ARISTO is an International Training Network (ITN) funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement. Pesticides are major environmental pollutants. For this reason, the European Commission has imposed a stringent pesticide regulatory scheme for pesticides authorisation, where risk assessment for aquatic organisms and terrestrial macro-organisms is well defined. In contrast the assessment of the toxicity of pesticides on soil microorganisms is lagging behind, still relying on an outdated protocol which fails to identify effects on key microbial functions and on microbial diversity, which can now be accurately determined through advanced and standardized methods introduced in soil microbiology in the last 10 years. EFSA identified soil microorganisms as an attribute to monitor during pesticides environmental risk assessment and stressed the need for novel tests to assess the toxicity of pesticides on soil microorganisms. The ARISTO project will fulfil this scientific and regulatory gap through a unique doctoral program, based on the strong interaction of academia and industry, aiming to train the next generation of Microbial Ecotoxicologists. These will produce benchmarking knowledge supporting the development of advanced tools and procedures, based on the response of key microbial indicator groups, for the comprehensive assessment of the toxicity of pesticides on soil microorganisms. ARISTO offers doctorate fellows a challenging training program build along 5 research objectives: (1) to develop pioneering in vitro tests, as a first conservative step, to assess the toxicity of pesticides on distinct ammonia-oxidizing microorganisms and arbuscular mycorrhizal fungi (2) to develop advanced lab and field tests to assess the toxicity of pesticides on natural soil assemblages of AOM and AMF, as a more realistic toxicity assessment step; (3) to develop an ecosystem-level toxicity assessment looking at pesticide effects at microbial networks and across different trophic levels along the soil food web (predator - prey); (4) to develop novel tools to determine the soil microbial toxicity of pesticide mixtures, and bio-pesticides; (5) to develop and validate advanced in silico tools for prioritizing pesticide transformation products with potential toxicity to soil microbes.
Available PhD positions:
- PhD position in Environmental Microbiology & Ecology – Project title: In vitro assessment of the toxicity of pesticides on ammonia oxidising microorganisms. Ecole Centrale de Lyon, University of Lyon, France & NCIMB Ltd., Scotland UK are offering a PhD scholarship in environmental microbiology with expected commencement March 2021 or as soon as possible thereafter. The PhD will be awarded by the Ecole Centrale de Lyon, France.
Project description: Nitrification is the microbial conversion of ammonium to nitrate and a key process in the global nitrogen cycle. In soil these reactions are mediated by two autotrophic functional groups of nitrifying microorganisms (ammonia oxidizers microorganisms (AOM) and nitrite-oxidizing bacteria (NOB)) or in one cell by complete ammonia oxidisers (comammox). As the activity of these organisms is essential for soil health, they are ideal candidates for testing the impact of pesticides on microbial communities and soil ecosystem functioning. The PhD programme will determine the ecotoxicological response of AOM as microbial indicators of pesticides toxicity. The objectives of the programme are to (i) to establish, optimize and standardize in vitro assays for assessing the toxicity of pesticides on AOM, (ii) to identify toxicity on other microorganisms participating in the nitrification process, (iii) to explore the toxicity mechanisms of pesticides on AOM. The work will utilize both cultivated nitrifier populations and soil microcosm incubations requiring the use of molecular ecology approaches (quantitative PCR, amplicon sequencing). The programme will also develop a novel screening platform for the analysis and determination of the functional health of soils and other environmental samples in response to pesticide amendment.
Principal supervisors: Prof. Graeme Nicol (graeme.nicol@ec-lyon.fr, +33 472 18 60 88) and Dr Carol Phillips (c.phillips@ncimb.com, +44 1224 009333).
