PhD fellowship/scholarship - Lessons from nature: Untapping the full potential of crop root microbiomes
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PhD fellowship/scholarship - Lessons from nature: Untapping the full potential of crop root microbiomes
Applicants are invited for a PhD fellowship/scholarship at Graduate School of Technical Sciences, Aarhus University, Denmark, within the Agroecology programme. The position is available from 01 August 2026 or later. You can submit your application via the link under 'how to apply'.
Title:
Lessons from nature: Untapping the full potential of crop root microbiomes
Research area and project description:
We are inviting candidates interested in performing a PhD that seeks to develop and apply cutting-edge machine learning techniques and AI methods to complex biological datasets. Specifically, we wish to apply them on crops and their associated root microbiomes, with the plan to make agriculture more resilient to climate change. The PhD is part of a larger project funded by the Villum Foundation that started in August 2024.
Agriculture is one of the leading sources of anthropogenic greenhouse gases. Fertiliser application is a major contributor the total emissions associated with agriculture, and if less can be applied, agriculture becomes more sustainable. Microbes can influence how plants respond to stress and can help plants uptake nutrients. Therefore, crops can be bred to cultivate ‘better’ microbial communities that can mitigate some of the environmental impact of agriculture. The overall aim of this project will be to study the co-evolution of wild crop relatives and their microbiome, and learn from this relationship to breed better crops.
In this project, you will explore host data (genomes, methylomes, transcriptomes, metabolomes) and microbiomes (metagenomes, metatranscriptomes). Others in the group have performed experiments in glasshouses, generated data and performed basic analyses using subsets of the data. Your role is to take these holistic datasets and use them to develop and implement methods of integrating them. We want to maximise their potential in predicting the crop phenotype, namely in understanding why different crop varieties respond differently to climatic stresses. We ultimately hope to use this information to ultimately breed better crops.
The PhD project specifically entails working with technicians, PhD students and postdocs that have generated primary data. They will primarily bring the system specific knowledge (the biological knowledge of plants and microbes), while your primarily bring knowledge of data analyses, however, an interest in plant microbiomes is also desired. There will be chances to participate in ongoing experiments to also gain some hands-on experience in sampling of plants and generating data in the lab, depending on the successful applicant’s level of interest. It should also be noted that we also have experienced researchers in the group, and in the wider department, which are experienced in integrating multi-omic datasets that can provide initial training and assistance in developing new methods.
As part of your training, budget and time is allocated for developing skills at within PhD summer schools and courses. Therefore, you will be given the opportunity to develop relevant skills in both scientific (data analysis, lab skills etc.) and non-scientific (communication, project management, use of AI tools) areas. Importantly, this work will be performed with project partners in Europe, Mexico and North Africa, and some research stays are required (3 months in total).
The PhD position is based in the village of Flakkebjerg (near Slagelse) within the Department of Agroecology, as part of Aarhus University. You will work daily with Associate Professor Christopher Barnes and Professor Mette Vestergård, working with a vibrant team of researchers studying different aspects of plant-microbe interactions. While working at home is permitted one day a week, attendance within the department will be required to build a group dynamic.
For technical reasons, you must upload a project description. Please simply copy the project description above, and upload it as a PDF in the application.
Qualifications and specific competences:
Applicants must have a relevant Master’s degree (120 ECTS) in Bioinformatics, computational biological, computer science, maths or similar and an interest in plants and microbes. It is required that applicants have documented experience with quantitative data analysis on large data sets with machine learning methods, AI methods, Matlab, R, Python or similar.
Good collaborative skills are required, since you are expected to perform complementary analyses with an active microbial ecology research group that you will become part of. We also expect you to be able to communicate in both written and oral English.
Place of employment and place of work:
The place of employment is Aarhus University, and the place of work is Department of Agroecology, Forsøgsvej 1, 4200 Slagelse, Denmark.
Contacts:
Applicants seeking further information regarding the PhD position are invited to contact:
How to apply:
Please follow this link to submit your application. Application deadline is 15 March 2026 23:59 CET.
