Introduction

Microbial communities are microorganisms (viruses, bacteria, fungi, algae) at the base of the food web pyramid, representing about 50 % of the total biomass on Earth. They are responsible for the biogeochemical cycles that shape the earth environment and of its aquatic systems, influencing the health of each trophic and ultimately human health, too.

In Europe, the good quality of surface waters is established under the Water Frame Directive (WFD) based on the monitoring either of chemical or the ecological status and pathogen detection for drinking and bathing waters. However, methods and techniques currently used for the water quality monitoring and potential biohazard detection present several limitations due to the i) need of highly skilled technicians, ii) long time for obtaining results, and iii) lack of tools for an integrated monitoring approach with biological and non biological parameters relevant to guide preventive and remediation actions by the water authorities.