Temporal dynamics in epipelic, pelagic and epiphytic algal production in a clear and a turbid shallow lake

SUMMARY 1. Pelagic and epipelic microalgal production were measured over a year in a pre-defined area (depth 0.5 m) in each of two lakes, one turbid and one with clear water. Further estimates of epiphytic production within reed stands were obtained by measuring production of periphyton developed on artificial substrata.
2. Total annual production of phytoplankton and epipelon was 34% greater in the turbid lake (190 g C m⁻² year⁻¹) than in the clearwater lake (141 g C m⁻² year⁻¹). However, the ratio of total production to mean water column TP concentration was two fold greater in the clearwater lake.
3. Phytoplankton accounted for the majority of the annual production (96%) in the turbid lake, while epipelic microalgal production dominated (77%) in the clear lake. The relative contribution of epipelic algae varied over the year, however, and in the turbid lake was higher in winter (11–25%), when the water was relatively clear, than during summer (0.7–1.7%), when the water was more turbid. In the clearwater lake, the relative contribution of epipelon was high both in winter, when the water was most clear, and in mid-summer, when phytoplankton production was constrained either by nutrients or grazing.
4. Compared with pelagic and epipelic primary production, epiphytic production within a reed stand was low and did not vary significantly between the lakes.
5. The study supports the theory of a competitive and compensatory trade-off between primary producers in lakes with contrasting nutrient concentrations, resulting in relatively small differences in overall production between clear and turbid lakes when integrating over the season and over different habitats.     

草藻型稳态转换对湖泊微生物结构及其碳循环功能的影响

湖泊是地球表层系统中水、土、气等各个圈层相互作用的联结点,对区域物质如碳等元素循环具有重要影响.微生物是湖泊等水生态系统中的重要组成部分,是湖泊等生态系统中碳等元素物质循环的主要驱动者,是深入了解湖泊碳循环过程的关键.受人类活动等影响,湖泊生态系统,尤其是浅水湖泊生态系统往往表现出以高等水生植物(草型)为主要初级生产者的清水稳定态和以浮游藻类(藻型)为主要初级生产者的浊水稳定态,而随着湖泊营养负荷和湖泊环境条件的变化,这两个不同的稳定态之间可以发生转换或者剧变,这种剧变不仅影响湖泊生态系统中的微生物结构,而且对湖泊中有机碳的形成、循环过程及其微生物驱动机制产生重大影响.本文重点就湖泊生态系统中有机碳的转换与微生物关系以及草藻型稳定态的转换对微生物结构及其碳循环功能的影响等进行综述,进一步分析其中的关键科学问题,以期为深入了解湖泊生态系统中碳等元素循环的微生物驱动过程与机制提供帮助.     

Alternative equilibria in shallow lakes

The turbidity of lakes is generally considered to be a smooth function of their nutrient status. However, recent results suggest that over a range of nutrient concentrations, shallow lakes can have two alternative equilibria: a clear state dominated by aquatic vegetation, and a turbid state characterized by high algal biomass. This bi-stability has important implications for the possibilities of restoring eutrophied shallow lakes. Nutrient reduction alone may have little impact on water clarity, but an ecosystem disturbance like foodweb manipulation can bring the lake back to a stable clear state. We discuss the reasons why alternative equilibria are theoretically expected in shallow lakes, review evidence from the field and evaluate recent applications of this insight in lake management.     

Restoring lakes by using artificial plant beds: habitat selection of zooplankton in a clear and a turbid shallow lake

