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Simple Summary  Microbial communities play a significant role in the functioning of the ecosystem in the cold mountain desert of Eastern Pamir, a region that is characterized by extreme environments with limited nutrient and water availability and sparse vegetation. This study aims to investigate the taxonomic composition and structure of bacterial endolithic (rock matrix colonizing) assemblages and soil-inhabiting communities that occur in the Eastern Pamir Mountains, and to compare the composition and structure of both types of communities looking for general patterns and trying to identify the connectivity between these types of microbial assemblages. The taxonomic composition of Pamirian endolithic communities and soil-inhabiting microbial consortia (biocrust communities) exhibit similarities to communities from cold and hot deserts, but they also harbor taxa, which are possibly novel species or which, so far, lack reference sequences in the databases. The endolithic communities occurring in three subregions of Eastern Pamir are characterized by high heterogeneity and cannot be grouped according to the subregion, while the distribution of Cyanobacteria in the soil crusts demonstrates the similarities between the communities within the subregion reflecting regional differences. We also found connectivity between both habitats concerning the occurrence the same taxa (e.g., Cyanobacteria).    Abstract  Microbial communities found in arid environments are commonly represented by biological soil crusts (BSCs) and endolithic assemblages. There is still limited knowledge concerning endoliths and BSCs occurring in the cold mountain desert of Pamir. The aim of the study was to investigate the composition and structure of endolithic bacterial communities in comparison to surrounding BSCs in three subregions of the Eastern Pamir (Tajikistan). The endolithic and BSC communities were studied using culture-independent and culture-dependent techniques. The structure of the endolithic bacterial communities can be characterized as Actinobacteria–Proteobacteria–Bacteroidetes–Chloroflexi–Cyanobacteria, while the BSCs’ can be described as Proteobacteria–Actinobacteria–Bacteroidetes–Cyanobacteria assemblages with low representation of other bacteria. The endolithic cyanobacterial communities were characterized by the high percentage of Chroococcidiopsaceae, Nodosilineaceae, Nostocaceae and Thermosynechococcaceae, while in the BSCs were dominated by Nodosilineaceae, Phormidiaceae and Nostocaceae. The analysis of 16S rRNA genes of the cyanobacterial cultures revealed the presence of possibly novel species of  Chroococcidiopsis ,  Gloeocapsopsis  and  Wilmottia . Despite the niches’ specificity, which is related to the influence of microenvironment factors on the composition and structure of endolithic communities, our results illustrate the interrelation between the endoliths and the surrounding BSCs in some regions. The structure of cyanobacterial communities from BSC was the only one to demonstrate some subregional differences.

Connectivity of Edaphic and Endolithic Microbial Niches in Cold Mountain Desert of Eastern Pamir (Tajikistan)