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A deep chlorophyll layer (DCL) is a common feature of many deep, oligotrophic lakes including Lake Superior. Mechanisms generating and maintaining DCLs are variable across lakes, and seasonal patterns and relationships of DCL structure to physical variables are not well described. Using vertical profile data for physical and biological variables from western and central Lake Superior, we described seasonal patterns in DCL structure and other physical and biological parameters and applied linear mixed-effects models to determine how different physical factors (surface temperature, thermocline depth, and 1% photosynthetically active radiation (PAR) depth) affect the depth, thickness, maximum concentration, and integrated chlorophyll of the DCL. We observed clear seasonal patterns in the development and degradation of the DCL that coincide with seasonal changes in light and temperature. Modeling analysis using linear mixed-effects models showed that the DCL thickness was best predicted by surface temperature (R2 = 0.51) followed by thermocline depth (R2 = 0.36), and the deep chlorophyll maximum (DCM) concentration was best predicted by surface temperature (R2 = 0.26). The 1% PAR depth was not implicated as an important predictor, but observations from seasonal data suggest that it plays a role in the depth of the DCM. While no relationship was found between surface temperature and DCL-integrated chlorophyll, DCL thickness decreased and DCM concentration increased with increasing surface temperature, which could have implications for productivity in the DCL as the lake continues to warm.

Changes in phytoplankton community composition and structure can have broad-scale ecosystem effects; however, drivers of species diversity in planktonic systems are not well understood. In lakes, a common but not thoroughly tested assumption is that shallow, nearshore waters are much more diverse and productive, and contribute considerably more material and energy to pelagic food webs than deeper waters farther offshore. Lake Superior is a large, cold, oligotrophic freshwater system which can provide insight into community organization under oligotrophic conditions. We used epilimnion and deep chlorophyll layer phytoplankton data from a lake-wide sampling program conducted in 2011 and 2016 to test whether assemblage composition, total algal biovolume, cell concentrations, diversity, and richness vary with depth. Although lake depth was an important factor in structuring assemblage composition, there were no clear nearshore-offshore gradients in cell density or biovolume despite the exposure of nearshore areas to higher concentrations of watershed-derived nutrients. Shannon diversity increased slightly with increasing depth, whereas richness was uncorrelated. Understanding of the nearshore-offshore patterns in phytoplankton community characteristics in the Great Lakes has implications for designing monitoring strategies and for considering how further changes in climate and nutrient deposition would affect the base of the food web.

Thermal stratification in meromictic Lake Tanganyika weakens during the cool, dry and windy season, allowing intrusions of deeper nutrient-rich waters into the upper mixed layer enhancing primary productivity. The current study examined the seasonal influence of thermal structure on the patterns of primary production in Lake Tanganyika. Two sites (Kigoma Bay and Mahale) were sampled on a monthly basis for 1 year. Water temperature and chlorophyll a fluorescence profiles (0–100 m) were measured using a multisonde. Water samples were taken every 20 m (0–100 m) to measure soluble reactive phosphorus (SRP), chlorophyll a and primary production. Pulse Amplitude Modulated Fluorometry was used for the measurements of primary production. The results show that the dry season coincided with higher wind speeds, elevated SRP and some peaks of chlorophyll a and primary production at both sites. During the wet season, high levels of chlorophyll a and primary production coincided with an increase in the euphotic depth, a deep chlorophyll maximum (DCM) and a contribution from metalimnetic areal production at both sites. Our results suggest that the vertical distribution of primary production in Lake Tanganyika is affected by the lake thermal structure, nutrient availability and the extent of the euphotic zone. In Lake Tanganyika, estimates of areal primary production were significantly affected by DCM and required estimation throughout the entire upper mixed layer and the metalimnion which extended to ~89 m.

Epilimnetic production has declined in Lake Ontario, but increased production in metalimnetic deep chlorophyll layers (DCLs) may compensate for these losses. We investigated the spatial and temporal extent of DCLs, the mechanisms driving DCL formation, and the use of physical variables for predicting the depth and concentration of the deep chlorophyll maximum (DCM) during April–September 2013. A DCL with DCM concentrations 2 to 3 times greater than those in the epilimnion was present when the euphotic depth extended below the epilimnion, which occurred primarily from late June through mid-August. In situ growth was important for DCL formation in June and July, but settling and photoadaptation likely also contributed to the later-season DCL. Supporting evidence includes: phytoplankton biovolume was 2.4 × greater in the DCL than in the epilimnion during July, the DCL phytoplankton community of July was different from that of May and the July epilimnion (p = 0.004), and there were concurrences of DCM with maxima in fine particle concentration and dissolved oxygen saturation. Higher nutrient levels in the metalimnion may also be a necessary condition for DCL formation because July metalimnetic concentrations were 1.5 × (nitrate) and 3.5 × (silica) greater than in the epilimnion. Thermal structure variables including epilimnion depth, thermocline depth, and thermocline steepness were useful for predicting DCM depth; the inclusion of euphotic depth only marginally improved these predictions. However, euphotic depth was critical for predicting DCM concentrations. The DCL is a productive and predictable feature of the Lake Ontario ecosystem during the stratified period.

