Differential rRNA gene metabarcoding of prokaryotic consortia in desert athalassohaline and thalassohaline brines

Culture-independent molecular study presented the first exploring and evaluation of prokaryotic communities in two desert brines; the athalassohaline Lake “Aghormy”, Siwa Oasis, Western Desert of Egypt, and the thalassohaline saltern “Sebeaka Sabkha”, Bardawil Lagoon, north coast of the Sinai. 16S rRNA gene metabarcoding generated a total of 488,828 reads from both sites, grouped into 17,741 operational taxonomic units (OTUs). 3030 OTUs were shared in both sites, while 2255 and 9426 OTUs were unique to Aghormy Lake and Sebeaka Sabkha, respectively. Both sites showed an abundance of Bacteroidetes, particularly the genera Salisaeta and Salinibacter in Aghormy and Sebeaka Sabkha, respectively. Aghormy brine was characterized by phylotypes belonging to Deinococcus-Thermus, Spirochaetes, Rhodovibrio, Piscirickettsiaceae and GMD14H09 (Deltaproteobacteria). While phylotypes assigned to AT12OctB3 (Bacteroidetes), Rhodobacteriaceae, Ectothiorhodospiraceae, and Xanthomonadaceae formed Sebeaka Sabkha bacterial community. A Cyanobacteria-like phylotype was assigned to genus Dactylococcopsis in both brines. The archaeal family, Halobacteriaceae, represented 4.8% of Sebeaka brine reads. Although some of the recorded phylotypes in both brines belonged to the same phyla, they differed in lower taxonomic ranks, implicating distant brine environments' impact on shaping halophilic communities. The metabolic prediction analyses showed a dominance of TCA cycle, branched amino acid biosynthesis and heme biosynthesis, common metabolic features for salt tolerance.