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: microbial cultivation, molecular biology, soil microbial ecology
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in agricultural science and bioengineering – Project title: In vitro assessment of the toxicity of pesticides on AMF. Université catholique de Louvain and Phytothreptiki SA, are offering a PhD scholarship in agricultural science and bioengineering with expected commencement March 2021 or as soon as possible thereafter. The PhD will be awarded by the Université catholique de Louvain (Belgium)
PhD Project description: Arbuscular mycorrhizal fungi (AMF) are key soil microorganisms associated to the vast majority of agricultural and horticultural crops, improving their growth and resistance to abiotic and biotic stresses. They are thus of wide importance in agricultural practices. At the same time, they seem to be responsive to pesticides, being negatively affected by them. The specific objectives of the PhD project will be (i) to establish, optimize and standardize a fast-track in vitro system to evaluate the toxicity of a broad-range of pesticides on AMF using a variety of specialized testing systems for AMF in vitro cultivation, (ii) to explore the impact of pesticides on functional attributes (i.e. transport of minerals) of AMF, (iii) to explore the mechanisms of toxicity. This is expected to lead to the establishment of first low-tier screening test for the soil microbial toxicity of pesticides using AMF as key microbial bioindicators.
Principal supervisors: Prof. Stéphane Declerck, Stephan.declerck@uclouvain.be, +32 10 47 46 44 and Dr Myrto Tsiknia, tsiknia.myrto@gmail.com, TEL +30 210 259 4105
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: agricultural sciences, microbiology, molecular biology, knowledge or experience on plant-microbe interactions will be a merit
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in soil microbial ecology – Project title: Assessment of the ecotoxicity of pesticides on nitrifiers in soil. Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden and SATT SAYENS (SAYENS), Dijon, France are offering a PhD position in soil microbial ecology, expected to start May 2021 or as soon as possible thereafter. The PhD will be awarded by the Swedish University of Agricultural Sciences.
Project description of the PhD student: To detect potential toxic effects of pesticides on natural microbial soil assemblages, bacteria and archaea involved in nitrification will be used as indicators. Toxic effects can be both direct and indirect, affecting the functioning of soils and their capacity to cope with additional stressors. The aim of the PhD student project is to assess the toxicity of pesticides on the function and diversity of ammonia oxidizing bacteria and archaea, and on other functional groups involved in nitrification in soil. Specific objectives are to identify (i) toxicity endpoints on activity, abundance and diversity of nitrifiers; (ii) toxicity mechanisms on ammonia oxidizing bacteria and archaea; (iii) interaction effects on functional groups involved in nitrification; (iv) stability of functional groups involved in nitrification (i.e. resistance and resilience to secondary stressors). This work goes beyond direct effects of pesticides on ammonia oxidizing bacteria and archaea and brings new knowledge on the use of stability of soil functioning as a bioindicator and establishes novel procedures for assessing pesticide toxicity on soil microorganisms. The PhD student will work with lab and field experiments using a range of molecular techniques (e.g. amplicon sequencing, qPCR) as well as bioinformatic and biostatistical tools.
Principal supervisor: Prof. Sara Hallin, sara.hallin@slu.se, and Dr. Abdelwahad Echairi, abdelwahad.echairi@sayens.fr
Key criteria for the assessment of candidates
● A master’s degree relevant to the subject area of the project
● Expertise in soil microbial ecology and skills in bioinformatics, biostatistics, molecular biology is desired
● Previous research publications are merits
● Other professional activities will be considered
● Language skills: fluency in English, both written and oral are required
- PhD position in arbuscular mycorrhizal fungi (AMF) ecology – Project title: Assessing the toxicity of pesticides on natural soil and plant assemblages of AMF. University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, Greece and INOQ GmbH, Germany are offering a PhD scholarship in soil microbial ecology and plant-microbe interactions with expected commencement May 2021 or as soon as possible thereafter. The PhD will be awarded by the University of Thessaly, Greece.
