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Sreenayana B, Mondal KK, Mathiyalagan N, Shanmugam KN, Kumar S, Shrinivas Reddy M, Mani C. Molecular characterization and evaluation of novel management options for Burkholderia glumae BG1, the causative agent of panicle blight of rice (Oryza sativa L.). Mol Biol Rep 2024; 51:519. [PMID: 38625424 DOI: 10.1007/s11033-024-09498-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Bacterial panicle blight, incited by Burkholderia glumae, has impacted rice production globally. Despite its significance, knowledge about the disease and the virulence pattern of the causal agent is very limited. Bacterial panicle blight is a major challenge in the rice-growing belts of North-western India, resulting in yield reduction. However, the management of B. glumae has become a challenge due to the lack of proper management strategies. METHODOLOGY AND RESULTS Twenty-one BG strains have been characterized using the 16S rRNA and the gyrB gene-based sequence approach in the present study. The gyrB gene-based phylogenetic analysis resulted in geographic region-specific clustering of the BG isolates. The virulence screening of twenty-one BG strains by inoculating the pathogenic bacterial suspension of 1 × 10-8 cfu/ml at the booting stage (55 DAT) revealed the variation in the disease severity and the grain yield of rice plants. The most virulent BG1 strain resulted in the highest disease incidence (82.11%) and lowest grain yield (11.12 g/plant), and the least virulent BG10 strain resulted in lowest disease incidence of 18.94% and highest grain yield (24.62 g/plant). In vitro evaluation of various biocontrol agents and nano copper at different concentrations by agar well diffusion method revealed that nano copper at 1000 mg/L inhibited the colony growth of B. glumae. Under net house conditions, nano copper at 1000 mg/L reduced the disease severity to 21.23% and increased the grain yield by 20.91% (31.76 g per plant) compared to the positive control (COC 0.25% + streptomycin 200 ppm). Remarkably, pre-inoculation with nano copper at 1000 mg/L followed by challenge inoculation with B. glumae enhanced the activity of enzymatic antioxidants viz., Phenyl ammonia-lyase (PAL), Polyphenol oxidase (PPO) and Peroxidase (POX) and non-enzymatic antioxidant phenol. Additionally, we observed a substantial transcript level upregulation of six defense-related genes to several folds viz., OsPR2, OsPR5, OsWRKY71, OsPAL1, OsAPX1, and OsPPO1 in comparison to the pathogen control and healthy control. CONCLUSIONS Overall, our study provides valuable insights into the potential and practical application of nano copper for the mitigation of bacterial panicle blight, offering promising prospects for commercial utilization in disease management.
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Affiliation(s)
- Bhaskaran Sreenayana
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Kalyan Kumar Mondal
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India.
- National Institute of Biotic Stress Management, Raipur, Chhattisgarh, India.
| | - Nivetha Mathiyalagan
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Sanjeev Kumar
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Chander Mani
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Ngalimat MS, Mohd Hata E, Zulperi D, Ismail SI, Ismail MR, Mohd Zainudin NAI, Saidi NB, Yusof MT. A laudable strategy to manage bacterial panicle blight disease of rice using biocontrol agents. J Basic Microbiol 2023; 63:1180-1195. [PMID: 37348082 DOI: 10.1002/jobm.202300182] [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: 04/04/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
Bacterial panicle blight (BPB) disease is a dreadful disease in rice-producing countries. Burkholderia glumae, a Gram-negative, rod-shaped, and flagellated bacterium was identified as the primary culprit for BPB disease. In 2019, the disease was reported in 18 countries, and to date, it has been spotted in 26 countries. Rice yield has been reduced by up to 75% worldwide due to this disease. Interestingly, the biocontrol strategy offers a promising alternative to manage BPB disease. This review summarizes the management status of BPB disease using biological control agents (BCA). Bacteria from the genera Bacillus, Burkholderia, Enterobacter, Pantoea, Pseudomonas, and Streptomyces have been examined as BCA under in vitro, glasshouse, and field conditions. Besides bacteria, bacteriophages have also been reported to reduce BPB pathogens under in vitro and glasshouse conditions. Here, the overview of the mechanisms of bacteria and bacteriophages in controlling BPB pathogens is addressed. The applications of BCA using various delivery methods could effectively manage BPB disease to benefit the agroecosystems and food security.