1. Return of large‐bodied zooplankton populations is of key importance for creating a shift from a turbid to a clear‐water state in shallow lakes after a nutrient loading reduction. In temperate lakes, recovery is promoted by submerged macrophytes which function as a daytime refuge for large zooplankton. However, recovery of macrophytes is often delayed and use of artificial plant beds (APB) has been suggested as a tool to enhance zooplankton refuges, thereby reinforcing the shift to a clear‐water state and, eventually, colonisation of natural plants. 2. To further evaluate the potential of APB in lake restoration, we followed the day–night habitat choices of zooplankton throughout summer in a clear and a turbid lake. Observations were made in the pelagic and littoral zones and in APB in the littoral representing three different plant densities (coverage 0%, 40% and 80%). 3. In the clear lake, the zooplankton (primarily Daphnia) were mainly found in the pelagic area in spring, but from mid‐May they were particularly abundant in the APB and almost exclusively so in mid‐June and July, where they appeared in extremely high densities during day (up to 2600 ind. L⁻¹). During night Daphnia densities were overall more equally distributed between the five habitats. Ceriodaphnia was proportionally more abundant in the APB during most of the season. Cyclopoids were more abundant in the high APB during day but were equally distributed between the five habitats during night. 4. In the turbid lake, however, no clear aggregation was observed in the APB for either of the pelagic genera (Daphnia and Bosmina). This may reflect a higher refuge effect in the open water due to the higher turbidity, reduced ability to orient to plant beds and a significantly higher fish density (mainly of roach, Rutilus rutilus, and perch, Perca fluviatilis) in the plant beds than in the clear lake. Chydorus was found in much higher proportions among the plants, while cyclopoids, particularly the pelagic Cyclops vicinus, dominated in the pelagic during day and in the pelagic and high density plants during night. 5. Our results suggest that water clarity is decisive for the habitat choice of large‐bodied zooplankton and that introduction of APB as a restoration measure to enhance zooplankton survival is only a useful tool when water clarity increases following loading reduction. Our results indicate that dense APB will be the most efficient.     

Total phosphorus thresholds for regime shifts are nearly equal in subtropical and temperate shallow lakes with moderate depths and areas

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Drought-induced changes in nutrient concentrations and retention in two shallow Mediterranean lakes subjected to different degrees of management

While extensive knowledge exists on the relationship between nutrient loading and nutrient concentrations in lakes in the cold temperate region, few studies have been conducted in warm lakes, not least in warm arid lakes. This is unfortunate as a larger proportion of the world’s lakes will be situated in arid climates in the future due to climate change and a larger proportion will suffer from a higher frequency of intensive drought. We conducted a comprehensive 11–13 year mass balance study in two interconnected shallow Mediterranean lakes in Turkey, covering a period with substantial changes in climate conditions. The upstream lake was only affected by natural changes in nutrient loading, while the downstream lake was additionally influenced by sewage diversion and restoration by fish removal. Contrasting to experience from north temperate lakes we found an increase in in-lake concentrations of total phosphorus and inorganic nitrogen (ammonia as well as nitrate) in dry years despite lower external nutrient loading, and submerged macrophytes did not increase the nitrogen retention capacity of the lakes. In contrast, fish removal modulated the nitrogen concentration as in north temperate lakes, but the effect was not long-lasting. Our results suggest that climate warming reduces the nutrient retention capacity of shallow lakes in the Mediterranean and exacerbates eutrophication. Lower thresholds of nutrient loading for shifting turbid shallow lakes to a clear water state are therefore to be expected in arid zones in a future warmer climate, with important management implications.     

Climate change effects on nitrogen loading from cultivated catchments in Europe: implications for nitrogen retention, ecological state of lakes and adaptation

Climate change might have profound effects on the nitrogen (N) dynamics in the cultivated landscape as well as on N transport in streams and the eutrophication of lakes. N loading from land to streams is expected to increase in North European temperate lakes due to higher winter rainfall and changes in cropping patterns. Scenario (IPCC, A2) analyses using a number of models of various complexity for Danish streams and lakes suggest an increase in runoff and N transport on an annual basis (higher during winter and typically lower during summer) in streams, a slight increase in N concentrations in streams despite higher losses in riparian wetlands, higher absolute retention of N in lakes (but not as percentage of loading), but only minor changes in lake water concentrations. However, when taking into account also a predicted higher temperature there is a risk of higher frequency and abundance of potentially toxic cyanobacteria in lakes and they may stay longer during the season. Somewhat higher risk of loss of submerged macrophytes at increased N and phosphorus (P) loading and a shift to dominance of small-sized fish preying upon the key grazers on phytoplankton may also enhance the risk of lake shifts from clear to turbid in a warmer North European temperate climate. However, it must be emphasised that the prediction of N transport and thus effects is uncertain as the prediction of regional precipitation and changes in land-use is uncertain. By contrast, N loading is expected to decline in warm temperate and arid climates. However, in warm arid lakes much higher N concentrations are currently observed despite reduced external loading. This is due to increased evapotranspiration leading to higher nutrient concentrations in the remaining water, but may also reflect a low-oxygen induced reduction of nitrification. Therefore, the critical N as well as P loading for good ecological state in lakes likely has to be lower in a future warmer climate in both north temperate and Mediterranean lakes. To obtain this objective, adaptation measures are required. In both climate zones the obvious methods are to change agricultural practices for reducing the loss of nutrients to surface waters, to improve sewage treatment and to reduce the storm-water nutrient runoff. In north temperate zones adaptations may also include re-establishment of artificial and natural wetlands, introduction of riparian buffer zones and re-meandering of channelised streams, which may all have a large impact on, not least, the N loading of lakes. In the arid zone, also restrictions on human use of water are urgently needed, not least on the quantity of water used for irrigation purposes.     

