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A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models., Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe; 1326

A one-dimensional numerical model and a two-dimensional numerical model of the hydrodynamic and thermal structure of Lake Shira during summer have been developed, with several original physical and numerical features. These models are well suited to simulate the formation and dynamics of vertical stratification and provide a basis for an ecological water-quality model of the lake. They allow for the quantification of the vertical mixing processes that govern not only the thermal structure but also the nutrient exchange, and more generally, the exchange of dissolved and particulate matter between different parts of the lake. The outcome of the calculations has been compared with the field data on vertical temperature and salinity distributions in Lake Shira. Lake Shira is meromictic and exhibits very stable annual stratification. The stratification is so stable because of the high salinity of the water. If the water in Lake Shira were fresh and other parameters (depth, volume, and meteorology) were the same, as now, the lake would be mixed in autumn. Using the newly developed models and using common meteorological parameters, we conclude that Lake Shira will remain stratified in autumn as long as the average salinity is higher than 3‰.

We describe the limnological changes between 1989 and 2006 in an urban, shallow lake, Laguna Alalay, located in the Andean valley of Cochabamba (Bolivia). Until 1960, water diversion to the lake was used to lower the inundation risk of Cochabamba city. In the 1980s and 1990s, the high waterfowl diversity and recreational services provided by the lake increased its conservation value. However, the population increase and the discharge of wastewater rich in nutrients increased eutrophication, and the lake became characterized by an annual alternation of submerged macrophytes and phytoplankton. The main aim of the present study is to analyze the response of the lake to manipulations implemented by local authorities: (a) sediment removal and accidental introduction of the exotic fish species Odontesthes bonariensis in 1997 and (b) manual mass removal of floating macrophytes during 2004–2006. The sediment removal and species introduction had several unpredictable consequences for the functioning of the lake, namely the transition to a permanent turbid water state and the persistent dominance of floating macrophytes. A general conclusion of our study is that any lake recovery measures in Bolivia should consider not only ecological, but also socio-economic and political aspects. Taking these into account, restoration of the submerged macrophyte-dominated state may not be that universally desirable as is widely held.

This Special Issue of Aquatic Ecology is an update on the ongoing limnological studies on the ecosystems of two saline, meromictic lakes, Lake Shira and Lake Shunet, both located in southern Siberia (Khakasia, Russia). Lake Shira can be termed as a ‘natural laboratory’ for investigations into the lower limits of biodiversity, in view of the complete absence of fish and cladoceran zooplankton in this water body (see below). Both Lake Shira and the neighbouring Lake Shunt have been the focus of limnological research by the Institute of Biophysics (IBP), Krasnoyarsk, Siberian Branch of the Russian Academy of Science (SB-RAS), since the late 1990s. Below, we provide a brief historical resume of this research programme and then focus on the main findings documented in this special issue. This first, international cooperative study on the Siberian lakes was carried out from 1999 to 2002 by the IBP and The Netherlands Institute of Ecology of the Royal Netherlands Academy of Science (NIOOKNAW), Nieuwersluis. The universities of Madrid, Spain (Prof. Antonio Quesada), Zurich, Switzerland (Prof. Friedrich Juttner) and the Institute of Computational Modelling, Krasnoyarsk (SB-RAS), were the other main participants. The study on Lake Shira during the first three-years (1999–2001) by this international research team was funded by the European Union (EU) INTAS Grant 97-O519 to the IBP. Two of the undersigned—Andrey G. Degermendzhy, head of the IBP, Krasnoyarsk, and Ramesh D. Gulati, of NIOO-KNAW, Nieuwersluis— were among most active collaborators in this early project. The complete study titled The structure and functioning of Lake Shira ecosystem: an example of Siberian brackish water lakes was published in Aquatic Ecology as a Special Issue (36/2) containing 18 papers (Gulati and Degermendzhy 2002). In addition to summarising studies on the bacterial production, protozoan bacterivory, phytoplankton, the growth of dominant zooplankton and the microbial food web of Lake Shira, this study described the geography and geology, as well as provided data on salient features of water chemistry of Khakasian lakes. The above-mentioned published study formed the basis of a concerted, follow-up research project between The Netherlands and Russia from 2005 to 2008. This new project was funded jointly by the Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWORFBR grant 047.017.012), with one of the undersigned (Wolf M. Mooij) as project coordinator. In Handling editor: Piet Spaak.

A feature of meromictic lakes is that several physicochemical and biological gradients affect the vertical distribution of different organisms. The vertical stratification of physical, chemical and biological components in saline, fishless meromictic lakes Shira and Shunet (Siberia, Russia) is quite different mainly because both mean depth and maximum depth of lakes differ as well as their salinity levels differ. The chemocline of the Lake Shira, as in many meromictic lakes, is inhabited by bacterial community consisting of purple sulphur and heterotrophic bacteria. As the depth of the chemocline is variable, the bacterial community does not attain high densities. The mixolimnion in Lake Shira, which is thermally stratified in summer, also creates different habitat for various species. The distribution of phytoplankton is non-uniform with its biomass peak in the metalimnion. The distribution of zooplankton is also heterogeneous with rotifers and juvenile copepods inhabiting the warmer epilimnion and older copepods found in the cold but oxic hypolimnion. The amphipod Gammarus lacustris which can be assigned to the higher trophic link in the fishless lake’s ecosystem, such as Lake Shira, is also distributed non-uniformly, with its peak density generally observed in the thermocline region. The chemocline in Lake Shunet is located at the depth of 5 m, and unlike in Lake Shira, due to a sharp salinity gradient between the mixolimnion and monimolimnion, this depth is very stable. The mixolimnion in Lake Shunet is relatively shallow and the chemocline is inhabited by (1) an extremely dense bacterial community; (2) a population of Cryptomonas sp.; and (3) ciliate community comprising several species. As the mixolimnion of Lake Shunet is not thermally stratified for long period, the phytoplankton and zooplankton populations are not vertically stratified. The gammarids, however, tend to concentrate in a narrow layer located 1–2 m above the chemocline. We believe that in addition to vertical inhomogeneities of both physicochemical parameters, biological and physical factors also play a role in maintaining these inhomogeneities. We conclude that the stratified distributions of the major food web components will have several implications for ecosystem structure and dynamics. Trophic interactions as well as mass and energy flows can be significantly impacted by such heterogeneous distributions. Species spatially separated even by relatively short distances, say a few centimetres will not directly compete. Importantly, we demonstrate that not only bacteria, phytoflagellates and ciliate tend to concentrate in thin layers but also larger-sized species such Gammarus (amphipods) can also under certain environmental conditions have stratified distribution with maxima in relatively thin layer. As the vertical structure of the lake ecosystem is rather complex in such stratified lakes as ours, the strategy of research, including sampling techniques, should consider potentially variable and non-homogeneous distributions.