1
|
Cellier G, Nordey T, Cortada L, Gauche M, Rasoamanana H, Yahiaoui N, Rébert E, Prior P, Chéron JJ, Poussier S, Pruvost O. Molecular Epidemiology of Ralstonia pseudosolanacearum Phylotype I Strains in the Southwest Indian Ocean Region and Their Relatedness to African Strains. PHYTOPATHOLOGY 2023; 113:423-435. [PMID: 36399027 DOI: 10.1094/phyto-09-22-0355-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The increasing requirement for developing tools enabling fine strain traceability responsible for epidemics is tightly linked with the need to understand factors shaping pathogen populations and their environmental interactions. Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is one of the most important plant diseases in tropical and subtropical regions. Sadly, little, outdated, or no information on its epidemiology is reported in the literature, although alarming outbreaks are regularly reported as disasters. A large set of phylotype I isolates (n = 2,608) was retrieved from diseased plants in fields across the Southwest Indian Ocean (SWIO) and Africa. This collection enabled further assessment of the epidemiological discriminating power of the previously published RS1-MLVA14 scheme. Thirteen markers were validated and characterized as not equally informative. Most had little infra-sequevar polymorphism, and their performance depended on the sequevar. Strong correlation was found with a previous multilocus sequence typing scheme. However, 2 to 3% of sequevars were not correctly assigned through endoglucanase gene sequence. Discriminant analysis of principal components (DAPC) revealed four groups with strong phylogenetic relatedness to sequevars 31, 33, and 18. Phylotype I-31 isolates were highly prevalent in the SWIO and Africa, but their dissemination pathways remain unclear. Tanzania and Mauritius showed the greatest diversity of RSSC strains, as the four DAPC groups were retrieved. Mauritius was the sole territory harboring a vast phylogenetic diversity and all DAPC groups. More research is still needed to understand the high prevalence of phylotype I-31 at such a large geographic scale.
Collapse
Affiliation(s)
- Gilles Cellier
- Anses, Plant Health Laboratory, Saint Pierre, Reunion Island
| | | | - Laura Cortada
- East Africa Hub, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Nematology Section, Department of Biology, Ghent University, Ghent, Belgium
| | - Mirana Gauche
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Hasina Rasoamanana
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Noura Yahiaoui
- Anses, Plant Health Laboratory, Saint Pierre, Reunion Island
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Emeline Rébert
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Philippe Prior
- INRAE, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint-Pierre, Reunion Island
| | - Jean Jacques Chéron
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Stéphane Poussier
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Olivier Pruvost
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| |
Collapse
|
2
|
Complete Genome Sequence of Ralstonia solanacearum Strain Bs715, a Member of Biovar 4 and a Strong Pathogen of Bacterial Wilt on Solanum lycopersicum. Microbiol Resour Announc 2023; 12:e0088322. [PMID: 36688649 PMCID: PMC9933660 DOI: 10.1128/mra.00883-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ralstonia solanacearum is a notorious pathogen of bacterial wilt on Solanum lycopersicum. Most isolates from diseased tomato tissues are biovar 3, and their genomes are publicly available; however, information on biovar 4 strains is limited. Here, the complete genome sequence of R. solanacearum Bs715, a biovar 4 strain, is presented.
