Training Course 1: Methods of Microorganism Detection in Soil, Water and Food (October 2020)

Banner for training course

SIMBA partners are happy to announce the first SIMBA training course that will take place online over four days (9-10th, 16-17th) in October 2020. The online course will focus on Methods of Microorganisms Detection in Soil, Water and Food.

See course flyer here

Course overview

How can microorganism and the microbiome be utilised to increase plant resilience and sustainability throughout the food system? During this free online training course, you will learn about the microbiome, and methods to detect and apply microorganism in soil, water and food to support more sustainable agriculture and food production through the implementation of novel biofertilizers (microbial consortia), and more efficient delivery methods (biochar, amendments, nanomaterials). This training course is organised by University of Parma (UNIPR), with lectures taught by experts from the SIMBA project, as well as international guests.

Course content and modules

This course aims to encourage scientists, technologists and practitioners to consider SIMBA project concepts for the development of a more sustainable agriculture and food production through the implementation of novel biofertilizers and more efficient delivery methods. All lectures will be held online and more details will be provided after acceptance to the course.

SIMBA partners from UNIPR, Luke, ENEA, NIOZ, NIVA, Bielefeld University and CCS Aosta will teach on lectures throughout training course.

An outline of the course modules is outlined here:

Module 1: The Natural &Anthropized Worlds of Microorganisms Friday 9/10/20, 13:00 – 18:00 (CET)
  • Introductory note of the SIMBA Project by Anne Pihlanto (Luke, SIMBA Project Coordinator)
  • Presentation of the training course by Prof Nelson Marmiroli (UNIPR, Scientific Coordinator of the Training Course)
  • Outline of the programme, activities and other business by Prof Elena Maestri (UNIPR, Training Course Acting Secretary)
  • Invited external expert:
    • Nanoscale amendments to enhance crop growth: Unintended consequences in the rhizosphere and plant microbiome – Prof Jason White, Director of Connecticut Agricultural Experiment Station, Connecticut, USA.
  • Topic covered in module:
    • Microorganisms in the environment – Nelson Marmiroli (UNIPR)
    • The new age of soil microbiome –Annamaria Bevivino (ENEA)
    • Sustainability in agriculture – Anne Pihlanto (Luke) and Nelson Marmiroli (UNIPR)
Module 2: Isolation, Cultivation and Monitoring Saturday 10/10/20, 09:00 – 13:00 (CET)
  • Topics covered in module:
    • Isolation of microorganisms from natural environments – Nelson Marmiroli (UNIPR)
    • Cultivation approaches – Silvia Tabacchioni (ENEA) and Antonella Del Fiore (ENEA)
    • Biofilms and microscopic observations – Marina Caldara (UNIPR)
    • Communities in marine and freshwater – Carlos Escudero (NIVA) and Henk Bolhuis (NIOZ)
  • Invited external expert: Organic amendments increase soil fertility and activity of marginal soils: a microbial vision – Prof François Rineau, Hasselt University, Belgium
Module 3: Into the Microbial X-omics Friday 16/10/20, 13:00 – 18:00 (CET)
  • Topics covered in module:
    • DNA analysis, targeted and untargeted methods in metagenomics – Annamaria Bevivino
    • X-omics approaches – Elena Maestri and Gianfranco Diretto (ENEA)
    • Overview of the assembly based Whole Genome Sequencing (WGS) Metagenomics Analyses – Alexander Sczyrba (CeBiTec, Bielefeld University)
    • Case study presentation – Giuseppe Aprea (ENEA)
  • Invited external expert:
    • The use of microbiomes in the sustainable cultivation of some major crops in USA – Prof Henry T. Nguyen, University of Missouri, USA
Module 4: Applicability, Costs, Benefits and Risk Saturday 17/10/20, 09:00 – 13:00 (CET)
  • Topics cover in this module:
    • Application of microbial processing in food and feed production – Vesa Joutsjoki (Luke)
    • Industrial experience and exploitation of useful consortia – Caterina Giovannetti (CCS Aosta)
    • The selection and characterization of microorganisms in marine environments and food – Minna Kahala (Luke) and Henk Bolhuis (NIOZ)
  • Invited external expert:
    • Microorganisms uses as phytosanitary products in agriculture. Risk assessment and EU Regulation – Dr J. Oriol Magrans, European Food Safety Authority (EFSA)
  • Training course wrap-up, discussion and conclusion

Practical Information

Location: Online training course, full details on how to access the course will be provided after acceptance to the course.

Format: The training course is composed of four modules, which will involve lectures and discussions. Course material will be distributed to all accepted participants prior to course commencement. Course tutors can be approached by email with any question regarding the course or provided material.

Date and Time: Friday 9th – Saturday 10th October, Friday 16th October – Saturday 17th October. Friday modules run from 13:00 – 18:00 and Saturday modules run from 09:00 – 13:00. Please note all times are set in Central European Summer Time.

Fees: Course registration and participation is free, thanks to the European Union Horizon 2020 funding.

Maximum number of participants: 30. Selection will be based on suitability for the course and availability to attend ALL four modules

GDPR: The SIMBA project partners are subject to the EU General Data Protection Regulation (GDPR) which came into force on 25th May 2018. Data that is collected and processed for the purposes of facilitating and administering SIMBA training courses is therefore subject to GDPR. Please review our Data Management Policy here.

It is a requirement of GDPR that all data subjects (i.e. training course applicants) give explicit consent to the storage and processing of their personal data. A separate GDPR Consent Form is therefore provided, and this must be completed by an individual applying for any SIMBA training course. This should be attached to the training course application.

Necessary documentation: To be eligible for the course, each applicant must complete in full and submit a registration form (here) and a GDPR consent form (here) to email to Scientific Coordinator Prof Nelson Marmiroli ( and School Secretary Prof Elena Maestri (


To register your interest in the SIMBA Training Course on Methods of Microorganism Detection in Soil, Water and Food, please complete in full:

Email both forms to the Scientific Coordinator of training course Prof Nelson Marmiroli ( and School Secretary Prof Elena Maestri ( Please indicate SIMBA/Training Course 1 application in the email subject line.


For any questions and queries please contact Scientific Coordinator of the training course Prof Nelson Marmiroli ( and School Secretary Prof Elena Maestri (