Large lowland rivers represent an important type of ecosystem that has been under a constant anthropogenic influence (industry, thermal power plants, untreated communal water, and agriculture) for centuries, which has led to most of them no longer meeting natural reference conditions. These pressures affect diatom communities which represent a reliable bioindicator of the overall degradation of water bodies. The current study provides detailed information about benthic diatoms from the large international lowland rivers Sava and Tisa, analyzed using digital microscopy. Using the digital method and the BIIGLE 2.0 image annotation system, a total of 205 and 206 diatom taxa in the Sava and Tisa rivers were identified, belonging to 65 and 63 genera, respectively. Some of the dominant genera in the Sava River were Achnanthidium, Cocconeis, Gyrosigma, and Navicula, while in the Tisa River, mostly centric diatoms (Discostella, Cyclotella, Stephanodiscus) were dominant. Most of the recorded species are alkaliphilic and characteristic of running waters with high trophic conditions. The presence of halophilic taxa was also noted (e.g. Bacillaria paxilifera, Tryblionella species, Nitzschia clausii, Navicula salinarum). These taxa are sensitive indicators of even short-term changes in lowland lotic ecosystems characterized by elevated conductivity. The diatom indices showed very consistent ecological status, mainly moderate in terms of the general pollution index IPS, and poor to bad ecological status according to trophic diatom indices (Rott TI and TDI).
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