PhD in Microbial and Chemical Ecology: Microfluidics and Plant-Microbe Interactions (RhizoTrack Project)

This PhD position at the Technical University of Denmark (DTU) offers an exciting opportunity to explore the dynamic interactions between soil microorganisms and plants, focusing on the chemical communication that underpins resilient plant-microbe partnerships. The DFF-funded RhizoTrack project investigates how soil microorganisms sense, differentiate, and transform plant root exudates, and how these chemical interactions influence microbial colonization of plant roots. By elucidating these mechanisms, the project aims to inform the development of microbial and chemical strategies to enhance plant health and reduce reliance on agrochemical inputs, contributing to sustainable agriculture. As a PhD candidate, you will work at the interface of microbiology, chemical ecology, and environmental science, developing advanced skills in microfluidics, molecular ecology, and environmental data analysis. The project introduces microfluidic in situ chemotaxis assays (ISCAs) to soil ecosystems, enabling direct measurement of microbial movement in natural soil matrices. Research activities will progress from synthetic communities and soil-analogue environments to complex natural soils, utilizing chemotaxis experiments, long-read sequencing, microbial community analysis, and LC-MS-based chemical characterization. You will join the Section for Microbial and Chemical Ecology (MCE) at DTU Bioengineering, which hosts internationally recognized groups in microbial ecology, environmental biotechnology, microfluidics, and chemical ecology. The section provides state-of-the-art facilities for environmental genomics, chemical analytics, and microbial cultivation, and fosters a vibrant, interdisciplinary environment with strong ties to Danish and international collaborators. The project includes a research visit to Dr. Jean-Baptiste Raina, co-inventor of the ISCA technique. Responsibilities include investigating soil microorganism responses to plant root exudates using microfluidic assays, molecular ecology, and chemical analysis, collaborating with experts in the field, contributing to coordinated work packages, and supporting the establishment of microfluidic-based workflows for soil environments. You will also participate in the supervision of BSc and MSc students involved in the project. Applicants must hold a two-year master’s degree (120 ECTS points) or equivalent in microbiology, microbial ecology, biotechnology, environmental biology, environmental engineering, or a related field. Required skills include molecular microbiology techniques (DNA extraction, PCR, sequencing workflows), and a structured approach to experimental work. Familiarity with microfluidics, flow cytometry, quantitative image-based data analysis, and microbial bioinformatics workflows is desirable. Strong communication skills in English and the ability to work both independently and collaboratively are essential. The PhD scholarship is subject to academic approval, and successful candidates will be enrolled in one of DTU’s general degree programmes. The position is funded for three years, with salary and appointment terms based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union. DTU offers a stimulating international environment, with a commitment to academic excellence, collegial respect, and academic freedom. Applications must be submitted online by 15 February 2026, including a cover letter, CV, grade transcripts, diplomas, a research statement, and at least one reference. For further information, contact Associate Professor Lars Behrendt ([email protected]) or Professor Lars Jelsbak ([email protected]). Additional details about DTU Bioengineering and working in Denmark can be found at the provided links. DTU Bioengineering is an international leader in biotechnology and biomedicine, with a strong focus on innovation, industry collaboration, and scientific services. The department is located at DTU Lyngby Campus and is committed to creating value through science and engineering for the benefit of society.