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Affiliation(s)
- Mohamad S Ngalimat
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Erneeza Mohd Hata
- Sustainable Agronomy and Crop Protection, Institute of Plantation Studies, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Dzarifah Zulperi
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siti I Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd R Ismail
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nur A I Mohd Zainudin
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor B Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd T Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Kouzai Y, Akimoto-Tomiyama C. A Seed-Borne Bacterium of Rice, Pantoea dispersa BB1, Protects Rice from the Seedling Rot Caused by the Bacterial Pathogen Burkholderia glumae. Life (Basel) 2022; 12:life12060791. [PMID: 35743824 PMCID: PMC9225591 DOI: 10.3390/life12060791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Seedling rot, caused by the bacterial pathogen Burkholderia glumae, is a major disease of rice. It originates from pathogen-contaminated seeds and is thus mainly controlled by pesticide treatments of seeds. We previously demonstrated that the seed-borne bacteria of rice may be a useful and sustainable alternative to pesticides to manage seedling rot, but they are limited in terms of variety. Here, we report that another seed-borne bacterium, Pantoea dispersa BB1, protects rice from B. glumae. We screened 72 bacterial isolates from rice seeds of three genetically different cultivars inoculated or non-inoculated with B. glumae. 16S rRNA gene sequencing revealed that pathogen inoculation affected the composition of culturable seed-borne bacterial communities and increased the presence of Pantoea and Paenibacillus species. Among three Pantoea and Paenibacillus isolates that exhibit tolerance to toxoflavin, a virulence factor of B. glumae, P. dispersa BB1 significantly mitigated the symptoms of rice seedling rot. The culture filtrate of BB1 inhibited the growth of B. glumae in vitro, suggesting that this isolate secretes antibacterial compounds. Seed treatment with BB1 suppressed pathogen propagation in plants, although seed treatment with the culture filtrate did not. Because BB1 did not show pathogenicity in rice, our findings demonstrate that BB1 is a promising biocontrol agent against seedling rot.
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Béna G, Fory PA, Rico JE, Mosquera GM. VNTR Typing of the Bacterial Rice Pathogen Burkholderia glumae Reveals the Coexistence of Several Diverging Lineages in a Single Field in Colombia. PLANT DISEASE 2021; 105:3466-3473. [PMID: 33797974 DOI: 10.1094/pdis-02-21-0235-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: 06/12/2023]
Abstract
Burkholderia glumae is responsible for the panicle blight disease of rice. This disease is present worldwide and can result in significant drop in yields. To estimate the genetic diversity of the bacterial strains present in a rice paddy field in Colombia, we sampled 109 strains from infected panicles. To detect fine genetic relationships among related haplotypes, and to overcome a very low nucleotide diversity detected in previous studies, we designed primers to amplify and sequence several highly variable minisatellite loci, or variable number tandem repeats (VNTRs), as well as part of the Toxoflavin toxA gene in all strains. Results show that the toxA nucleotide diversity defined four lineages and was similar to that detected in several fields in Japan; data suggest that B. glumae has spread from Asia to America without major loss of genetic diversity, and that five VNTR loci discriminated the strains within the field revealing single and multi-infections of the rice panicles with a wide distribution of the haplotypes among the different plots. Even though disease levels vary considerably from year to year, the bacterial genetic diversity is maintained within a field. We do not detect any geographical structuring within the field, nor any effect of the rice cultivar on the observed diversity. The consequences on the origin and evolution of the bacteria are discussed.
