Postdoc in Environmental Microbiology and Soil Microbial Ecology: Greece

The Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly is offering a Postdoc position in soil microbial ecology with expected commencement October 2021 or as soon as possible thereafter. The project is funded by SYNGENTA and it has a duration of 24 months starting in September 2021. The project main objective is to setup a database which will encompass all available literature data on the toxicity of pesticides on soil microorganisms, curate and use it for meta-analysis of potential toxicity endpoints for pesticide risk assessment.

Brief Project Description

Pesticides interact with soil microbes in various ways spanning from energy-gain biodegradation to toxicity. Although soil microorganisms have been identified as key modulator of soil functioning, the toxicity of pesticides on this group of organisms has been largely overlooked at regulatory level. The assessment of the toxicity of pesticides on soil microorganisms has attracted a lot of attention in the last 10 years with the upsurge and standardization, at various levels, of novel biochemical and molecular tools. At the same time it has resulted in the production of a lot of fragmented knowledge which needs to be gathered, assessed in a systematic way in order to allow the development of tools that would be used for defining new target organisms in the mikrobiokosmos of soil.

The proposed project will work at two levels aiming (a) to provide a thorough literature review of the current knowledge regarding the toxicity of pesticides on soil microorganisms and (b) to put together a database of amplicon sequencing data from relevant studies that would be used as a tool for meta-analysis of the effects of pesticides on the soil microbial community. These two goals will result in the development of a dual database composed of (a) literature information linking pesticide chemicals with effects on soil microorganisms as reported in studies critically assessed as of standard quality and (b) a database of curated amplicon sequencing data for bacteria and fungi that would be used for multi-purpose meta-analysis using standard and higher tier ecotoxicology approaches in order to define microbial groups responsive to pesticide exposure or general statistically relevant trends of effects of pesticides on soil microorganisms (even across trophic levels in the soil food web). The ultimate goal will be the production of a user interface that would enable access to the scientific community. In the longer term the amplicon sequencing database would expand to the diversity of functional microbial groups like ammonia-oxidizing microbes, arbuscular mycorrhizal fungi and even protists for which amplicon sequencing data are available or are in the process of being generated.

Principal supervisor: Prof. Dimitrios Karpouzas,, +30-2410565294

Collaborating Partners: Dr Claudio Screpanti, SYNGENTA

Duration: The position is available for 18 months with the possible extension for 6 more months

Job description and tasks

The selected candidate is expected to:

  • Employ a literature survey to gather all relevant publications related to effects of pesticides on soil microorganisms
  • Employ a quality screening of the publications (based on predetermined criteria), identify relevant toxicity endpoints measured and present the gathered data in a user friendly mode
  • Gather all studies looking at the effects of pesticides on soil microbial diversity using amplicon sequencing, gather and quality screen the data
  • Employ a meta-analysis to identify key microbial groups responsive to pesticides as indicators of microbial toxicity
  • Work together with the industrial partner in the preparation of a user interface for public access to the dataset

Key criteria for the assessment of candidates

  • PhD in Environmental Microbiology or Microbial Ecology
  • Experience in IT tools for handling big data and literature analysis
  • Experience in bioinformatics and ecological statistics
  • Experience in molecular microbial ecology omic tools or pesticides will be a merit

Terms of employment

Recruitment and Terms of appointment will be done according to the national rules and regulations. The stipend of the fellow will be 2000 € gross (the net salary will depend on the type of contract signed ie. Fellowship, Free-launch-type contract or IDOX).

Place of Employment

University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Larissa, GREECE, Website:

Application Procedure

The application, must be submitted by mail to and later through the submission system of the University of Thessaly when the call will be officially open. Please include a full CV including studies, research experience, work experience and publications along with 3 professional referees (Name, address, telephone & email)

The University of Thessaly wish our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of age, gender, race, religion or ethnic background.

Recruitment Process: After the expiry of the deadline for applications, the project manager will provide all applications to the members of the recruitment committee which will evaluate all applications and select the best three candidates based on the quality of the candidates’ previous training, qualifications and skills (as listed above), CV. The best three candidates will be interviewed by the recruitment committee which will select the best applicant for the position. The applicants will be notified of the final selection by the Project Manager and will be given 7 days to accept or decline

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