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Gosset-Erard C, Han G, Kyrko D, Hueber A, Nay B, Eparvier V, Touboul D. Structural characterization of N-acyl-homoserine lactones from bacterial quorum sensing using LC-MS/MS analyses after Paternò-Büchi derivatization in solution. Anal Bioanal Chem 2024:10.1007/s00216-024-05355-0. [PMID: 38842688 DOI: 10.1007/s00216-024-05355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
Bacterial quorum sensing is a chemical language allowing bacteria to interact through the excretion of molecules called autoinducers, like N-acyl-homoserine lactones (AHLs) produced by Gram-negative Burkholderia and Paraburkholderia bacteria known as opportunistic pathogens. The AHLs differ in their acyl-chain length and may be modified by a 3-oxo or 3-hydroxy substituent, or C = C double bonds at different positions. As the bacterial signal specificity depends on all of these chemical features, their structural characterization is essential to have a better understanding of the population regulation and virulence phenomenon. This study aimed at enabling the localization of the C = C double bond on such specialized metabolites while using significantly lower amounts of biological material. The approach is based on LC-MS/MS analyses of bacterial extracts after in-solution derivatization by a photochemical Paternò-Büchi reaction, leading to the formation of an oxetane ring and subsequently to specific fragmentations when performing MS/MS experiments. The in-solution derivatization of AHLs was optimized on several standards, and then the matrix effect of bacterial extracts on the derivatization was assessed. As a proof of concept, the optimized conditions were applied to a bacterial extract enabling the localization of C = C bonds on unsaturated AHLs.
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Affiliation(s)
- Clarisse Gosset-Erard
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Guanghui Han
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Dimitra Kyrko
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Amandine Hueber
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - Bastien Nay
- Laboratoire de Synthèse Organique (LSO), CNRS UMR 7652, Ecole Polytechnique, ENSTA, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Véronique Eparvier
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, CNRS, Institut de Chimie Des Substances Naturelles, UPR 2301, 91198, Gif-Sur-Yvette, France.
- Laboratoire de Chimie Moléculaire (LCM), CNRS UMR 9168, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.
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Radjasa OK, Steven R, Humaira Z, Dwivany FM, Nugrahapraja H, Trinugroho JP, Kristianti T, Chahyadi A, Natanael Y, Priharto N, Kamarisima, Sembiring FAPB, Dwijayanti A, Kusmita L, Moeis MR, Suhardi VSH. Biosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites. Sci Rep 2023; 13:19273. [PMID: 37935710 PMCID: PMC10630419 DOI: 10.1038/s41598-023-44603-8] [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: 02/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.
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Affiliation(s)
- Ocky Karna Radjasa
- Research Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation Agency, Jakarta, 14430, Indonesia.
| | - Ray Steven
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Zalfa Humaira
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Fenny Martha Dwivany
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia.
| | - Husna Nugrahapraja
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Joko Pebrianto Trinugroho
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Tati Kristianti
- Institut Pendidikan Indonesia, Garut, West Java, 44151, Indonesia
| | - Agus Chahyadi
- University Center of Excellence for Nutraceuticals, Bioscience and Biotechnology Research Center, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Yosua Natanael
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Neil Priharto
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Kamarisima
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | | | - Ari Dwijayanti
- CNRS@CREATE Ltd., 1 Create Way, #08-01 Create Tower, Singapore, 138602, Singapore
| | - Lia Kusmita
- STIFAR Yayasan Pharmasi Semarang, Semarang, Central Java, 50124, Indonesia
| | - Maelita R Moeis
- Department of Biotechnology, Faculty of Science and Technology, Universitas Muhammadiyah Bandung, Bandung, West Java, 40262, Indonesia
| | - V Sri Harjati Suhardi
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
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Webster G, Mullins AJ, Petrova YD, Mahenthiralingam E. Polyyne-producing Burkholderia suppress Globisporangium ultimum damping-off disease of Pisum sativum (pea). Front Microbiol 2023; 14:1240206. [PMID: 37692405 PMCID: PMC10485841 DOI: 10.3389/fmicb.2023.1240206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023] Open
Abstract
Extensive crop losses are caused by oomycete and fungal damping-off diseases. Agriculture relies heavily on chemical pesticides to control disease, but due to safety concerns multiple agents have been withdrawn. Burkholderia were successfully used as commercial biopesticides because of their fungicidal activity and plant protective traits. However, their potential for opportunistic pathogenicity led to a moratorium on their registration as biopesticides. Subsequently, Burkholderia were shown to produce multiple specialised metabolites including potent antimicrobial polyynes. Cepacin A, a polyyne produced by Burkholderia ambifaria biopesticide strains was shown to be an important metabolite for the protection of germinating peas against Globisporangium ultimum (formerly Pythium) damping-off disease. Recently, there has been an expansion in bacterial polyyne discovery, with the metabolites and their biosynthetic gene pathways found in several bacterial genera including Burkholderia, Collimonas, Trinickia, and Pseudomonas. To define the efficacy of these bacterial polyyne producers as biopesticidal agents, we systematically evaluated metabolite production, in vitro microbial antagonism, and G. ultimum biocontrol across a panel of 30 strains representing four bacterial genera. In vitro polyyne production and antimicrobial activity was demonstrated for most strains, but only Burkholderia polyyne producers were protective within the in vivo G. ultimum damping-off pea protection model. B. ambifaria was the most effective cepacin-expressing biopesticide, and despite their known potential for plant pathogenicity Burkholderia gladioli and Burkholderia plantarii were uniquely shown to be protective as caryoynencin-producing biopesticides. In summary, Burkholderia are effective biopesticides due to their suite of antimicrobials, but the ability to deploy polyyne metabolites, caryoynencin and cepacin, is strain and species dependent. Graphical Abstract.
