The molecular laboratories offer a wide range of facilities needed for handling, preparing and analysing a wide variety of DNA and/or RNA samples. The lab is well-equipped, and in addition to the general molecular laboratory there are several specialised laboratories such as an MLII Lab, an RNA Lab and a PCR lab with UV-cupboards.

Two of the most pervasive human impacts on ecosystems are alteration of global nutrient budgets and changes in the abundance and identity of consumers. In spite of the global impacts of these human activities, there have been no globally coordinated experiments to quantify the general impacts on ecological systems. The Nutrient Network (NutNet) is a grassroots, global research effort to address these questions within a coordinated research network comprised of more than 130 grassland sites worldwide.

The Marker Wadden is a newly constructed archipelago in lake Markermeer, which aims to improve the lake’s degrading food web by stimulating primary productivity. The archipelago consists of five islands that add a currently missing habitat type to the lake: shallow, sheltered waters with high nutrient availability and gradual land-water transitions.

The Aqua-flex Arena is a fenced terrain (2500 m2; 80 x 32m) for performing outdoor mesoscosm experiments throughout the year, in the immediate promixity of the NIOO Aquatic Laboratories. Experiments can be performed with > 100 experimental units. There is great flexibility in the spatial set up of experimental units.

The limnotrons are nine stainless steel indoor mesocosms with a high level of control. The dimensions are: 0.97 m in diameter, depth between 1.32 m (side) and 1.37 m (centre), volume of 922 L. The vessels can be closed with a removable PMMA flange lid. In addition to the possibility of sampling vertically with specifically designed integrated water samples, sampling can also be done by using the sampling ports positioned at three depths.

The Netherlands Institute of Ecology (NIOO-KNAW) houses 36x10L microcosms (transparent polycarbonate carboys; NALGENE, Rochester, USA) for plankton research. The microcosms can be temperature-controlled in water baths (at 0.5 °C temperature resolution), and automatically stirred through magnetic stirrers mounted below the water baths.

Flowcytometry (FCM) is a technique that distinguishes individual particles based on light scatter and fluorescence. A large advantage is that FCM can analyse and sort cells at a very high speed of up to 10,000 cells/second.

Chemostats are bioreactors used for cultivation of phytoplankton and/or zooplankton. They can be operated as batch (no dilution rate), as chemostat (fixed dilution rate) or as turbidostats (dilution rate dependent on turbidity). They can be operated as open or closed system, and also axenically.

The aquatic laboratories facilitate researchers working with aquatic samples, sediments or organisms. They include laboratories with specialised equipment for aquatic analyses, dedicated rooms for controlled experiments, and they give access to separate storage areas for field equipment, sample storage, chemicals and disposables stocks.

The Netherlands Institute of Ecology (NIOO-KNAW) houses 8 long glass aquaria (180 x 40 x 40 cm in length x width x height, 288L) and 24 shorter glass aquaria (90 × 50 × 50 cm in length x width x height, 225L). The aquaria can be kept at different temperatures which can be controlled by an automatic control system (Cascade Automation Systems, Ridderkerk, the Netherlands).