Abstract
Microbial dark matter (MDM) represents a vast, uncultured fraction of microbial life with largely unknown ecological roles, particularly in extreme environments. This study investigates MDM in the hypersaline microbial mats of Solar Lake, Taba, Egypt, using shotgun metagenomics (∼70 M reads/sample; triplicate sampling across four sites). A total of 364 metagenome-assembled genomes (MAGs) were recovered, of which 116 (∼30 %) were classified as MDM, comprising 55 % archaeal and 45 % bacterial lineages. Functional annotation revealed that ∼14 % of the MDM MAGs had the genetic potential to fix carbon. The genetic makeup of Ca. Lokiarchaeota (5 MAGs, 4.3 %) and Heimdallarchaeota (1 MAG, 0.86 %) suggest a mixotrophic lifestyle. Some non-methanogenic MAGs had the genetic capacity to utilize methanol and glycine-betaine as carbon sources. In addition, Ca. Marinisomatota MAGs had the genetic potential to degrade polysaccharides, while KSB1 MAGs harbored genes for carbohydrate degradation, denitrification, and nitrogen fixation. The high relative abundance of the SOX gene complex, in Ca. Asgardarchaeota and Ca. Coatesbacteria (RBG-13-66-14), highlights MDM community involvment in thiosulfate oxidation. Additionally, a novel Myxococcota MAG encoded a complete photosynthetic gene cluster, including photosystem II, suggesting phototrophic activity along with Cyanobacteria. Collectively, the genetic makeup of the Solar Lake MDM community underpins key processes such as carbon cycling, sulfur reduction, thiosulfate oxidation, nitrogen fixation, and denitrification, driving the biogeochemical dynamics of this unique hypersaline ecosystem.