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Abstract In tropical lakes, deep water-column mixing exerts great influence on nutrient dynamics and food-web structure, and on the probability for hazardous accumulation of bio- or geogenic gases in the hypolimnion. However, conventional criteria to infer a lake's mixing regime in temperate regions, such as the changing seasonal position of the thermocline or the depth to anoxia, often lead to faulty conclusions when applied to stratifying tropical lakes. The water column of these lakes tends to exhibit multiple thermoclines, and deep-water anoxia tends to spread quickly throughout the hypolimnion in all but the least productive lakes, complicating the interpretation of isolated temperature and dissolved-oxygen profiles. Here, multiple depth profiles of temperature, dissolved oxygen and conductivity from a diverse selection of 11 small tropical crater lakes in western Uganda are combined with time series of temperature-logger data to determine the occurrence and maximum depth of water-column mixing within a given time period. We propose three reliable indicators of past mixing: 1) presence of oxygen below the photic zone; 2) evidence of recent cooling at a given depth; and 3) disappearance of previously documented thermo- and chemoclines. The greatest depth of mixing can only be inferred with a fair degree of certainty from a chronosequence of at least two sets of profiles. Highlights • Criteria to determine mixing depth in tropical lakes using physical-property profiles. • Based on evidence of cooling, oxygenation and elimination of thermo- and chemoclines. • Mixing criteria commonly used in temperate lakes are less suitable in tropical lakes. • A chronosequence of profiles is essential for reliable assessment of mixing regime. [ABSTRACT FROM AUTHOR]

High-throughput DNA sequencing (HTS) and photosynthetic marker-pigment analysis can provide cost-and time-efficient alternatives for morphology-based microscopic identification and counting of lacustrine phytoplankton. However, application of particularly HTS in tropical lakes is still uncommon. We analyzed the community composition of cyanobacterial and eukaryotic phytoplankton in relation to trophic status and other environmental factors in 15 tropical crater lakes in western Uganda, using both high-performance liquid chromatography (HPLC) of photosynthetic marker pigments and HTS of 16 S and 18 S small subunit rRNA genes. We then compared the results with phytoplankton composition data based on microscopic identification and cell counting to evaluate whether the two former methods can be alternative or complementary approaches to analyze these lakes' phytoplankton communities. HTS recorded 105 operational taxonomic units (OTUs) of cyanobacteria, and 197 OTUs of autotrophic eukaryotes mainly from dinoflagellates, cryptophytes and green algae. Ochrophyta (chrysophytes and diatoms) were present in low abundances only, and the few remaining sequences belonged to Streptophyta and Haptophyta. Marker pigment distribution among samples reflected the widespread and often dominant presence of cyanobacteria (primarily zeaxanthin, myxoxanthophyll and echinenone), followed by green algae (chlorophyll b , lutein, antheraxanthin, neoxanthin) and diatoms (fucoxanthin, diato-diadinoxanthin), and with cryptophyta (alloxanthin) important in some of the lakes. Direct and indirect ordinations of the OTUs and marker pigments revealed that, similar to patterns observed in cell counts, phytoplankton community composition differed between deep oligotrophic lakes and shallower more productive lakes, even though the distribution of cyanobacterial OTUs was more related to lake water conductivity and season than to trophic status. Procrustes analyses of the composition of green algae and Ochrophyta, the two dominant eukaryotic groups, based on HTS data showed patterns significantly similar to composition data based on cell counts, but no significant correlations were found between the complete eukaryotic or cyanobacterial HTS data and cell count data. While the latter discrepancies can be attributed to method-related biases in both HTS and microscopy, in contrast to the microscopic approach HTS failed to identify trophic indicator species and did not assign all lakes to the correct trophic category. Composition data based on marker pigments clustered the 15 lakes according to their trophic level only when pigment abundances were expressed as absolute concentrations, not when expressed as fractional abundances. We attribute this lower discriminating power partly to the wide distribution of cyanobacteria in these tropical crater lakes, besides the pigments' low taxonomic resolution. Nevertheless, as the compositional patterns in relation to environmental variation observed in marker pigments and OTUs of the dominant eukaryotic phytoplankton groups are similar to those in cell count data, both methods hold potential for ecosystem-level monitoring of tropical crater lakes. However, the high-resolution HTS approach is handicapped by non-uniform amplification of gene sequences, while the low-resolution marker-pigment approach is handicapped by the widespread dominance of cyanobacteria in these systems irrespective of their trophic status. • Phytoplankton in Ugandan crater lakes was analyzed using DNA and pigments. • High-resolution DNA, while limited by non-uniform amplification of gene sequences, shows otherwise "hidden" taxa. • In these systems, the widespread dominance of cyanobacteria limits marker pigment results, irrespective of trophic status. • DNA and pigment analysis can complement but not replace morphological analysis. [ABSTRACT FROM AUTHOR]