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Affiliation(s)
- Gilles Béna
- Plant Health Institute Montpellier (PHIM), Université de Montpellier, French National Research Institute for Sustainable Development (IRD), National Research Institute for Agriculture, Food and Environment (INRAE), French Agricultural Research Centre for International Development (CIRAD), Institut Agro, Montpellier, France
| | - Paola A Fory
- Agrobiodiversity Program, International Center for Tropical Agriculture (CIAT), Cali 763537, Palmira, Colombia
| | - Johanna Echeverri Rico
- The National Federation of Rice Growers of Colombia (FEDEARROZ), 110911 Bogota, Colombia
| | - Gloria M Mosquera
- Agrobiodiversity Program, International Center for Tropical Agriculture (CIAT), Cali 763537, Palmira, Colombia
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Echeverri-Rico J, Petro E, Fory PA, Mosquera GM, Lang JM, Leach JE, Lobaton JD, Garcés G, Perafán R, Amezquita N, Toro S, Mora B, Cuasquer JB, Ramirez-Villegas J, Rebolledo MC, Torres EA. Understanding the complexity of disease-climate interactions for rice bacterial panicle blight under tropical conditions. PLoS One 2021; 16:e0252061. [PMID: 34038435 PMCID: PMC8153475 DOI: 10.1371/journal.pone.0252061] [Citation(s) in RCA: 3] [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: 01/11/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022] Open
Abstract
Bacterial panicle blight (BPB) caused by Burkholderia glumae is one of the main concerns for rice production in the Americas since bacterial infection can interfere with the grain-filling process and under severe conditions can result in high sterility. B. glumae has been detected in several rice-growing areas of Colombia and other countries of Central and Andean regions in Latin America, although evidence of its involvement in decreasing yield under these conditions is lacking. Analysis of different parameters in trials established in three rice-growing areas showed that, despite BPB presence, severity did not explain the sterility observed in fields. PCR tests for B. glumae confirmed low infection in all sites and genotypes, only 21.4% of the analyzed samples were positive for B. glumae. Climate parameters showed that Montería and Saldaña registered maximum temperature above 34°C, minimum temperature above 23°C, and Relative Humidity above 80%, conditions that favor the invasion model described for this pathogen in Asia. Our study found that in Colombia, minimum temperature above 23°C during 10 days after flowering is the condition that correlates with disease incidence. Therefore, this correlation, and the fact that Montería and Saldaña had a higher level of infected samples according to PCR tests, high minimum temperature, but not maximum temperature, seems to be determinant for B. glumae colonization under studied field conditions. This knowledge is a solid base line to design strategies for disease control, and is also a key element for breeders to develop strategies aimed to decrease the effect of B. glumae and high night-temperature on rice yield under tropical conditions.
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Affiliation(s)
| | - Eliel Petro
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | - Paola A. Fory
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | - Gloria M. Mosquera
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | - Jillian M. Lang
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States of America
| | - Jan E. Leach
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States of America
| | - Juan D. Lobaton
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | | | | | | | | | - Brayan Mora
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | - Juan B. Cuasquer
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
| | - Julián Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), c/o CIAT, Cali, Colombia
| | - Maria Camila Rebolledo
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
- CIRAD, UMR AGAP, F-34398 Montpellier, France. AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Edgar A. Torres
- International Center for Tropical Agriculture (CIAT), Agrobiodiversity Research Area, Cali, Colombia
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Lee HH, Park J, Jung H, Seo YS. Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. Microorganisms 2021; 9:1123. [PMID: 34067383 PMCID: PMC8224644 DOI: 10.3390/microorganisms9061123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.
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Affiliation(s)
- Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
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Ortega L, Rojas CM. Bacterial Panicle Blight and Burkholderia glumae: From Pathogen Biology to Disease Control. PHYTOPATHOLOGY 2021; 111:772-778. [PMID: 33206007 DOI: 10.1094/phyto-09-20-0401-rvw] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial panicle blight (BPB), caused by the bacterium Burkholderia glumae, has affected rice production worldwide. Despite its importance, neither the disease nor the causal agent are well understood. Moreover, methods to manage BPB are still lacking. Nevertheless, the emerging importance of this pathogen has stimulated research to identify the mechanisms of pathogenicity, to gain insight into plant disease resistance, and to develop strategies to manage the disease. In this review, we consolidate current information regarding the virulence factors that have been identified in B. glumae and present a model of the disease and the pathogen. We also provide an update on the current research status to develop methods to control the disease especially through biological control approaches and through the development of resistant cultivars.
