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Moshe M, Gupta CL, Sela N, Minz D, Banin E, Frenkel O, Cytryn E. Comparative genomics of Bacillus cereus sensu lato spp. biocontrol strains in correlation to in-vitro phenotypes and plant pathogen antagonistic capacity. Front Microbiol 2023; 14:996287. [PMID: 36846749 PMCID: PMC9947482 DOI: 10.3389/fmicb.2023.996287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Bacillus cereus sensu lato (Bcsl) strains are widely explored due to their capacity to antagonize a broad range of plant pathogens. These include B. cereus sp. UW85, whose antagonistic capacity is attributed to the secondary metabolite Zwittermicin A (ZwA). We recently isolated four soil and root-associated Bcsl strains (MO2, S-10, S-25, LSTW-24) that displayed different growth profiles and in-vitro antagonistic effects against three soilborne plant pathogens models: Pythium aphanidermatum (oomycete) Rhizoctonia solani (basidiomycete), and Fusarium oxysporum (ascomycete). To identify genetic mechanisms potentially responsible for the differences in growth and antagonistic phenotypes of these Bcsl strains, we sequenced and compared their genomes, and that of strain UW85 using a hybrid sequencing pipeline. Despite similarities, specific Bcsl strains had unique secondary metabolite and chitinase-encoding genes that could potentially explain observed differences in in-vitro chitinolytic potential and anti-fungal activity. Strains UW85, S-10 and S-25 contained a (~500 Kbp) mega-plasmid that harbored the ZwA biosynthetic gene cluster. The UW85 mega-plasmid contained more ABC transporters than the other two strains, whereas the S-25 mega-plasmid carried a unique cluster containing cellulose and chitin degrading genes. Collectively, comparative genomics revealed several mechanisms that can potentially explain differences in in-vitro antagonism of Bcsl strains toward fungal plant pathogens.
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Affiliation(s)
- Maya Moshe
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Chhedi Lal Gupta
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Noa Sela
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Ehud Banin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omer Frenkel
- Institute of Plant Pathology and Weed Research, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel
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Rodríguez M, Reina JC, Sampedro I, Llamas I, Martínez-Checa F. Peribacillus castrilensis sp. nov.: A Plant-Growth-Promoting and Biocontrol Species Isolated From a River Otter in Castril, Granada, Southern Spain. FRONTIERS IN PLANT SCIENCE 2022; 13:896728. [PMID: 35812926 PMCID: PMC9262404 DOI: 10.3389/fpls.2022.896728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
A strictly aerobic, chemoheterotrophic, endospore-forming, Gram-positive, rod-shaped bacterial strain N3T was isolated from the feces of a river otter in Castril (Granada, southern Spain). It is halotolerant, motile, and catalase-, oxidase-, ACC deaminase-, and C4- and C8-lipase-positive. It promotes tomato plant growth and can reduce virulence in Erwinia amylovora CECT 222T and Dickeya solani LMG 25993T through interference in their quorum-sensing systems, although other antagonistic mechanisms could also occur. A phylogenetic analysis of the 16S rRNA gene sequence as well as the phenotypic and phylogenomic analyses indicated that the strain N3T is a novel species of the genus Peribacillus, with the highest 16S rRNA sequence similar to that of Bacillus frigoritolerans DSM 8801T (99.93%) and Peribacillus simplex DSM 1321T (99.80%). Genomic digital DNA-DNA hybridization (dDDH) between the strain N3T and Bacillus frigoritolerans DSM 8801T and Peribacillus simplex was 12.8 and 69.1%, respectively, and the average nucleotide identity (ANIb) of strain N3T and Bacillus frigoritolerans DSM 8801T and Peribacillus simplex was 67.84 and 93.21%, respectively. The genomic G + C content was 40.3 mol%. Its main cellular fatty acids were anteiso-C15:0 and iso-C15:0. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with the chemotaxonomic and phenotypic data, we demonstrated that the type strain N3T (=CECT 30509T = LMG 32505T) is a novel species of the genus Peribacillus and the name Peribacillus castrilensis sp. nov. is proposed.
