HYDROMIC - HYDROsystem MICrobiomes under Morphological and Catchment Pressures
Context:
Freshwater hydrosystems—including rivers, streams, lagoon, floodplains, and connected wetlands—provide essential ecosystem services such as water purification, nutrient cycling, biodiversity conservation, and climate regulation. These functions are strongly mediated by microbial communities, which drive key biogeochemical processes including carbon turnover, nitrogen transformation, and contaminant degradation. As the foundation of aquatic ecosystem functioning, microbiomes respond rapidly to environmental change and may therefore serve as sensitive indicators of ecosystem health.
Gaps:
Recent advances in high-throughput sequencing and environmental genomics have created unprecedented opportunities to characterize and monitor aquatic microbiomes. Nevertheless, one of the less-know-taxa and there remains limited understanding of how hydrosystem microbiomes evolve and change under the combined influence of physical habitat alteration, pollution gradients, and land-use patterns across catchments. Developing this understanding is essential for improving ecosystem assessment and informing sustainable river management and restoration strategies. Although numerous studies have examined individual drivers of microbial diversity in freshwater ecosystems, most focus on isolated factors such as nutrient enrichment or specific contaminants. Comparatively few studies integrate hydromorphological status, pollution pressure, and catchment-scale land use within a unified analytical framework. Moreover, many investigations provide only static snapshots of microbial communities, without considering their spatial variability across connected hydrosystems or their temporal dynamics. The links between microbiome composition, ecosystem functioning, and indicators of ecological quality remain poorly resolved, limiting the application of microbial indicators in environmental monitoring. Another important gap concerns the interaction between local environmental conditions and broader landscape characteristics. It is unclear whether catchment land use exerts direct effects on microbiome structure or whether these effects are mediated through changes in hydrology, sediment transport, and pollutant delivery. Understanding these multi-scale relationships is critical for predicting ecosystem responses to environmental change and designing effective restoration measures.
Main Research Question:
How do hydromorphological conditions, pollution levels, and catchment land-use patterns shape the composition, diversity, and evolution of freshwater microbiomes within hydrosystems?
Objectives:
The overall objective of this research is to develop a comprehensive understanding of the factors governing hydrosystem microbiomes and their evolution in response to morphological alteration, pollution, and catchment land use.
Specifically, the project will deliver:
- A characterization of microbial community composition and diversity across hydrosystems exhibiting contrasting hydromorphological conditions, pollution levels, and land-use contexts.
- An integrated analysis identifying the relative contribution and interactions of physical, chemical, and landscape drivers influencing dynamics of microbiome structure.
- Predictive models linking catchment characteristics and environmental pressures to microbial community responses and ecosystem functioning.
- Identification of microbial taxa or community signatures that can serve as indicators of hydrosystem health and ecological integrity.
- Recommendations for incorporating microbiome information into freshwater monitoring, river restoration, and watershed management frameworks.
The primary beneficiaries of these outputs include environmental agencies responsible for water quality assessment, river basin managers and restoration practitioners seeking science-based decision tools, policymakers implementing integrated watershed management strategies, and the scientific community investigating ecosystem resilience and microbial ecology.