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Smith HAB, Mullins AJ, Webster G, Sapsford D, Gaskin P, Monis PT, Hoefel D, Saint CP, Weightman AJ. Sphingopyxis Species Isolated from Sand Filter Biofilm at an Australian Drinking Water Treatment Works. Microbiol Resour Announc 2023; 12:e0024923. [PMID: 37341619 PMCID: PMC10353388 DOI: 10.1128/mra.00249-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/01/2023] [Indexed: 06/22/2023] Open
Abstract
Three strains isolated by geosmin enrichment from a sand filter in an Australian drinking water treatment works were genome sequenced to identify their taxonomic placement, and a bench-scale batch experiment confirmed their geosmin-degrading capability. Using the average nucleotide identity based on the MUMmer algorithm (ANIm), pairwise digital DNA-DNA hybridization (dDDH), and phylogenomic analyses, the strains were identified as Sphingopyxis species.
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Affiliation(s)
- Holly-Anne B. Smith
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
| | - Devin Sapsford
- School of Engineering, Queen’s Buildings, Cardiff University, Cardiff, Wales, United Kingdom
| | - Paul Gaskin
- Dwr Cymru Welsh Water, Coed Kernew, Newport, Wales, United Kingdom
| | - Paul T. Monis
- Australian Water Quality Centre, SA Water, Adelaide, Australia
| | - Daniel Hoefel
- Australian Water Quality Centre, SA Water, Adelaide, Australia
| | - Christopher P. Saint
- Future Industries Institute, University of South Australia, Adelaide, Australia
- UniSA STEM, University of South Australia, Adelaide, Australia
| | - Andrew J. Weightman
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
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Compilation of the Antimicrobial Compounds Produced by Burkholderia Sensu Stricto. Molecules 2023; 28:molecules28041646. [PMID: 36838633 PMCID: PMC9958762 DOI: 10.3390/molecules28041646] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Due to the increase in multidrug-resistant microorganisms, the investigation of novel or more efficient antimicrobial compounds is essential. The World Health Organization issued a list of priority multidrug-resistant bacteria whose eradication will require new antibiotics. Among them, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae are in the "critical" (most urgent) category. As a result, major investigations are ongoing worldwide to discover new antimicrobial compounds. Burkholderia, specifically Burkholderia sensu stricto, is recognized as an antimicrobial-producing group of species. Highly dissimilar compounds are among the molecules produced by this genus, such as those that are unique to a particular strain (like compound CF66I produced by Burkholderia cepacia CF-66) or antimicrobials found in a number of species, e.g., phenazines or ornibactins. The compounds produced by Burkholderia include N-containing heterocycles, volatile organic compounds, polyenes, polyynes, siderophores, macrolides, bacteriocins, quinolones, and other not classified antimicrobials. Some of them might be candidates not only for antimicrobials for both bacteria and fungi, but also as anticancer or antitumor agents. Therefore, in this review, the wide range of antimicrobial compounds produced by Burkholderia is explored, focusing especially on those compounds that were tested in vitro for antimicrobial activity. In addition, information was gathered regarding novel compounds discovered by genome-guided approaches.
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Petrova YD, Zhao J, Webster G, Mullins AJ, Williams K, Alswat AS, Challis GL, Bailey AM, Mahenthiralingam E. Cloning and expression of Burkholderia polyyne biosynthetic gene clusters in Paraburkholderia hosts provides a strategy for biopesticide development. Microb Biotechnol 2022; 15:2547-2561. [PMID: 35829647 PMCID: PMC9518984 DOI: 10.1111/1751-7915.14106] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/27/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022] Open
Abstract
Burkholderia have potential as biocontrol agents because they encode diverse biosynthetic gene clusters (BGCs) for a range of antimicrobial metabolites. Given the opportunistic pathogenicity associated with Burkholderia species, heterologous BGC expression within non-pathogenic hosts is a strategy to construct safe biocontrol strains. We constructed a yeast-adapted Burkholderia-Escherichia shuttle vector (pMLBAD_yeast) with a yeast replication origin 2 μ and URA3 selection marker and optimised it for cloning BGCs using the in vivo recombination ability of Saccharomyces cerevisiae. Two Burkholderia polyyne BGCs, cepacin (13 kb) and caryoynencin (11 kb), were PCR-amplified as three overlapping fragments, cloned downstream of the pBAD arabinose promoter in pMLBAD_yeast and mobilised into Burkholderia and Paraburkholderia heterologous hosts. Paraburkholderia phytofirmans carrying the heterologous polyyne constructs displayed in vitro bioactivity against a variety of fungal and bacterial plant pathogens similar to the native polyyne producers. Thirteen Paraburkholderia strains with preferential growth at 30°C compared with 37°C were also identified, and four of these were amenable to genetic manipulation and heterologous expression of the caryoynencin construct. The cloning and successful heterologous expression of Burkholderia biosynthetic gene clusters within Paraburkholderia with restricted growth at 37°C opens avenues for engineering non-pathogenic biocontrol strains.
