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We examined the spatial and temporal variability of ciliate community in a subtropical estuary by rRNA and rDNA-based high throughput sequencing of 97 samples collected along the entire salinity gradient at two-month intervals in 2014. Community divided statistically into three groups: freshwater (salinity < 0.5‰), oligohaline and mesohaline (0.5‰ < salinity < 18‰), and polyhaline and euhaline (18‰ < salinity < 40‰). Across all three groups, salinity explained most of the community variability. Within each group, seasonal shifts in community formed cool (spring and winter) and warm (summer and autumn) subgroups, indicating that spatial variability overrode seasonal changes in determining community composition. Cool and warm groups showed opposite associations with temperature and prey proxies, suggesting distinct seasonal niche separation. The community reassembly of cool and warm groups was essentially due to transitions between intermediate (with relative abundance of 0.01–1%) and abundant (with relative abundance > 1%) OTUs. Further analyses demonstrated that the intermediate group not only encompassed comparable OTU richness to that of the total community and maintained high metabolic activity but also had the highest proportion in transition, either to abundance or rarity, thus offering a first view on how it varies across space and time and revealing the essential role it played in maintaining stability and functionality within the community.

Marked seasonality and high spatial variation in estuarine ciliates are driven by exchanges between the ‘abundant’ and ‘intermediate’ biospheres