International Summer School

Plant-based approaches to clean up contaminated environments

Exploring plant-microbe interactions

Programme schedule

Wednesday 20th July

13:30 - 14:00 Registration and welcome with food and drinks

14:00 - 15:15 Keynote lecture 1 (remotely): “Phytoremediation of contaminated soils: form lab to brownfield”. Prof. Michel Labrecque, Institut de recherche en biologie végétale, Jardin botanique de Montréal

15:15 - 15:30 Coffee break

15:30 - 18:30 Introduction to the Lab experience

Hands-on learning (Lab experience), DNA Extraction from rhizosphere samples.

DNA from rhizosphere samples will be extracted and purified using a commercial kit for direct extraction of nucleic acid from soil based on mechanical cell lysis and matrix purification. The presence of inhibitors and the optimal dilution for downstream analysis will be assessed by PCR.

18:30 - 19:45 Keynote lecture 2: "Plants and soil microbes a quid pro quo relationship: implications for phytoremediation" Prof José M. Becerril, Dpt. of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain

Fishbowl conversations by inviting speakers

Thursday 21th July

9:00-10:30 Hands-on learning (Lab experience) – PCR amplification of marker genes, according with Illumina sequencing protocol.

Using the extracted DNA as a template, two taxonomic and phylogenetic markers for the study of bacterial and fungal community, respectively, will be amplified by PCR. The amplicons size and quality will be assessed by electrophoresis.

10:30-10:45 Coffee break

10:45-12:00 Keynote lecture 3: "How to make better use of plant-microbe interactions for phytoremediation” dr Sofie Thijs, Dpt. of Biology Center for Environmental Sciences Hasselt University Belgium

Fishbowl conversations by inviting speakers

12:00-13:00 Lunch at the UNIMIB

13:00 - 16:30 Hands-on learning (Lab experience) – Sequencing library preparation and overview of sequencing platform (Illumina MiSeq).

The obtained amplicon will be used to prepare the DNA libraries for the Illumina sequencing. Adaptors and index will be added to the amplicons and the quality of the libraries will be assesses by DNA fragment analyser.

16:30 - 16:45 Coffee break

16:45 - 19:30 Hands-on learning (Data analysis experience) – Amplicon data elaboration.

The amplicons reads obtained by Illumina MiSeq instrument will be analyses in a bioinformatic laboratory. A linux-based bioinformatics pipeline will be applied to obtain the structure of the bacterial and fungal community of the analysed samples.

Friday 22nd July

8:30 - 13:00 Visit to sites under phytoremediation (in collaboration with HPC and ENI Companies)

13:00 - 14:00 Farewell with food and drinks

Click here to download a printable version of the program.