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Here, we used transcriptomics to investigate the response of\n                      <jats:italic toggle=\"yes\">Enterococcus faecalis<\/jats:italic>\n                      to Al\n                      <jats:sub>2<\/jats:sub>\n                      O\n                      <jats:sub>3<\/jats:sub>\n                      and SiO\n                      <jats:sub>2<\/jats:sub>\n                      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 (log\n                      <jats:sub>2<\/jats:sub>\n                      FC range from 3.8 to 4.2) concurrent with oxidative stress defenses (catalase, thiol peroxidase, and NADH oxidase) is suggestive of an \u201ciron paradox,\u201d which is potentially attributable to mineral-mediated nutrient sequestration and steric hindrance of membrane transporters alongside interfacial reactive oxygen species generation. To adapt,\n                      <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                      orchestrated a coordinated metabolic shift, repressing serine catabolism (log\n                      <jats:sub>2<\/jats:sub>\n                      FC = \u22122.7) while investing nitrogen into glutathione biosynthesis (cystathionine synthase genes, log\n                      <jats:sub>2<\/jats:sub>\n                      FC = 3.7). Correlation analysis identified an o\n                      <jats:italic toggle=\"yes\">mpR<\/jats:italic>\n                      \u2013s\n                      <jats:italic toggle=\"yes\">igV<\/jats:italic>\n                      axis through which\n                      <jats:italic toggle=\"yes\">E. faecalis<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        Even in the absence of utilizable nutrients, non-nutritive minerals such as Al\n                        <jats:sub>2<\/jats:sub>\n                        O\n                        <jats:sub>3<\/jats:sub>\n                        and SiO\n                        <jats:sub>2<\/jats:sub>\n                        can profoundly influence the transcriptional responses of\n                        <jats:italic toggle=\"yes\">Enterococcus faecalis<\/jats:italic>\n                        . 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.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/aem.00954-26","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T13:04:27Z","timestamp":1787144667000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["The iron paradox and particle size sensing: transcriptomic response of\n                    <i>Enterococcus faecalis<\/i>\n                    to non-nutritive 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