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Affiliation(s)
- Miguel Rodríguez
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - José Carlos Reina
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Inmaculada Sampedro
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Inmaculada Llamas
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Biomedical Research Centre (CIBM), Institute of Biotechnology, University of Granada, Granada, Spain
| | - Fernando Martínez-Checa
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
- Biomedical Research Centre (CIBM), Institute of Biotechnology, University of Granada, Granada, Spain
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Kalia VC, Patel SKS, Kang YC, Lee JK. Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 2018; 37:68-90. [PMID: 30471318 DOI: 10.1016/j.biotechadv.2018.11.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/19/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Abstract
The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Achari GA, Ramesh R. Characterization of bacteria degrading 3-hydroxy palmitic acid methyl ester (3OH-PAME), a quorum sensing molecule of Ralstonia solanacearum. Lett Appl Microbiol 2015; 60:447-55. [PMID: 25580768 DOI: 10.1111/lam.12389] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 01/05/2015] [Accepted: 01/05/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED Bacterial wilt pathogen Ralstonia solanacearum causes severe crop loss of eggplant, which is of economic importance in India. 3-hydroxy palmitic acid methyl ester (3OH-PAME) is the main quorum sensing molecule governing the expression of virulence factors in R. solanacearum. Ability of 164 bacterial isolates from the xylem of eggplant (Solanum melongena L.), chilli pepper (Capsicum annuum L.) and wild eggplant (Solanum torvum Sw.) to degrade 3OH-PAME was tested by disc diffusion assay. Enzymatic degradation of 3OH-PAME by five bacteria was confirmed by High-Performance Liquid Chromatography-Mass Spectrometry analysis. 3OH-PAME degrading bacteria were identified as Stenotrophomonas maltophilia, Pseudomonas aeruginosa and Rhodococcus corynebacterioides. 3OH-PAME degrading bacteria reduced the expression of virulence factors (exopolysaccharides and endoglucanase) of R. solanacearum in vitro and reduced wilt incidence in eggplant seedlings under greenhouse conditions. Isolates with quorum quenching activity successfully re-colonized eggplant seedlings. Quorum quenching bacteria produced antagonistic compounds, which may act synergistically with quorum quenching in reducing bacterial wilt in eggplant. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report on endophytic bacteria of class Gammaproteobacteria and phylum Actinobacteria having 3OH-PAME degrading activity. This study demonstrates the potential use of endophytic bacteria as quorum quenching biocontrol agents for management of bacterial wilt in eggplant.
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Affiliation(s)
- G A Achari
- ICAR Research Complex for Goa, Old Goa, Goa, India; Department of Microbiology, Goa University, Taleigao Plateau, Goa, India
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Kumar P, Patel SK, Lee JK, Kalia VC. Extending the limits of Bacillus for novel biotechnological applications. Biotechnol Adv 2013; 31:1543-61. [DOI: 10.1016/j.biotechadv.2013.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 07/01/2013] [Accepted: 08/05/2013] [Indexed: 12/28/2022]
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Abstract
Cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. Its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. With the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. An antivirulence approach by which quorum sensing is impeded has caught on as a viable means to manipulate bacterial processes, especially pathogenic traits that are harmful to human and animal health and agricultural productivity. The identification and development of chemical compounds and enzymes that facilitate quorum-sensing inhibition (QSI) by targeting signaling molecules, signal biogenesis, or signal detection are reviewed here. Overall, the evidence suggests that QSI therapy may be efficacious against some, but not necessarily all, bacterial pathogens, and several failures and ongoing concerns that may steer future studies in productive directions are discussed. Nevertheless, various QSI successes have rightfully perpetuated excitement surrounding new potential therapies, and this review highlights promising QSI leads in disrupting pathogenesis in both plants and animals.
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Araújo FDDS, Esper LMR, Kuaye AY, Sircili MP, Marsaioli AJ. N-acyl-homoserine lactones from Enterobacter sakazakii (Cronobacter spp.) and their degradation by Bacillus cereus enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:585-592. [PMID: 22132860 DOI: 10.1021/jf203846f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A chemical study of acyl-homoserine lactones (acyl-HSLs) produced by Enterobacter sakazakii resulted in the identification of three molecules: (S)-N-heptanoyl-HSL, (S)-N-dodecanoyl-HSL and (S)-N-tetradecanoyl-HSL. Mixed cultures of E. sakazakii and Bacillus cereus depleted E. sakazakii acyl-HSLs, suggesting acyl-HSL degradation by B. cereus hydrolases (hydrolysis of the lactone or amide moiety). The expression of B. cereus acyl-HSL lactonase and acyl-homoserine acylase was confirmed by monitoring the biotransformation of (S)-N-dodecanoyl-HSL into (S)-N-dodecanoyl-homoserine, dodecanoic acid and homoserine in the presence of B. cereus whole cells, using electrospray-mass spectrometry (ESI-MS).
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Uroz S, Dessaux Y, Oger P. Quorum Sensing and Quorum Quenching: The Yin and Yang of Bacterial Communication. Chembiochem 2009; 10:205-16. [DOI: 10.1002/cbic.200800521] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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The maintenance of the list of QPS microorganisms intentionally added to food or feed - Scientific Opinion of the Panel on Biological Hazards. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.923] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Zhou Y, Choi YL, Sun M, Yu Z. Novel roles of Bacillus thuringiensis to control plant diseases. Appl Microbiol Biotechnol 2008; 80:563-72. [DOI: 10.1007/s00253-008-1610-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/08/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
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