Genome analysis of a Bacillus subtilis strain reveals genetic mutations determining biocontrol properties

Bettina Bóka,Kadaikunnan Shine,Jamal M Khaled,Sándor Kocsubé,László Kredics,Csaba Vágvölgyi,Naiyf S Alharbi,László Manczinger,Martin Münsterkötter

doi:10.1007/s11274-019-2625-x

Abstract

Several Bacillus strains are used as biocontrol agents, as they frequently have strong antagonistic effects against microbial plant pathogens. Bacillus strain SZMC 6179J, isolated from tomato rhizosphere, was previously shown to have excellent in vitro antagonistic properties against the most important fungal pathogens of tomato (Alternaria solani, Botrytis cinerea, Phytophthora infestans and Sclerotinia sclerotiorum) as well as several Fusarium species. Taxonomic investigations revealed that it is a member of the B. subtilis subsp. subtilis group and very closely related with the reference type strain B. subtilis subsp. subtilis 168. The sequenced genome of strain SZMC 6179J contains the genes responsible for the synthesis of the extracellular antibiotics surfactin, fengycin and bacilysin. Compared to strain 168, a prophage-like region is missing from the genome of SZMC 6179J, while there are 106 single nucleotide polymorphisms and 23 deletion-insertion polymorphisms. The high biocontrol potential of strain SZMC 6179J may results from a single base deletion in the sfp gene encoding the transcription factor of the surfactin and fengycin operons. Hypermutated regions reflecting short-time evolutionary processes could be detected in SZMC 6179J. The deletion-insertion polymorphism in the sfp gene and the detected hypermutations can be suggested as genetic determinants of biocontrol features in B. subtilis.Graphical

Highlights

Bacillus strains are successful biological pest control agents by competition for nutrients and the ecological niche in the rhizosphere
The investigation of the reference strain’s genome for the distribution of prophage sequences by PHAST (Phage Search Tool) did not reveal any prophages or prophage traces. The presence of this region was examined in other Bacillus strains by BLAST (Basic Local Alignment Search Tool) and the results were visualized with Kablammo, which revealed that besides B. subtilis subsp. subtilis 168, only 11 other strains have this prophage-like region in an intact form, while it is entirely missing from Szeged Microbiology Collection (SZMC) 6179J and a series of other B. subtilis strains
The genome of SZMC 6179J is closely related with the reference type strain B. subtilis subsp. subtilis str. 168—a tryptophan-requiring auxotrophic strain widely used in academic research, which was isolated from B. subtilis subsp. subtilis Marburg after

Summary

Introduction

Bacillus strains are successful biological pest control agents by competition for nutrients and the ecological niche in the rhizosphere. They produce various antibiotics and extracellular enzymes and induce systemic resistance mechanisms in plants (Cawoy et al 2011, 2015; Emmert and Handelsman 1999; Jourdan et al 2009; Kloepper et al 2004; Shoda 2000). Complete genome sequences are available for some biocontrol strains of the genus Bacillus (Borriss 2015). Earl et al (2012) published full genomes of four B. subtilis strains The W23 genome has 157 accessory (non-core) genome segments that are not found in B. subtilis subsp. subtilis 168, while its genome has 141 segments not found in strain W23. Deng et al (2011) presented the complete genome sequence of B. subtilis strain BSn5 isolated from

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Results

Conclusion