Do we need to standardize extraction procedures for community level physiological profiling?

Microorganisms are essential regulators of soil functioning, as they are involved in many crucial processes such as organic matter decomposition, nutrient cycling, soil structure and fertility. Currently, there is a growing interest in functional diversity, such as the number and type of substrates used for energy metabolism (CLPP-community level physiological profiling). Such metabolic diversity of heterotroph soil bacteria is frequently investigated through Biolog Ecoplates, containing 31 of the most useful carbon sources for the soil community. The metabolic diversity of soil bacteria might be an interesting biological indicator of soil quality, and also a useful tool for investigating the link between land use change, climate warming, soil carbon, microbial diversity and activity.
Methods related to Biolog-CLPP reported in the literature differ in the suspension medium and extraction method, the type and density of inoculums, the inoculation procedures and conditions of incubations. For example, various combinations of extraction methods and suspension media are being used for the first bacterial extraction step. Despite such methodological differences, Biolog-CLPP data are often compared across studies. The development of a standardised method for Biolog-CLPP is however essential improving the relevance and significance of results across studies. In this work, we investigated the influence of extraction procedures on microbial extraction efficiency for further use in CLPP. The microbial extraction efficiency was tested by plate counts for a total of twelve combinations of three suspension media and four extraction methods. The experiment was performed on four soils differing in organic matter content.

The aims of this study were to:
• Synthesize extraction procedures used for Biolog-CLPP
• Measure the effect of extraction procedures on microbial extraction efficiency (plate counts) in four soil types
• Investigate a possible interaction between the suspension media and the extraction method used
• Evaluate whether a standardized extraction procedure can be recommended across soil types