Different responses of lake microbial assemblages to climate changes and human activities are not well understood due to the scarcity of long-term biodiversity records. In this study, an approach of paleolimnology and metagenomic sequencing of sedimentary ancient DNA was combinedly used to investigate environmental changes, lake primary productivity, and cyanobacterial community succession over the last ∼500 years in Lake Daihai, northern China. The results show a different response of cyanobacterial communities to climate change and anthropogenic activities on different timescales. Lake primary productivity, biodiversity, and trophic status were in a generally natural state and were mainly controlled by temperature and precipitation before ∼1850 CE, but were clearly affected by human activities thereafter. Overall microbial diversity values gradually increased after ∼1850 CE, and ordination analysis further indicates that the present community is substantially dissimilar to that observed before ∼1850 CE. The structure of cyanobacterial communities was relatively stable prior to ∼1850 CE, followed by prominent decadal scale fluctuations that were broadly synchronous with the sedimentary organic matter molecular compositions. These molecular proxies reveal that anthropogenic forcing, rather than climate, may be the primary controls of cyanobacterial communities over the past one more century. Enhanced land-use change and cropland runoff, and increased discharges of industrial wastewater and human sewage are likely the main factors driving changes in lake primary productivity and cyanobacterial community composition. Our finding highlights the sensitive responses of lake ecosystem to anthropogenic disturbance in the monsoon marginal zone, and proper exogenous nutrient control (e.g., thresholds for agricultural runoff) is necessary to maintain the sustainability of the regional aquatic ecosystems.
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