TABLE 3.

Utility and limitations of some community analysis methods

Type	Example	Utility	Limitations
Culture dependent	Plating	Isolates obtained for further study	Only a small proportion of community detected, isolates not necessarily reflective of a specific metabolic function
	MPN	Metabolic function of interest detected	No isolates obtained for further study, selective media may limit proportion of community detected
	Biolog	Overall metabolic activity detected, rapid and easy to use	No isolates obtained for further study, selective media may limit proportion of community detected, may not include substrates of interest, sensitive to inoculum size and incubation effects
Culture independent	Phospholipid fatty acid analysis	Changes in fingerprint can indicate change in community structure	No isolates obtained for further study
	Protein banding	No selection pressure if extracted directly	No measurement of community function, difficult to link fingerprints to specific microbial groups
	Fluorescence in situ hybridization	Spatially visualize specific microorganisms in an environment, no bias from culture media	Not necessarily detecting active microorganisms, laborious technique
	Staining for active microbes	Enumerate live microorganisms, no bias from culture media	Does not differentiate microorganisms with catabolic activity of interest
	RSGPa	Quantitative analysis of specific microorganisms in environmental samples, no bias from culture media	Limited to those microorganisms included in the screen
	PCR followed by gel electrophoresis	No bias from culture media, can identify microorganisms by sequencing resolved bands, bulk changes in community structure detected	Differential DNA or RNA extraction from different cells, differential amplification during PCR, no information on activity; no isolates for study
	Probes for specific metabolic genes	Detect genes with function of interest, mRNA detection can reveal information about expression	Limited to known genes, activity cannot be inferred from presence of genes alone
	Promoter-reporter systems	Gene expression detected, treatment effects on total cell function can be monitored	Nature of promoter must be known, easier to apply when whole genome sequences are available, monitors only those strains with reporter genes inserted

^aRSGP, reverse sample genome probing.