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Affiliation(s)
- Laura Ortega
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701
| | - Clemencia M Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701
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8
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Kim N, Mannaa M, Kim J, Ra JE, Kim SM, Lee C, Lee HH, Seo YS. The In Vitro and In Planta Interspecies Interactions Among Rice-Pathogenic Burkholderia Species. PLANT DISEASE 2021; 105:134-143. [PMID: 33197363 DOI: 10.1094/pdis-06-20-1252-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Burkholderia glumae, B. plantarii, and B. gladioli are responsible for serious diseases in rice crops and co-occurrence among them has been reported. In this study, in vitro assays revealed antagonistic activity among these organisms, with B. gladioli demonstrating strong inhibition of B. glumae and B. plantarii. Strains of B. glumae and B. plantarii that express green fluorescent protein were constructed and used for cocultivation assays with B. gladioli, which confirmed the strong inhibitory activity of B. gladioli. Cell-free supernatants from each species were tested against cultures of counterpart species to evaluate the potential to inhibit bacterial growth. To investigate the inhibitory activity of B. gladioli on B. glumae and B. plantarii in rice, rice plant assays were performed and quantitative PCR (qPCR) assays were developed for in planta bacterial quantification. The results indicated that coinoculation with B. gladioli leads to significantly reduced disease severity and colonization of rice tissues compared with single inoculation with B. glumae or B. plantarii. This study demonstrates the interactions among three rice-pathogenic Burkholderia species and strong antagonistic activity of B. gladioli in vitro and in planta. The qPCR assays developed here could be applied for accurate quantification of these organisms from in planta samples in future studies.
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Affiliation(s)
- Namgyu Kim
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Mohamed Mannaa
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Juyun Kim
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Ji-Eun Ra
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea
| | - Chaeyeong Lee
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241, Korea
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea
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Ortega L, Walker KA, Patrick C, Wamishe Y, Rojas A, Rojas CM. Harnessing Pseudomonas protegens to Control Bacterial Panicle Blight of Rice. PHYTOPATHOLOGY 2020; 110:1657-1667. [PMID: 32852258 DOI: 10.1094/phyto-02-20-0045-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial panicle blight of rice is a seedborne disease caused by the bacterium Burkholderia glumae. This disease has affected rice production worldwide and its effects are likely to become more devastating with the continuous increase in global temperatures, especially during the growing season. The bacterium can cause disease symptoms in different tissues and at different developmental stages. In reproductive stages, the bacterium interferes with grain development in the panicles and, as a result, directly affects rice yield. Currently, there are no methods to control the disease because chemical control is not effective and completely resistant cultivars are not available. Thus, a promising approach is the use of antagonistic microorganisms. In this work, we identified one strain of Pseudomonas protegens and one strain of B. cepacia with antimicrobial activity against B. glumae in vitro and in planta. We further characterized the antimicrobial activity of P. protegens and found that this activity is associated with bacterial secretions. Cell-free secretions from P. protegens inhibited the growth of B. glumae in vitro and also prevented B. glumae from causing disease in rice. Although the specific molecules associated with these activities have not been identified, these findings suggest that the secreted fractions from P. protegens could be harnessed as biopesticides to control bacterial panicle blight of rice.
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Affiliation(s)
- Laura Ortega
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Katherine A Walker
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Casey Patrick
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Yeshi Wamishe
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR 72160, U.S.A
| | - Alejandro Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Clemencia M Rojas
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
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[Genetic characterization of rice endophytic bacteria (Oryza sativa L.) with antimicrobial activity against Burkholderia glumae]. Rev Argent Microbiol 2020; 52:315-327. [PMID: 32147231 DOI: 10.1016/j.ram.2019.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/17/2019] [Accepted: 12/20/2019] [Indexed: 11/21/2022] Open
Abstract
The aim of the present study was to isolate, select and characterize endophytic bacteria in rice inhibiting Burkholderia glumae THT as well as to characterize the genetic diversity and virulence factors in strains of B. glumae and Burkholderia gladioli of rice. Rice plants were collected in 4 departments from the northern region of Peru, isolating endophytic bacteria, after tissue sterilization, at 30°C (48h) in Trypticase Soy Agar (TSA), evaluating the antimicrobial activity against B. glumae THT, production of siderophores, resistance of toxoflavine and partial sequencing of the 16S rRNA gene. Furthermore, B. glumae and B. gladioli were isolated in selective medium (pH 4.5) at 41°C/72h. Molecular identification was performed using BOX-PCR and sequencing of the 16S rRNA gene, in addition to the production of extracellular enzymes, motility tests and sensitivity/resistance to bactericides. One hundred and eighty nine (189) endophytic bacteria were isolated, and only 9 strains showed antimicrobial activity against B. glumae THT, highlighting Burkholderia vietnamiensis TUR04-01, B. vietnamiensis TUR04-03 and Bacillus aryabhattai AMH12-02. The strains produced siderophores and at least 55.5% were resistant to toxoflavin. Additionally, 17 strains were grouped into 9 BOX-PCR profiles, where 16 had similarity with B. glumae LMG2196T (100%) and 1 with B. gladioli NBRC 13700T (99.86%). High diversity was found according to geographical origin and virulence factors. In conclusion, strains of the genus Bacillus and Burkholderia are potential biocontrol agents against B. glumae.
