This dataset provides long-term information about Iberian ibex (Capra pyrenaica hispanica Schimper, 1848) presence in Sierra Nevada (SE Iberian Peninsula), as a result of annual sampling from 1993 to 2018 done by the managers of the Sierra Nevada Natural and National Park. They carried out the transects collecting different variables such as the number of individuals observed, the perpendicular distance of each group of goats to the transect line and, at an individual level and sex as well as age of individuals in the case of males. These data enabled the calculation of population parameters such as density, sex ratio, birth rate and age structure. These parameters are key for Iberian ibex conservation and management, given that Sierra Nevada harbours the largest population of this species in the Iberian Peninsula. The data set we present is structured using the Darwin Core biological standard, which contains 3,091 events (582 transect walk events and 2,509 group sighting events), 5,396 occurrences, and 2,502 measurements. The occurrences include the sightings of 11,436 individuals (grouped by sex and age) from 1993 to 2018 in a total of 88 transects distributed along Sierra Nevada, of which 33 have been continuously sampled since 2008.

Bidighinzu Lake is a warm monomitic and hypereutrophic reservoir located in northwestern Sardinia at 334 m a.s.l. Built in 1956, it is mainly used for drinking water for a population of about 160,000 users. Bidighinzu Lake covers a surface area of 1.7 × 10⁶ m² and has a maximum volume of 12.2×10⁶ m³ and a mean depth of 7.3 m. According to ECOSTAT, it belongs to the LM7 category (altitudes <800 m a.s.l., mean depths >15 m, conductivity <2.5 mS cm−1). Its watershed has a surface area of 52 km² with a geological substrate consisting of basalt, limestone, and shale. The supplies of water from the catchment to the lake are insufficient to make up for the losses and human demands. Consequently, the lake receives additional water from Temo Lake and Rio Mannu-Su Tulis river lock, localized in different watersheds. Problems of potabilization have arisen since the early years of the reservoir’s use, particularly in summer-autumn, because of hypolimnic deoxygenation and the excessive presence of algae in the epilimnion. To face this situation, different restoration actions were carried out in Bidighinzu Lake. Among the most important: the installation in 1966 of an aeration system in the area around the water intake tower and in 1987 the reduction of nutrient loads from the watershed by the diversion of civil and industrial wastewater downstream of the dam. A comparison among data collected from just before to about 10 years after this last action the site did not show any improvement in the trophic status. Since 2006, the lake is managed by the Sardinia Water Authority (ENAS) and is part of LTER-Italy. The site has real-time remote monitoring station equipped with a multiparameter probe housed on floating platform. The main scientific purposes at present concern the relationships between trophic status, abundance of cyanobacteria and the presence of toxins; the assessment of climate change and local factors on the phytoplankton dynamics; the development of territorial indicators related to the trophic conditions based on the land cover and use of catchment areas. Recently in Lake Bidighinzu it was conducted an experimental activity, with an aeration system with micro-bubbles. The aim was to maintain sufficient oxygen in the hypolimnetic waters, especially in the summer months, in order to improve the purification process, prevent phosphorus release from sediments and mitigate eutrophication. Available data sets include information on phytoplankton and limnological variables since the last 70.

