PhD Agrochemical impacts on microbial carbon cycling in aquatic ecosystems

Universiteit van Amsterdam; Amsterdam; On-site; EUR 38,000 - 49,000; Full time

Benefits offered by this job

8% holiday allowance

8.3% year-end allowance

30% ruling for non-Dutch applicants

ABP pension support

housing assistance

Job summary

University of Amsterdam, IBED, invites applications for a PhD candidate to study agrochemical impacts on aquatic microbial carbon cycling in drainage ditch sediments. You will join a multidisciplinary team bridging ecotoxicology, environmental chemistry, and microbial ecology.

The position offers a 38-hour week contract for 4 years, with a plan including courses, international meetings, teaching, and a structured educational program. Curious applicants should apply by 18 October 2026.

Qualifications

• MSc in Ecology, Environmental Science, Microbiology, or related field.
• Background spanning Ecotoxicology and Microbial Ecology preferred.
• Experience with field and/or lab work and data analysis.

Responsibilities

• Co-design field sampling, measurements, lab experiments, analyses.
• Process large datasets and perform statistical analyses.
• Communicate with researchers, water authorities, stakeholders.
• Present work at national/international conferences.
• Publish in peer-reviewed journals; mentor students.

Skills

Ecotoxicology

Microbial Ecology

Data analysis

Scripting

Education

MSc in Ecology

Tools

R

Python

Bash

Job description

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.

About the position

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).

What are you going to do?

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:

• Co-designing and conducting field sampling and measurements, lab experiments, and instrumental analyses;
• Conducting large dataset processing and statistical analyses;
• Communicating with local researchers, water authorities, and stakeholders;
• Presenting work at national and international symposia and scientific conferences;
• Writing publications for peer-reviewed journals;
• Mentoring BSc and MSc students.

Your profile

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:

• MSc in Ecology, Environmental Science, Microbiology, or a related field;
• Strong background and experience in Ecotoxicology and/or Microbial Ecology;
• Experience with field and/or lab work;
• Experience with data analysis, such as statistics, data management, etc.;
• Experience in scripting/programming (e.g., R, Bash, Python);
• Strong interest in understanding human impacts on ecological processes, biodiversity, and ecosystem health;
• Proficiency in scientific writing;
• Experience or strong interest in transdisciplinary research;
• Ability to speak and communicate in English at an academic level.

Our offer

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:

• 232 holiday hours per year (based on full‑time) and extra holidays between Christmas and 1 January;
• multiple courses to follow from our Teaching and Learning Centre;
• a complete educational program for PhD students;
• multiple courses on topics such as leadership for academic staff;
• multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
• 7 weeks birth leave (partner leave) with 100% salary;
• partly paid parental leave;
• the possibility to set up a workplace at home;
• a pension at ABP for which UvA pays two‑thirds of the contribution;
• the possibility to follow courses to learn Dutch;
• help with registration at UvA‑Housing for a studio or small apartment when you’re moving from abroad.

Are you curious to read more about our extensive package of secondary employment benefits? Take a look here.

About us

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.

Applications should be received by 18 October 2026.

Do you have any questions, or do you require additional information?

Dr. Milo L. de Baat, [e-mail], [phone]

Dr. Paula Dalcin Martins, [e-mail], [phone]