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Liu JX, Cai YN, Jiang WY, Li YG, Zhang QF, Pan HY. Population Structure and Genetic Diversity of Fungi Causing Rice Seedling Blight in Northeast China Based on Microsatellite Markers. PLANT DISEASE 2020; 104:868-874. [PMID: 31935343 DOI: 10.1094/pdis-08-19-1620-re] [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
Rice seedling blight, which is caused by diverse pathogenic microorganisms, occurs worldwide and is the most important seedling disease affecting rice production in Northeast China. To further characterize the population structure and genetic diversity of the fungi responsible for rice seedling blight in Northeast China, 225 fungal strains were isolated from diseased rice seedlings collected from various rice-producing areas. The isolated strains included Fusarium oxysporum (48.0%), F. verticillioides (11.6%), F. tricinctum (8.0%), F. redolens (6.7%), F. equiseti (6.2%), F. solani (6.2%), Rhizoctonia solani (6.7%), Alternaria alternata (4.0%), and Curvularia coatesiae (2.7%). F. oxysporum was the dominant fungal species causing rice seedling blight, with most isolates exhibiting moderate pathogenicity. Moreover, to our knowledge, this is the first study to identify A. alternata and C. coatesiae as causal agents of rice seedling blight in Northeast China. None of the F. oxysporum isolates were sensitive to 10 μg/ml of carbendazim, implying that carbendazim is ineffective for controlling rice seedling blight in Northeast China. The F. oxysporum isolates were divided into nine groups based on a simple sequence repeat analysis involving 14 primer pairs. In addition, an analysis of molecular variance revealed a significant correlation between the F. oxysporum population and geographical location, which had a significant effect on the differentiation of the dominant isolate population. The results of this study provide insights into the genetic diversity of F. oxysporum strains causing rice seedling blight and may be useful for selecting isolates to screen for disease-resistant rice varieties, evaluating fungicide efficacy, and developing effective disease management strategies.
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Affiliation(s)
- J X Liu
- Agricultural College, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Y N Cai
- Agricultural College, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - W Y Jiang
- Agricultural College, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Y G Li
- Agricultural College, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Q F Zhang
- Heilongjiang Plant Quarantine and Plant Protection Station, Harbin 150036, People's Republic of China
| | - H Y Pan
- College of Plant Sciences, Jilin University, Changchun 150000, People's Republic of China
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Suárez-Moreno ZR, Vinchira-Villarraga DM, Vergara-Morales DI, Castellanos L, Ramos FA, Guarnaccia C, Degrassi G, Venturi V, Moreno-Sarmiento N. Plant-Growth Promotion and Biocontrol Properties of Three Streptomyces spp. Isolates to Control Bacterial Rice Pathogens. Front Microbiol 2019; 10:290. [PMID: 30858835 PMCID: PMC6398372 DOI: 10.3389/fmicb.2019.00290] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 02/04/2019] [Indexed: 11/23/2022] Open
Abstract
Bacterial Panicle Blight caused by Burkholderia glumae is a major disease of rice, which has dramatically affected rice production around the world in the last years. In this study we describe the assessment of three Streptomyces isolates as biocontrol agents for B. glumae. Additionally, the presence of other plant-growth promoting abilities and their possible beneficial effects upon their inoculation on rice plants was evaluated as an ecological analysis for their future inoculation in rice crops. Two isolates (A20 and 5.1) inhibited growth of virulent B. glumae strains, as well as a wide range of bacterial and fungal species, while a third strain (7.1) showed only antifungal activity. In vitro tests demonstrated the ability of these strains to produce siderophores, Indoleacetic acid (IAA), extracellular enzymes and solubilizing phosphate. Greenhouse experiments with two rice cultivars indicated that Streptomyces A20 is able to colonize rice plants and promote plant growth in both cultivars. Furthermore, an egfp tagged mutant was generated and colonization experiments were performed, indicating that Streptomyces A20 –GFP was strongly associated with root hairs, which may be related to the plant growth promotion observed in the gnotobiotic experiments. In order to characterize the antimicrobial compounds produced by strain A20 bacteria, mass spectrometry analyses were performed. This technique indicated that A20 produced several antimicrobial compounds with sizes below 3 kDa and three of these molecules were identified as Streptotricins D, E and F. These findings indicate the potential of Streptomyces A20 as a biocontrol inoculant to protect rice plants against bacterial diseases.
