Microbial food webs regulate marine carbon cycling by linking trophic interactions with bacterial transformation of dissolved organic matter (DOM). However, whether changes in microbial food-web configuration alter the coupling between bacterial succession and DOM dynamics remains poorly understood, particularly in vertically heterogeneous coastal waters.
We conducted seven-day dark incubations using deep chlorophyll maximum (DCM) and near-bottom seawater collected off eastern Hainan in the South China Sea. Microbial food-web configuration was experimentally modified through size-fractionated filtration, generating a protozoan-reduced 0.7-μm treatment and a <20-μm assemblage retaining small heterotrophic eukaryotes. Bacterial abundance, bacterial and eukaryotic community composition, fluorescent dissolved organic matter (FDOM), and chromophoric dissolved organic matter (CDOM) absorption were monitored throughout the incubation.
Food-web configuration altered both the magnitude and trajectory of bacterial succession. In the <20-μm assemblage, bacterial abundance showed maximum declines of approximately 22% in DCM-derived water by day 5 and 53% in near-bottom-derived water by day 7. At the end of incubation, bacterial richness and diversity were lower in the <20-μm assemblage than in the 0.7-μm treatment in near-bottom-derived water, suggesting that differences in microbial food-web configuration influenced bacterial community assembly. Furthermore, dominant bacterial taxa, including Rhodobacteraceae, Cyclobacteriaceae, and Alteromonadaceae, exhibited contrasting succession patterns between the two size-fractionated treatments, with distinct trajectories observed in near-bottom waters.
DOM optical properties changed concurrently with bacterial succession. During the early incubation stage (day 1), fluorescent components (C1, C2, and C3) and the CDOM absorption coefficient (a300) were higher in the <20-μm assemblage than in the 0.7-μm treatment, followed by gradual decreases toward stable levels. Redundancy analysis revealed depth- and size-fractionation-dependent associations between bacterial communities and DOM characteristics. Notably, C2 was significantly associated with bacterial community variation only in the <20-μm assemblage, where shifts in heterotrophic eukaryotic communities were also linked to bacterial succession, suggesting that microbial food-web configuration altered bacteria-DOM coupling patterns.
Together, these results demonstrate that microbial food-web configuration regulates not only bacterial succession but also its coupling with DOM optical dynamics. The contrasting responses of DCM- and near-bottom-derived communities further indicate that trophic regulation of microbial carbon processing depends on the initial ecological context of the source water.

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