Supplementary Materials of "Unravelling the genomic and functional arsenal of Bacilli endophytes from plants with different lifestyles"

The ongoing environmental crisis requires sustainable farming to ensure food security. Endophytes, and in particular endophytic species of the Bacilli class, exhibit promising agricultural potential by promoting plant growth, controlling challenging plant pathogens, and producing a substantial variety of secondary metabolites. Unraveling the phylogeny of this class in conjunction with genome mining and comparative genomics provides unique insights into the evolutionary relationships among its members and can reveal novel traits that will be crucial for future biotechnological and agrifood applications. We thoroughly study 25 novel endophytic Bacilli strains that we isolated from various halophytic plants and olive trees on Crete and Chrysi island. We evaluate the ability of these isolates to grow under increased salinity, to inhibit the growth of economically important phytopathogens in vitro, and enhance plant tolerance against biotic and abiotic stress. We employ a hybrid sequencing approach that combines Illumina short-reads and PacBio long-reads, to accurately reconstruct the complete genome of each isolate. Genome mining and comparative genomics analyses identify genes that are associated with plant-growth promotion, production of secondary metabolites as well as antimicrobial compounds, and an increased genetic novelty among the genomes of our isolates. Furthermore, we infer a well-supported phylogeny that includes our isolates as well as publicly available Bacilli representatives. We identified four putatively novel species and show that these isolates and even isolates of already well-studied species (e.g., Bacillus thuringiensis) may harbor yet unidentified protein-coding genes and secondary metabolites. Our study highlights the increased genetic, functional, and taxonomic novelty that reside within endophytic strains of a well-studied class and emphasizes the value of deep exploration of endophytic microbial genomes and communities for microbiology, ecology and agriculture.