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Affiliation(s)
| | | | | | | | - Freddy A Ramos
- Departamento de Química. Universidad Nacional de Colombia, Bogotá, Colombia
| | - Corrado Guarnaccia
- Biotechnology Development Unit, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giuliano Degrassi
- Bacteriology and Plant Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Vittorio Venturi
- Bacteriology and Plant Bacteriology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
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13
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Jaiswal S, Singh DK, Shukla P. Gene Editing and Systems Biology Tools for Pesticide Bioremediation: A Review. Front Microbiol 2019; 10:87. [PMID: 30853940 PMCID: PMC6396717 DOI: 10.3389/fmicb.2019.00087] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/16/2019] [Indexed: 01/15/2023] Open
Abstract
Bioremediation is the degradation potential of microorganisms to dissimilate the complex chemical compounds from the surrounding environment. The genetics and biochemistry of biodegradation processes in datasets opened the way of systems biology. Systemic biology aid the study of interacting parts involved in the system. The significant keys of system biology are biodegradation network, computational biology, and omics approaches. Biodegradation network consists of all the databases and datasets which aid in assisting the degradation and deterioration potential of microorganisms for bioremediation processes. This review deciphers the bio-degradation network, i.e., the databases and datasets (UM-BBD, PAN, PTID, etc.) aiding in assisting the degradation and deterioration potential of microorganisms for bioremediation processes, computational biology and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation experiments. Besides, the present review also describes the gene editing tools like CRISPR Cas, TALEN, and ZFNs which can possibly make design microbe with functional gene of interest for degradation of particular recalcitrant for improved bioremediation.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Dileep Kumar Singh
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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14
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Pedraza LA, Bautista J, Uribe-Vélez D. Seed-born Burkholderia glumae Infects Rice Seedling and Maintains Bacterial Population during Vegetative and Reproductive Growth Stage. THE PLANT PATHOLOGY JOURNAL 2018; 34:393-402. [PMID: 30369849 PMCID: PMC6200043 DOI: 10.5423/ppj.oa.02.2018.0030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/05/2018] [Accepted: 05/25/2018] [Indexed: 05/31/2023]
Abstract
Rice world production is affected due to the growing impact of diseases such as bacterial panicle blight, produced by Burkholderia glumae. The pathogen-induced symptoms include seedling rot, grain rot and leaf-sheath browning in rice plants. It is currently recognized the entrance of this pathogen to the plant, from infected seeds and from environmental sources of the microorganism. However, it is still not fully elucidated the dynamics and permanence of the pathogen in the plant, from its entry until the development of disease symptoms in seedlings or panicles. In this work it was evaluated the infection of B. glumae rice plants, starting from inoculated seeds and substrates, and its subsequent monitoring after infection. Various organs of the plant during the vegetative stage and until the beginning of the reproductive stage, were evaluated. In both inoculation models, the bacteria was maintained in the plant as an endophyte between 1 × 101 and 1 × 105 cfu of B. glumae.g-1 of plant throughout the vegetative stage. An increase of bacterial population towards initiation of the panicle was observed, and in the maturity of the grain, an endophyte population was identified in the flag leaf at 1 × 106 cfu of B. glumae.g-1 fresh weight of rice plant, conducting towards the symptoms of bacterial panicle blight. The results found, suggest that B. glumae in rice plants developed from infected seeds or from the substrate, can colonize seedlings, establishing and maintaining a bacterial population over time, using rice plants as habitat to survive endophyticly until formation of bacterial panicle blight symptoms.
