The generation of organic matter (OM) occurs synchronously with phytoplankton growth. Characterization of the generated particulate and dissolved OM during algal blooms in eutrophic lakes is crucial for better understanding the carbon cycle but remains limited. We speculate that sediments play a critical role in the biogeochemical transformation of OM derived from algal blooms in shallow lakes. In this study, changes in OM quantity and quality and the concentrations of biogenic elements (nutrients and metals) during algal blooms, were studied in situ in a shallow eutrophic lake (Lake Chaohu, China). Two enclosure treatments in the presence and absence of sediments were compared, and the cause-effect relationships among sediment, nutrients, metals, phytoplankton, particulate OM (POM), and dissolved OM (DOM) were revealed by a partial least square-path model (PLS-PM). The results showed that the changes in nutrients and metals concentrations over time were consistent with that of chlorophyll a (Chl a), and at the end of the treatment, the concentrations of Chl a, nutrients, and metals in Treatment S (with sediments) were approximately 3–5 times of those in Treatment N (without sediments). The high concentration of Chl a in Treatment S resulted in a high quantity of POM, which showed low molecular weight, low humification, and was enriched in protein-like components (∼ 70%). For DOM, the quantity increased after the decrease in POM, and DOM quality showed a significantly higher abundance of humic-like components and a higher molecular weight than POM did. The PLS-PM results showed that the significant positive effects of sediment on nutrients, metals, phytoplankton, POM, and DOM were 0.28, 0.37, 0.28, 0.25, and 0.25, respectively, suggesting that sediment had an important role in the biogeochemical cycles of these substances. The significant negative relationship between POM and DOM (-0.62) and the distinct difference in POM and DOM quality implied the efficient transformation of the freshly generated OM to those with a higher molecular weight, higher humification, and potentially refractory. Our results depicted the quick biogeochemical transformation of nutrients, metals, and the potential formation of refractory organic carbon in water column, as driven by the couple of the algae pump with the microbial carbon pump.
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