In silico search for the hallmarks of plant‐associated phenotypes in Bacillus strains

Abstract

Gram-positive bacteria of Bacillus genus exploit various ecological strategies, ranging from soil saprotrophy to pathogenecity in animal species. Some of the Bacillus strains dwelling in the soil or associated with the plant tissues have been demonstrated to belong to the so-called plant growth-promoting bacteria (PGPB), ameliorating plant growth by either phytohormone production, nutrient uptake enhancement, or response to pathogens. The molecular bases for these features have been thoroughly characterized in different PGPB species; however, the actual distribution of growth promoting potential among the bacterial species has yet to be estimated. Recently, our research group has elaborated a tool named CryProcessor designed to rapidly mine genes encoding for Cry entomocidal toxins. Here we demonstrate the extension of its utility to find the genes determining PGPB-related phenotypes in Bacillus strains. Gene sequences associated with plant growth promotion and/or pathogen suppression were selected based on the literature evidence and presence in the confirmed PGPB strains’ genomes. These sequences were further used to construct hidden Markov models (HMMs) using HMMer v3.3.1, which were subsequently wrapped in a master script similar to that of CryProcessor. The resulting tool is capable of assessing the presence of PGPB genetic features in both raw sequencing data and complete genome assemblies. The preliminary tests of its functionality revealed the diversity of genes involved in allelopathic interactions with bacterial and fungal species in Bacillus strains. What is more, a hidden presence of genes encoding for the primary steps of phytohormones in the non-PGPB strains was observed, prompting further evaluation of their putative beneficial effects on plant growth. Although the resulting tool was not tested on genomic data for species outside the Bacillus genus, we suggest that it can be used for the assessment of the PGPB-associated traits in various bacterial species, facilitating the discovery of novel beneficial strains.