South-West Bulgaria, Mediterranean catchment

Lake Tovel has a long history of limnological research and over 300 publications since the late 1800s, including an intensive study by E. Baldi in the 1930s, document the continued interest in this lake. Tovel is famous for its clear waters and past red dinoflagellate blooms (Flaim et al. 2004. Phycologia 43:737–743) that no longer occur due to changes in land use (Borghi et al. 2006. Studi Trent. Sci. Nat., Acta Biol. 81:1-472). Besides its intrinsic biological value, Lake Tovel provides irrigation water and electrical energy to the local population, and its location in the heart of the Adamello Brenta Natural Park makes it an important tourist attraction. Following several sporadic surveys, since 1995 the lake is part of an ongoing long-term limnological study conducted by the Fondazione E. Mach (FEM) at S. Michele all’Adige TN, that includes temperature profiling, chemical and biological data taken at monthly intervals during the ice-free period and occasional winter sampling. FEM is well equipped for limnological field work with dinghy with electrical motor, multi-parameter probe, fluoroprobe, underwater quantum sensor, Eckman dredge, plankton nets, water sampling bottles, etc. Laboratory facilities include microscopy (bright field, phase contrast, interferential, fluorescent, inverted microscopes and stereoscopes) with image analysing software, a wet lab and a fine chemistry lab for nutrients and major ions in water as well as organics by ion chromatography and liquid chromatography-Mass Spectrometry (LC-MS). Also available are molecular laboratories equipped with basic (PCR, electrophoresis) and advanced techniques (Sanger and NG sequencing). Limnological data are supported by meteorological data provided by a meteorological station situated in the lake and active since 1976. Recently, sensors for high frequency data (HFD) for temperature, dissolved oxygen, light (at various depths) and water level have been installed on a central lake platform. Notwithstanding its modest altitude (1178 m asl), Tovel has characteristics similar to a 'high altitude' lake because its waters are particularly cold and transparent. The lake is oligotrophic (PT <10 µg/L) with a high biodiversity of plankton, especially of flagellates (Hansen & Flaim 2007J Limnol 66:107-141)and rotifers (Obertegger et al. 2008 J Plank Res 30:633–643). Cold-water dinoflagellates from the lake have been studied for their life cycles (Flaim et al. 2009 Hydrobiologia 639:85–98), lipid profiles (Flaim et al. 2012 Hydrobiologia 698: 285-293) and their response to stressors such as UVR (Obertegger et al. 2011 J. Phycol. 47:811–820). Furthermore, marked water level fluctuations due to the input of snowmelt water are influential in structuring the plankton community (Obertegger et al. 2007. Aquat. Sci. 69:575 – 583). Lake Tovel is an ideal ‘natural laboratory’ where we study the biotic and abiotic parameters tied to climate change and verify ecological theories.

How do freshwater ecosystems react to changing environmental conditions and to what extent can these changes be captured in the dynamics of eco-evolutionary processes? The project REES ('Rhine Eco-Evolutionary System') aims at the long-term assessment of eco-evolutionary interactions in the Rhine as a limnic habitat under consideration of diverse associated water bodies. The study area includes the main flow channel of the Rhine (km 845, North Rhine-Westphalia), as well as Rhine oxbows, Rhine water-fed gravel pit lakes in ecological succession and the surrounding floodplain (Rees, district of Kleve). The Ecological Research Station Rees-Grietherbusch of the Institute of Zoology (University of Cologne) and the Nature Conservation Center District Kleve e.V. form the central infrastructure of the study area. In addition, the Ecological Rhine Station of the University under the direction of Prof. Dr. Arndt is also associated to the project, which enables direct sampling and experimental recording of the main Rhine flow channel. The extensive system of standing and flowing freshwater bodies covered in the REES study site allows the investigation of dynamic variations in biodiversity composition at all levels, from species diversity of communities to genomic diversity at the molecular level of individuals and populations. Along a selected trophic cascade, representative species will be long-term observed and analyzed ecologically and especially also (population-)genomically. The incorporation of ecological genomics is the core aspect of this LTER-D project, which is intended to capture the feedback of evolutionary changes on the ecological system. Population genomic approaches can be used to infer both evolutionary and ecological processes from genomic data. To cope with the dimension of this project, REES is designed as an interdisciplinary collaboration project and currently counts seven project partners with corresponding subordinate projects.

The WelFin LTER-site is located at the Hanko peninsula, at the entrance to the Gulf of Finland. The activities are largely focused to the coastal areas surrounding Tvärminne Zoological Station (University of Helsinki); a marine station established in 1902. The site is well equipped to meet the research demands, offering differently sized research vessels, field equipment, a range of climate chambers, and modern analytical instrumentation. A large part of the surrounding area is a nature reserve, to be used only for science and education. Many of the partners of this site have a long history of scientific collaboration. Although high-quality basic research continues to be at the heart of the site’s activities, many of the research questions nowadays include aspects of human induced long-term change.

