The Use of Carbon Substrate Utilization Patterns in Environmental and Ecological Microbiology

Abstract

Carbon substrate utilization patterns have found increasing use in environmental and ecological microbiology over the past five years. Ninety six-well microtiter plates containing various carbon substrates permit these patterns to be determined quickly, economically, and effectively. The use of these patterns to characterize and differentiate strains isolated from the environment has been very effective in providing information on the culturable fraction of the microbial community. Another approach involves the direct inoculation of natural samples into these microtiter plates; this approach has several fundamental problems. The inoculation of low cell densities into the wells means that the technique is a culture-based method in which the biases of enrichment culture may render the results unrepresentative of the native microbiota. The physiological state of the inoculated microbes may affect the kinetics and pattern of substrate utilization. As a measure of the functional diversity of microbial communities, this approach suffers because the tested substrates do not accurately represent the types of substrates present in ecosystems, and the metabolic redundancy of species implies that changes in the response may only crudely represent the actual microbial population dynamics. Therefore, although this approach can be used to determine whether environmental samples differ in their response patterns, it is unclear how it can be used to provide fundamental information on questions of microbial diversity.