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Highlights • Colonization dynamics in community functioning showed different models among four depths. • Temporal variations in functional distinctness showed different trends among four depths. • The homogeneity of mature samples showed a decreasing trend from depths 1 to 5 m. • The functional distinctness is a useful tool to determine the homogeneity of ciliate communities. • The approach is needed to make an optimal sampling strategy for ciliate colonization surveys. Abstract Functional diversity/distinctness, as important biodiversity parameters of a community, have proved to be a feasible tool to summarize ecosystem functions and community structures both ecological research and monitoring program. For determining the homogeneity in community functioning of periphytic ciliates during colonization process, a 1-month baseline survey was conducted at four depths of 1, 2, 3.5 and 5 m in coastal waters of the Yellow Sea, northern China. The colonization dynamics in functional trait distribution of periphytic ciliates generally showed different temporal variations during colonization period at four depths. The functional diversity (Δ χ), functional distinctness (Δ* χ), average functional distinctness (Δ χ +) and variation in functional distinctness (Λ χ +) indices generally represented different models within colonization process at four depths. Ellipse test on the paired functional distinctness measures (Δ χ + - Λ χ +) revealed that the mature samples (14–28 days) were inside the expected patterns of community functioning at only one water depth (1 m), although the 14-day communities were fallen into the contours of 10 sub-list size at the other two water layers (2 and 3.5 m). These findings suggest that the functional distinctness measures might be a useful indicator to determine the optimal sampling strategy with high homogeneity of community functioning in colonization surveys for marine bioassessment. [ABSTRACT FROM AUTHOR]