DGGE Fingerprinting of Cultivable Bacteria as a Potentially Valuable Indicator of Soil Perturbation.

The relevance of culture-based techniques in contemporary microbial ecology has been questioned because only 0.1-5% of environmental bacteria can grow on culture media. However, populations of readily-cultivable zymogenous microbes are known to be responsive to changes in carbon and nutrient availability, and may serve as useful general indicators of environmental perturbation. We compared culture-dependent (CD) DGGE and culture-independent (CI) DGGE fingerprints of soil microbial communities in two separate experiments. Both the 16S rRNA gene and a nitrite reductase gene (nirk) were used to evaluate the effect of earthworm (Lumbricus terrestris) activity on microbial community composition. CD DGGE and CI DGGE detected distinct bacterial communities; however, cluster analysis revealed nearly identical relationships between the treatments in CD and CI profiles. In a second study, CD DGGE fingerprints of the 16S rRNA gene, community level physiological profiling (CLPP), microbial biomass carbon (MBC), and potentially mineralizable nitrogen (PMN), were used to compare cultivable microbial communities in organic farm and pasture soils subjected to differing fertility regimes. Overall, MBC, PMN, and CLPP were most responsive to additions of compost and manure, while CD DGGE resolved differences in legume cropping and inorganic fertilization. Multiple and simple correlation analyses revealed significant relationships between MBC, PMN, and variables derived from principal component analysis (PCA) of CLPP data, as well as non-metric multidimensional scaling (NMDS) of CD DGGE data. These results suggest that changes in cultivable bacterial communities are linked to the dynamics of the non-cultivable bacteria as well as widely employed measures of soil quality such as MBC and PMN; therefore, CD DGGE may be a useful technique to monitor environmental perturbations.