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The sedimentary Marl mudstone soil is composed primarily of CaCO3, and is an important pedologic and geomorphologic element known as Marl, extensively dispersed in slopes and ridges in the northern Negev Desert, Israel. The wide Marl soil-layer areas are barren, with well-developed streamsides and no perennial vegetation cover. Soil systems in the Negev Desert have been widely studied, yet very little information was collected on Marl soils, and even less on the microbiome present in the Negev. Thus, an evaluation of the microbial-community inhabitants in a Marl soil layer was conducted in an attempt to distinguish between Marl with surface green mat and bare Marl soil layer. Our objective was to investigate the microbiome and abiotic components of the upper layer (0–5 cm) of Marl and Marl-with-green-mat soil collected in the Negev Desert. Plate-counting enabled the estimation of fungal and bacterial population size, while nested polymerase chain reaction (nPCR) and Ion Torrent sequencing were used to analyze biological diversity. The results indicate significant differences in microbial biomass and microbial-community diversity between Marl and Marl-green mat, despite similar pH levels. Further study is needed to enhance understanding of the activity of the biotic components and their contribution to slope stabilization. [ABSTRACT FROM AUTHOR]