Zooplankton in small tropical lakes has been little studied and its variation during the year may respond to different factors. In this study, the zooplankton of a small neotropical lake was studied at different times during one year and compared with changes in the lake conditions and in phytoplankton composition. The lake stratifies from March until September, and mixes during the hemispherical winter, from October until February. Besides the lake show a seasonal fluctuation in water level according to the seasonality of rains. Zooplankton was composed of at least 13 species, four Cladocerans, three Copepods, four Rotifers and other groups such as an Ostracod and the larvae of Chaoborus. The most abundant were Thermocyclops sp., Daphnia sp. and Keratella tropica. Their abundance fluctuated along the year, probably in response to changes in lake level and changes in hydrological conditions, increasing during dry season when the main outlet of the lake dried up. Changes in phytoplankton composition do not seem to be as relevant for zooplankton variation in this small lake.

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Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.