Project description: Pesticide toxicity on soil microorganisms is insufficiently evaluated as yet, due to the lack of recognized key microbial indicator. Arbuscular mycorrhizal fungi (AMF) represent the most ubiquitous plant symbiotic microorganism that associate with almost 80% of plant species in beneficial interactions that can promote plant growth, and resilience to stresses. At the ecosystem level, AMF could affect the composition and productivity of plant communities with reciprocal effects on nutrient cycling, which in turn has an impact on soil microbiota. Thus, AMF have been identified as key species indicators for soil microbial toxicity of pesticides. Natural AMF soil assemblages will be used to develop assessment protocols in experimental lab and field tests. The effects on the AMF diversity will be determined by developing suitable molecular profiles at the highest possible resolution by amplicon NGS, by qPCR protocols and microscopy protocols at a soil community level. The impact of pesticides directly to AMF or via the plant host will also be evaluated. The experimental process will involve collaboration with other fellows’ projects providing a holistic assessment of the soil microbial toxicity of pesticides on AMF.
Principal supervisor: Prof. Kalliope Papadopoulou, kalpapad@bio.uth.gr, +30-2410565244 and Dr Carolin Schneider, schneider@inoq.de , +0 58 42-98 16 72
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: experience with AMF, plant biology, microbial ecology, bioinformatics, biostatistics, experience on pesticide analytics will be a merit
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in soil microbial ecology – Project title: Studying the toxicity of pesticides on soil microbial networks. Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dijon, France and Syngenta Crop Protection AG, Switzerland are offering a PhD scholarship in soil microbial ecology with expected commencement May 2021 or as soon as possible thereafter. The PhD will be awarded by the University of Bourgogne, France.
Project description of the PhD student: In nature, microorganisms are assembled into complex and diverse communities in which subpopulations are intertwined by different types of interactions. Therefore, a toxic pesticide will not only directly affect the vulnerable microbes but also indirectly those they are interacting with. This can lead to cascading effects in the soil microbial network, which can potentially affect ecosystem functions. The objectives of the PhD student are to identify (i) indicator groups within bacterial and fungal networks of the pesticide’s impact and (ii) keystone members whose response to pesticides will have major impact on the maintenance and function of microbial networks. This work will bring novel concepts in community assembly for a high-resolution evaluation of pesticides toxicity using microbial networks as potential bioindicators for higher tier risk assessment. Specifically, the PhD student will perform lab experiments with soil microcosms for assessing the impact of pesticides on microbial co-occurrence networks and soil functions using a range of molecular tools (e.g. amplicon sequencing, qPCR) and advanced biostatistics and bioinformatics analytical methods. The experimental process will involve collaboration with other fellows’ projects providing a holistic assessment of the soil microbial toxicity.
Principal supervisor: Dr Laurent Philippot, laurent.philippot@inrae.fr, +33-3 80 60 33 46 and Dr Claudio Screpanti, claudio.screpanti@syngenta.com,
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: soil microbial ecology, bioinformatics, biostatistics, molecular biology
● Previous research publications
● Other professional activities
Language skills: fluency in English
- PhD position in microbial ecology – Project title: Assessment of pesticides impact on microbial function in a soil food-web context. Helmholtz Centre for Environmental Research – UFZ and HYDREKA, are offering a PhD scholarship in microbial ecology with expected commencement May 2021 or as soon as possible thereafter. The PhD will be awarded by the University of Leipzig, Germany
Project description: Most studies have assessed the toxicity of pesticides either on individual bacterial taxa and functional groups separately or in the context of a biochemical pathway, ignoring the ecological dimensions of the effects observed. The project will look into the impact of pesticides in a microbial food web context. Specifically, the focus will be on interacting trophic levels, including bacteria, predatory microbes (e.g., protists) and viruses. In this frame, lab microcosm studies of different complexities will be established. The responses of interacting trophic levels upon pesticide exposure and the cascading effects on the dynamics, diversity and adaptation of both predator and prey levels and on related soil ecosystem functions will be followed using microbiological, stable-isotope, molecular biological (amplicon sequencing, genomics, metagenomics, q-PCR, FISH, SIP) and analytical methods as well as biocomputational and statistical tools. The experimental process will involve collaboration with other fellows’ projects.
