Desert soil around the black stones is highly complex, which substantially affects the diversity and composition of inhabiting microbes. The existence of black stones in the southern part of the Black Gobi desert of China could provide microhabitats for diverse bacterial communities that remain unexplored. Hence, Illumina MiSeq sequencing was used to determine the differences in bacterial communities associated within microhabitats in three sites of the Black Gobi desert, China. Our results show that bacterial communities are significantly affected by each microhabitat. For instance, the a-diversity of bacterial communities indicated more remarkable diversity and richness in these microhabitats. Considering beta-diversity, variances were reported mainly in the Proteobacteria (30%), Actinobacteria (26%), Chloroflexi (19%), and Firmicutes (9%). Firmicutes were markedly enriched in the upper surface, especially in site 1. Compared to other microhabitats, the relative abundance of Proteobacteria was greater in the subsurface, and they were also more dominant in the other two sites. Network analysis of soil factors and bacterial genera showed that the most significant-occurrences were positively correlated, demonstrating potential synergistic interactions. Collective with the predicted function profiles and the redundancy analysis, these results indicated the highest variances in bacterial community structure and function in Black Gobi Desert ecosystems. These differences are likely closely related to the soil parameters, mainly water content, total carbon, and total nitrogen, and might be associated with black stones. This study concludes that microhabitats formed by black stones support highly diverse and biologically active bacterial communities. These microhabitats with extreme environmental conditions deliver new opportunities to explore soil bacterial communities at relevant spatial scales in the Black Gobi desert.

The Qaidam Basin of the Qinghai-Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The alpha-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general,Firmicuteswas dominant in the west region, whileProteobacteriaandAcidobacteriawere dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.