This abstract summarizes the results of the microbial community composition in deep subsurface (>7,000ft.) black shales based on analyses of membrane lipid biomarkers. The membrane phospholipid and diglyceride fatty acids (PLFA and DGFA) represent some of the most important proxies for microbial signatures in natural environmental systems. Samples were acquired from the Marcellus Shale Energy and Environment laboratory and the West Virginia Geological Survey. To improve recovery and reproducibility of lipid biomarkers from subsurface shales, characterized by low biomass density and complex matrices, we tested and compared performance of seven lipid extraction procedures. Procedures tested were; the Bligh-Dyer, the Folch, and the Microwave extraction methods together with respective biochemical amendments and buffer modifications. The intact phospholipid-amended modified Bligh Dyer treatment had the highest yield and best reproducibility compared to the other lipid extraction procedures. We further used the diversity and concentration of the lipid biomarkers to interpret microbial community structure and distribution within three geologic zones of the Marcellus Shale. We differentiated the membrane lipid profiles in the shale rock samples from the drilling muds and provided evidence of rock-hosted microbial signatures. The lipid composition of the samples consisted of Gram (+), Gram (-), and high stress indicative biomarkers. The presence of stress indicative biomarkers provide evidence of physiological adaptation to stress associated with deep subsurface systems. We further investigated the possible effects that different sampling and storage conditions could have on the distribution of subsurface microbial community. Core samples collected and stored at room temperature conditions (WV 6) were compared with samples collected and stored at -80 degrees (MSEEL). The variety and concentration of lipid biomarker were higher in the MSEEL samples compared to the WV 6 samples. More so, stress biomarkers like the oxiranes, dimethyl esters and keto lipid were only present in MSEEL samples. The microbial species in WV 6 samples modified their membrane lipid structures in response to low temperature and pressure conditions associated with the surface conditions. The better we know about the microbial community composition of deep subsurface shales like the Marcellus Shale, the better we can improve biocide performance in shale gas development, microbial colonization, and enhanced gas recovery.