Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants

Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. Here we traced the fate and microbiome responses to {superscript 1}3C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% {+/-} 15.5% removed within 25 days, producing primarily {superscript 1}3CO2 and some {superscript 1}3CH. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation ([~]85% {+/-} 5% remaining), yet its 13C-labeled N-methyl groups fueled {superscript 1}3CH production, coinciding with enrichment of Bathyarchaeia and Methanosarcina. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.