Most known lipid biomarkers were found by analysis of pure bacterial cultures in vitro. The practical impact of a biomarker including possible interferences should be tested in extensive research of target strains in real ecosystems. Phospholipid fatty acids identified in river sediments, activated sludge and waterworks sand filters correspond with those proposed previously as biomarkers typical of expected microorganisms. Two ether lipids regarded as specific biomarkers of the Archaea kingdom were identified in digested sludge from a sewage water plant.