Six offshore stations in southeastern Lake Michigan were sampled during a pre quagga mussel Dreissena rostriformis bugensis period (1995–2000) and a post quagga mussel period (2007–2011). Chlorophyll a fluorescence profiles were used to characterize chlorophyll a concentrations during early (June–July) and late (August–September) summer stratification. During the early summer period the average whole water column chlorophyll a , the deep chlorophyll maximum, and the size of deep chlorophyll layer decreased 50%, 55%, and 92%, respectively, between 1995–2000 and 2007–2011. By contrast, in late summer there were no changes in these metrics between periods. Surface mixed layer chlorophyll a in early and late summer did not differ between time periods. On the other hand, chlorophyll a in the near bottom zone (bottom 20 m) declined 63% and 54% between 1995–2000 and 2007–2011 in early and late summer respectively. Changes in total phosphorus between 1995–2000 and 2007–2011 were less dramatic, with declines of 22–27% in early summer and 11–30% in late summer. Changes in the chlorophyll a conditions were attributed to dreissenid mussels which reduced material available from the spring bloom and disrupted the horizontal transport of nutrients to the offshore. Although light availability increased (i.e., increased secchi depths), reduced nutrient availability and spring diatom abundance resulted in a much smaller deep chlorophyll layer in 2007–2011.

The deep chlorophyll maximum (DCM) is a near ubiquitous feature in Lake Superior during the summer stratified season. Previous studies have elucidated observable characteristics of the DCM in Lake Superior but the physical and biological mechanisms controlling the creation and maintenance of the DCM remained unclear. We use a three-dimensional hydrodynamic model of Lake Superior coupled to an ecological model to perform sensitivity runs exploring the influence of photoadaptation, photoinhibition, zooplankton grazing, and phytoplankton sinking on the vertical distribution of chlorophyll in the water column. The role of a nutricline in determining the presence and nature of the DCM is also explored. The presence of the DCM is dependent upon the presence of thermal stratification in the model. The sensitivity runs reveal that photoadaptation plays a primary role in determining the depth of the DCM in the model while zooplankton grazing and phytoplankton sinking affected the magnitude but not the presence or depth of the DCM. Photoinhibition showed negligible effects on chlorophyll concentration distribution. The presence of a nutricline in the model is also a necessary condition for the formation of the DCM and it influences both the depth and magnitude of the DCM.

Water column primary production is a major term in the organic carbon cycle, particularly in large lakes with relatively reduced shoreline and near-shore influence. Presently, there is a large imbalance in the known inputs vs. outputs of organic carbon in Lake Superior. This study examined primary production in offshore Lake Superior using in situ incubations over a range of conditions representing an annual cycle. Primary producers were dominated by small (

Summer surveys conducted on Lake Superior from 1996–2001 indicated that a deep chlorophyll maximum (DCM) is a common feature of the offshore waters. The DCM was usually observed in the upper hypolimnion between 23 and 35 m, a region lacking a pronounced density gradient. Chlorophyll a concentrations in the DCM were typically 1.5–2.5 (median = 2.0) times epilimnetic concentrations, although these were associated with minimal or no increases in particulate organic carbon concentrations. Seston carbon:phosphorus ratios were consistently lower in the DCM than in the epilimnion, indicating increased phosphorus content of DCM phytoplankton. This could have resulted from either improved nutrient conditions or light limitation at depth. A phosphorus-rich phytoplankton community at depth could serve as a resource for the large, deep-living calanoid copepods that constitute the majority of summer zooplankton biomass. The phytoplankton communities at the level of the DCM were taxonomically distinguishable from those in the epilimnion, with the most notable difference being a relative reduction in the abundance of Cyclotella species in the DCM.

Evolution of the paradigm regarding the relative importance of allochthonous and autochthonous sources of organic matter in aquatic systems has rekindled interest in the role of bacteria in energy transfer. The development of material budget calculations characterizing conditions of net heterotrophy requires knowledge of spatiotemporal dynamics in the bacterial community. Here we present results from three years of measurement of bacterioplankton abundance and production at three locations on the south shore of Lake Superior. In general, bacterial numbers (0.63 × 10 6 ± 0.29 × 10 6 cells·mL −1 ) and production (0.037 ± 0.055 mgC·m −3 ·hr −1 ) were comparable to those reported previously for Lake Superior and were consistent with the system's place along the trophic gradient. Interannual differences in abundance and production were apparently related to the timing and magnitude of seasonal phytoplankton dynamics. There was no inter-transect variation or systematic nearshore-offshore gradients in bacterial activity despite substantial differences in proximity to sources of terrigenous materials (between transects) and in phytoplankton biomass (with distance offshore). The most striking signals in bacterial activity were those evidenced by peaks in bacterial production associated with the deep chlorophyll maximum and with the decline in the phytoplankton community with the approach to turnover. It is hypothesized that bacterioplankton activity in Lake Superior exists in a near steady state, fueled by labile organic matter produced through phytoplankton excretion and the photolytic processing of refractory terrigenous materials. Superimposed on this rather stable signal are peaks in bacterial production apparently related to senescence of the phytoplankton community and, perhaps, the generation of nutrients by the grazing community.