Collapse
|
3
|
Characterization and Assessment of 2, 4-Diacetylphloroglucinol (DAPG)-Producing Pseudomonas fluorescens VSMKU3054 for the Management of Tomato Bacterial Wilt Caused by Ralstonia solanacearum. Microorganisms 2022; 10:microorganisms10081508. [PMID: 35893565 PMCID: PMC9330548 DOI: 10.3390/microorganisms10081508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022] Open
Abstract
Microbial bio-products are becoming an appealing and viable alternative to chemical pesticides for effective management of crop diseases. These bio-products are known to have potential to minimize agrochemical applications without losing crop yield and also restore soil fertility and productivity. In this study, the inhibitory efficacy of 2,4-diacetylphloroglucinol (DAPG) produced by Pseudomonas fluorescens VSMKU3054 against Ralstonia solanacearum was assessed. Biochemical and functional characterization study revealed that P. fluorescens produced hydrogen cyanide (HCN), siderophore, indole acetic acid (IAA) and hydrolytic enzymes such as amylase, protease, cellulase and chitinase, and had the ability to solubilize phosphate. The presence of the key antimicrobial encoding gene in the biosynthesis of 2,4-diacetylphloroglucinol (DAPG) was identified by PCR. The maximum growth and antimicrobial activity of P. fluorescens was observed in king’s B medium at pH 7, 37 °C and 36 h of growth. Glucose and tryptone were found to be the most suitable carbon and nitrogen sources, respectively. DAPG was separated by silica column chromatography and identified by various methods such as UV-Vis, FT-IR, GC-MS and NMR spectroscopy. When R. solanacearum cells were exposed to DAPG at 90 µg/mL, the cell viability was decreased, reactive oxygen species (ROS) were increased and chromosomal DNA was damaged. Application of P. fluorescens and DAPG significantly reduced the bacterial wilt incidence. In addition, P. fluorescens was also found effective in promoting the growth of tomato seedlings. It is concluded that the indigenous isolate P. fluorescens VSMKU3054 could be used as a suitable biocontrol agent against bacterial wilt disease of tomato.
Collapse
|
4
|
Abebe AM, Choi J, Kim Y, Oh CS, Yeam I, Nou IS, Lee JM. Development of diagnostic molecular markers for marker-assisted breeding against bacterial wilt in tomato. BREEDING SCIENCE 2020; 70:462-473. [PMID: 32968349 PMCID: PMC7495205 DOI: 10.1270/jsbbs.20027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
Bacterial wilt, caused by the Ralstonia pseudosolanacearum species complex, is an important vascular disease that limits tomato production in tropical and subtropical regions. Two major quantitative trait loci (QTL) of bacterial wilt resistance on chromosome 6 (Bwr-6) and 12 (Bwr-12) were previously identified in Solanum lycopersicum 'Hawaii 7996'; however, marker-assisted breeding for bacterial wilt resistance is not well established. To dissect the QTL, six cleaved amplified polymorphic sites (CAPS) and derived CAPS (dCAPS) markers within the Bwr-6 region and one dCAPS marker near Bwr-12 were developed, and resistance levels in 117 tomato cultivars were evaluated. Two markers, RsR6-5 on chromosome 6 and RsR12-1 on chromosome 12, were selected based on the genotypic and phenotypic analysis. The combination of RsR6-5 and RsR12-1 effectively distinguishes resistant and susceptible cultivars. Furthermore, the efficiency of the two markers was validated in the F3 generation derived from the F2 population between E6203 (susceptible) and Hawaii 7998 (resistant). Resistant alleles at both loci led to the resistance to bacterial wilt. These markers will facilitate marker-assisted breeding of tomato resistant to bacterial wilt.