Successful restoration of water level and surface area restored migrant bird populations in a Hungarian wetland

Water level and water surface area fluctuations are important factors determining abundance of bird populations and bird assemblages structure in a wetland habitat. The water level and water surface area of the Marsh T?m?rd (West Hungary) changed drastically between 1998 and 2008, and the marsh dried out because of scarce rainfall in 2000 and 2001. A habitat restoration in winter 2001 repaired the waterholding capacity of the marsh. We analyzed changes in parameters of bird assemblages in investigated wetland area in relation of environmental factors. We used full redundancy analysis (RDA) on number of caugth migratory birds per year, species richness, diversity and evenness of bird assemblages to examine correlations among water level, water surface area and vegetation core. Species like water rail, common snipe, river warbler, Savi’s warbler, great reed warbler, reed warbler, marsh warbler, sedge warbler, reed bunting showed high and positive linear correlations with the water level and water surface area in the postbreeding period. Some wetland species, sedge warbler, Savi’s warbler and reed bunting as well as total number of caugth birds per year and total numbers of caugth species per year were clearly associated with thick marsh vegetation. According to our results the bird species composition of the wetland might have returned to the prerestoration levels and surface areas.     

Ciliate community structure and interactions within the planktonic food web in two alpine lakes of contrasting transparency

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Relative importance of periphyton and phytoplankton in turbid and clear vegetated shallow lakes from the Pampa Plain (Argentina): a comparative experimental study

We analyzed experimentally the relative contribution of phytoplankton and periphyton in two shallow lakes from the Pampa Plain (Argentina) that represent opposite scenarios according to the alternative states hypothesis for shallow lakes: a clear lake with submerged macrophytes, and a turbid lake with high phytoplankton biomass. To study the temporal changes of both microalgal communities under such contrasting conditions, we placed enclosures in the littoral zone of each lake, including natural phytoplankton and artificial substrata, half previously colonized by periphyton until a mature stage and half clean to analyze periphyton colonization. In the clear vegetated shallow lake, periphyton chlorophyll a concentrations were 3–6 times higher than those of the phytoplankton community. In contrast, phytoplankton chlorophyll a concentrations were 76–1,325 times higher than those of periphyton in the turbid lake. Here, under light limitation conditions, the colonization of the periphyton was significantly lower than in the clear lake. Our results indicate that in turbid shallow lakes, the light limitation caused by phytoplankton determines a low periphyton biomass dominated by heterotrophic components. In clear vegetated shallow lakes, where nitrogen limitation probably occurs, periphyton may develop higher biomass, most likely due to their higher efficiency in nutrient recycling.     

Precipitation-Induced Alternative Regime Switches in Shallow Lakes of the Boreal Plains (Alberta,Canada)

