What are biomarkers?
The biomass of complex microbial consortia can be determined by measuring the concentrations of the components of cell membranes. The detailed analysis of universal components, such as the lipids found in all cell membranes, yields detailed patterns of components that have been established as biomarker "signatures" for specific groups of microbes. The detailed patterns can be utilized as quantitative definitions of microbial community structure. Detection/identification is independent of cell culture and growth. Cell lysis also facilitates nucleic acid recovery from the same samples. Automated systems utilizing successive enhanced extractions can be coupled to GC/MS or, providing even greater specificity/sensitivity, to HPLC/electrospray/MS/MS. With the electrospray ionization and in ideal conditions, sensitivity is near single microbe levels. Shifts of signature component patterns can be followed as responses to environmental perturbations. Rates of formation or utilization of endogenous storage compounds such as triglyceride or poly -hydroxy alkanoate can be utilized as measures of the community nutritional status. Rates of formation and turnover of specific components can be utilized as measures of metabolic activities by utilizing labeled precursors. This signature lipid biomarker analysis has recently been supplemented by DNA gene probe analysis for functional (enzyme gene probes), and specific organism probes based on genes for 16S rRNA.
Current research utilizing the signature lipid biomarker analysis is involved in examination of the origins of the deep subsurface microbial communities, effects of nutrients and elevated CO2 on the rhizosphere microbiota and the lability of soil carbon, the quantitative definition of soil "quality" based on the microbial ecology, effects of bioturbation on estuarine sedimentary microbiota, culture independent defining of human fecal pollution in urban runoff, detection of injured and noncultured pathogens in drinking water distribution systems, rapid ultrasensitive detection/identification of pathogens like Mycobactria and Legionella in clinical and environmental systems, quantitative detection/identification of organisms, allergens, and immune potentiators in indoor air, characterization of biofilms that initiate microbially influenced corrosion, in monitoring effectiveness and predicting success of in situ bioremediation, and in monitoring bioprocesses and waste treatment.
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