Microbial Insights

MI offers three categories of cultivation independent analyses to characterize microbial communities: PLFA, DGGE, and CENSUS.  Although the target biomarker molecules (phospholipids vs. DNA) and procedures (GC/MS vs. PCR) are extremely different, the overlying difference in the results provided by each technique is in the degree of resolution or specificity.  Choosing between these approaches, therefore, depends primarily upon the specificity of questions that need to be addressed and the current state of knowledge regarding the microbial process in question.

Phospholipid fatty acid (PLFA) analysis provides a robust measure of total biomass and a broad-based profile of the microbial community composition grouped into general categories such as anaerobic Gram negative bacteria, eukaryotes, and Proteobacteria.  Other than for stable isotope probing (SIP) studies, PLFA analysis is best suited for addressing more general questions such as whether a treatment increased (or decreased) total biomass or substantially changed redox conditions.

CENSUS results, on the other hand, are very specific – quantification of specific organisms (e.g. Dehalococcoides) and genes encoding specific functions (e.g. vinyl chloride reductases).  Thus, CENSUS analysis is most appropriate for answering targeted questions relating to reasonably well characterized microbial processes.  For example, CENSUS assays have been developed to quantify specific bacteria and functional genes responsible for biodegradation of a wide variety of common groundwater contaminants.

In some respects, the resolution of DGGE analysis is somewhere in the middle of PLFA and CENSUS.  DGGE and sequence analysis provides a DNA based profile of the microbial community and allows identification of the predominant organisms generally to the family or genus level but cannot quantify specific organisms or microbial functions.  DGGE profiles are used to visually display differences or shifts in microbial community composition over time or in response to treatment.  Subsequent sequence analysis is somewhat exploratory, seeking to answer the question “Who is there?”.  Most often, DGGE analysis is performed when identification of the predominant organisms is required but little is known about the microbial community of the sample prior to analysis.