This study focused on unraveling the natural mechanism for the frequent shifts in alternative regimes in pristine shallow lakes of the Boreal Plains, Alberta, Canada. The lakes tend to be clear and dominated by submerged aquatic vegetation (SAV) or turbid and dominated by phytoplankton. We report on the inter-annual response of 23 lakes from 2001 to 2007. We explore the effect of fluctuations in annual precipitation on the lake response including water depth, total phosphorus (TP) concentration, turbidity, phytoplankton biomass, SAV biomass, and the proportion of clear and turbid lakes. The regime switches appear driven by the transient dynamics of phytoplankton, and dilution of nutrients, phytoplankton biomass, and turbidity during wet years, and evapoconcentration during dry years. Increased precipitation was correlated with decreased phytoplankton biomass, TP concentration, chloride concentration, and turbidity. In 2005, the wettest year, no phytoplankton-dominated lakes were observed. During the driest year (2002), the phytoplankton-dominant regime (>18 μg chl-a L^?1) occurred in 22% of lakes, which was higher than the study period average. SAV biomass was not directly affected by precipitation, but was negatively associated with phytoplankton biomass and positively associated with the previous year’s SAV growth. SAV biomass was carried over from year-to-year, and the occurrence of SAV-dominated (>25% cover) lakes was significantly higher in 2007 (90%) following 3 years of high precipitation levels.     

Climate-related differences in the dominance of submerged macrophytes in shallow lakes

It has been suggested that shallow lakes in warm climates have a higher probability of being turbid, rather than macrophyte dominated, compared with lakes in cooler climates, but little field evidence exists to evaluate this hypothesis. We analyzed data from 782 lake years in different climate zones in North America, South America, and Europe. We tested if systematic differences exist in the relationship between the abundance of submerged macrophytes and environmental factors such as lake depth and nutrient levels. In the pooled dataset the proportion of lakes with substantial submerged macrophyte coverage (> 30% of the lake area) decreased in a sigmoidal way with increasing total phosphorus (TP) concentration, falling most steeply between 0.05 and 0.2 mg L⁻¹. Substantial submerged macrophyte coverage was also rare in lakes with total nitrogen (TN) concentrations above 1–2 mg L⁻¹, except for lakes with very low TP concentrations where macrophytes remain abundant until higher TN concentrations. The deviance reduction of logistic regression models predicting macrophyte coverage from nutrients and water depth was generally low, and notably lowest in tropical and subtropical regions (Brazil, Uruguay, and Florida), suggesting that macrophyte coverage was strongly influenced by other factors. The maximum TP concentration allowing substantial submerged macrophyte coverage was clearly higher in cold regions with more frost days. This is in agreement with other studies which found a large influence of ice cover duration on shallow lakes' ecology through partial fish kills that may improve light conditions for submerged macrophytes by cascading effects on periphyton and phytoplankton. Our findings suggest that, in regions where climatic warming is projected to lead to fewer frost days, macrophyte cover will decrease unless the nutrient levels are lowered.     

Modeling nutrients,oxygen and critical phosphorus loading in a shallow reservoir in China with a coupled water quality – Macrophytes model

Many macrophyte-dominated clear lakes switch to a phytoplankton-dominated turbid state when the lake becomes eutrophic. An existing Yuqiao Reservoir Water Quality Model (YRWQM) and the macrophyte submodel were coupled to simulate the effect of submerged macrophytes on nutrients and dissolve oxygen cycles in a shallow reservoir in China. The level of phosphorus loading in a transition from a clear to turbid state was addressed using the integrated model. The model runs from seedling establishment until dying out, from March 1 to July 18 in 2009. The simulations were performed for a contingent range of P loadings, starting from three different initial conditions. The results indicated that the integrated model improves accuracy of predictions compared to YRWQM. The concentrations of nutrients declined slightly during the macrophyte growth period in the reservoir and dissolved oxygen increased slightly. Although nutrient concentrations increased by submerged macrophyte release during the extinction period, the effect on the nutrients was less than that of transfer with nutrient-rich water. More released nutrients may enhance increases in substantial abundance. The critical phosphorus loading level during a switch from the clear to turbid state was estimated by these scenarios. The threshold for the switch is ∼6.1 mgP m⁻² d⁻¹ with an initial total phosphorus concentration of 160 μg l⁻¹. Moreover, the results demonstrated that the switch was also dependent on the initial total phosphorus concentration. These results suggest that the reservoir in a clear water state is at risk of a switch as nutrient levels are close to the critical levels.     

