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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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Ontoy JC, Shrestha B, Karki HS, Barphagha I, Angira B, Famoso A, Ham JH. Genetic Characterization of the Partial Disease Resistance of Rice to Bacterial Panicle Blight and Sheath Blight by Combined QTL Linkage and QTL-seq Analyses. PLANTS (BASEL, SWITZERLAND) 2023; 12:559. [PMID: 36771643 PMCID: PMC9920235 DOI: 10.3390/plants12030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Bacterial panicle blight (BPB) and sheath blight (SB) are major diseases of rice and few cultivars have shown a high level of resistance to these diseases. A recombinant inbred line (RIL) population developed from the U.S. cultivars Jupiter (moderately resistant) and Trenasse (susceptible) was investigated to identify loci associated with the partial disease resistance to BPB and SB. Disease phenotypes in BPB and SB, as well as the days-to-heading (DTH) trait, were evaluated in the field. DTH was correlated to BPB and SB diseases, while BPB was positively correlated to SB in the field trials with this RIL population. Genotyping was performed using Kompetitive Allele Specific PCR (KASP) assays and whole-genome sequence (WGS) analyses. Quantitative trait locus (QTL) mapping and bulk segregant analysis using a set of WGS data (QTL-seq) detected a major QTL on the upper arm of chromosome 3 for BPB, SB, and DTH traits within the 1.0-1.9 Mb position. Additional QTLs associated with BPB and SB were also identified from other chromosomes by the QTL-seq analysis. The QTLs identified in this study contain at least nine candidate genes that are predicted to have biological functions in defense or flowering. These findings provide an insight into the complex nature of the quantitative resistance to BPB and SB, which may also be closely linked to the flowering trait.
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Affiliation(s)
- John Christian Ontoy
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Bishnu Shrestha
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Hari Sharan Karki
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Inderjit Barphagha
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, LSU AgCenter, Rayne, LA 70578, USA
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, LSU AgCenter, Rayne, LA 70578, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
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Park J, Jung H, Mannaa M, Lee SY, Lee HH, Kim N, Han G, Park DS, Lee SW, Lee SW, Seo YS. Genome-guided comparative in planta transcriptome analyses for identifying cross-species common virulence factors in bacterial phytopathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:1030720. [PMID: 36466249 PMCID: PMC9709210 DOI: 10.3389/fpls.2022.1030720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Plant bacterial disease is a complex outcome achieved through a combination of virulence factors that are activated during infection. However, the common virulence factors across diverse plant pathogens are largely uncharacterized. Here, we established a pan-genome shared across the following plant pathogens: Burkholderia glumae, Ralstonia solanacearum, and Xanthomonas oryzae pv. oryzae. By overlaying in planta transcriptomes onto the pan-genome, we investigated the expression profiles of common genes during infection. We found over 70% of identical patterns for genes commonly expressed by the pathogens in different plant hosts or infection sites. Co-expression patterns revealed the activation of a signal transduction cascade to recognize and respond to external changes within hosts. Using mutagenesis, we uncovered a relationship between bacterial virulence and functions highly conserved and shared in the studied genomes of the bacterial phytopathogens, including flagellar biosynthesis protein, C4-dicarboxylate ABC transporter, 2-methylisocitrate lyase, and protocatechuate 3,4-dioxygenase (PCD). In particular, the disruption of PCD gene led to attenuated virulence in all pathogens and significantly affected phytotoxin production in B. glumae. This PCD gene was ubiquitously distributed in most plant pathogens with high homology. In conclusion, our results provide cross-species in planta models for identifying common virulence factors, which can be useful for the protection of crops against diverse pathogens.
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Affiliation(s)
- Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Namgyu Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Gil Han
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Dong-Soo Park
- Paddy Crop Division, National Institute of Crop Science, Rural Development Administration, Miryang, South Korea
| | - Sang-Won Lee
- Department of Plant Molecular Systems Biotech & Crop Biotech Institute, KyungHee University, Yongin, South Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
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Sidoruk KV, Levitin EI, Sviridov BV, Piksasova OV, Shustikova TE. A Method of DNA Extraction from a Wide Range of Objects via Treatment with Ammonium Salts. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821080056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Genome Sequence and Adaptation Analysis of the Human and Rice Pathogenic Strain Burkholderia glumae AU6208. Pathogens 2021; 10:pathogens10020087. [PMID: 33498266 PMCID: PMC7909282 DOI: 10.3390/pathogens10020087] [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: 12/01/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/01/2022] Open
Abstract
Burkholderia glumae causes rice (Oryza sativa) bacterial panicle blight, which is an increasingly economically important disease worldwide. As the first B. glumae strain isolated from patients with chronic infections, AU6208 has been reported as an opportunistic clinic pathogen. However, our understanding of the molecular mechanism underlying human pathogenesis by B. glumae remains rudimentary. In this study, we report the complete genome sequence of the human-isolated B. glumae strain AU6208 and compare this to the genome of the rice-pathogenic B. glumae type strain LMG 2196T. Analysis of the average nucleotide identity demonstrated 99.4% similarity between the human- and plant-pathogenic strains. However, the phenotypic results from this study suggest a history of niche adaptation and divergence. In particular, we found 44 genes were predicted to be horizontally transferred into AU6208, and most of these genes were upregulated in conditions that mimic clinical conditions. In these, the gene pair sbnAB encodes key enzymes in antibiotic biosynthesis. These results suggest that horizontal gene transfer in AU6208 may be responsible for selective advantages in its pathogenicity in humans. Our analysis of the AU6208 genome and comparison with that of LMG 2196T reveal the evolutionary signatures of B. glumae in the process of switching niches from plants to humans.