Preferred starting date is 1 August 2026.
Please note:
Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants. All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.
Title:
Lessons from nature: Untapping the full potential of crop root microbiomes
Research area and project description:
We are inviting candidates interested in performing a PhD that seeks to develop and apply cutting-edge machine learning techniques and AI methods to complex biological datasets. Specifically, we wish to apply them on crops and their associated root microbiomes, with the plan to make agriculture more resilient to climate change. The PhD is part of a larger project funded by the Villum Foundation that started in August 2024.
Agriculture is one of the leading sources of anthropogenic greenhouse gases. Fertiliser application is a major contributor the total emissions associated with agriculture, and if less can be applied, agriculture becomes more sustainable. Microbes can influence how plants respond to stress and can help plants uptake nutrients. Therefore, crops can be bred to cultivate ‘better’ microbial communities that can mitigate some of the environmental impact of agriculture. The overall aim of this project will be to study the co-evolution of wild crop relatives and their microbiome, and learn from this relationship to breed better crops.
In this project, you will explore host data (genomes, methylomes, transcriptomes, metabolomes) and microbiomes (metagenomes, metatranscriptomes). Others in the group have performed experiments in glasshouses, generated data and performed basic analyses using subsets of the data. Your role is to take these holistic datasets and use them to develop and implement methods of integrating them. We want to maximise their potential in predicting the crop phenotype, namely in understanding why different crop varieties respond differently to climatic stresses. We ultimately hope to use this information to ultimately breed better crops.
The PhD project specifically entails working with technicians, PhD students and postdocs that have generated primary data. They will primarily bring the system specific knowledge (the biological knowledge of plants and microbes), while your primarily bring knowledge of data analyses, however, an interest in plant microbiomes is also desired. There will be chances to participate in ongoing experiments to also gain some hands-on experience in sampling of plants and generating data in the lab, depending on the successful applicant’s level of interest. It should also be noted that we also have experienced researchers in the group, and in the wider department, which are experienced in integrating multi-omic datasets that can provide initial training and assistance in developing new methods.
As part of your training, budget and time is allocated for developing skills at within PhD summer schools and courses. Therefore, you will be given the opportunity to develop relevant skills in both scientific (data analysis, lab skills etc.) and non-scientific (communication, project management, use of AI tools) areas. Importantly, this work will be performed with project partners in Europe, Mexico and North Africa, and some research stays are required (3 months in total).
The PhD position is based in the village of Flakkebjerg (near Slagelse) within the Department of Agroecology, as part of Aarhus University. You will work daily with Associate Professor Christopher Barnes and Professor Mette Vestergård, working with a vibrant team of researchers studying different aspects of plant-microbe interactions. While working at home is permitted one day a week, attendance within the department will be required to build a group dynamic.
For technical reasons, you must upload a project description. Please simply copy the project description above, and upload it as a PDF in the application.
Qualifications and specific competences:
Applicants must have a relevant Master’s degree (120 ECTS) in Bioinformatics, computational biological, computer science, maths or similar and an interest in plants and microbes. It is required that applicants have documented experience with quantitative data analysis on large data sets with machine learning methods, AI methods, Matlab, R, Python or similar.
Good collaborative skills are required, since you are expected to perform complementary analyses with an active microbial ecology research group that you will become part of. We also expect you to be able to communicate in both written and oral English.
Place of employment and place of work:
The place of employment is Aarhus University, and the place of work is Department of Agroecology, Forsøgsvej 1, 4200 Slagelse, Denmark.
Contacts:
Applicants seeking further information regarding the PhD position are invited to contact:
- Associate Professor Christopher Barnes (main supervisor)
How to apply:
Please follow this link to submit your application. Application deadline is 15 March 2026 23:59 CET.
Preferred starting date is 1 August 2026.
Please note:
- Only documents received prior to the application deadline will be evaluated. Thus, documents sent after deadline will not be taken into account.
- The programme committee may request further information or invite the applicant to attend an interview.
- Shortlisting will be used, which means that the evaluation committee only will evaluate the most relevant applications.
Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants. All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.