10 fully-funded PhD positions in the MSCA Doctoral Network "ROOTED"

Applications are invited for 10 PhD positions (Doctoral Researchers) in the Marie Sklodowska-Curie Root Phenotyping Integrated Educational Doctoral Network “ROOTED".

Background 

A deeper understanding of the interactions between soils and plants, especially at the root zone, where they take up water and nutrients may support sustainable intensification of agricultural production. Research is indicating that a greater understanding of roots and soil functions may lead to increases in crop yields, reductions in greenhouse gas emissions from soils, enhanced productivity in grasslands and reductions in fertilizer requirements to land. However, data gaps remain in our understanding of how plant roots interact with their environment from a physiological and phenotypic perspective. The challenge of ensuring food security provides the impetus for ROOTED (Root Phenotyping Integrated Educational Doctoral Network). ROOTED will apply deep learning and artificial intelligence to speed up data generation in root phenotyping.

Network 

ROOTED consolidates the complimentary expertise of an international, interdisciplinary, multisectoral team to train a new generation of creative, resilient, adaptive multi-skilled scientists capable of innovating the fields of plant and soil sciences to actively contribute to the goal of doubling food production in a sustainable manner by 2050. Soil health and food is one of the 5 mission areas for Horizon Europe and the findings from ROOTED would be directly applicable to the EU’s Green deal and a Soil Deal for Europe. ROOTED graduates will have a level of scientific, communication and digital skills mastery that enables them to move straight into employment in agri-food businesses, seed and breeding companies, advisory and scientific roles.

To achieve the objectives of the network, each Doctoral Researcher will undertake a combination of individual and collaborative research work, at least one secondment and workshops on scientific and applied skills facilitated by the academic/non-academic members of the consortium.

Location 

The 10 Doctoral Researcher positions will be hosted by University College Dublin (UCD), Ireland (ROOTED Coordinator) - 2 positions, Helmholtz Centre for Environmental Research (UFZ), Germany- 1 position, Aarhus University, (AU), Denmark- 1 position, University of Tartu, (UT), Estonia- 1 position, Institut National de la Recherche pour l’agriculture, l’alimentation et l’environnement, (INRAE), France- 1 position, Université Catholique de Louvain, (UCLouvain), Belgium- 1 position, Forschungszentrum Jülich (FZJ), Germany- 1 position, Wageningen University & Research (WU), Netherlands- 1 position, Origin Enterprises, (ORIGIN) Ireland- 1 position 

Details of the 10 positions available 

• For detailed information on each position, including how to apply and the application deadline, please refer to each position description below. Please note that the application deadline varies for each position. 
• If you wish to apply to more than one position, please apply individually to each position.
• All applicants must include this application form as part of their application for any of the positions below (to download a copy, click File→Download)
• Please note, in some institutions PhD programmes are for a 48 month period – please see individual requirements in the position descriptions below. 

DOCTORAL RESEARCHER 1- Legacy of perennials in structuring soils – what we can learn for sustainability of cropping systems

Host and PhD Awarding institution: Helmholtz Centre for Environmental Research (UFZ), Germany

Primary Supervisor: Prof. Dr. Doris Vetterlein

Project duration: 36 months 

Project description: The specific task of this PhD position is 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 how far and whether at all the exploration of the subsoil can be improved by perennial root systems. It will also be investigated whether this results in differences in respect to infiltration or exploitation of soil water. 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.

Secondment(s): University of Nottingham

Required applicant profile: Master’s degree in Agriculture, Biology, Soil Science, Geoscience or related natural sciences. 

Informal inquiries: doris.vetterlein@ufz.de

Application deadline: 21st April 2023

Full details of this position and how to apply: https://recruitingapp-5128.de.umantis.com/Vacancies/2681/Description/2

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DOCTORAL RESEARCHER 2- Roots of plant species mixtures to mitigate soil compaction in a changing climate

Host and PhD Awarding institution: Aarhus University, (AU), Denmark

Primary Supervisor: Prof. Dr. Lars J. Munkholm

Project duration: 36 months

Project description: Soil degradation due to subsoil compaction is a major challenge in agriculture as natural recovery is very slow. Thus, targeted strategies are needed to promote and speed up the recovery of compacted subsoils. Previous studies have shown recovery effects of deep-rooted plant species such as chicory,lucerne and lupin grown in monoculture. We anticipate that growing plant mixtures with different root growth patterns and varying symbiosis with arbuscular mycorrhizal fungi can increase the extent and rate of subsoil recovery after compaction. Yet, there is a lack of knowledge of the potential of such plant species mixtures to aid the recovery of compacted subsoils. The project will explore interactions between soil and roots as well as the impact of the root growth patterns on soil functioning using state-of- the-art methods.

