Reclassification of the biocontrol agents Bacillus subtilis BY-2 and Tu-100 as Bacillus velezensis and insights into the genomic and specialized metabolite diversity of the species.

Alex J Mullins,Xing Liao,Gordon Webster,Chiming Gu,Lu Qin,Lihua Xie,Xiaojia Hu,Eshwar Mahenthiralingam,Yinshui Li

doi:10.1099/mic.0.000986

Abstract

The genomes of two historical Bacillus species strains isolated from the roots of oilseed rape and used routinely in PR China as biocontrol agents to suppress Sclerotinia disease were sequenced. Average nucleotide identity (ANI) and digital DNA–DNA hybridization analyses demonstrated that they were originally misclassified as Bacillus subtilis and now belong to the bacterial species Bacillus velezensis . A broader ANI analysis of available Bacillus genomes identified 292 B. velezensis genomes that were then subjected to core gene analysis and phylogenomics. Prediction and dereplication of specialized metabolite biosynthetic gene clusters (BGCs) defined the prevalence of multiple antimicrobial-associated BGCs and highlighted the natural product potential of B. velezensis . By defining the core and accessory antimicrobial biosynthetic capacity of the species, we offer an in-depth understanding of B. velezensis natural product capacity to facilitate the selection and testing of B. velezensis strains for use as biological control agents.

Highlights

Phytopathogens are a major constraint on global food production, causing plant disease in the field and during post-harvest storage
The clade II B. amyloliquefaciens group contains strains that are more proficient at rhizosphere colonization and biocontrol than other members of the B. subtilis species complex [8, 12], and average nucleotide identity (ANI), digital DNA–DNA hybridization and core gene phylogeny demonstrate that clade II comprises three discrete but closely
Both BY-2 and Tu-100 were similar (≥95 % ANI) to Bacillus genomes classified as B. velezensis

Summary

Introduction

Phytopathogens are a major constraint on global food production, causing plant disease in the field and during post-harvest storage. Several micro-organisms have been developed as biopesticides and used routinely in the field, and among the most successful are members of the Bacillus subtilis species complex, known to suppress disease caused by bacterial, fungal, viral and nematode plant pathogens [2,3,4,5]. Comparison of the complete 16S rRNA gene sequences of Bacillus amyloliquefaciens DSM 7T and B. subtilis 168T revealed >99 % sequence identity [7]. The clade II B. amyloliquefaciens group contains strains that are more proficient at rhizosphere colonization and biocontrol than other members of the B. subtilis species complex [8, 12], and average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH) and core gene phylogeny demonstrate that clade II comprises three discrete but closely

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