
Are you interested in the impacts of agricultural land use on microbial communities? Do you want to understand the effects of pesticides and nutrients on carbon cycling in aquatic ecosystems? The Institute of Biodiversity and Ecosystem Dynamics is looking for a highly motivated PhD candidate to investigate agrochemical impacts on microbial carbon cycling in lowland agricultural drainage ditch sediments.
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Are you interested in the impacts of agricultural land use on microbial communities? Do you want to understand the effects of pesticides and nutrients on carbon cycling in aquatic ecosystems? The Institute of Biodiversity and Ecosystem Dynamics is looking for a highly motivated PhD candidate to investigate agrochemical impacts on microbial carbon cycling in lowland agricultural drainage ditch sediments.
Agricultural land use strongly alters the functioning and biodiversity of the surrounding landscape. Conventional practices rely heavily on chemical inputs, such as fertilizers and pesticides, which readily make their way into adjacent waterways. Yet how these agrochemicals affect aquatic microbial communities and their functioning remains poorly understood. This is a pressing research priority, since the Netherlands has approximately 300,000 km of drainage ditches. These ditches hold huge ecological potential, supporting ecosystem services such as carbon cycling and water transport, but they are also most heavily exposed to agrochemical inputs — a combination that may threaten biodiversity and undermine the very services they provide.
This PhD position will focus on aquatic microbial ecotoxicology, aiming to unravel the effects of agrochemicals on the structure and functioning of microbial and viral communities in agricultural ditch sediments and the linked ecosystem function of carbon cycling. It incorporates pesticide mixture toxicity, which is severely understudied, especially to viruses, bacteria, archaea, and fungi. As such, it goes beyond the effects of single chemicals on single organisms and takes a wide scope of microbial diversity and a key ecosystem function – carbon cycling, including both sediment carbon pools and greenhouse gas emissions. This project will broaden our understanding of the impacts of agrochemicals from being toxic to aquatic life to the intertwined consequences for global warming.
The position will be based at the Institute for Biodiversity and Ecosystem Dynamics (IBED) of the University of Amsterdam, bridging the Departments of Freshwater and Marine Ecology (FAME) and Ecosystem and Landscape Dynamics (ELD).

Agricultural land use strongly alters the functioning and biodiversity of the surrounding landscape. Conventional practices rely heavily on chemical inputs, such as fertilizers and pesticides, which readily make their way into adjacent waterways. Yet how these agrochemicals affect aquatic microbial communities and their functioning remains poorly understood. This is a pressing research priority, since the Netherlands has approximately 300,000 km of drainage ditches. These ditches hold huge ecological potential, supporting ecosystem services such as carbon cycling and water transport, but they are also most heavily exposed to agrochemical inputs — a combination that may threaten biodiversity and undermine the very services they provide.
This PhD position will focus on aquatic microbial ecotoxicology, aiming to unravel the effects of agrochemicals on the structure and functioning of microbial and viral communities in agricultural ditch sediments and the linked ecosystem function of carbon cycling. It incorporates pesticide mixture toxicity, which is severely understudied, especially to viruses, bacteria, archaea, and fungi. As such, it goes beyond the effects of single chemicals on single organisms and takes a wide scope of microbial diversity and a key ecosystem function – carbon cycling, including both sediment carbon pools and greenhouse gas emissions. This project will broaden our understanding of the impacts of agrochemicals from being toxic to aquatic life to the intertwined consequences for global warming.
The position will be based at the Institute for Biodiversity and Ecosystem Dynamics (IBED) of the University of Amsterdam, bridging the Departments of Freshwater and Marine Ecology (FAME) and Ecosystem and Landscape Dynamics (ELD).
You will address this multidisciplinary topic using state-of-the-art analytical techniques and data processing and analysis, guided by the highly qualified support staff at IBED. Together with your supervisors, you will bridge the fields of aquatic ecotoxicology, environmental chemistry, and microbial ecology. This requires thinking outside the traditional spheres of these fields, and demands creativity and flexibility as well as a strong motivation to address this challenge using multiple lines of evidence.
Tasks and responsibilities:
We seek a motivated PhD candidate to work at the interface of Ecotoxicology and Microbial Ecology. You hold a Master's degree in Ecology, Environmental Science, Microbiology, or a related field, with a background spanning both disciplines. Ideally, you have experience with microbial community analysis (e.g., sequencing, bioinformatics) and/or assessing chemical stressor effects on organisms or ecosystems, along with solid skills in experimental design and data analysis.
You are genuinely curious about how anthropogenic chemicals shape microbial communities and their functioning, and eager to bridge the conceptual and methodological gap between Ecotoxicology and Microbial Ecology. As an independent, proactive thinker who thrives in interdisciplinary collaboration, you are excited to contribute new insight into this understudied but ecologically highly relevant research field.
Your experience and profile:
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. The preferred starting date is as soon as possible. For this position, the University Job Classification profile “Promovendus” (PhD candidate) applies. Your salary will be €3,204 gross per month in the first year and will increase to €4,051 in the final year, based on full-time employment of 38 hours per week. In addition, you will receive an 8% holiday allowance and 8.3% year-end allowance.
A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants.
The Collective Labour Agreement of Universities of the Netherlands is applicable.
Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:
Are you curious to read more about our extensive package of secondary employment benefits? Take a look here.
You will address this multidisciplinary topic using state-of-the-art analytical techniques and data processing and analysis, guided by the highly qualified support staff at IBED. Together with your supervisors, you will bridge the fields of aquatic ecotoxicology, environmental chemistry, and microbial ecology. This requires thinking outside the traditional spheres of these fields, and demands creativity and flexibility as well as a strong motivation to address this challenge using multiple lines of evidence.
