Genetic, Functional and Structural diversity of Bacteria

Genetic diversity in bacteria is commonly explored through the analysis of 16S rDNA genes, which are universally present and exhibit variations in base composition among species (Nielsen et al., 2002).

To assess structural diversity, phospholipid fatty acids (PLFAs), stable components of microbial cell walls, are extracted from soil samples and subsequently analysed by gas chromatography. This method enables the identification and quantification of specific PLFAs, providing sensitive and reproducible measurements. It characterizes the numerically dominant segment of soil microbial communities without the need for cultivation (Nielsen et al., 2002).

Functional diversity is evaluated by examining carbon utilization patterns using the BIOLOGTM assay. In this process, a soil extract is incubated with up to 95 different carbon sources in a microtiter plate, and microbial activity is indicated by a redox dye. Specifically selected sets of carbon sources are employed to study soil microbial communities. The assay yields a qualitative physiological profile of potential functions within the microbial community, and variations in these profiles can be analysed using multivariate statistics (Nielsen et al., 2002).

Systematic sampling ensures that the entire site being sampled is well represented by the individual samples. The analytical variability between laboratories can be controlled by analysing all samples by one specific method within one specific laboratory as done in the Dutch Soil Monitoring Programme (Nielsen et al., 2002).