Principal supervisor: Prof. Antonis Chatzinotas, antonis.chatzinotas@ufz.de, +49 341 2351324 and Dr. Cédric Malandain, +33 472 531153, cmalandain@hydreka.fr
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: microbiology, microbial ecology, molecular biology, bioinformatics, statistics knowledge and experience in ecology theory is considered a merit
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in soil microbial ecology – Project title: Assessment of the toxicity of pesticide mixtures on soil microorganisms. Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dijon, France and ECT Oekotoxicologie GmbH, Flörsheim am Main, Germany are offering a PhD scholarship in pesticide soil ecotoxicology with expected commencement May 2021 or as soon as possible thereafter. The PhD will be enrolled in the doctoral school ‘Environments – Santé’ and will be awarded by the University of Bourgogne, France.
Project description of the PhD student: In soil, microorganisms are abundant and diverse and accomplish key functions supporting ecosystem services. They are interacting with other organisms living in soils forming complex interactions supporting soil foodweb. Exposure to pesticides applied to crops to control various pests can impact the abundance, diversity of activity of soil microorganisms as well as their interactions with macroorganisms. Although soil organisms are exposed to complex mixtures of pesticide residues, most of the studies to assess the ecotoxicity of pesticide towards soil microorganisms are still done in silo one active substance by one, not considering neither complex mixtures nor interactions with macroorganisms. Within this context, the two main objectives of the PhD student are (i) to identify and to develop methods, procedures and tools to assess the toxicity of pesticide mixtures on soil microorganisms and (ii) to assess the toxicity of pesticides on soil microorganisms and potential interactions with terrestrial macro-organisms. This work will be carried out under a lab-to-field experimental design with a two-tier scenario of exposure. Two microbial guilds (AOM and AMF) will be studied in details as well as their possible interactions with soil macroorganisms (arthropod or earthworm). Specifically, the PhD student will perform lab experiments with planted soil microcosms and field experiment for assessing the impact of pesticide mixtures on the abundance (qPCR), diversity (amplicon sequencing) and activity of these two microbial guilds and advanced biostatistics and bioinformatics analytical methods. The experimental process will involve collaboration with other fellows’ projects (notably ESR8 working on the assessment of the toxicity of biopesticides on soil microorganisms) to provide a comprehensive scheme of assess the ecotoxicity of complex mixtures of active substances of chemical and/or natural origin.
Principal supervisor: Dr Aymé Spor, ayme.spor@inrae.fr, +33-3 80 69 30 94, Dr Marion Devers, marion.devers@inrae.fr, +33 80 69 xxxx (co-supervisor), and Dr Jörg Römbke, ECT Oekotoxikologie GmbH, j-roembke@ect.de,
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: soil microbial ecology, bioinformatics, biostatistics, molecular biology
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in soil microbial ecology – Project title: Assessing the toxicity of bio-pesticides on soil microorganisms. University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology and Metabolic Insights Ltd, Ness Ziona Industrial Park, Israel are offering a PhD scholarship in soil microbial ecology with expected commencement May 2021 or as soon as possible thereafter. The PhD will be awarded by the University of Thessaly, Greece.
PhD project description: To date biopesticides including microbe-based pesticides and natural products (or botanicals) are gaining interest in the pesticide market. They are considered environmentally safe although solid evidence for their reduced off-target toxicity are still lacking. The project will (i) examine the hypothesis that bio-pesticides are non-toxic, or less toxic than synthetic pesticides, to soil microorganisms and (ii) assess the overall soil microbial toxicity of bio-pesticides on functional microbial endpoints. In this frame lab microcosm and field tests will be undertaken to examine the toxicity of a range of biopesticides (vs synthetic pesticides) on the overall soil microbial diversity and on functional microbial diversity (e.g. ammonia-oxidizing microorganisms and arbuscular mycorrhizal fungi) using a range of molecular tools (amplicon sequencing, metagenomics, q-PCR), microscopy and advanced analytical methods. The experimental process will involve collaboration with other fellows’ projects providing a holistic assessment of the soil microbial toxicity.
