Iron oxides are crucial to soil organic carbon (SOC) sequestration in wetland ecosystems. Whether vegetation drives soil microorganisms to regulate iron–carbon interactions and influence SOC sequestration capacity remains controversial. Thus, this study investigated iron–carbon coupling processes and their microbial drivers in the Caohai alpine freshwater closed wetland, Guizhou Province, China. Using metagenomic sequencing and physicochemical analyses, we compared vegetated areas (
Phragmites australis and
Scirpus tabernaemontani) with bare flats (BF). Levels of SOC, microbial necromass carbon (MNC), and plant-derived carbon (PC) in vegetated soils were significantly higher than those in BF (
p < 0.05). In all study regions, the PC/SOC ratio (PA: 27.89 ± 3.59 %; ST: 24.58 ±1.86 %; BF: 24 ±2.82 %) exceeded the MNC/SOC ratio (PA: 15.58 ± 0.94 %; ST: 15.95 ± 0.73 %; BF: 13.06 ±1.30 %). The PC/SOC and MNC/SOC ratios were higher in vegetated areas than in BF areas. Compared with BF, vegetation enhanced wetland SOC stability and promoted carbon sequestration. Iron-bound organic carbon
content was substantially greater in vegetated soils (PA:0.34 ± 0.08 g/kg; ST:1.07 ± 0.58 g/kg) than in BF (0.14 ± 0.08 g/kg) (
p < 0.05). Based on the
/
ratio (PA: 22.87 ± 14.00 %; ST: 23.00 ± 13.90%; BF: 5.36 ± 3.40 %),
associations in vegetated soils were dominated by stable coprecipitation, whereas unstable adsorption prevailed in BF. In all study regions, the abundances of iron-reducing bacteria (FeRB) and iron-oxidizing bacteria (FeOB) peaked in BF. Several FeRB genera, including
Thiobacillus,
Intrasporangium,
Gallionella, and
Nocardioides, were significantly and positively correlated with
(
p < 0.05). Conversely,
Geobacter and
Nitrospira exhibited significant negative correlations with
and PC (
p < 0.05). The FeOB genera—
Thioalkalivibrio,
Thiohalobacter, and
Pseudomonas—were negatively correlated with
. Vegetation presence appears to influence microbial metabolic potentials through the provision of rhizodeposits and the modulation of rhizosphere conditions, thereby affecting
associations and contributing to SOC sequestration in wetland soils to some extent. These findings provide critical insights into plant–microbe–mineral interactions and a scientific framework for predicting carbon sink dynamics in wetland ecosystems.
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