Secondment(s): University College Dublin (Ireland) and DLF-Seed (Denmark)

Required applicant profile: Highly motivated, independent and enthusiastic doctoral researcher with relevant Master's degree (Soil Science, Crop Science,Agronomy or closely related fields), excellent track record of academic achievement and a strong interest in conducting original research. Interest in soil structure and soil-plant-microbiome interactions is essential. Experience of working with experimental work in the field and laboratory is desirable.

Informal inquiries: lars.munkholm@agro.au.dk

Application deadline: 30th April 2023

Full details of this position and how to apply: https://phd.tech.au.dk/for-applicants/apply-here/saeropslag/phd-in-root…   

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DOCTORAL RESEARCHER 3- New insights into the plant hormones that govern root system exploration in soil

Host and PhD Awarding institution: University College Dublin, (UCD), Ireland

Primary Supervisor: Dr. Saoirse Tracy

Project duration: 36 months 

Project description: The aim of this 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. A greater understanding of the hormonal activators of root interactions with soil compaction is required. New state-of-the-art techniques and software for the reconstruction of 3D root systems in X-ray CT will be utilised for the quantification of root exploration. A shared library of root images in soil and associated ground truth data for training of AI models will be created.
 

Secondment(s): University of Nottingham (UK) 

Required applicant profile: We are looking for a highly motivated, independent and enthusiastic doctoral researcher with a relevant bachelor or masters degree in Biological, Agricultural or Environmental sciences. A degree subject that combines computer science and biology would be preferred. An excellent track record of academic achievement and a strong interest in conducting original research on root system interactions with soils is essential. Must be comfortable with the application of technologies e.g. imaging technologies. However, full training will be given. Interest in plant growth, soil science and computer science are essential.Experience of working on or contributing to using imaging technologies or computer programming to answer agricultural or environmental problems is desirable.

Informal inquiries: saoirse.tracy@ucd.ie 

Application deadline: 12th May 2023

Full details of this position and how to apply are available here

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DOCTORAL RESEARCHER 4- Temporal observations of soil: root interactions with arbuscular mycorrhizal fungi

Host and PhD Awarding institution: University of Tartu, (UT), Estonia

Primary Supervisor: Dr. Maarja Öpik 

Project duration: 36 months paid (+ 12 months optional, with additional pay potentially available)

Project description: Monitor root system architecture in relation to root-symbiotic arbuscular mycorrhizal (AM) fungal performance (diversity, composition, abundance, activity) in the context of indigenous and introduced (inocula) AM fungi and under different agricultural practices in different areas. Fundamental new knowledge will be gained on root-symbiotic arbuscular mycorrhiza under various agricultural practices in different areas. We hypothesise different interaction characteristics between the indigenous and introduced (inocula) into the plant: soil environments.

Secondment(s): University College Dublin (Ireland)

Required applicant profile: Highly motivated, independent and enthusiastic doctoral researcher with relevant master's degree, excellent track record of academic achievement and a strong interest in conducting original research on root system interactions with soils and soil biota. Must be comfortable with the application of technologies, e.g. DNA based sequencing technologies, and imaging technologies. However, full training will be provided. Interest in agriculture and plant and fungal ecology are essential. Experience of working on or contributing to using DNA sequencing technologies to answer agricultural or environmental problems is desirable.

Informal inquiries: Dr. Maarja Öpik, maarja.opik@ut.ee

Application deadline: 15^th May 2023

Full details of this position are available here and details of how to apply are available here 

**Please note that applications will be accepted from 20th April 2023**

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DOCTORAL RESEARCHER 5- Investigating the role of the 3D soil matrix in mediating root to root interactions

Host and PhD Awarding institution: University College Dublin, (UCD), Ireland

Primary Supervisor: Dr. Saoirse Tracy

Project duration: 36 months

Project description: The aim of this project is to understand how plants interact with neighbouring plants. Above-ground interactions are well defined while below-ground interactions are less well understood. Using X-ray CT, we can investigate the changes in root architecture and positioning in the presence of a neighbouring plant. We will test the role of nutrient availability and soil matrix in mediating root to root interactions between wheat and a known weed (blackgrass, Alopecurus myosuroides). A new standardised method for root phenotyping in the presence of neighbouring plants will be used. Measurement of soil porosity in the rhizosphere and root architecture and positioning of wheat plants grown under different nutrient and soil matrix treatment combinations will be conducted.

