Even a low concentration of sodium dodecyl sulfate (SDS), a widely used bactericidal surfactant, can significantly change the species, quantity and genetic functions of microorganism communities in natural waters. Lake–terrestrial ecotones are areas where microorganisms are highly active, and they are also the lake areas most vulnerable to SDS pollution. Because microorganisms are very sensitive to environmental changes, their activities vary greatly among lakes and laboratories, so it is difficult to simulate their real dynamics using small-scale experiments. To study the interaction between SDS and microorganisms in a lake–terrestrial ecotone, a large artificial simulation device was used to analyse microbial community structure, phospholipid fatty acid (PLFA) content, gene function and ability to degrade SDS in a lake–terrestrial ecotone contaminated with SDS. The results showed that (1) the period from 2 to 4 days after the beginning of the experiment was the key stage for the biodegradation of SDS. The biodegradation cycle of SDS in the natural environment is shorter than that in small-scale experimental setups, and more than 90% of SDS was removed within 4 days in the simulation device. (2) Low-level SDS pollution (≤ 6 mg/L) has different effects on different types of lacustrine microorganisms. The presence of SDS can lead to a significant decrease in microbial diversity and biomass in lake–terrestrial ecotones with a high density of aquatic plants, but the opposite is true in ecosystems with degraded aquatic plant communities. (3) After SDS pollution occurred, pollution-resistant bacteria such as Chitinophaga and Flavobacterium became dominant. The relative abundance of carbon cycle functional genes increased rapidly in microorganisms, while the relative abundance of nitrogen cycle functional genes decreased. These changes were not readily reverse even after 20 days, although the communities recovered to a certain extent.
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