Habitat Preferences and Short‐Term Dynamics of Alien Fishes Revealed by Environmental DNA in River Floodplains

Czeglédi, István and Funk, Andrea and Pont, Didier and Hein, Thomas and Meulenbroek, Paul and Preiszner, Bálint and Valentini, Alice and Erős, Tibor (2026) Habitat Preferences and Short‐Term Dynamics of Alien Fishes Revealed by Environmental DNA in River Floodplains. ENVIRONMENTAL DNA, 8 (2). ISSN 2637-4943

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Abstract

Floodplains are among the most diverse freshwater ecosystems, yet they are increasingly threatened by human‐induced alterations. Recent research has shown that the ecological impacts of alien species in these systems can rival those of other anthropogenic disturbances. Effective management and mitigation strategies depend on accurate assessments of the distribution and temporal dynamics of alien species. However, traditional fish sampling methods are often inadequate in floodplains because their high spatial and temporal heterogeneity makes it impossible to apply a single traditional method effectively across different habitat types. In this study, we investigated how local habitat characteristics and regional‐scale processes influence habitat use and the temporal dynamics of alien fish abundance inferred from environmental DNA in Danubian floodplain systems. By integrating community‐ and species‐level analyses, we found that lateral hydrological connectivity is a key driver shaping alien fish community assembly, although the influence of other environmental factors, such as the local habitat structure, water chemistry, and land use, varied across taxa. We also revealed that the temporal dynamics of alien species were generally independent of local‐ and regional‐scale drivers. This suggests that extrinsic factors like hydrology, connectivity, and resource availability may have only a limited influence on short‐term eDNA‐derived abundance fluctuations of alien fishes in floodplains. These findings have practical implications: management effectiveness is likely to vary across spatial scales and species, and control efforts may be more successful in areas where alien fish populations are less stable. Importantly, our study demonstrates that eDNA metabarcoding is a powerful tool for monitoring alien species in complex and dynamic environments such as floodplains. It enables efficient, non‐invasive, and fine‐scale detection of spatial and temporal patterns that would be challenging to capture through conventional sampling, thereby enhancing our ability to inform targeted and adaptive management strategies.

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