Lake Garda has the largest volume (49 billions of cubic meters) and the most extensive area (368 km2) of Italian lakes. Along with lakes Orta, Maggiore, Lugano, Como, Iseo and Idro, it forms part of the group of deep lakes located south of the Alps in one of the most densely populated and highly productive area of Italy. With a total volume of over 124 billions of cubic meters, these lakes constitute one of the largest freshwater supplies in Europe. Their waters are used for agriculture, industry, fishery and drinking. Moreover, they are an important resource for recreation and tourism thanks to both attractive landscape and water quality. In Lake Garda, sporadic studies were carried out irregularly by various Institutions up to the end of the 1980s. Since the beginning of the 1990s, continuous monthly samplings and measurements were carried out by the Department of Biology of the Padova University (Responsible, Nico Salmaso), with the collaboration of ARPAV. Since 2005 the whole limnological research is performed by the Limnological research group of the Agrarian Institute of S. Michele all’Adige – E. Mach Foundation (S. Michele all’Adige, Trento; coordinator, Nico Salmaso). Since the 1970s, Lake Garda showed an increase in the trophic status, with mean annual concentrations of total phosphorus in the whole water column increasing from ca. 10 µg P/L to 20 µg P/L. In the last 4-5 years of observations, TP showed a stabilisation of the concentrations, around 18 µg P/L. At the community level, annual phytoplankton cycles underwent a unidirectional and slow shift mainly due to changes in the species more affected by the nutrient enrichment of the lake. After a first and long period of dominance by conjugatophytes (Mougeotia) and diatoms (Fragilaria), phytoplankton biomass in recent years was sustained by cyanobacteria (Planktothrix). Other important modifications in the development of phytoplankton were superimposed on this pattern due to the effects of annual climate fluctuations principally mediated by the deep mixing events at spring overturn. Main specific research objectives in this LTER station include: -Changes in the physical, chemical and biological variables at different temporal scales, from months to decades and centuries (paleoecology). Update of the time series of hydrological, climatological and limnological data, whith special attention to lake evolution and effects on biotic communities in relation to ongoing climatic changes. Definition of predictive models. - Identification of the environmental and biotic mechanisms favouring the development of cyanobacteria (including the recent appearence of blooms and new species). Identification of the factors selecting for the development of toxic strains, the production and concentrations of epato- and neurotoxins, and their impact on trophic webs and water usability. The limnological field facilities of the limnological research group include 2 rubber dinghies, 2 multi-parameter probes, a fluoroprobe, a FlowTracker Handheld ADV Sonntek, underwater Quantum sensors, a Kajak corer and an Eckman dredge for sediment sampling. The unit also has several laboratories. These include the hydrobiology and microscopy laboratory, equipped for analyses of basic limnological variables (photosynthetic pigments, dry weight, dissolved oxygen, water turbidity, macrophytes) and of phytoplankton, picoplankton and periphyton samples (microscopes, invertoscopes, fluorescent microscopy, image analysis). The analytical and environmental chemistry laboratory is equipped for analysis of the major ions and nutrients (phosphorus, nitrogen and silica), as well as organic molecules (with focus on cyanotoxins) by means of spectrophotometry, ion chromatography and Liquid Chromatography-Mass Spectrometry (LC-MS). We have access to genetic laboratories equipped with the principal analytical tools, i.e. PCR, electrophoresis, and sequencing. The data collected at monthly frequency since 1991 includes water temperature and oxygen. Phytoplankton was collected since 1993, while complete data recording (including chemistry and zooplankton) begun in 1995.

Rich fen and grassland communites formerly used for haymaking in the transition between the middle boreal and northern boreal vegetation zone, and in the transition between oceanic and continental vegetation sections in Central Norway

In order to combat the eutrophication of Lake Balaton, the Kis-Balaton Water Protection System (KBWPS) was initiated in the early 1980s. Originally, the KBWPS consisted of an 18 km2 shallow (less than 1.3 m) artificial lake system (Lake Hídvégi) and a 16 km2 wetland, which were constructed on the site of the former Kis-Balaton wetland in the mid-1980s. Later, the wetland part of the KBWPS was significantly enlarged (over 50 km2). Lake Hídvégi was designed to retain nutrients and provide ideal conditions for algae growth, while the wetland component of the KBWPS prevented these algae from entering Lake Balaton. Regular limnological, ornithological, ichthyological and plant ecological measurements are carried out in both Lake Hídvég and the wetland part of the KBWPS.

Large-scale opencast mining of brown coal represents a significant and devastating intervention in the natural environment. As a close to nature and economically acceptable method of reclamation of residual mine pits, the hydric method of reclamation is used, when lakes are created from quarries. The creation of a new lake in a former mining area essentially represents a large-scale ecological experiment, during which a number of specific factors are involved with impacts on individual organisms, multiple trophic levels and interactions, even entire food chains, and ultimately the lake water quality. Post-mining lakes (Medard Lake – 490 ha, max. depth 50 m, 400 m a.s.l., Milada Lake – 245 ha, max. depth 25 m, 145 m a.s.l., Most Lake – 310 ha, max. depth 75 m, 199 m a.s.l.) thus represent unique LTER areas for studying ecological processes in large natural lentic ecosystems. The ongoing research is focused mainly on (i) the structuring effect of submerged macrophytes on trophic relationships and distribution of fish in deep lakes, (ii) the effects of intra- and interspecific interactions on the succession of fish communities, and (iii) the effects of anthropogenic use and long-term changes on water quality, composition, periphyton composition and phytoplankton structure and biomass.