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Fresh water biodiversity is an increasing concern due to growing human impact. Herein, we report a long-term survey (ca. 90 years) of sedimentary diatoms and the modern flora from surface sediments and their biodiversity changes along a eutrophication gradient. Study was carried out in one of the most important water supply reservoirs (Guarapiranga Reservoir) of Sao Paulo Metropolitan Region, Brazil. Results are based on 75 core subsamples (subfossil assemblages from core) previously dated by 210Pb and 14 samples from surface sediments (modern assemblages). Overall, 84 taxa were reported, belonging to 30 genera, 71 species and eight non-typical varieties, besides five probable new taxa. Results expanded two new additions for the Brazilian diatom flora (Chamaepinnularia submuscicula and Stauroneis acidoclinata) and 30 infrageneric taxa for the state of Sao Paulo. 47.6% of total taxa inventoried were accounted exclusively for the subfossil assemblages indicating a significant biodiversity change over time. Access to past oligotrophic conditions and to contemporary mesotrophic regions of the Guarapiranga Reservoir accounted for these new additions representing 25% of the total diatom flora. Decline in the total species number along the trophic state gradient occurred for subfossil and modern assemblages. This pattern was even clearer when considering the changes in species richness over time.Eunotia with 21 taxa was the far most represented genera particularly in the oligotrophic phase. During the transitional period (1947-1974), richness gradually declined. With the onset (in the 1970s) and the major eutrophication period (since ca. 1990) occurred a drastic reduction in richness and the replacement of oligotrophic to eutrophic species. Human management also caused abrupt changes in richness. Marked decline occurred (1933) assotiated with hydrological impacts (water discharge increase) with the initial use of the reservoir as a public water supply. Unlike, sudden increase occurred probably associated with the application of algaecide to control cyanobacterial blooms. Present findings highlight the need for surveying the diatom assemblages in protected environments or in less degraded conditions for biodiversity assessment. Furthermore, reinforce the use of paleolimnological approach as in many cases the only tool to assess biodiversity changes encompassing time scales relevant to human-induced degradation and pre-anthropogenic impacts.

Composition and distribution of diatom assemblages from core and surface sediments of a water supply reservoir in Southeastern Brazil