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.

Nematode communities play an important role in soil ecology research. To analyse different type of plant-soil nematodes, NIOO has a facility for extracting soil and root nematodes by Oostenbrink funnel and mistifier.

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 Passerine testing facility offers a unique oportunity to house and measure passerine birds for an array of behavioural tests in a controlled environment.

The NIOO Phytotron is a complex of greenhouses and climate chambers. In addition to offering controlled growing and rearing environments, the Phytotron offers rooms to process, prepare, harvest or store experiments. The Phytotron also provides physiological analysis- and field equipment, ovens and has a large stock of disposables which can be used.

The ecotron consists of 60 cilinders with intact (non-disturbed) sand, peat or sea clay cores (20 each). For each soil treatment, ten of the cilinders are inoculated with soil from species-rich grassland with the same soil type. The other ten are inoculated with sterile soil from the same grassland. The cilinders are buried in an experimental garden.

The sperm lab houses state-of-the-art equipment used for the analysis of sperm.This includes a computer-assisted sperm-analysis (CASA) system for accurate and automatic assessment of sperm motility and a microscope/camera/software combination for digital image analysis of sperm morphology.

SPI-Birds Network & Database, or the Studies of Populations of Individuals – Birds, is a grassroots initiative connecting those working on populations of individually-marked breeding birds. SPI-Birds is a metadata registry of individually-marked breeding bird studies and the people involved in these studies, and a central hub for data on individually-marked breeding birds.

The NIOO stable isotope facility is part of the chemical analytical lab, with equipment and facilities to perform stable isotope tracer experiments. Stable isotopes (13C) can be analysed in PLFA, gases (CO2/CH4) , (13C/15N) solid material (e.g. soil, plant material, bird feathers) as well as in DNA and RNA and breath samples of birds (D/H).

This is a systematic collection of eight plant species from five grassland sites in the Veluwe, for which some tissue from individual plants is stored at -80 °C. For each site, up to 10 individuals from each species have been sampled along a transect at two time points (late May and early August).

Vogeltrekstation (Dutch Centre for Avian Migration and Demography) is a cooperation between NIOO-KNAW and the Ringersvereniging (bird banding society). It arranges the daily practicalities with relation to catching and ringing of wild birds for science, policy and conservation.

Plants and microorganisms emit a wide range of chemically diverse volatile compounds. These volatiles mediate swift chemical interactions and communication in both aquatic and terrestrial environments, and carry out important ecological functions.