The phytoplankton community structure is potentially influenced by both environmental and spatial processes. In addition, the relative importance of these two processes to phytoplankton assemblage will be affected by hydrological connectivity. However, the impacts of anthropogenic activities on phytoplankton beta diversity and the relative importance of these two processes to phytoplankton are still poorly understood, especially in water conservation areas. Here, we examined the relative importance of local and regional environmental control and spatial structuring of phytoplankton communities in five rivers with different degrees of disturbance during wet and dry seasons. We found that community structure and local environmental conditions varied greatly in seasons and rivers. The reference river (with minimum disturbance) had the highest homogeneity of environmental conditions and phytoplankton assemblage, while the excessive disturbance rivers (sand mining activities) had the greatest environmental heterogeneity and species dissimilarity between sites. Variation partitioning analysis showed that the phytoplankton community variation was mainly explained by the spatial variables in the wet season (summer and autumn) and winter, while the local environmental variables explained the largest variation of phytoplankton community in the dry season (spring). However, broad-scale variables were selected by redundancy analysis in both dry and wet seasons, which indicates that long-distance scales always have low river connectivity, regardless of whether the river is overflowing or drying up. Local environmental processes explained the most variation in phytoplankton community within all of the rivers, suggesting that deterministic processes usually work on relatively small spatial scales. However, this effect would be weakened by anthropogenic activities, especially sand mining activities. We inferred that sand mining activities increased the environmental heterogeneity and species dissimilarity between sites by causing watercourse habitat patches and obstructing river connectivity. On the other hand, as the excessive disturbance, sand mining activities significantly reduced the species richness and abundance of phytoplankton.

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