The sea floor is a unique and diverse ecosystem to investigate how geochemical processes affect the diversity of biological life. Red Sea brine pools are water bodies characterized by a unique multitude of extreme conditions, including high temperature, high salinity, and unusual high concentration of heavy metals. We performed a comparative metagenomic analysis of the microbial communities in the sea floor of the Atlantis II (2168 m; 68oC), Discovery Deep (2166 m; 48oC) brine pools and two non-brinesites (1,856 m; 21.93°C and 1,937 m; 31.87°C) in the Red Sea. Each brine core wasvertically dissected into seven distinct subsections. CHN&S profiles showed significant fluctuations in sulfur and nitrogen levels in two of the brine pool subsections. A comprehensive 16S rDNA analysis of about one million 16S rDNA reads, allowed the identification of an exclusive assemblage of microbial communities in the sulfur rich Atlantis II and the nitrogen rich Discovery Deep brine pool subsections when compared to adjacent brine and non-brine sediments. Proteobacteria, Actinobacteria, Cyanobacteria,and Deferribacteres were the most abundant bacterial phyla. Interestingly, the S-rich Atlantis II subsection showed distinctive abundance of the recently identified Chloroflexiorder Anaerolineales, Fusobacteria and OP1. Crenarchaeota dominated all the sediment samples with the exception to the S-rich Atlantis II and the N-rich Discovery Deep sample that was dominated by Euryarchaeota. Our study illustrates a distinct stratification of the microbial communities in both the nitrogen rich and the sulfur rich brine subsections. However, the lack of apparent stratification in the remaining layers of the brine and non-brine sediments despite variations in metals and CHN&S profiles implies that sulfur and nitrogen are the major players that dictate the microbial assemblage in the Red Sea
