Unravelling the genomic and functional arsenal of Bacilli endophytes from plants with different lifestyles and their antimicrobial potential

Endophytic microbiomes of crop wild relatives (CWRs) adapted to extreme environments, such as halophytes, are promising
sources of plant-beneficial bacteria and secondary metabolites for sustainable food production. Here, we analysed 25 Bacilli isolates
obtained from CWRs, halophytes and other plant species in Crete, Greece. Using a hybrid Illumina–PacBio sequencing approach, we
generated high-quality genomes and performed comparative genomics, phylogenetic and pangenome analyses, complemented by
in vitro assays. We identified 312 biosynthetic gene clusters (BGCs), nearly 60% of which showed no similarity to known clusters,
revealing extensive unexplored biosynthetic potential. These unique BGCs may constitute an adaptive feature enabling endophytic
Bacilli to colonize and interact with host plants. The isolates spanned diverse genera (Bacillus, Paenibacillus, Peribacillus, Neobacillus,
Cytobacillus and Rossellomorea), including three novel species. Phenotypic assays of our isolates demonstrated high salinity toler-
ance (up to 17.5% wt/v NaCl) and strong antagonism against major bacterial and fungal phytopathogens. Genome mining further
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revealed a broad array of putatively plant-beneficial traits related to growth promotion, stress adaptation, host interaction and
inhibition of pathogens. Together, these findings show that Bacilli endophytes from wild and halophytic plants possess exceptional
phylogenetic novelty, functional diversity and biosynthetic capacity, providing new genomic and ecological insights into Bacilli asso-
ciated with plants inhabiting extreme environments.