Secondment(s): NIAB Regional Trial Network (UK)

Required applicant profile: We are looking for a highly motivated, independent and enthusiastic doctoral researcher with a relevant bachelor or master’s degree in biological, agricultural or environmental sciences. An excellent track record of academic achievement and a strong interest in conducting original research on root system interactions with soils. Must be comfortable with the application of technologies e.g. imaging technologies. However, full training will be given.  Interest in agriculture and plant growth are essential. Experience of working on or contributing to using imaging technologies or computer programming to answer agricultural or environmental problems is desirable.

Informal inquiries:saoirse.tracy@ucd.ie 

Application deadline: 9th July 2023

Full details of this position and how to apply are available here 

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DOCTORAL RESEARCHER 6- Towards the optimization of legume nodulated root system architecture for water and nitrogen acquisition under drought conditions.

Host: Institut National de la Recherche pour l’agriculture, l’alimentation et l’environnement, (INRAE), France

PhD Awarding institution: University of Burgundy Franche-Comté, France

Primary Supervisor: Dr. Marion Prudent

Project duration: 36 months

Project description: Grain legumes are cultivated for their protein-rich seeds, used for feed or food. These species do not need N fertilizers, thanks to their ability to fix atmospheric N2 in symbiosis with soil bacteria (rhizobia) in newly-formed root organs called nodules. With a functional-structural approach focused on the nodulated root system, we will investigate transient nutrient deficiencies and drought effect on root architecture, water and nutrient uptake, and rhizodeposition. The molecular underlying regulations will be deciphered by multi-omics approaches including RNAseq and metabolomics analysis.

Secondment(s): University of Burgundy Franche-Comté (France)

Required applicant profile: Highly motivated and enthusiastic doctoral researcher with a plant biology Master's degree, excellent academic track record and an appeal for integrative biology. The PhD topic will focus on the legume root system and its interaction with rhizobia using whole plant physiology/ecophysiology, high-throughput phenotyping but also several omics approach. Therefore applicant must be comfortable with image analysis and/or biostatistics of large and heterogenous datasets.

Informal inquiries: marion.prudent@inrae.fr 

Application deadline: 28th April 2023

Full details of this position and how to apply: https://jobs.inrae.fr/en/ot-18015

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DOCTORAL RESEARCHER 7- Root plasticity as an optimal trait in adverse environments

Host and PhD Awarding institution: UCLouvain, Louvain-la-Neuve, Belgium

Primary Supervisor: Prof Mathieu Javaux and Xavier Draye

Project duration: 36 + 12 months

Project description: This project aims at deciphering plant root architectural and hydraulic response functions to soil water distribution. Using a unique automated rhizotron phenotypic platform, we will investigate how Maize genotypes cope with soil heterogeneity. Root response functions will be implemented in a Functional Structural plant root model to discover Maize ideotypes better adapted to drought under different pedo-climatic conditions.

Required applicant profile: Highly motivated and enthusiastic student with a MSc degree in biology, soil science, bioscience engineering, physics or applied mathematics, excellent track record of academic achievement and a strong interest in conducting original research on root system interactions with soils. Must be comfortable with the application of technologies e.g. imaging technologies. However, full training will be given. Interest in plant growth, soil science and computer science are essential. Experience of working on or contributing to using imaging technologies or computer programming to answer agricultural or environmental problems is desirable.

Application deadline: 31st May 2023

Full details of this position and how to apply here

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DOCTORAL RESEARCHER 8- Root plasticity responses to low P as modulated by N availability

Host: Forschungszentrum Jülich (FZJ), Germany

PhD Awarding institution: Université Catholique de Louvain, (UCLouvain), Belgium

Primary Supervisor: Dr Johannes Postma

Project duration: 36 months 

Required applicant profile: We are looking for candidates with a Master’s degree in Agriculture, Plant Biology, Soil Science, related natural sciences.

You have a deep interest in how plants optimize nutrient acquisition and acclimate to different soil conditions. You are curious about root functioning and preferably have some experience within plant root research, for example during your master thesis work. You enjoy designing, conducting, and analysing experiments. You enjoy math and quantitative approaches in science and have some affinity with modelling and or computer programming.

