Microorganisms have the ability to control the biophysical properties of their membrane lipids to thrive in natural environments. Different microbial species possess different membrane lipid compositions, even the composition of a single species is not always constant, but depends on the habitat conditions. Microorganisms adjust their membrane lipid composition by modifying the types of glycerol backbone (chain length, saturation, and branching) and head groups. Therefore, signatures of membrane lipids in the environmental samples could be used as biomarkers reflecting the physicochemical conditions and the community structures. With the increasing knowledge of lipid structures and their properties, the interpretation of lipid-based biomarker in environmental samples would be more accurate. By using lipidomics, this thesis aimed at (i) identifying new lipid isomers to help improve the precision of its derived proxy, (ii) expanding the application of lipid biomarkers to the terrestrial subsurface critical zone for tracing the signal of surface down, (iii) providing a full lipid profile in the soils, investigating their sources and potential possibility as novel chemotaxonomic markers for bacteria.