Training School 2025 (Nitra)
Training School “Metabarcoding of Plant Microbiomes II”
The 3rd Training School of the MiCropBiomes COST Action on “Rhizosphere Analysis: Metabarcoding with ONT and Culturomics” will take place in Nitra, Slovakia, from July 14 to 18, 2025.
Training School series will be focused on gaining direct, hands-on experience with current techniques used in the analysis of plant-associated microbial communities. These include Oxford Nanopore Technologies (ONT) sequencing of 16S rRNA and ITS amplicons, and bacterial cultivation with MALDI-TOF MS identification. Through the full workflow—from field sampling to sequence data—the training will offer both technical competence and critical insight into experimental design, troubleshooting, and data interpretation.
Beyond the technical content, the training school is also intended to foster networking and peer learning in a supportive, collaborative environment. Participants will work together to address a real experimental question: “How does the rhizosphere microbiome change following compost application?” This experience will provide valuable context for applying these methods in your own research.
The techniques introduced during the training school represent the state-of-the-art in studying plant–microbe interactions. Amplicon sequencing using ONT allows for flexible and real-time analysis of microbial communities, while cultivation-based methods combined with MALDI-TOF MS provide valuable insight into functional and taxonomic properties of cultivable microbes. Together, these approaches enable researchers to explore both the diversity and activity of microbial populations in the rhizosphere. The skills acquired during this training can be directly applied in a range of research and applied contexts — from fundamental studies in microbial ecology to the development of sustainable agricultural practices, including microbial inoculants and soil health monitoring.
Trainers:
| Name | Institution | Location and country |
| Dr. Ting He | Faculty of Science and Engineering Chemical and Pharmaceutical Biology | Groningen (The Netherlands) |
| Dr. Joël Pothier | Zürich University of Applied Sciences, School of Life Sciences and Facility Management | Wädenswil (Switzerland) |
| Dr. Renata Artimová, Dr. Marek Barta | Institute of Forest Ecology Slovak Academy of Sciences, Department of Plant Pathology and Mycology | Nitra (Slovakia) |
| Prof. Miroslava Kačániová, Prof. Jana Žiarovská, Dr. Lucia Urbanová, and Dr. Juraj Medo | Slovak University of Agriculture in Nitra | Nitra (Slovakia) |
The deadline for application is 20 June 2025.
Further information can be found in the first circular dated 28 May 2025: Poster_Third Training School (First Circular)