In order to understand the ecological functioning of lake ecosystems, little is more crucial than knowledge of their mixing regime. However in tropical regions, this information is scarce for all except the largest lakes, and often inferred from occasional observation of physical water-column properties. In this study, a total of 276 water-column profiles of temperature, conductivity and dissolved oxygen collected between 2000 and 2017 in 60 volcanic crater lakes in equatorial western Uganda are used to classify these lakes according to mixing regime. Most study lakes are small (on average 29 ha), but together they cover a spectacularly large gradient in maximum depth (Z max) between 1.4 m and > 220 m, and consequently they display a wide range of mixing regimes. We identified four lakes as continuous warm polymictic, 12 as discontinuous warm polymictic, and 11 other lakes mix completely once or twice each year. We classify these 11 lakes as equatorial dimictic, because they experience deep mixing during both dry seasons separated by long periods of stable stratification, while the season of complete mixing may differ between years and among neighbouring lakes. The 33 remaining lakes do not usually mix completely and are thus meromictic. Relative depth (Z r) is the main factor controlling the mixing regime of these lakes. The presence of a shallow permanent chemocline reduces mixing depth, and the smallest meromictic lakes (< 3 ha) tend to occasionally mix deeper than predicted by Z r. Based on these variables, predictions can be made about the mixing dynamics of Ugandan crater lakes not covered by our dataset. Previous suggestions that the mixing depth of tropical crater lakes is strongly influenced by the wind shelter provided by a high crater rim or by water-column transparency could not be confirmed. [ABSTRACT FROM AUTHOR]

• Ugandan crater lakes cover wide gradients of aquatic productivity and human impact. • Most lakes are dominated by cyanobacteria, including those that are least productive. • Phytoplankton communities can be clustered in four groups linked to trophic level. • Their chl-a boundaries are higher than those between traditional trophic categories. • Each cluster contains one or more primary and/or accessory indicator species. The freshwater crater lakes of western Uganda represent an important natural resource for the region's rural communities, but their capacity to provide drinking-quality water and other ecosystem services is being threatened by rapidly intensifying human activity within their catchments. This study investigated the relationship between the composition of pelagic phytoplankton communities in these lakes and their trophic status, to assess how phytoplankton surveys with recognition of indicator species can assist in the assessment of water-resource vulnerability to human impact. For this purpose we analyzed 70 phytoplankton samples with linked environmental data from 26 crater lakes spanning the entire regional gradients of primary productivity and land-use intensity, with each lake sampled two to four times and during both dry and rainy seasons. At this equatorial location, nutrient concentrations and phytoplankton biomass (measured as the concentration of chlorophyll-a) showed no consistent seasonal pattern. In total we recorded 118 phytoplankton taxa from 72 genera, and from 20 to 54 taxa per lake. The phytoplankton community of most lakes and in most seasons was dominated by cyanobacteria (on average 78% of total cell counts) followed by green algae (17%) and diatoms (4%); euglenophytes, dinoflagellates, chrysophytes and cryptophytes together contributed less than 1% on average. Many species were found to have a wide distribution along the productivity gradient, which complicated characterization of phytoplankton communities typical of different trophic states. Cluster analysis revealed four groups of samples, of which two broadly represented the least and most highly productive lakes. The two other groups comprised a mixture of lakes with intermediate productivity, suggesting that phytoplankton composition in these lakes is structured by other factors in addition to nutrient availability. In total 25 taxa displayed a significant association with one of these groups, but only 12 of them can be considered robust indicators of a particular trophic level; among these, the cyanobacteria Planktolyngbya limnetica and Microcystis aeruginosa qualify as strong indicator species for lakes with low and high productivity, respectively. Based on the distributional turnover between indicator species, we propose that the fresh Ugandan crater lakes comprise four trophic levels, of which the boundaries are situated higher up the chlorophyll-a gradient than those between the four classic trophic levels defined for temperate-region lakes. For practical use, Ugandan crater lakes with a chlorophyll-a concentration up to 6 µg/L can be defined as oligotrophic; similarly, we situate the mesotrophic/eutrophic boundary at ca 20 µg/L, and the eutrophic/hypertrophic boundary at ca 60 µg/L. [ABSTRACT FROM AUTHOR]