Despite of the importance of understanding the sediment quality for lacustrine management, the source evaluation of sedimentary organic matter (SOM) in freshwater lakes is still insufficient. In this study, two shallow eutrophic lakes of Lake Taihu, China and Lake Izunuma, Japan were systematically investigated. Results of fatty acid profiles demonstrated that a wide range of organic matters, varying ecotypically, was inputted into the sediments of both lakes. Interestingly, there was a strong contribution from terrestrial plants to the sediments across ecotypes, with an approximate input from bacteria, and a relatively minor input from microalgae mainly included cyanobacteria, green algae, diatom and dinoflagellates. In addition, isotopic mixing model depicted a complementary picture that a significant, but spatially variable, amount of organic matter was derived from emergent and floating-leaf plants of Phragmites, Nelumbo, Nymphoides and Trapa L in Lake Izunuma. A general indicator selection procedure for the source assignments of SOM in freshwater ecosystems was therefore proposed: fatty acids could be a valid biomarker when the potential sources are unknown or unavailable; stable isotopes could be an effective supplement approach when assessing the special or defined organic sources.
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