Zooplankton, phytoplankton and the microbial food web in two turbid and two clearwater shallow lakes in Belgium

Components of the pelagic food web in four eutrophic shallow lakes in two wetland reserves in Belgium (Blankaart and De Maten) were monitored during the course of 1998–1999. In each wetland reserve, a clearwater and a turbid lake were sampled. The two lakes in each wetland reserve had similar nutrient loadings and occurred in close proximity of each other. In accordance with the alternative stable states theory, food web structure differed strongly between the clearwater and turbid lakes. Phytoplankton biomass was higher in the turbid than the clearwater lakes. Whereas chlorophytes dominated the phytoplankton in the turbid lakes, cryptophytes were the most important phytoplankton group in the clearwater lakes. The biomass of microheterotrophs (bacteria, heterotrophic nanoflagellates and ciliates) was higher in the turbid than the clearwater lakes. Biomass and community composition of micro- and macrozooplankton was not clearly related to water clarity. The ratio of macrozooplankton to phytoplankton biomass – an indicator of zooplankton grazing pressure on phytoplankton – was higher in the clearwater when compared to the turbid lakes. The factors potentially regulating water clarity, phytoplankton, microheterotrophs and macrozooplankton are discussed. Implications for the management of these lakes are discussed.     

A conceptual ecological model to aid restoration of Cootes Paradise Marsh,a degraded coastal wetland of Lake Ontario,Canada

An ecological model is derived from recent studies, based on 60 years of empirical observations and experimental data, that conceptualizes how Cootes Paradise Marsh was transformed from a lush emergent marsh with considerable ecological diversity in all trophic levels, to one that is currently turbid, devoid of vegetation, and dominated by a few exotic plant and fish species. This conceptual model contains 17 key components that interact and contribute to the overall unhealthy state of the marsh. The most influential component is high water level which caused the initial loss of emergent vegetation in the 1940s and 1950s. In the absence of plants to attenuate sediment and assimilate nutrients, the marsh became turbid and windswept, and this led to the disappearance of submergent vegetation over the next two decades. Currently, high water turbidity is being maintained by wind re-suspension, high sediment loading from the watershed during the summer, high algal biomass resulting from excessive nutrient loads from sewage effluent and surface runoff, and the feeding and spawning activities of a very large population of common carp ( Cyprinus carpio). Due to vegetation loss, the substrate has become mostly loose sediment that is no longer suitable for the diverse assemblage of aquatic insect larvae that lived on the plants and detrital material in the 1940s. Benthic grazers have been kept in low abundances due to predation by benthivorous carp; consequently, epiphytic algae have proliferated and further contribute to light limitation of macrophytes. High nutrient loadings contribute to high diurnal fluxes in dissolved oxygen levels that tend to select against less tolerant organisms such as insect larvae (other than chironomids) and piscivores (northern pike and largemouth bass). Without piscivores in the marsh, the planktivores have become dominant and have virtually eliminated all of the large herbivorous zooplankton (e.g., Daphnia), except for a few pockets in the marsh inlets close to residual macrophyte beds. Because of the dominance of small-bodied inefficient grazers (rotifers and small cladocerans), algal biomass is high, and the community has a large proportion of heterotrophic forms that tolerate low light environments. This ecological model suggests that the current turbid un-vegetated state of Cootes Paradise may be very stable. It will persist as long as water levels remain unfavorable for natural re-colonization by the emergent flora, and/or water turbidities remain sufficiently high to suppress the growth of submergent vegetation. Using this conceptual model, I developed a model of how Cootes Paradise Marsh may have functioned as a healthy marsh prior to the 1940s, and use these models as a basis to explore a number of restoration and management options and discuss their implications on the aquatic foodweb.     

Changes in physicochemical and biological factors during regime shifts in a restoration demonstration of macrophytes in a small hypereutrophic Chinese lake

Shallow, eutrophic lakes are usually characterized by a turbid state devoid of submerged vegetation subject to human-induced eutrophication. In most cases, it is rather hard to restore a vegetated clear state due to reduced resilience caused by a blend of complicated factors. In this study, we successfully reestablished a plant community in a small hypereutrophic lake over a certain period. In winter and spring with transparency of >55 cm and temperature of <20 °C, a submerged stands bed formed gradually under strong human interventions. The reestablished plant bed displayed obvious seasonal succession and prolonged the clear-water stage until July 2005, when it collapsed. The regime shift to a turbid state was mainly attributed to the decreasing biomass of stands bed and mechanical damage brought about by the elimination of Spirodela polyrhiza, increasing water temperature, P concentration as well as periphyton biomass, etc. The reestablishment also changed the aquatic ecosystem greatly. A ‘clear-water’ stage was characterized by higher NO₃^?–N, NH₄⁺–N, electrical conductivity, transparency and TN/TP level and more cladocerans (mainly Daphnia pulex), while the turbid state was characterized by higher temperature, chlorophyll a and TP level and more abundant rotifers. It is thus viable to restore submerged macrophytes in such lakes in winter and spring, when transparency is relatively high while temperature and water level are low. Nevertheless, to obtain a long-term, vegetated clear state, control of internal nutrient loading by means of obstruction, purification, dredging or solidification, is extremely necessary since nutrients play an important role in regime shifts as evidenced by the present case, too.     

