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As global changes begin to affect the biosphere profoundly, the impacts on ecosystem health will become more significant. Understanding the sequence of functional species loss along an environmental or ecological gradient remains a research priority for ecosystem conservation. In this paper, nestedness, beta-diversity and its components in diatom communities are used as ecological indicators of the dynamic change in functional species along environment gradients in 76 lakes of the lower Yangtze River basin, China. The results indicate that species turnover is typically the dominant component of beta-diversity and that the influence of nestedness is generally low. However, changes in nestedness denote a significant threshold of lake eutrophication at a total phosphorus (TP) level of 0.06 mg/l, which is lower than the threshold indicated by diatom diversity. This finding was coupled with theoretical predictions about the successive proportional loss of 'canary' and 'keystone' species, which are replaced by 'weedy' species. These results show that nestedness of diatom communities can provide an additional metric for evaluating lake ecosystem health in this region. As management targets for nutrient control have already been introduced in the region, a revision of the identified critical phosphorus level (i.e., TP = 0.087-0.1 mg/l) to TP = 0.06 mg/l is proposed to keep lakes under low risk. (C) 2018 Elsevier B.V. All rights reserved.