Genomic Insights Into the Multimetal Resilience and Biofilm-Templated Nanorod Biosynthesis of Stenotrophomonas bentonitica BII-R7: Bioremediation and Green Nanotechnology Implications.

While microbial metal reduction is widely documented, the genomic determinants that govern the morphological transition from disordered phases to structured nanocrystals remain elusive. Here, we present an integrative study of Stenotrophomonas bentonitica BII-R7, a strain exhibiting exceptional metal resistance and the unique capacity to synthesize crystalline trigonal selenium (t-Se) nanorods. Comparative pangenomic analysis of 38 Stenotrophomonas strains revealed that BII-R7 possesses a notably large accessory genome of 2311 exclusive singletons. We identify a specialized genomic toolkit, absent in all related strains, comprising key metal resistance determinants (e.g., copB, copF, and czcA) alongside extracellular remodelling enzymes (Wzyligase and GH92-glycosyl hydrolase). This unique repertoire confers BII-R7 with significantly higher Cu and Ni tolerance compared to related Stenotrophomonas species, which we hypothesize is fundamental for maintaining metabolic activity in polymetallic environments. RT-qPCR and functional assays confirm that these singletons are not only upregulated under metal stress (e.g., czcA: 42.2-fold) but are also consistent with a critical role in maintaining biofilm resilience. Crucially, we propose a mechanistic model where this unique genetic repertoire governs the assembly of a compositionally distinctive Extracellular Polymeric Substance (EPS). Using a three-state (biofilm, planktonic, EPS-depleted) experiment, we provide direct phenotypic evidence that an intact EPS matrix is required for the efficient transition from amorphous nanospheres to highly ordered crystalline nanorods, and we propose that it acts as a molecular template directing the anisotropic growth of selenium. By bridging genomics and bionanotechnology, this work positions BII-R7 as a promising candidate for sustainable green synthesis and bioremediation, while defining the targeted gene-knockout and complementation experiments now required to establish direct causal roles for the candidate determinants.