Nico Salmaso (

Claudio Donati (

via Mach 1, San Michele all'Adige - Italy

Integrating ‘Omics’ Technologies into Aquatic Ecology:

New perspectives in Metagenomic, Metabolomic and Bioinformatic applications

in the study of aquatic ecosystems


The course is aimed to provide both the theoretical foundations and examples of applications of the “Omics” in aquatic ecology, with a focus on the genetic analysis of genomes (metagenomics), proteins and metabolites (proteomics, metabolomics) in biological and environmental aquatic samples. These topics are relevant not only for the advancement of freshwater ecology, but also for the monitoring and management of water resources and the associated biological communities.

The techniques that will be described are commonly used in the analysis of environmental DNA (eDNA) extracted from a variety of aquatic and terrestrial environments, as well as biological hosts. Therefore, to broaden the scope of the course, a few lectures will focus on the use of metagenomics/metabolomics in other complementary research fields.

At the end of the course, participants will have acquired knowledge, skills and competence on:
- The state of the art of modern ‘Omics’ technologies and their role in the advancement of modern aquatic ecology and establishment of new theoretical foundations.
- The field of application of ‘Omics’ technologies, with practical applied ecology case studies from aquatic, terrestrial and gut microbiota environments, critically commented, and highlighting pros and cons of different methods and their possible combinations.
- The inclusion of ‘Omics’ in research projects and in different ecological/environmental “problem solving” issues, complementing or challenging traditional approaches; deciding which approach could be the best in function of the final aim of a study.
- The principal bioinformatic pipelines available to analyse High Throughput Sequencing data.

Specific fields of application of the ‘Omics’ approaches in ecology will include, among the others, the quantitative evaluation and functions of biodiversity in ecosystems; the impact of climate change, anthropogenic stressors, and pollutants; the introduction and early detection of alien species; and characterization of active metabolites (e.g. cyanotoxins synthetized by cyanobacteria). Introductory lectures will be followed by the presentation and critical discussion of case studies, and by the organization of practical laboratory sessions (including bioinformatic pipelines, and guided practice in the laboratories of genomics and metabolomics).

The course will be completed by a mid-course field excursion with sampling (Lake Garda).

Participants are requested to bring their laptop with them.

Download the summer course flyer!