Las Tablas de Daimiel National Park (TDNP, Iberian Peninsula) is a semi-arid wetland of international significance for waterfowl and serves as a migratory route for various bird species. However, TDNP presents strong anthropization and fluctuating water levels, making it a highly fragile ecosystem. Water physico-chemical parameters and microbial diversity of the three domains (Bacteria-Archaea- Eukarya) were analysed in Zone A and Zone B of the wetland (a total of eight stations) during spring and summer, aiming to determine how seasonal changes influence the water quality, trophic status and ultimately, the microbial community composition. Additionally, Photosynthetically Active Radiation (PAR) was used to determine the trophic status instead of transparency using Secchi disk, setting the threshold to 20–40 μmol/sm2 for benthic vegetation growth. In spring, both zones of the wetland were considered eutrophic, and physico-chemical parameters as well as microbial diversity were similar to other wetlands, with most abundant bacteria affiliated to Actinobacteriota, Cyanobacteria, Bacteroidota, Gammaproteobacteria and Verrumicrobiota. Methane-related taxa like Methanosarcinales and photosynthetic Chlorophyta were respectively the most representative archaeal and eukaryotic groups. In summer, phytoplankton bloom led by an unclassified Cyanobacteria and mainly alga Hydrodictyon was observed in Zone A, resulting in an increase of turbidity, pH, phosphorus, nitrogen, chlorophyll-a and phycocyanin indicating the change to hypertrophic state. Microbial community composition was geographical and seasonal shaped within the wetland as response to changes in trophic status. Archaeal diversity decreases and methane-related species increase due to sediment disturbance driven by fish activity, wind, and substantial water depth reduction. Zone B in summer suffers less seasonal changes, maintaining the eutrophic state and still detecting macrophyte growth in some stations.This study provides a new understanding of the interdomain microbial adaptation following the ecological evolution of the wetland, which is crucial to knowing these systems that are ecological niches with high environmental value.
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