The iron paradox and particle size sensing: transcriptomic response of Enterococcus faecalis to non-nutritive...

Minerals are known to influence microbial metabolism as nutrient sources or redox partners, yet whether chemically inert, non-nutritive minerals can regulate microbial physiology, and through what mechanisms, remains poorly understood. Here, we used transcriptomics to investigate the response of Enterococcus faecalis to Al₂O₃ and SiO₂ particles spanning nanoscale to millimeter scale. Mineral exposure triggered extensive transcriptional reprogramming across hundreds of differentially expressed genes. Notably, a massive upregulation of iron acquisition genes (log₂FC range from 3.8 to 4.2) concurrent with oxidative stress defenses (catalase, thiol peroxidase, and NADH oxidase) is suggestive of an "iron paradox," which is potentially attributable to mineral-mediated nutrient sequestration and steric hindrance of membrane transporters alongside interfacial reactive oxygen species generation. To adapt, E. faecalis orchestrated a coordinated metabolic shift, repressing serine catabolism (log₂FC = -2.7) while investing nitrogen into glutathione biosynthesis (cystathionine synthase genes, log₂FC = 3.7). Correlation analysis identified an ompR-sigV axis through which E. faecalis discriminates mineral particle size, with nanoscale particles eliciting stronger transcriptional responses than their larger counterparts. This stress response additionally upregulated virulence-associated genes and antibiotic resistance genes without direct antimicrobial selection pressure. These findings suggest that non-nutritive minerals shape microbial physiology through physical and surface-chemical cues independent of their nutritional value, highlighting the need for further exploration of the non-nutritional functions of minerals in microbial ecology.IMPORTANCEEven in the absence of utilizable nutrients, non-nutritive minerals such as Al₂O₃ and SiO₂ can profoundly influence the transcriptional responses of Enterococcus faecalis. Using transcriptomic sequencing, we show that these inert minerals regulate microbial transcription, enhancing iron acquisition, oxidative stress repair, pathogenicity, and antibiotic resistance. Mineral-mediated transcriptional control is driven primarily by physical contact, surface chemistry, and particle size sensing, rather than conventional metabolic interactions. These findings identify inert minerals as signaling molecules that actively modulate microbial transcription, playing a proactive role in microbial evolution and environmental adaptation. This study redefines inert minerals as active carriers of transcriptional regulation, filling a critical gap in geomicrobiology and providing new insights into microbial environmental responses, biogeochemical cycling, and the mechanisms underlying microbial functional evolution and maintenance.