Collapse
Affiliation(s)
- Alebel Mekuriaw Abebe
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Jinwoo Choi
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Youngjun Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, Gyeonggi-do 17104, South Korea
| | - Inhwa Yeam
- Department of Horticulture and Breeding, Andong National University, Andong, Gyeongbuk, 36729, South Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 57922, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea
| |
Collapse
|
5
|
The Entner-Doudoroff and Nonoxidative Pentose Phosphate Pathways Bypass Glycolysis and the Oxidative Pentose Phosphate Pathway in Ralstonia solanacearum. mSystems 2020; 5:5/2/e00091-20. [PMID: 32156794 PMCID: PMC7065512 DOI: 10.1128/msystems.00091-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Understanding the metabolic versatility of Ralstonia solanacearum is important, as it regulates the trade-off between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on the potential roles of glycolysis and the oxidative pentose phosphate pathway (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis that the Entner-Doudoroff pathway and non-OxPPP bypass glycolysis and OxPPP during the oxidation of glucose, a component of the host xylem pool that serves as a potential carbon source (5). The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood. In Ralstonia solanacearum, a devastating phytopathogen whose metabolism is poorly understood, we observed that the Entner-Doudoroff (ED) pathway and nonoxidative pentose phosphate pathway (non-OxPPP) bypass glycolysis and OxPPP under glucose oxidation. Evidence derived from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis supported the observations. Comparative metabolic network analysis derived from the currently available 53 annotated R. solanacearum strains, including a recently reported strain (F1C1), representing the four phylotypes, confirmed the lack of key genes coding for phosphofructokinase (pfk-1) and phosphogluconate dehydrogenase (gnd) enzymes that are relevant for glycolysis and OxPPP, respectively. R. solanacearum F1C1 cells fed with [13C]glucose (99% [1-13C]glucose or 99% [1,2-13C]glucose or 40% [13C6]glucose) followed by gas chromatography-mass spectrometry (GC-MS)-based labeling analysis of fragments from amino acids, glycerol, and ribose provided clear evidence that rather than glycolysis and the OxPPP, the ED pathway and non-OxPPP are the main routes sustaining metabolism in R. solanacearum. The 13C incorporation in the mass ions of alanine (m/z 260 and m/z 232), valine (m/z 288 and m/z 260), glycine (m/z 218), serine (m/z 390 and m/z 362), histidine (m/z 440 and m/z 412), tyrosine (m/z 466 and m/z 438), phenylalanine (m/z 336 and m/z 308), glycerol (m/z 377), and ribose (m/z 160) mapped the pathways supporting the observations. The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. IMPORTANCE Understanding the metabolic versatility of Ralstonia solanacearum is important, as it regulates the trade-off between virulence and metabolism (1, 2) in a wide range of plant hosts. Due to a lack of clear evidence until this work, several published research papers reported on the potential roles of glycolysis and the oxidative pentose phosphate pathway (OxPPP) in R. solanacearum (3, 4). This work provided evidence from 13C stable isotope feeding and genome annotation-based comparative metabolic network analysis that the Entner-Doudoroff pathway and non-OxPPP bypass glycolysis and OxPPP during the oxidation of glucose, a component of the host xylem pool that serves as a potential carbon source (5). The outcomes help better define the central carbon metabolic network of R. solanacearum that can be integrated with 13C metabolic flux analysis as well as flux balance analysis studies for defining the metabolic phenotypes. The study highlights the need to critically examine phytopathogens whose metabolism is poorly understood.
Collapse
|
6
|
Li Y, Guo Q, He F, Li Y, Xue Q, Lai H. Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota. MICROBIAL ECOLOGY 2020; 79:134-147. [PMID: 31165188 DOI: 10.1007/s00248-019-01388-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Soil Actinomycetes have been used as biocontrol agents against soil-borne plant diseases, yet little is known about their effects on the structure of the rhizosphere microbiota and the long-term effects on crop yield and disease intensity after the application of Actinomycetes is stopped. Here, we conducted 3-year plot experiments to investigate the roles of two Actinomycetes strains (Streptomyces pactum Act12 and Streptomyces rochei D74) in the biocontrol of soil-borne root diseases and growth promotion of monkhood (Aconitum carmichaelii). We also examined their long-term effects after soil application of a mixed Actinomycetes preparation (spore powder) was completed. High-throughput sequencing was used to analyze shifts in the rhizosphere microbiota. The antifungal activity and root colonization ability of the two Actinomycetes were also tested. Disease severity of southern blight and root rot decreased following application of the Actinomycetes preparation, whereas biomass yield of tubers increased compared with the control group. Significant effects of disease control and plant growth promotion were also observed after application was stopped. The Actinomycetes preparation induced marked increases in the abundance of beneficial microbes and decreases in the abundance of harmful microbes in rhizosphere soil. Adding cell-free culture filtrates of both strains Act12 and D74 inhibited the growth of fungal pathogens capable of causing southern blight (Sclerotium rolfsii) and root rot (Fusarium oxysporum) in A. carmichaelii. A GFP-labeled strain was used to show that D74 can colonize roots of A. carmichaelii. In conclusion, a preparation of two Actinomycetes plays a role in the biocontrol of root diseases and growth promotion of A. carmichaelii by inhibiting pathogen growth and shaping the rhizosphere microbiota.
