Ammonium availability may alter microbial access to persistent dissolved organic matter (DOM), but the response capacity of indigenous deep-water microbial communities remains poorly constrained. We used dark microcosms established with South China Sea seawater from 500 and 2000 m to examine microbial and DOM responses to ammonium enrichment. Microcosms received 50 μM ammonium nitrogen (NH4+-N) and were incubated without agitation at 24 °C for 90 days alongside unamended controls. Nutrient and dissolved organic carbon (DOC) measurements were integrated with optical DOM characterization, 16S rRNA gene profiling, and semiquantitative molecular formula profiling by Fourier transform ion cyclotron resonance mass spectrometry. Ammonium-amended microcosms showed 46-50 μM net NH4+-N depletion, accumulation of oxidized nitrogen, and numerically greater 90-day DOC loss than controls (11-12 vs 5-6 μM), although DOC trajectories did not differ significantly between treatments. These changes coincided with increased relative representation of Thaumarchaeota and Bacteroidetes, stronger tyrosine-like and tryptophan-like fluorescence signals, and pronounced shifts in detectable molecular formula composition. Collectively, these coordinated responses reveal latent DOM-processing capacity in indigenous deep-water communities and are consistent with an ammonium-associated priming-like response potentially involving ammonia oxidation and autotroph-heterotroph coupling.
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