Mortality-dependent diversification and compound-selective mineral retention of microbial necromass

Microbial necromass is a principal source of carbon and nitrogen sustaining the oligotrophic subsurface, yet its composition and retention remain poorly resolved, leaving it underrepresented in carbon-cycling models. Using Bacillus subtilis 168 and Rhodanobacter sp. FW104-10B01, we profiled extracellular metabolites under four turnover and stress conditions: untreated growth-phase turnover, metal stress (aluminum), antibiosis (kanamycin) and phage exposure. Untargeted and targeted metabolomics (2,787 features; 80 authentic standards), combined with matched transcriptomics and proteomics, revealed compositionally distinct extracellular pools across treatments (55.5% of features differing significantly from respective controls), associated with producer identity and stress mode. Although matched compounds showed similar retention across producers, the overall metabolite profiles remained distinct after sediment exposure. Across natural sediment, clay and ferrihydrite, retention varied with compound class, suggesting that mineral surfaces modify necromass composition without erasing its biological origin. Microbial turnover and stress therefore diversify extracellular pools, while mineral interactions selectively alter its subsequent fate.