Tasks and responsibilities:
We seek a motivated PhD candidate to work at the interface of Ecotoxicology and Microbial Ecology. You hold a Master's degree in Ecology, Environmental Science, Microbiology, or a related field, with a background spanning both disciplines. Ideally, you have experience with microbial community analysis (e.g., sequencing, bioinformatics) and/or assessing chemical stressor effects on organisms or ecosystems, along with solid skills in experimental design and data analysis.
You are genuinely curious about how anthropogenic chemicals shape microbial communities and their functioning, and eager to bridge the conceptual and methodological gap between Ecotoxicology and Microbial Ecology. As an independent, proactive thinker who thrives in interdisciplinary collaboration, you are excited to contribute new insight into this understudied but ecologically highly relevant research field.
Your experience and profile:
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. The preferred starting date is as soon as possible. For this position, the University Job Classification profile “Promovendus” (PhD candidate) applies. Your salary will be €3,204 gross per month in the first year and will increase to €4,051 in the final year, based on full-time employment of 38 hours per week. In addition, you will receive an 8% holiday allowance and 8.3% year-end allowance.
A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants.
The Collective Labour Agreement of Universities of the Netherlands is applicable.
Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:
Are you curious to read more about our extensive package of secondary employment benefits? Take a look here.
The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of eight research institutes of the Faculty of Science at the University of Amsterdam. The research at IBED aims to unravel how ecosystems function in all their complexity, and how they change due to natural processes and human activities. At its core lies an integrated systems approach to study biodiversity, ecosystems and the environment. IBED adopts this systems approach to ecosystems, addressing abiotic (soil and water quality) and biotic factors (ecology and evolution of plants, animals, and microorganisms), and the interplay between those. The IBED vision includes research encompassing experimental and theoretical approaches at a wide variety of temporal and spatial scales, i.e., from molecules and microorganisms to patterns and processes occurring at the global scale. The University of Amsterdam has excellent high-performance computing facilities. Furthermore, IBED has a dedicated computational support team with specialized knowledge of bioinformatics, (geo)database management and scientific programming. IBED also works with non-academic partners to deliver transdisciplinary science for society.
The position will be based in two IBED departments:
Department of Freshwater and Marine Ecology. The Department of Freshwater & Marine Ecology aims to increase our understanding of the biodiversity and dynamics of freshwater and marine ecosystems from the level of molecules and genes to entire ecosystems.
Department of Ecosystem and Landscape Dynamics. The Ecosystem and Landscape Dynamics research department improves our understanding of the functioning and dynamics of abiotic and biotic components of (geo-)ecosystems across landscapes through time.
Want to know more about our organisation? Read more about working at the University of Amsterdam.
The Institute for Biodiversity and Ecosystem Dynamics (IBED) is one of eight research institutes of the Faculty of Science at the University of Amsterdam. The research at IBED aims to unravel how ecosystems function in all their complexity, and how they change due to natural processes and human activities. At its core lies an integrated systems approach to study biodiversity, ecosystems and the environment. IBED adopts this systems approach to ecosystems, addressing abiotic (soil and water quality) and biotic factors (ecology and evolution of plants, animals, and microorganisms), and the interplay between those. The IBED vision includes research encompassing experimental and theoretical approaches at a wide variety of temporal and spatial scales, i.e., from molecules and microorganisms to patterns and processes occurring at the global scale. The University of Amsterdam has excellent high-performance computing facilities. Furthermore, IBED has a dedicated computational support team with specialized knowledge of bioinformatics, (geo)database management and scientific programming. IBED also works with non-academic partners to deliver transdisciplinary science for society.
The position will be based in two IBED departments:
Department of Freshwater and Marine Ecology. The Department of Freshwater & Marine Ecology aims to increase our understanding of the biodiversity and dynamics of freshwater and marine ecosystems from the level of molecules and genes to entire ecosystems.
Department of Ecosystem and Landscape Dynamics. The Ecosystem and Landscape Dynamics research department improves our understanding of the functioning and dynamics of abiotic and biotic components of (geo-)ecosystems across landscapes through time.
Want to know more about our organisation? Read more about working at the University of Amsterdam.
If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the ‘Apply’-button on the vacancy’s webpage. We accept applications until and including 18 October 2026.
Applications should include the following information (all files besides your CV should be submitted in one single PDF file):
Only complete applications received within the response period via the link below will be considered.
A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). The interviews are expected to take place in late October and November. We will send out the invitations to the selected candidates shortly after the closing date.
Do you have any questions, or do you require additional information? Please contact:
Dr. Milo L. de Baat, [email protected], +31639734035
Dr. Paula Dalcin Martins, [email protected], +31657614902
If you feel the profile fits you, and you are interested in the job, we look forward to receiving your application. You can apply online via the ‘Apply’-button on the vacancy’s webpage. We accept applications until and including 18 October 2026.
Applications should include the following information (all files besides your CV should be submitted in one single PDF file):
Only complete applications received within the response period via the link below will be considered.
A knowledge security check can be part of the selection procedure (for details: national knowledge security guidelines). The interviews are expected to take place in late October and November. We will send out the invitations to the selected candidates shortly after the closing date.
Do you have any questions, or do you require additional information? Please contact:
Dr. Milo L. de Baat, [email protected], +31639734035
Dr. Paula Dalcin Martins, [email protected], +31657614902
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