Shallow lakes theory revisited: various alternative regimes driven by climate,nutrients, depth and lake size

Shallow lakes have become the archetypical example of ecosystems with alternative stable states. However, since the early conception of that theory, the image of ecosystem stability has been elaborated for shallow lakes far beyond the simple original model. After discussing how spatial heterogeneity and fluctuation of environmental conditions may affect the stability of lakes, we review work demonstrating that the critical nutrient level for lakes to become turbid is higher for smaller lakes, and seems likely to be affected by climatic change too. We then show how the image of just two contrasting states has been elaborated. Different groups of primary producers may dominate shallow lakes, and such states dominated by a particular group may often represent alternative stable states. In tropical lakes, or small stagnant temperate waters, free-floating plants may represent an alternative stable state. Temperate shallow lakes may be dominated alternatively by charophytes, submerged angiosperms, green algae or cyanobacteria. The change of the lake communities along a gradient of eutrophication may therefore be seen as a continuum in which gradual species replacements are interrupted at critical points by more dramatic shifts to a contrasting alternative regime dominated by different species. The originally identified shift between a clear and a turbid state remains one of the more dramatic examples, but is surely not the only discontinuity that can be observed in the response of these ecosystems to environmental change.     

Predicting the effect of climate change on temperate shallow lakes with the ecosystem model PCLake

Global average surface temperatures are expected to rise by about 1.4–5.8°C from the present until the year 2100. This temperature increase will affect all ecosystems on earth. For shallow lakes—which can be either in a clear water or a turbid state—this climate change will expectedly negatively affect water transparency though the prediction is far from conclusive and experimental investigations elucidating the potential climatic effects on shallow lakes are still rare. The aim of this study was to further shape and sharpens hypotheses on the impact of climate change on shallow lakes by applying an existing and well-calibrated ecosystem model, PCLake. We focused on asymptotic model behaviour for a range of temperature and loading scenarios in a factorial design. We conclude that climate change will likely lead to decreased critical nutrient loadings. Combined with an expected increase in the external nutrient loading, this will increase the probability of a shift from a clear to a turbid state. As the model predicts a higher summer chlorophyll-a concentration, a stronger dominance of cyanobacteria during summer and a reduced zooplankton abundance due to climate change, the turbid state itself is likely to become even more severe.     

Enhanced Input of Terrestrial Particulate Organic Matter Reduces the Resilience of the Clear-Water State of Shallow Lakes: A Model Study

The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent.     

Planktonic ciliate community structure in shallow lakes of lowland Western Europe

Temperate shallow meso- to eutrophic lakes can exist in one of two alternative states with contrasting foodwebs, referred to as the clear-water and the turbid state. We describe the planktonic ciliate communities of such lakes based on a survey of 66 northwestern European lakes. Ciliates were enumerated and identified to species level according to the quantitative protargol staining technique. Ciliate biomass was on average twice as high in the turbid than in the clear-water lakes. The ciliate communities were dominated by oligotrichs and protostomatids, and no differences in functional composition or α-diversity could be detected between turbid and clear-water lakes, although β-diversity tended to be higher in the latter. At the species level, however, community structure strongly differed between turbid and clear-water lakes, and several indicator species could be identified for the different lake categories. Variation partitioning showed that nutrient status did not explain ciliate community structure independent of the alternative states, while lake area was identified as an additional structuring factor for the ciliate communities. These results stress the importance of the ecosystem structure in shaping ciliate communities in temperate shallow lakes and suggest that nutrient status has little direct effect on ciliate community structure in such lakes.