Solar salterns consist of a series of basins in which seawater is gradually concentrated until precipitation of table salt or halite, the main product of the activity, occurs. After the collection of halite, the basins remain with bittern, until recently considered an aseptic environment due to its high content of magnesium salts. The aim of our work was to describe the microbial diversity in the Sečovlje salterns (archaea, bacteria, fungi, other eukaryotes) present in the brine of various concentrations and in the bittern. For the detection of all mentioned groups, except for the other eukaryotes, we used classical cultivation methods and identification of pure cultures with molecular markers. For all the above mentioned groups, we also used the cultivation independent metagenomic approach with amplicon sequencing (next generation sequencing or NGS). With cultivation we identified 34 fungal isolates (7 genera) from brines and two isolates (two genera) from bitterns. Among them, fungi from the phylum Ascomycota predominate, with the most numerous genera being Cladosporium, Aspergillus, Penicillium, and the basidiomycetous genus Wallemia. Black yeasts (Dothideales) and non-melanized asco- and basidiomycete yeasts are also present. Using amplicon sequencing of the ITS2 region, we detected 73 fungal genera, however we did not detect black yeasts. From brines of different salinity we isolated 45 bacterial isolates from the genera Bacillus, Chromohalobacter, Cobetia, Halomonas, Larsenimonas, Salicola, Salinicola and Staphylococcus, and 7 archaea from the genera Halorubrum and Halococcus. Using amplicon sequencing of the variable regions of 16S rDNA, we showed that in the brine and bittern within the crystallization ponds, the predominant bacterial genera are Salinibacter and Salinivenus, while the predominant archaeal genus is Halorubrum. As salinity increases, alpha diversity of bacteria, archaea and other eukaryotes decreases, while alpha diversity of fungi is lowest at moderate salinity (10–20 % NaCl).
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