Monitoring marine microbial communities and their relationships with ecosystem functions in coastal areas

Coastal transitional ecosystems are among the most dynamic and highly stressed environments on Earth, influenced by the interplay of natural variability and intense human activities. Detecting ecological change early in these systems requires monitoring approaches that are scalable, comparable across space and time, and able to capture not only biodiversity patterns, but also signals of change in the ecosystem functioning. This thesis develops and applies a molecular monitoring framework for coastal areas. It integrates environmental DNA (eDNA), microbial community metabarcoding, and metagenomics to establish reference baselines, evaluate how methodological choices shape inference, and assess community responses in relation to ecosystem processes under different environmental conditions. The thesis is organized into five studies. Two of them provide information about the Venice Lagoon – a unique Italian coastal transitional ecosystem subject to multiple pressures and management actions – by characterizing benthic biodiversity (from surface-water eDNA) and prokaryotic communities across sites and seasons (from water and sediment). The objective is to establish a reference framework for future comparisons in a system where spatial heterogeneity and temporal variability are naturally high, and to highlight the complementary ecological information provided by different matrices. A third case study focuses on methodological optimization, assessing how streamlining sampling and laboratory workflows affects microbial community patterns recovered in different environmental contexts and providing guidance for protocol standardisation in long-term monitoring. The last two case studies investigate functional questions regarding microbial responses to natural environmental variability or to stressors: salt marsh sediments are used to evaluate whether strong diel physicochemical oscillations translate into detectable taxonomic or functional shifts, while a controlled mesocosm experiment tests how nutrient enrichment combined with warming can reshape turf-associated microbiomes and their metabolic balance. By integrating baseline establishment, methodological optimization, and functional interpretation under realistic stress conditions, this thesis provides an integrated view of how molecular-based monitoring can support coastal ecosystem preservation by improving understanding of ecosystem dynamics and enabling the assessment of restoration outcomes.