Molecular evidence for depth‐dependent microbial transformation of dissolved organic matter into carboxyl‐rich alicyclic molecules in coastal marginal seas

Abstract Marine dissolved organic matter (DOM) represents a primary reservoir in the biogeochemical cycle, and marine microorganisms are essential to the transformation and long‐term sequestration of DOM as recalcitrant dissolved organic matter (RDOM). In China's marginal seas, DOM levels are affected by coastal productivity and terrestrial inputs, yet the molecular mechanisms driving the DOM to RDOM transformation remain insufficiently characterized. This study aimed to elucidate the mechanisms behind the DOM transformation mediated by marine microorganisms in the Bohai and Yellow Seas, particularly focusing on molecular‐level characterizations of microbial carbon cycling processes. Here, using 16S rDNA amplicon sequencing, we analyzed the bacterial communities across the surface and deep layers. Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) was used to molecularly characterize the DOM. Our findings revealed distinct bacterial diversity and functional profiles between the surface and deep layers, with deep layers exhibiting higher microbial diversity. Furthermore, the deep layers were characterized by higher proportions of RDOM, with molecular indicators such as carboxyl‐rich alicyclic molecules (CRAM) suggesting enhanced carbon stability. This study highlights the role of microbial processes in shaping the molecular characteristics of DOM across depths, supporting the microbial carbon pump (MCP) framework and characterizing the Bohai and Yellow Seas as significant carbon sinks in the coastal region. These findings advance our mechanistic understanding of oceanic carbon sequestration, particularly in coastal marginal seas.