Principal supervisors: Prof. Dimitrios Karpouzas, dkarpouzas@uth.gr, +30-2410565294 and Dr G. Wittenberg, gal@metabolic-insights.com,
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: soil microbial ecology, bioinformatics, biostatistics, knowledge or prior experience to biopesticides will be a merit
● Previous research publications
● Other professional activities
● Language skills: fluency in English
- PhD position in environmental chemistry & cheminformatics – Project title: Development of tools for in silico prioritization of pesticide TPs for soil microbial ecotoxicity testing. Eawag, Switzerland and enviPath UG & Co.KG, Germany are offering a PhD scholarship in environmental chemistry and cheminformatics with expected commencement May 2021 or as soon as possible thereafter. The PhD will be awarded by the University of Zurich, Switzerland.
PhD project description: Pesticide transformation may lead to the formation of transformation products (TPs) that are equally or more toxic than the parent compound. The introduction of advanced analytical tools, e.g., high-resolution mass spectrometry, has enabled a more accurate annotation of the transformation pathways of pesticides. Based on these data, in silico tools have been developed that support the prediction of TPs for analytical suspect screening and also risk assessment purposes. The objectives of the project are to optimize enviPath, a publically available model for prediction of pesticides TPs jointly developed by Eawag and enviPath UG & Co.KG, and to expand it with in silico tools for predicting the soil microbial toxicity of pesticide TPs. Predictions will be validated for selected pesticides with experimental biotransformation studies carried out by the PhD student in collaboration with other fellows in the ARISTO project. The project will thus contain experimental work (including batch assays with activated sludge and soil, analytical chemistry) but its emphasis will lie on developing cheminformatics tools for transformation and toxicity prediction based on existing databases and new data generated within the ARISTO project.
Principal supervisor: Prof. Kathrin Fenner, kathrin.fenner@eawag.ch, +41-587655058 and T. Lorsbach, lorsbach@envipath.com.
Key criteria for the assessment of candidates
● A master’s degree related to the subject area of the project
● The grade point average achieved should be more than 75 % of the maximum
● Professional qualifications relevant to the PhD programme
o Relevant skills: environmental chemistry, cheminformatics, analytical chemistry
● Previous research publications
● Other professional activities
● Language skills: fluency in English
All positions involve employment for 36 months. PhD students recruited will spend 50% of their time in an academic and another 50% of their time in an industrial partner. Please visit the PhD position webpage given for more information.
Formal requirements and eligibility for all available positions
At the time of commencement, it is required that the candidate shall at the date of recruitment, be in the first four years[1] (full time equivalent research experience) of their research careers and have not been awarded a doctoral degree. Furthermore, the candidate must not have resided or carried out their main activity (work, studies, etc.) in the countries where the hosting organizations are located for more than 12 months in the 3 years immediately prior to their recruitment. Short stays, such as holidays, are not taken into account.
Terms of employment
Recruitment and Terms of appointment will be done according to the rules and regulations of the hosting institutions and according to the rules and regulations laid down by European Union’s Horizon 2020 Marie Curie Initial Training Networks. The stipend includes a living allowance (3270 €, adjusted by a country correction factor), mobility allowance (600 €) and family allowance (500 €), the latter allowance depending on the family status of the fellow. All PhD fellowships available involves a split PhD studentship between an academic and an industrial partner, while the fellow will also spend time to other partners through short secondments.
Application Procedure
The application, in English, must be submitted by email to the supervisors of each advertised position and the coordinator of the project dkarpouzas@uth.gr. You are encouraged to apply for more than one of the available positions. In this case please indicate the position for which you are applying.
For your application please include
● Motivation Letter, stating which PhD project you are applying, why you want to pursue a PhD career in academic and industrial sectors, and to what extent does the given project complies with your skills and ambition.
● A statement if (and which) you have applied for other ARISTO PhD fellowships
● Full CV including studies, research experience, work experience and publications if any
● Diploma and transcripts of records (BSc and MSc)
● 3 professional referees (Name, address, telephone & email)
● Documentation of English language qualifications