While the effect of the global biodiversity crisis on local species loss is still debated, there is empirical evidence for major changes in local biodiversity attributed to increased species turnover. In communities exposed to a climate stressor, species turnover can lead to increased dominance of well-adapted species and consequently to an overall decline in species diversity. Despite the known importance of species turnover for community dynamics and functioning, experimental results on the connection between biodiversity loss and species turnover are scarce. We still do not fully understand which specific factors increase the rate of change in species composition, especially when considering natural compared to artificially lab assembled communities. In the present study, we experimentally tested whether a heatwave and dispersal increased species turnover and decreased species diversity in natural benthic diatom communities with different initial species compositions. We found that on the local scale, dispersal had overall positive effects on species richness while the relationship between exposure to the heatwave, species turnover, and diversity depended on initial community composition. However, on the regional (i.e. metacommunity) scale, exposure to the heatwave and dispersal both increased turnover and decreased Shannon diversity by almost 50%. Turnover in these metacommunities was not caused by a loss of species, but rather by a change in dominance patterns leading to homogenization, and consequently decreased diversity. Our study shows that climate change can destabilize community composition and degrade species diversity, but still after ca. 15 generations does not decrease the number of species in the community, demonstrating that the response of species diversity and richness to changing conditions can be fundamentally decoupled on ecological time scales.

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