Minerals function as signals to modulate microbial adaptation

Minerals are pivotal environmental factors influencing the adaptation and evolution of microbial communities. Conventional wisdom has long regarded the impact of minerals as a byproduct of their role in providing nutrients and energy to organisms, largely overlooking the significance of non-nutritive and energy-neutral mineral species. In this study, we explore the influence of minerals on microbial development in nutrient- and energy-rich media through a serial passage evolution experiment. Our results show both the inert mineral kaolinite and the energy/nutrient-rich olivine exert evident effects on the microorganisms. Both minerals induced substantial shifts in community structure. Notably, kaolinite and olivine selectively enriched specific taxa, including Acinetobacter and Clostridium. Metatranscriptomic analyses revealed substantial changes in gene expression, with both minerals enriching unique metabolic pathways. Interestingly, kaolinite specifically enriched pathways related to streptomycin biosynthesis. Both minerals stimulated the expression of antibiotic resistance genes (ARGs), particularly those associated with multidrug and macrolide resistance. Furthermore, both minerals induced the upregulation of genes involved in the degradation of complex organic matter, highlighting their potential role in soil carbon cycling. These findings underscore the intricate interplay between minerals and microbes, challenging the conventional notion that minerals function solely as material sources for organism growth. Inert mineral kaolinite and the energy/nutrient-rich olivine change microbial community structure, stimulate the antibiotic resistance genes, and regulate the degradation of complex organic matter, according to a serial passage evolution experiment in nutrient and energy-rich media.