Storage, transformation and removal of nutrients and organic matter are key processes in aquatic ecosystem functioning, able to affect biogeochemical cycles. In rivers, the above processes are influenced by habitat structure, hydro-morphology and flow conditions. In lakes, highly sensitive to trophic changes, the basin morphology, the water circulation and turnover time are the more relevant factors. The marine ecosystem functioning is strongly influenced by water masses origin and dynamics. Overall, climate changes affect biogeochemical cycles. In all the aquatic ecosystems the biological communities take on a crucial role in the nutrient cycling. IRSA’s research activities in inland waters are related to:

1. diffusion and fate of nutrients and organic matter in rivers and lakes;
2. physical and biological processes occurring in the riparian zone, able to remove nitrogen and phosporous released by agriculture practices;
3. chemical processes removing nutrients in the river hyporheic zone in the Mediterranean area and in the Po Valley;
4. trophic status changes in lakes, with special attention to factors controlling algal growth and to nutrients and carbon dynamics.

Research studies carried out in the marine environment have the goal to describe the planktonic community role in CO₂ circulation in areas characterised by a different trophic status ranging from the ultra-oligotrophic conditions of the Cilician basin (Eastern Meditearranean) to the eutrophic conditions of the coastal areas in the Adriatic Sea.

The evaluation of Biological Communities in aquatic environments (e.g. invertebrates, fish, macrophytes, algae) is crucial for understanding the effects of both large scale variations and more local anthropogenic activities. Also, the uncovering of cause-effect relationships, that determine structural and functional aspects of aquatic ecosystems, is essential for any effective environmental management. In this overall context, IRSA activities are mainly focused on the development of biological methods, on the characterization of river habitats, on aquatic invertebrates ecology and on the selection of appropriate bioindicators. Particular emphasis is given to the implementation of the Water Framework Directive (WFD: 2000/60/CE), at the Italian and European scale. Particularly, scientific support to monitoring planning (surveillance, operational and investigative) and ecological status classification are provided. IRSA is involved in setting up criteria and guidelines for the implementation of environmental laws, in the developing and validation of qualitative and quantitative methods for specific ecological variables in rivers and lakes and, finally, in the definition of procedures and tools - including databases and softwares - for the ecological classification of water bodies.

The study of aquatic microbial communities contributes to a better understanding of the ecosystemic processes involved in carbon and nutrients cycling, organic matter mineralization and the energy transfer trough the aquatic food web. At IRSA, the research is oriented toward a better comprehension of the functional role of the aquatic microorganisms and their response to local perturbations (e.g. pollutants, flood & drought) and global changes. Moreover, the dynamics of microbial species, that might be identified as early warning indicators of environmental stress, have been investigating. By bio-molecular techniques, the activity (at bulk and single-cell level) and the diversity of microbial assemblages have been assessed both in planktonic communities and biofilms, including pathogenic organisms. The research activities on temporary rivers, coastal and marine environments are mainly focused on:

• the analysis of functional characteristics, with the aim to describe the microbial community capacity to degrade organic matter and compounds under different environmental conditions, including degradation of hazardous substances;
• the analysis of microbial community composition, with the aim to the describe how the community adapts to environmental changes and to water pollution.

Dystrophic phenomena may favour the growth of potentially toxic phytoplanktonic species in lakes, artificial reservoirs and coastal waters. Particular attention has been paid to cyanophytes (or cyanobacteria) prokaryote organisms able to perform photosynthesis. Some species of this group, indeed, produce cyano-toxins as a defence against herbivorous organisms such as zooplankton and fish. These toxins also exert toxic effects on target human organs and system such as liver, lungs and nervous system. IRSA carries out researches on this topic in three main areas: environmental factors behind the proliferation of cyanophytes, fast methods for detection of cyanophytes and impact of cyano-toxins on ecosystems. The role of nutrients in controlling the development of phytoplankton biomass is evaluated using the Algal Growth Potential test (Pseudokirchneriella subcapitata). Analytical protocols based on immunoenzymatic screening (ELISA) and quantitative analyses by HPLC are instead used to quantify the cyano-toxins concentrations. The potential toxicity of cyano-toxins is, then, tested on target organisms such as the crustacean Thamnocephalus platyurus. The research results are integrated into guidelines for the management of the ecosystem. IRSA has recently conducted research activities on cyanophytes in Lake Pusiano, Lake Como and, more recently, in Lake Occhito, where massive blooms of the cyanophyte Planktothrix rubescens occurred.