Doctoral Researchers 

Supervisors: Prof. Dr Doris Vetterlain, Dr Steffen Schlüter

Research project: Legacy of perennials in structuring soils – what we can learn for sustainability of cropping systems

My name is Abebaw Misganaw Ambaw, and I am originally from Ethiopia. Having completed my Bachelor of Science degree in Biotechnology at the University of Gondar in Ethiopia in 2012, I joined the Ethiopian Institute of Agricultural Research (EIAR) as a Junior Researcher specializing in plant biotechnology. In December 2020, I completed my MSc degree in Agricultural Sciences from the University of Bonn in Germany, with funding support from DAAD. In  2021, I pursued further academic enrichment by obtaining a second Master's degree in Plant Biotechnology from Addis Ababa University, Ethiopia.

This research project is aimed to investigate root-associated soil structural changes in perennial crops as compared to annual crops, more specifically permanent grasslands versus agricultural crops. This will show to which degree biopore networks are destroyed by tillage in annual cropping and how far and whether at all the exploration of the subsoil can be improved by perennial root systems. These land use comparisons will be carried out at several long-term field trials in Germany to assess the impact of texture and other site conditions on these effects. It will also be investigated whether the land use effect results in differences with respect to infiltration or exploitation of soil water. This project will cover the work package of root phenotyping, imaging and processing through the application of AI algorithms to explore root and its biological environment.  A shared library of root images obtained via non-destructive X-ray CT scanning of root systems in soil will be created to improve the current state-of-the-art in root image analysis. Our project aims to investigate root-associated soil structural changes in perennial crops versus annual crops, to evaluate the impact of soil type and texture on biopore formation and root diameter distribution in both perennial and agricultural crops, to differentiate the impact of vegetation and soil cultivation on soil microstructure and to explore whether soil properties like soil pH, soil carbon, and nitrogen content have to be considered as co-variables. 

Supervisors: Prof. Lars Munkholm, Associate Prof. Sabine Ravnskov, Dr Loraine ten Damme 

Research project: Roots of Plant Species Mixtures to Mitigate Soil Compaction in a Changing Climate

Camila is a doctoral researcher at the Department of Agroecology at Aarhus University in Denmark. She holds a bachelor's degree in Agronomic Engineering from the University of the Llanos, Colombia, a master’s degree in Geomatic and Geoinformation Engineering from the University of Jaen, Spain, and an Erasmus Mundus Master's in Soil Science from the University of Agriculture in Krakow (Poland) and Ondokuz Mayis University (Turkey).

She aims to evaluate the role of plants in soil compaction recovery via root growth patterns and symbiosis with arbuscular mycorrhizal fungi. Her research will focus on root phenotyping by linking root traits to soil physical, mechanical and morphological patterns. She will analyse a combination of laboratory and field measurements with micro-CT images.

Supervisor: Associate Prof. Saoirse Tracy 

Research Project: New insights into the plant hormones that govern root system exploration in soil

Renaud graduated in 2022 with Magna cum Laude from the Université catholique de Louvain (UCLouvain) as a bioengineer in Agricultural Sciences. He then worked as a research assistant on a wheat screening project at UCLouvain before joining a non-profit organisation to help implement field trials on maize. Passionate about research, he decided to pursue a PhD and joined the RootEd doctoral network in 2023 as a doctoral candidate. 

The aim of his project is to observe soil exploration by plant roots in compacted soil to deduce the impacts of different plant hormones on this ability to overcome sub-optimum soil conditions. To do so, Renaud will develop new software and techniques for an AI-based approach for the reconstruction of 3D root systems in X-ray CT scans and use these new tools to quantify root exploration of tomato mutants under compacted soil conditions.

Supervisors: Prof. Maarja Opik, Prof. Ivika Ostonen 

Research project -Temporal observations of soil: root interactions with arbuscular mycorrhizal fungi

Sarkal Jyakhwa is a junior research fellow in the Soil Ecology Workgroup at the University of Tartu, Estonia. He comes from Nepal. He holds a bachelor’s degree in agriculture from the Himalayan College of Agricultural Sciences and Technology (HICAST), Kathmandu, Nepal. In 2022, he graduated with a prestigious Erasmus Mundus master’s degree in plant breeding (emPLANT) from the Institute Polytechnique Unilasalle, France, and the University of Helsinki, Finland.

The aims of his project are (i) to identify how AM fungal diversity changes due to crop rotation and fertilization (ii) to test if indigenous and introduced AM fungi differentially modify the host’s root system architecture; and (iii) to monitor temporal changes in the abundance, diversity, and community composition of AM fungi under different agricultural practices in Estonia. His research methodology will include field collecting soil samples, subsequent DNA-based analysis of AM fungal diversity to characterize the AM fungal communities, X-ray CT scans, and other root analysis approaches.

Supervisor: Associate Prof. Saoirse Tracy 

Research project: Investigating the role of the 3D soil matrix in mediating root to root interactions

With a Bachelor of Science degree in Biochemistry from West University of Timisoara (Romania), followed by a Master of Science degree in Plant Biotechnology from Wageningen University & Research (the Netherlands), Denis possesses a solid academic foundation in plant physiology, molecular biology, and bioinformatics. 