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Affiliation(s)
- Luz Adriana Pedraza
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
| | - Jessica Bautista
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
| | - Daniel Uribe-Vélez
- Instituto de Biotecnología, Universidad Nacional de Colombia, A.A 14-490, Bogotá D.C.,
Colombia
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15
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Flórez LV, Scherlach K, Miller IJ, Rodrigues A, Kwan JC, Hertweck C, Kaltenpoth M. An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles. Nat Commun 2018; 9:2478. [PMID: 29946103 PMCID: PMC6018673 DOI: 10.1038/s41467-018-04955-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Microbial symbionts are often a source of chemical novelty and can contribute to host defense against antagonists. However, the ecological relevance of chemical mediators remains unclear for most systems. Lagria beetles live in symbiosis with multiple strains of Burkholderia bacteria that protect their offspring against pathogens. Here, we describe the antifungal polyketide lagriamide, and provide evidence supporting that it is produced by an uncultured symbiont, Burkholderia gladioli Lv-StB, which is dominant in field-collected Lagria villosa. Interestingly, lagriamide is structurally similar to bistramides, defensive compounds found in marine tunicates. We identify a gene cluster that is probably involved in lagriamide biosynthesis, provide evidence for horizontal acquisition of these genes, and show that the naturally occurring symbiont strains on the egg are protective in the soil environment. Our findings highlight the potential of microbial symbionts and horizontal gene transfer as influential sources of ecological innovation.
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Affiliation(s)
- Laura V Flórez
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany.
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Ian J Miller
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Andre Rodrigues
- Department of Biochemistry and Microbiology, UNESP-São Paulo State University, Av. 24A, n. 1515-Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Jason C Kwan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, 777 Highland Ave, Madison, WI, 53705-2222, USA
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
- Natural Product Chemistry, Friedrich Schiller University, 07743, Jena, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 13, 55128, Mainz, Germany
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16
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Nguyen TT, Chon TS, Kim J, Seo YS, Heo M. Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species. J Microbiol 2017; 55:568-582. [PMID: 28664514 DOI: 10.1007/s12275-017-7085-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/02/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
Abstract
Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)-based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea
| | - Tae-Soo Chon
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
| | - Muyoung Heo
- Department of Physics, Pusan National University, Busan, 46241, Republic of Korea.
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17
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Cui Z, Ojaghian M, Tao Z, Kakar K, Zeng J, Zhao W, Duan Y, Vera Cruz C, Li B, Zhu B, Xie G. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice. J Appl Microbiol 2016; 120:1357-67. [DOI: 10.1111/jam.13094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/04/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Z. Cui
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - M.R. Ojaghian
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - Z. Tao
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - K.U. Kakar
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - J. Zeng
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - W. Zhao
- Chinese Academy of Inspection and Quarantine; Beijing China
| | - Y. Duan
- USDA-ARS-USHRL; Fort Pierce FL USA
| | - C.M. Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division; International Rice Research Institute; Metro Manila Philippines
| | - B. Li
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
| | - B. Zhu
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation; College of Life Science; Zhejiang Sci-Tech University; Hangzhou China
| | - G. Xie
- State Key Laboratory of Rice Biology; Institute of Biotechnology; Zhejiang University; Hangzhou China
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18
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Naughton LM, An SQ, Hwang I, Chou SH, He YQ, Tang JL, Ryan RP, Dow JM. Functional and genomic insights into the pathogenesis of B
urkholderia
species to rice. Environ Microbiol 2016; 18:780-90. [DOI: 10.1111/1462-2920.13189] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Lynn M. Naughton
- School of Microbiology; Biosciences Institute; University College Cork; Cork Ireland
| | - Shi-qi An
- Division of Molecular Microbiology; College of Life Sciences; University of Dundee; Dundee UK
| | - Ingyu Hwang
