Whole Genome Sequence of Seaweed Endophyte Bacillus Halotolerans Strain AUPP for Antagonistic Activity Against Fusarium Incarnatum Causing Chilli Fruit Rot

Overview

Journal Sci Rep

Specialty Science

Date 2024 Dec 31

PMID 39738420

Authors

Hudson Ann Suji

Karuppiah Manikandan

Appusami Sudha

Arjunan Muthukumar

Chelladurai Jeyalakshmi

Muniyandi Charumathi

Manickam Rajesh

Thankaraj Suthin Raj

Affiliations

Soon will be listed here.

Abstract

Endophytes isolated from seaweeds emerge as promising biocontrol agents against broad spectrum of plant diseases. The endophytic bacteria were isolated from the seaweed (Sargassum wightii) to manage the chilli fruit rot pathogen Fusarium incarnatum. The antifungal activity of the isolated bacteria was tested by dual culture assay and plant growth-promoting activity was also tested by the standard paper towel method. The biocontrol strain AUPP displayed strong antifungal against Fusarium incarnatum (80.23%) and plant growth-promoting activity including seed germination (97.60%) and vigour index (1287.34) under in-vitro conditions. The identity of the endophytic bacteria was established through whole genome sequence analysis which showed promising biocontrol and plant growth-promoting activity. Whole genome sequence analysis of the biocontrol Bacillus halotolerans strain AUPP revealed the genomic information including 4,166,288 bp genome size, 18 contigs and 43.6% GC content. Genome analysis revealed the 15 secondary metabolite regions associated with the production of secondary metabolites and genes responsible for the antifungal activity. Furthermore, we identified multiple antibiotics, multidrug-resistant genes and a CRISPR sequence. This study presents the first whole genome sequence of B. halotolerans isolated from seaweed in India. These findings highlight its potential for broad-spectrum plant disease control.

References

Wattam A, Davis J, Assaf R, Boisvert S, Brettin T, Bun C . Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res. 2016; 45(D1):D535-D542. PMC: 5210524. DOI: 10.1093/nar/gkw1017. View

Meier-Kolthoff J, Goker M . TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019; 10(1):2182. PMC: 6522516. DOI: 10.1038/s41467-019-10210-3. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Chen X, Vater J, Piel J, Franke P, Scholz R, Schneider K . Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J Bacteriol. 2006; 188(11):4024-36. PMC: 1482889. DOI: 10.1128/JB.00052-06. View

Meier-Kolthoff J, Auch A, Klenk H, Goker M . Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013; 14:60. PMC: 3665452. DOI: 10.1186/1471-2105-14-60. View

Saggese A, Culurciello R, Casillo A, Corsaro M, Ricca E, Baccigalupi L . A Marine Isolate of Secretes a Pumilacidin Active against . Mar Drugs. 2018; 16(6). PMC: 6025400. DOI: 10.3390/md16060180. View

Feng Z, Xu M, Yang J, Zhang R, Geng Z, Mao T . Molecular characterization of a novel strain of protecting wheat from sheath blight disease caused by . Front Plant Sci. 2022; 13:1019512. PMC: 9618607. DOI: 10.3389/fpls.2022.1019512. View

Gao W, Liu F, Zhang W, Quan Y, Dang Y, Feng J . Mutations in genes encoding antibiotic substances increase the synthesis of poly-γ-glutamic acid in Bacillus amyloliquefaciens LL3. Microbiologyopen. 2016; 6(1). PMC: 5300885. DOI: 10.1002/mbo3.398. View

Wu X, Wu H, Wang R, Wang Z, Zhang Y, Gu Q . Genomic Features and Molecular Function of a Novel Stress-Tolerant Strain Isolated from an Extreme Environment. Biology (Basel). 2021; 10(10). PMC: 8533444. DOI: 10.3390/biology10101030. View

10.

Castillo D, Rorbo N, Jorgensen J, Lange J, Tan D, Kalatzis P . Phage defense mechanisms and their genomic and phenotypic implications in the fish pathogen Vibrio anguillarum. FEMS Microbiol Ecol. 2019; 95(3). DOI: 10.1093/femsec/fiz004. View

11.

Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee S . antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019; 47(W1):W81-W87. PMC: 6602434. DOI: 10.1093/nar/gkz310. View

12.

Ben Slama H, Cherif-Silini H, Bouket A, Qader M, Silini A, Yahiaoui B . Screening for Antagonistic Bacteria From Contrasting Niches Designated the Endophyte as Plant Warden Against . Front Microbiol. 2019; 9:3236. PMC: 6336696. DOI: 10.3389/fmicb.2018.03236. View

13.

Alcock B, Huynh W, Chalil R, Smith K, Raphenya A, Wlodarski M . CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2022; 51(D1):D690-D699. PMC: 9825576. DOI: 10.1093/nar/gkac920. View

14.

Masand M, Jose P, Menghani E, Jebakumar S . Continuing hunt for endophytic actinomycetes as a source of novel biologically active metabolites. World J Microbiol Biotechnol. 2015; 31(12):1863-75. DOI: 10.1007/s11274-015-1950-y. View

15.

Tsalgatidou P, Thomloudi E, Baira E, Papadimitriou K, Skagia A, Venieraki A . Integrated Genomic and Metabolomic Analysis Illuminates Key Secreted Metabolites Produced by the Novel Endophyte Cal.l.30 Involved in Diverse Biological Control Activities. Microorganisms. 2022; 10(2). PMC: 8877463. DOI: 10.3390/microorganisms10020399. View

16.

Juhmani A, Vezzi A, Wahsha M, Buosi A, De Pascale F, Schiavon R . Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice. Microorganisms. 2020; 8(11). PMC: 7693704. DOI: 10.3390/microorganisms8111657. View

17.

Overbeek R, Olson R, Pusch G, Olsen G, Davis J, Disz T . The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2013; 42(Database issue):D206-14. PMC: 3965101. DOI: 10.1093/nar/gkt1226. View

18.

Magno-Perez-Bryan M, Martinez-Garcia P, Hierrezuelo J, Rodriguez-Palenzuela P, Arrebola E, Ramos C . Comparative Genomics Within the Bacillus Genus Reveal the Singularities of Two Robust Bacillus amyloliquefaciens Biocontrol Strains. Mol Plant Microbe Interact. 2015; 28(10):1102-16. DOI: 10.1094/MPMI-02-15-0023-R. View

19.

Grant J, Enns E, Marinier E, Mandal A, Herman E, Chen C . Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 2023; 51(W1):W484-W492. PMC: 10320063. DOI: 10.1093/nar/gkad326. View

20.

Jin Q, Jiang Q, Zhao L, Su C, Li S, Si F . Complete genome sequence of Bacillus velezensis S3-1, a potential biological pesticide with plant pathogen inhibiting and plant promoting capabilities. J Biotechnol. 2017; 259:199-203. DOI: 10.1016/j.jbiotec.2017.07.011. View