Denis’s current research focuses on studying how the nutrient availability of the soil matrix affects root-to-root interactions between wheat and blackgrass, a notorious herbicide-resistant weed. The aims of his project are (i) to investigate how soil nutrient availability mediates the root-to-root interaction; (ii) to determine the blackgrass-susceptibility of agronomically important wheat cultivars; and (iii) to assess the role of different root architecture in the weed-crop interaction. 

To address these aims, Denis will be conducting a series of phenotyping experiments by co-cultivating wheat and blackgrass in distinct soil-based growing systems, such as soil columns, field plots, and rhizotrons. By delving into these complexities, Denis’s work not only enhances our understanding of plant-soil interactions, but also holds potential implications for crop resilience and management strategies inagricultural systems.

Supervisors: Prof. Mathieu Javaux, Prof. Xavier Draye 

Research Project: Investigating plant root structural and functional plastic responses to soil water

Erfan has a comprehensive background in soil sciences, sustainable agriculture, and plant cell biology. He earned his bachelor’s degree in soil sciences and engineering from Isfahan University of Technology, Iran focusing on phytoremediation strategies to mitigate soil toxicity.

His master’s degree in sustainable agriculture at the University of Padova, Italy deepened his understanding of agricultural sustainability and included research on the effects of plasma-activated water on plant-microbe interactions.

His international experience through an IAESTE Internship in Berlin, Germany, and an ERASMUS exchange at the Czech University of Life Sciences Prague has enriched his perspectives and skills, highlighting Erfan’s commitment to continuous learning and collaborative research in the field.

Erfan’s project at UCLouvain (Belgium) aims at investigating plant root structural and functional plastic responses to soil water. Erfan will investigate, using a unique automated rhizotron phenotypic platform, how Maize genotypes respond to heterogeneous soil water patterns. In addition, root response functions will be implemented in a Functional Structural plant root model (FSPM) to investigate  how local root response affect Maize development and define ideotypes better adapted to drought under different pedo-climatic conditions.

Supervisors: Prof. Dr Viola Williamsen, Dr Rick Van De Zedde 

Research project : High-throughput Rhizotron data from environmental challenged root systems towards AI

Fengjiao from China, is currently based at Wageningen University. She completed her master's degree in Artificial Intelligence in Hungary in July 2023. Before that, she completed her bachelor's degree in Software Engineering in China and received her undergraduate degree in June of 2020. In the Rooted project, she will utilize AI to study the root architecture of various crops under different environmental conditions. She aims to develop good practices for data acquisition methods and imaging protocols, as well as apply deep learning models to analyze rhizotron root images.

  Supervisors: Dr Johannes Postma, Dr Guillaume Lobet

  Research Project: Root plasticity responses to low P as modulated by N availability in Arabidopsis      thaliana

Maurene’s core interests are plant physiology and modeling. As part of her thesis, she developed a functional structural plant model for Episcia cupreata to conclude her Masters in Botany (Minor in Horticulture) in the University of the Philippines, Los Baños, Philippines. 

For her PhD, she will investigate root plasticity responses of A. thaliana as a function of combined phosphate and nitrate concentrations via 1) experimental observation in gel medium growth systems, and 2) functional structural plant modeling at the scales of root system architecture (RSA) and root tip.

Supervisors: Prof. Fiona Doohan (UCD), Prof. Jimmy Burke (Origin) 

Research Project: Exploration of the relationship between genotype, microbiome, root development and crop performance under reduced nutrient inputs

Suzan graduated from Hajee Mohammad Danesh Science and Technology University (HSTU), Bangladesh, with a Bachelor's degree in agricultural science. He completed an Erasmus Mundus Master Program in plant breeding (emPLANT) from UniLaSalle, France and University of Helsinki, Finland. He undertook a research internship at The Institute of Crop Science and Resource Conservation, University of Bonn, Germany. The primary goal of his Master's thesis was to identify how the zinc-finger transcription factor NTT/WIP2 affected cambial activity and xylem proliferation. He is passionate about understanding the genetic basis of root traits, developing new varieties of plants that are more resilient to environmental stresses and that have improved nutrient use efficiency.

Through this doctoral project he will investigate the impact of nutrient deficiencies on root growth of wheat.  To fulfil the project objectives, first he will optimize high-throughput rhizotron assay for screening root development within diverse wheat genotypes. Afterwards he will focus on identifying genetic factors controlling nutrient (phosphorus) utilization efficiency in wheat. His first hypothesis is that there is genetic variability within critical nutrient acquisition-associated traits in the root system and these can be used to develop wheat varieties with increased phosphorus utilization efficiency. The second hypothesis to be tests is that nutrient uptake and use can be enhanced through manipulation of formulations and biostimulant application. Successful completion of the project will provide a comprehensive understanding of the impact of genotype-based root variation, nutrient formulation and the microbiome on crop development. This project combines crop genomics, crop phenotyping, microbiome research, molecular biology, and crop nutrition.