- Institute of Biochemistry and Department of Agricultural Biotechnology; Seoul National University; Seoul 151-921 South Korea
| | - Shan-Ho Chou
- National Chung Hsing University Biotechnology Center; National Chung Hsing University; Taichung 40227 Taiwan
| | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources; The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering; College of Life Science and Technology; Guangxi University; 100 Daxue Road Nanning Guangxi 530004 China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources; The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering; College of Life Science and Technology; Guangxi University; 100 Daxue Road Nanning Guangxi 530004 China
| | - Robert P. Ryan
- Division of Molecular Microbiology; College of Life Sciences; University of Dundee; Dundee UK
| | - J. Maxwell Dow
- School of Microbiology; Biosciences Institute; University College Cork; Cork Ireland
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19
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Lee J, Park J, Kim S, Park I, Seo YS. Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli. MOLECULAR PLANT PATHOLOGY 2016; 17:65-76. [PMID: 25845410 PMCID: PMC6638467 DOI: 10.1111/mpp.12262] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Burkholderia gladioli is a causal agent of bacterial panicle blight and sheath/grain browning in rice in many countries. Many strains produce the yellow pigment toxoflavin, which is highly toxic to plants, fungi, animals and microorganisms. Although there have been several studies on the toxoflavin biosynthesis system of B. glumae, it is still unclear how B. gladioli activates toxoflavin biosynthesis. In this study, we explored the genomic organization of the toxoflavin system of B. gladioli and its biological functions using comparative genomic analysis between toxoflavin-producing strains (B. glumae BGR1 and B. gladioli BSR3) and a strain not producing toxoflavin (B. gladioli KACC11889). The latter exhibits normal physiological characteristics similar to other B. gladioli strains. Burkholderia gladioli KACC11889 possesses all the genes involved in toxoflavin biosynthesis, but lacks the quorum-sensing (QS) system that functions as an on/off switch for toxoflavin biosynthesis. These data suggest that B. gladioli has evolved to use the QS signalling cascade of toxoflavin production (TofI/TofR of QS → ToxJ or ToxR → tox operons) similar to that in B. glumae. However, some strains may have evolved to eliminate toxoflavin production through deletion of the QS genes. In addition, we demonstrate that the toxoflavin biosynthetic system enhances the virulence of B. gladioli. These findings provide another line of evidence supporting the differential regulation of the toxoflavin system in Burkholderia strains.
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Affiliation(s)
- Jongyun Lee
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 609-735, South Korea
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20
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Kajiwara H. Direct detection of the plant pathogens Burkholderia glumae, Burkholderia gladioli pv. gladioli, and Erwinia chrysanthemi pv. zeae in infected rice seedlings using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods 2016; 120:1-5. [DOI: 10.1016/j.mimet.2015.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 11/27/2022]
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21
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Lee HH, Park J, Kim J, Park I, Seo YS. Understanding the direction of evolution in Burkholderia glumae through comparative genomics. Curr Genet 2015; 62:115-23. [DOI: 10.1007/s00294-015-0523-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/02/2015] [Accepted: 10/03/2015] [Indexed: 12/11/2022]
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22
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Seo YS, Lim JY, Park J, Kim S, Lee HH, Cheong H, Kim SM, Moon JS, Hwang I. Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts. BMC Genomics 2015; 16:349. [PMID: 25943361 PMCID: PMC4422320 DOI: 10.1186/s12864-015-1558-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/20/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages. RESULTS We first sequenced the complete genome of B. plantarii ATCC 43733T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems. CONCLUSIONS The complete genome sequence of B. plantarii ATCC 43733T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other animal and human Burkholderia species.
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Affiliation(s)
- Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Jae Yun Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Sunyoung Kim
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan, 609-735, Republic of Korea.
| | - Hoon Cheong
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon, 443-400, Republic of Korea.
| | - Sang-Mok Kim
- Yeongnam Regional Office, Animal and Plant Quarantine Agency, Busan, 600-016, Republic of Korea.
| | - Jae Sun Moon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-633, Republic of Korea.
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, Republic of Korea.
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