Carbon, nitrogen, and sulfur cycling unveil deep-sea microbial niches in the Atacama Trench

Deep-sea sediments host microbial communities essential to nitrogen, sulfur, and carbon cycling, yet those in the Southern Hemisphere remain understudied. In this work, we analyze sediments from an oceanic trench off northern Chile using metatranscriptomics, aiming to relate community composition with functional activity. Most assayed sites form part of a broadly uniform deep-sea ecosystem fueled by the degradation of marine snow through diverse aerobic and anaerobic pathways. Nitrogen cycling within them is driven by archaeal nitrification and bacterial dissimilatory nitrate reduction. One site, however, appears to be a sulfur-based cold seep inhabited by mats of thiotrophs and vesicomyid clams within darker sediments. In this site, ANME archaea are largely absent despite the presence of dolomite crystals, which are typically associated with anaerobic methane oxidation. Instead, abundant subsurface pyrite and active sulfate reduction point to substantial sulfur cycling. Across the region, heterotrophic communities dependent on marine snow transition to chemosynthetic ones supported by reduced sulfur in a sulfur-driven cold seep with minimal fluid flow.