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Affiliation(s)
| | - Jinlian Zhao
- Department of Chemistry, University of Warwick, Coventry, UK
| | | | | | | | - Amal S Alswat
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK.,Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia
| | - Andy M Bailey
- School of Biological Sciences, University of Bristol, Bristol, UK
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Ayhan K, Coşansu S, Orhan-Yanıkan E, Gülseren G. Advance methods for the qualitative and quantitative determination of microorganisms. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Jones C, Webster G, Mullins AJ, Jenner M, Bull MJ, Dashti Y, Spilker T, Parkhill J, Connor TR, LiPuma JJ, Challis GL, Mahenthiralingam E. Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles. Microb Genom 2021; 7:mgen000515. [PMID: 33459584 PMCID: PMC8115902 DOI: 10.1099/mgen.0.000515] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/22/2020] [Indexed: 01/22/2023] Open
Abstract
Burkholderia gladioli is a bacterium with a broad ecology spanning disease in humans, animals and plants, but also encompassing multiple beneficial interactions. It is a plant pathogen, a toxin-producing food-poisoning agent, and causes lung infections in people with cystic fibrosis (CF). Contrasting beneficial traits include antifungal production exploited by insects to protect their eggs, plant protective abilities and antibiotic biosynthesis. We explored the genomic diversity and specialized metabolic potential of 206 B. gladioli strains, phylogenomically defining 5 clades. Historical disease pathovars (pv.) B. gladioli pv. allicola and B. gladioli pv. cocovenenans were distinct, while B. gladioli pv. gladioli and B. gladioli pv. agaricicola were indistinguishable; soft-rot disease and CF infection were conserved across all pathovars. Biosynthetic gene clusters (BGCs) for toxoflavin, caryoynencin and enacyloxin were dispersed across B. gladioli, but bongkrekic acid and gladiolin production were clade-specific. Strikingly, 13 % of CF infection strains characterized were bongkrekic acid-positive, uniquely linking this food-poisoning toxin to this aspect of B. gladioli disease. Mapping the population biology and metabolite production of B. gladioli has shed light on its diverse ecology, and by demonstrating that the antibiotic trimethoprim suppresses bongkrekic acid production, a potential therapeutic strategy to minimize poisoning risk in CF has been identified.
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Affiliation(s)
- Cerith Jones
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Present address: School of Applied Sciences, Faculty of Computing, Engineering and Science, University of South Wales, Pontypridd, CF37 4BD, UK
| | - Gordon Webster
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Alex J. Mullins
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Matthew Jenner
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew J. Bull
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Present address: Pathogen Genomics Unit, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Yousef Dashti
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Present address: The Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Present address: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Thomas R. Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - John J. LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gregory L. Challis
- Department of Chemistry and Warwick Integrative Synthetic Biology Centre, University of Warwick, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Eshwar Mahenthiralingam
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
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Burkholderia gladioli CGB10: A Novel Strain Biocontrolling the Sugarcane Smut Disease. Microorganisms 2020; 8:microorganisms8121943. [PMID: 33297590 PMCID: PMC7762381 DOI: 10.3390/microorganisms8121943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, we isolated an endophytic Burkholderia gladioli strain, named CGB10, from sugarcane leaves. B. gladioli CGB10 displayed strong inhibitory activity against filamentous growth of fungal pathogens, one of which is Sporisorium scitamineum that causes sugarcane smut, a major disease affecting the quality and production of sugarcane in tropical and subtropical regions. CGB10 could effectively suppress sugarcane smut under field conditions, without itself causing any obvious damage or disease, thus underscoring a great potential as a biocontrol agent (BCA) for the management of sugarcane smut. A toxoflavin biosynthesis and transport gene cluster potentially responsible for such antifungal activity was identified in the CGB10 genome. Additionally, a quorum-sensing gene cluster was identified too and compared with two close Burkholderia species, thus supporting an overall connection to the regulation of toxoflavin synthesis therein. Overall, this work describes the in vitro and field Sporisorium scitamineum biocontrol by a new B. gladioli strain, and reports genes and molecular mechanisms potentially involved.
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