in rice leaves without causing symptoms. Identification of this novel species can be accomplished by using diagnostic primer sets or by gyrB gene sequence analysis. We propose to classify these rice- and grass-associated bacteria as Xanthomonas maliensis sp. nov. with strain M97(T) = CFBP7942(T) = LMG27592(T) as the type strain.
Collapse
|
44
|
Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 PMCID: PMC4468381 DOI: 10.3389/fpls.2015.00431] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/05/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
Collapse
Affiliation(s)
- Jonathan M. Jacobs
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- Department of Applied Microbiology, Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu TropicalSaint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- *Correspondence: Ralf Koebnik, Institut de Recherche pour le Développement, UMR Interactions – Plantes – Microorganismes – Environnement, Génomique et Transcriptomique des Interactions Plantes-Procaryotes, 921 avenue Agropolis, 34394 Montpellier, France
| |
Collapse
|
45
|
Bonasera JM, Asselin JAE, Beer SV. Identification of bacteria pathogenic to or associated with onion (Allium cepa) based on sequence differences in a portion of the conserved gyrase B gene. J Microbiol Methods 2014; 103:138-43. [PMID: 24925602 DOI: 10.1016/j.mimet.2014.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/01/2014] [Accepted: 06/01/2014] [Indexed: 11/17/2022]
Abstract
We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from onion bulbs and leaves and soil in which onions were grown.
Collapse
Affiliation(s)
- Jean M Bonasera
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jo Ann E Asselin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Steven V Beer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
46
|
Wonni I, Cottyn B, Detemmerman L, Dao S, Ouedraogo L, Sarra S, Tekete C, Poussier S, Corral R, Triplett L, Koita O, Koebnik R, Leach J, Szurek B, Maes M, Verdier V. Analysis of Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity. PHYTOPATHOLOGY 2014; 104:520-31. [PMID: 24199713 DOI: 10.1094/phyto-07-13-0213-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on 'Kitaake' rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.
Collapse
|
47
|
Scientific Opinion on the risk to plant health of Xanthomonas citri pv. citri and Xanthomonas citri pv. aurantifolii for the EU territory. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3556] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
48
|
Structural and physiological analyses of the alkanesulphonate-binding protein (SsuA) of the citrus pathogen Xanthomonas citri. PLoS One 2013; 8:e80083. [PMID: 24282519 PMCID: PMC3839906 DOI: 10.1371/journal.pone.0080083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 10/09/2013] [Indexed: 11/19/2022] Open
Abstract
Background The uptake of sulphur-containing compounds plays a pivotal role in the physiology of bacteria that live in aerobic soils where organosulfur compounds such as sulphonates and sulphate esters represent more than 95% of the available sulphur. Until now, no information has been available on the uptake of sulphonates by bacterial plant pathogens, particularly those of the Xanthomonas genus, which encompasses several pathogenic species. In the present study, we characterised the alkanesulphonate uptake system (Ssu) of Xanthomonas axonopodis pv. citri 306 strain (X. citri), the etiological agent of citrus canker. Methodology/Principal Findings A single operon-like gene cluster (ssuEDACB) that encodes both the sulphur uptake system and enzymes involved in desulphurisation was detected in the genomes of X. citri and of the closely related species. We characterised X. citri SsuA protein, a periplasmic alkanesulphonate-binding protein that, together with SsuC and SsuB, defines the alkanesulphonate uptake system. The crystal structure of SsuA bound to MOPS, MES and HEPES, which is herein described for the first time, provides evidence for the importance of a conserved dipole in sulphate group coordination, identifies specific amino acids interacting with the sulphate group and shows the presence of a rather large binding pocket that explains the rather wide range of molecules recognised by the protein. Isolation of an isogenic ssuA-knockout derivative of the X. citri 306 strain showed that disruption of alkanesulphonate uptake affects both xanthan gum production and generation of canker lesions in sweet orange leaves. Conclusions/Significance The present study unravels unique structural and functional features of the X. citri SsuA protein and provides the first experimental evidence that an ABC uptake system affects the virulence of this phytopathogen.
Collapse
|
49
|
Roy JK, Mukherjee AK. Applications of a high maltose forming, thermo-stable α-amylase from an extremely alkalophilic Bacillus licheniformis strain AS08E in food and laundry detergent industries. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.06.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
50
|
van de Vossenberg BTLH, Westenberg M, Bonants PJM. DNA barcoding as an identification tool for selected EU-regulated plant pests: an international collaborative test performance study among 14 laboratories. ACTA ACUST UNITED AC 2013. [DOI: 10.1111/epp.12031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. T. L. H. van de Vossenberg
- National Plant Protection Organization; Netherlands Food and Consumer Product Safety Authority; P.O. Box 9102; 6700 HC; Wageningen; the Netherlands
| | - M. Westenberg
- National Plant Protection Organization; Netherlands Food and Consumer Product Safety Authority; P.O. Box 9102; 6700 HC; Wageningen; the Netherlands
| | - P. J. M. Bonants
- Plant Research International; P.O. Box 69; 6700 AB; Wageningen; the Netherlands
| |
Collapse
|