Abstract
The application of biocontrol biopesticides based on plant growth–promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable and ecologically safe. Recent advances in genome sequencing by third-generation sequencing technologies, e.g., Pacific Biosciences’ Single Molecule Real-Time (PacBio SMRT) platform, have allowed researchers to gain deeper insights into the molecular and genetic mechanisms of PGPR activities, and to compare whole genome sequences and global patterns of epigenetic modifications. In the current work, this approach was used to sequence and compare four Bacillus strains that exhibited various PGPR activities including the strain UCMB5140, which is used in the commercial biopesticide Phytosubtil. Whole genome comparison and phylogenomic inference assigned the strain UCMB5140 to the species Bacillus velezensis. Strong biocontrol activities of this strain were confirmed in several bioassays. Several factors that affect the evolution of active PGPR B. velezensis strains were identified: (1) horizontal acquisition of novel non-ribosomal peptide synthetases (NRPS) and adhesion genes; (2) rearrangements of functional modules of NRPS genes leading to strain specific combinations of their encoded products; (3) gain and loss of methyltransferases that can cause global alterations in DNA methylation patterns, which eventually may affect gene expression and regulate transcription. Notably, we identified a horizontally transferred NRPS operon encoding an uncharacterized polypeptide antibiotic in B. velezensis UCMB5140. Other horizontally acquired genes comprised a possible adhesin and a methyltransferase, which may explain the strain-specific methylation pattern of the chromosomal DNA of UCMB5140.
Key points
• Whole genome sequence of the active PGPR Bacillus velezensis UCMB5140.
• Identification of genetic determinants responsible for PGPR activities.
• Role of methyltransferases and epigenetic mechanisms in evolution of bacteria.
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Acknowledgments
We gratefully acknowledge K. Dietel (ABiTEP GmbH, Berlin, Germany) for preparing samples for mass spectroscopic measurements, and Daniel Frei and Juerg E. Frey (Agroscope, Switzerland) for the Illumina MiSeq sequencing.
Funding
O.N.R. was funded by the South African National Research Foundation (NRF) grants 93134 and 93664; O.N.R., Sy.L., and D.T. received funds from the joint NRF/COSTECH (Tanzanian Commission for Science and Technology) grant 86905 and from joint TIA (Technology Innovation Agency of South Africa)/COSTECH grant TIA 2018-FUN-0050. A.D.M. acquired PhD and MSc student fellowship grants from Southern African Biochemistry and Informatics for Natural Products (SABINA, http://www.sabina-africa.org/). C.H.A. acknowledges support from Agroscope through its research program Microbial Biodiversity.
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O.N.R.—DNA and RNA sequencing, genome assembly, annotation, epigenetic profiling, funding acquisition, student supervision; S.A.L.—UCMB5140 isolation and characterization; A.D.M.—PGPR assays; D.M.—PGPR assays, student supervision; Sy.L.—PGPR assays, student supervision; W.Y.C.—mass spectrometry studies; St.L.—PacBio and Illumina MiSeq sequencing, genome assembly; C.H.A.—funding acquisition, PacBio and Illumina MiSeq sequencing, genome assembly; J.V.—mass spectroscopic measurements; R.B.—mass spectrometry and study supervision. All co-authors took part in the manuscript writing and edition.
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The authors declare that they have no conflict of interest. This article does not contain any studies with human participants or animals performed by any of the authors. All genome sequences obtained during the present study were made publicly accessible from NCBI database.
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Reva, O.N., Larisa, S.A., Mwakilili, A.D. et al. Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains. Appl Microbiol Biotechnol 104, 7643–7656 (2020). https://doi.org/10.1007/s00253-020-10767-w
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DOI: https://doi.org/10.1007/s00253-020-10767-w