Research group Environmental Metagenomics
Environmental Metagenomics develops and implements cutting-edge DNA technologies to map complex biological ecosystems in air, water, soil, humans, and animals. We do not develop these methodologies alone: the Environmental Metagenomics research group is a joint initiative of University of Applied Sciences Leiden (Hogeschool Leiden) and Naturalis Biodiversity Center.
Working Method
Metagenomics technology utilises DNA and RNA to identify which (micro)organisms are present in an environment. Due to its wide array of applications, metagenomics serves as a key enabling technology within life sciences. It provides essential insights for the responsible management and conservation of our ecosystems.
Our core focus lies in developing innovative methods for field sampling, sample preparation, and next-generation DNA sequencing. In parallel, we actively work on data management, pipeline development, and bioinformatics.
Team
- Arjen Speksnijder – Professor (Lector)
- Marijn Knip
- Anita Dirks
- Marc Besseling
- Rob Pastoor
- Ken Kraaijeveld
Impact
The intrinsic link between biodiversity and health (of humans, animals, and plants) is a central scientific theme within Environmental Metagenomics. This aligns directly with major innovation challenges: agriculture, water & food security, and healthcare. In addition, transferring knowledge directly into education is a fundamental objective of our research group.
Education
In close collaboration with education managers, lecturers, and students, we enrich life sciences degree programmes at University of Applied Sciences Leiden with state-of-the-art scientific insights. Through our research group, biodiversity has earned an integral place in educational curricula, broadening career opportunities for students in non-medical sectors such as water management, ecological conservation, agriculture, and horticulture.
- Curriculum committees: The Professor (Lector) sits on the Professional Advisory Committee for the Biology and Medical Laboratory Research (Biologie en Medisch Laboratoriumonderzoek - BM) programme.
- Secondary education outreach: We contribute to the pre-university HAVO beta talent programme.
- Biodiversity surveys: We coordinate biodiversity field surveys across the city of Leiden during the introduction week for first-year BM students.
- Specialised coursework & research integration: In 2022, we introduced the biodiversity module within the minor Biodiversity and Health, which progressed into the elective course Microbial Dynamics. This course serves as an active platform for integrating hands-on research directly into teaching. Students also participate in research projects, internships, and capstone theses.
Key research projects
School Greenovation: Building the Sustainable School of the Future Together
How can we transform outdated school facilities into healthy, climate-resilient environments where children learn with and from nature daily? University of Applied Sciences Leiden has joined forces with leading Dutch partners for this pioneering initiative, turning conventional school buildings into active, green educational ecosystems.
Omics in the Polder (Completed)
The peat meadow landscape (veenweidegebied) in the Netherlands is ecologically unique yet facing immense strain from agriculture, residential needs, recreation, infrastructure, and water storage. Amid climate change, biodiversity loss, soil subsidence, and housing demands, this project investigated alternative spatial management strategies to make local agriculture more sustainable and restore natural ecosystems.
BENIGN
The BluE and greeN Infrastructure desiGned to beat the urbaN heat (BENIGN) project aims to enhance our understanding of how blue and green infrastructure at the building and neighborhood scale impacts urban living conditions and promotes public health.
Hidden Biodiversity
Urban landscapes harbor significant amounts of undocumented biodiversity. Led by Naturalis Biodiversity Center, this collaborative initiative unites municipalities, industry partners, universities, and universities of applied sciences to uncover and map hidden urban biodiversity.
Biostimulants: From Bulb to Soil (Completed)
The ornamental bulb cultivation sector faces high demand for sustainable practices, aiming to drastically reduce dependence on chemical crop protection products by 2030. This project explored the efficacy of biostimulants - containing microbial substances, non-microbial compounds, or a combination of both - which improve plant nutrient uptake and enhance soil nutrient availability.
Network & partners
Arjen Speksnijder
Professor of Environmental Metagenomics
Contact & information
The Environmental Metagenomics group is part of the Leiden Centre for Applied Bioscience (LCAB) at University of Applied Sciences Leiden. Email: [email protected]
Key knowledge partners of the Environmental Metagenomics research group and Naturalis Biodiversity Center include:
- Leiden University
- Radboud University
- Wageningen University & Research (WUR)
- TU Delft
- Leiden University Medical Center (LUMC)
- LIOS
- Land van Ons
- Rijnland District Water Control Board (Hoogheemraadschap van Rijnland)
- Holland Rijnland Regional Partnership (Samenwerkingsorgaan Holland-Rijnland)
- Municipality of Leiden