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NMR-based metabolic profiling to follow the production of anti-phytopathogenic compounds in the culture of the marine strain Streptomyces sp. PNM-9. Microbiol Res 2020; 239:126507. [DOI: 10.1016/j.micres.2020.126507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
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Warming increases Bacterial Panicle Blight (Burkholderia glumae) occurrences and impacts on USA rice production. PLoS One 2019; 14:e0219199. [PMID: 31295286 PMCID: PMC6623956 DOI: 10.1371/journal.pone.0219199] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Bacterial Panicle Blight (BPB), caused by Burkholderia glumae, is a bacterial disease in rice (Oryza sativa) that reduces rice yield and quality for producers and consequently creates higher market prices for consumers. BPB is caused by the simultaneous occurrence of high daily minimum temperatures (~22°C) and relative humidity (~77%), which may increase under the current scenario of global warming. This study hypothesized that the economic damage from warming may cause an increase in economic losses, though at a decreasing rate per degree. Thus, this study estimates the yield losses associated with BPB occurrences at the county level in the Mid-South United States (US) for annual rice production in 2003–2013 and under +1–3°C warming scenarios using daily weather information with appropriate thresholds. From the estimated losses, the total production potential of a BPB-resistant rice was quantified using a spatial equilibrium trade model to further estimate market welfare changes with the counterfactual scenario that all US county-level rice production were BPB resistant. Results from the study indicate that the alleviation of BPB would represent a $69 million USD increase in consumer surplus in the US and a concomitant increase in rice production that would feed an additional 1.46 million people annually assuming a global average consumption of 54 Kg per person. Under the 1°C warming scenario, BPB occurrences and production losses would cause price increases for rice and subsequently result in a $112 million USD annual decrease in consumer surplus in the US and a loss of production equivalent to feeding 2.17 million people. Under a 3°C warming scenario, production losses due to BPB cause an annual reduction of $204 million USD in consumer surplus in the US, and a loss in production sufficient to feed 3.98 million people a year. As global warming intensifies, BPB could become a more common and formidable rice disease to combat, and breeding for BPB resistance would be the primary line-of-defense as currently no effective chemical options are available. The results of this study inform agriculturalists, policymakers, and economists about the value of BPB-resistance in the international rice market and also help support efforts to focus future breeding toward climate change impact resilience.
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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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Lee YH, Ko SJ, Cha KH, Park EW. BGRcast: A Disease Forecast Model to Support Decision-making for Chemical Sprays to Control Bacterial Grain Rot of Rice. THE PLANT PATHOLOGY JOURNAL 2015; 31:350-62. [PMID: 26672893 PMCID: PMC4677744 DOI: 10.5423/ppj.oa.07.2015.0136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 05/22/2023]
Abstract
A disease forecast model for bacterial grain rot (BGR) of rice, which is caused by Burkholderia glumae, was developed in this study. The model, which was named 'BGRcast', determined daily conduciveness of weather conditions to epidemic development of BGR and forecasted risk of BGR development. All data that were used to develop and validate the BGRcast model were collected from field observations on disease incidence at Naju, Korea during 1998-2004 and 2010. In this study, we have proposed the environmental conduciveness as a measure of conduciveness of weather conditions for population growth of B. glumae and panicle infection in the field. The BGRcast calculated daily environmental conduciveness, Ci , based on daily minimum temperature and daily average relative humidity. With regard to the developmental stages of rice plants, the epidemic development of BGR was divided into three phases, i.e., lag, inoculum build-up and infection phases. Daily average of Ci was calculated for the inoculum build-up phase (Cinf ) and the infection phase (Cinc ). The Cinc and Cinf were considered environmental conduciveness for the periods of inoculum build-up in association with rice plants and panicle infection during the heading stage, respectively. The BGRcast model was able to forecast actual occurrence of BGR at the probability of 71.4% and its false alarm ratio was 47.6%. With the thresholds of Cinc = 0.3 and Cinf = 0.5, the model was able to provide advisories that could be used to make decisions on whether to spray bactericide at the pre- and post-heading stage.
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Affiliation(s)
- Yong Hwan Lee
- Disaster Management Division, Rural Development Administration, Jeonju 54875,
Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
| | - Sug-Ju Ko
- Jeonnam Agricultural Research and Extension Services, Naju 58213,
Korea
| | - Kwang-Hong Cha
- Jeonnam Agricultural Research and Extension Services, Naju 58213,
Korea
| | - Eun Woo Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826,
Korea
- Interdisciplinary Program in Agricultural and Forest Meteorology, Seoul National University, Seoul 08826,
Korea
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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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