For inquiries contact Johannes Postma at OSR@fz-juelich.de

Full details of this position and how to apply here

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DOCTORAL RESEARCHER 9- High throughput Rhizotron data from environmental challenged root systems towards AI

Host and PhD Awarding institution: Wageningen University & Research

Primary Supervisor: Dr. Viola Willemsen

Project duration: 36 months

Project description: The aim of this project is to gain understanding in environmental effects on root architecture in soil using high throughput 2D soil rhizotron image data, which will be generated in the growth room based rhizotron system in module 4, which is part of the Netherlands Plant Eco-phenotyping Centre (NPEC).
More info: https://www.npec.nl/tool/five-htp-growth-rooms/

During the project standard operating procedures for data acquisition, imaging protocols and data labelling for deep learning and artificial intelligence (AI) applications on root systems will be established. NPEC makes accurate, high-throughput studies of plant performance possible in relation to relevant biotic (microbiome interactions, competition, disease) and abiotic (light quantity and quality, nutrients, temperature, moisture, soil pH and atmospheric CO2 level) factors across a range of scales using different model crops systems and mutant lines.

Required applicant profile: 

You have a Master’s degree in biology or will possess a Master’s degree by the intended start date.
You also possess:

• Knowledge of image analysis procedures for root trait extraction, preferably with classical machine-learning (classifiers, clustering, feature selection/reduction, dimensionality reduction) and up-to-date deep learning-based algorithms.
• Demonstrable coding ability in Python, C++, Java or similar programming languages, and experience with software version control and notebooks.
• Strong interest in plant biology
• The international MSCA component which funds your PhD demands you have been trained outside of the Netherlands. Rooted is coordinated by University College Dublin.
• The potential to become an independent scientist with proficient critical thinking skills
• A relevant master’s degree in Biological, Agricultural or Environmental sciences.
• A degree subject that combines computer science and biology is a must.

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognised Certificate of Proficiency in the English Language. More information can be found here.

Application deadline: 28th April 2023

Full details of this position and how to apply here 

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DOCTORAL RESEARCHER 10- Micronutrient deficiencies and the implications for wheat crop yields

Host: Origin Enterprises, (ORIGIN) Ireland

PhD Awarding institution: University College Dublin, (UCD), Ireland

Primary Supervisor: Prof. James I. Burke, Origin Enterprises plc, Prof. Fiona Doohan, University College Dublin.

Project duration: 36 months

Project description: The aim of this project is to investigate the impact of soil nutrient deficiencies on crop yields, where the impact on soil microbes and the uptake and assimilation of N and other nutrients will be assessed. It is envisaged that the student will adapt the high throughput assay developed at UCD to phenotype the growth of a diversity panel of wheat cultivars under reduced nutrient input scenarios as well as their ability to form microbial associations. Field and glasshouse studies will also investigate the effect of using nitrogen fertilisers coated with micro-nutrients that act as metallo-catalysts in the N cycle, e.g. Mo, Co, Fe, Cu & Ni and their impact on soil microbes, specifically certain enzymes and bacteria (e.g. Urease, Nitrate reductase, Nitrosomonas, Nitrobacter, Nitrococcus, etc.). The research will include nitrogen uptake, efficiency, assimilation, partitioning, and effect on root and shoot characteristics of different wheat germplasm and the relationship existing between growth under these conditions and the rhizosphere microbiome, in the presence and absence of plant-growth promoting microbes. The student will gain skills in crop genomics, microbiome studies, crop phenotyping, molecular biology, and crop nutrition.

Required applicant profile: 

We are looking for a highly motivated, independent and enthusiastic doctoral researcher with the following:

• Applicants should possess at least an upper second class honours primary degree or the equivalent and/or Master's degree or its equivalent in Biological, Agricultural or Environmental sciences. 

• An excellent track record of academic achievement and a strong interest in conducting original research on root system interactions with soils. Must be comfortable with the application of technologies e.g. imaging technologies. However, full training will be given during this study.

• Interest in plant growth, soil science and computer science are essential.

• Experience in plant molecular biology.

• Experience of working on or contributing to using imaging technologies or computer programming to answer agricultural or environmental problems is desirable.

Application deadline: 12th July 2023

Full details of this position and how to apply here