Collapse
Affiliation(s)
- Yulong Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Qiao Guo
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Fei He
- School of Modern Agriculture and Biotechnology, Ankang University, Ankang, 725000, China
| | - Yunzhou Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Quanhong Xue
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
7
|
Sabbagh CRR, Carrere S, Lonjon F, Vailleau F, Macho AP, Genin S, Peeters N. Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ 2019; 7:e7346. [PMID: 31579561 PMCID: PMC6762002 DOI: 10.7717/peerj.7346] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/25/2019] [Indexed: 12/21/2022] Open
Abstract
Background The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology). Methods Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors. Results We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.
Collapse
Affiliation(s)
| | | | - Fabien Lonjon
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Alberto P Macho
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Stephane Genin
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-tolosan, France
| | - Nemo Peeters
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-tolosan, France
| |
Collapse
|
8
|
Cho H, Song ES, Heu S, Baek J, Lee YK, Lee S, Lee SW, Park DS, Lee TH, Kim JG, Hwang I. Prediction of Host-Specific Genes by Pan-Genome Analyses of the Korean Ralstonia solanacearum Species Complex. Front Microbiol 2019; 10:506. [PMID: 30930881 PMCID: PMC6428702 DOI: 10.3389/fmicb.2019.00506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
The soil-borne pathogenic Ralstonia solanacearum species complex (RSSC) is a group of plant pathogens that is economically destructive worldwide and has a broad host range, including various solanaceae plants, banana, ginger, sesame, and clove. Previously, Korean RSSC strains isolated from samples of potato bacterial wilt were grouped into four pathotypes based on virulence tests against potato, tomato, eggplant, and pepper. In this study, we sequenced the genomes of 25 Korean RSSC strains selected based on these pathotypes. The newly sequenced genomes were analyzed to determine the phylogenetic relationships between the strains with average nucleotide identity values, and structurally compared via multiple genome alignment using Mauve software. To identify candidate genes responsible for the host specificity of the pathotypes, functional genome comparisons were conducted by analyzing pan-genome orthologous group (POG) and type III secretion system effectors (T3es). POG analyses revealed that a total of 128 genes were shared only in tomato-non-pathogenic strains, 8 genes in tomato-pathogenic strains, 5 genes in eggplant-non-pathogenic strains, 7 genes in eggplant-pathogenic strains, 1 gene in pepper-non-pathogenic strains, and 34 genes in pepper-pathogenic strains. When we analyzed T3es, three host-specific effectors were predicted: RipS3 (SKWP3) and RipH3 (HLK3) were found only in tomato-pathogenic strains, and RipAC (PopC) were found only in eggplant-pathogenic strains. Overall, we identified host-specific genes and effectors that may be responsible for virulence functions in RSSC in silico. The expected characters of those genes suggest that the host range of RSSC is determined by the comprehensive actions of various virulence factors, including effectors, secretion systems, and metabolic enzymes.
Collapse
Affiliation(s)
- Heejung Cho
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Eun-Sung Song
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Sunggi Heu
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - JeongHo Baek
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Young Kee Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Seungdon Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Seon-Woo Lee
- Department of Applied Biology, Dong-A University, Busan, South Korea
| | - Dong Suk Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Tae-Ho Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jeong-Gu Kim
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| |
Collapse
|