1.6 Microbial diversity in soil

The word ‘diversity’ when used in relation to organisms in a habitat describes complexity and variability at different levels of biological organisation:

  • Genetic variability within taxons (which may be species).
  • The number (also called richness) of taxons.
  • Relative abundance (or evenness) of taxons.
  • And number and abundance of functional groups.

Important aspects of diversity at the ecosystem level are:

  • The range of processes.
  • Complexity of interactions.
  • Number of trophic levels.

Thus, measurements of microbial diversity must include multiple methods, integrating measures at the total community level and partial approaches that target subsets of the community having specific structural or functional attributes. For example, you might be trying to assess all decomposers, or all leaf-eaters, all root diseases, etc.; each of which will give you just a partial view of the community in the habitat.

Simply attempting to count the number of micro-organisms in soil raises difficulties. Because they are microscopic counting and identifying them with conventional techniques requires them to be cultivated. Yet not all can be cultivated; some have growth requirements that are so fastidious they may be difficult or impossible to provide and it seems that in many other cases the growth requirements are simply unknown. The filamentous nature of most fungi creates the additional difficulty of recognising an individual fungus, and disentangling an extensive mycelial network from the substratum it is exploring and penetrating. Techniques based on chemical analysis to quantify some characteristic component of the fungal cell have been successfully used to quantify fungal biomass in soils, composts (in mushroom farming) and timber. Measurement of chitin (as amino sugar) can be used where confusion with arthropod exoskeletons can be excluded; but measurement of ergosterol, which is a characteristic component of fungal membranes, is more generally applicable. More recently, novel methods based on RNA and DNA probes and PCR have been developed to identify particular organisms and to reveal an immense diversity of microbes in natural habitats (Anderson & Parkin, 2007; Prosser, 2002; Torsvik & Øvreås, 2002; Wellington et al., 2003). Frequently, less than 1% of the micro-organisms detected this way can be cultivated and characterised as live cultures (Fig. 1).

Fluorescence micrograph of soil micro-organisms
Fig. 1. This picture (from Torsvik & Øvreås, 2002) shows an epifluorescence micrograph of soil micro-organisms stained with DAPI, which detects intact DNA. This sample had a visible count of 4 ×1010 cells gram-1 soil (dry weight); but the viable count was 4 × 106 colony-forming units gram-1 soil (dry weight) by plating on agar media.

This contrast between the numbers of microbes (of all sorts) that can be seen to be alive and the numbers that can be cultivated is not unusual, and certainly applies to fungi (Anderson & Parkin, 2007; Mitchell & Zuccaro, 2006; Prosser, 2002). There may be several reasons for it, including fastidious growth requirements of presently unknown nature and our current inability to break the dormancy of many of the living cells that can be detected.

Updated December 16, 2016