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Microorganisms are important drivers of material and energy circulation in freshwater ecosystems. Altered aquatic sedimentary environments disturbed by human activities affect microbial community composition. Concentrations of heavy metals, and sediment physicochemical properties, are described for 25 sediment samples collected from five habitat types (residential, duck farm, lotus pond, fish farm, and a reference reserve shallow freshwater lake site) around Baiyangdian Lake, China. Bacterial and fungal communities in sediments were determined using 16S rRNA and 18S rRNA high-throughput sequencing technology. Sediment physicochemical properties and heavy metal concentrations vary significantly among habitat types. Bacterial genera involved in S and N cycles are most abundant, followed by those that degrade organic pollutants, and are tolerant of heavy metals. Sediment bacterial Chao1 index is predominantly regulated by cobalt concentrations. The microbial communities within replicate samples within habitats are more similar to each other than they are between habitats. Redundancy analysis indicates Zn, pH, and TP are the main environment factors structuring bacterial communities, while fungal communities are most significantly influenced by Co and TP. The genus Cryptomonas is a food source for small zooplankton and fishes, and is mainly distributed in fish farm and lotus pond habitats. Species of Pseudallescheria that cause mycetoma, maduromycosis, and other infections in humans are highly abundant in duck farm and residential habitats. Species of Aleuria are saprobes; decompose organic matter, dead organisms, or biological excrement; and are highly accumulated in duck farm habitat.

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