The research on soil biodiversity and its link with ecosystems has concentrated on investigating the role of a few taxonomic groups and indicator organisms.  In many cases, the research has been hampered by the lack of suitable tools, particularly with microbial species. Many of the early techniques applied to soil microorganisms were originally developed for working with pure cultures of microorganisms. However, the complex soil environment exhibits a significant problem for studying the effects of microorganisms (Rillig, 2004).  For example, it is thought that soil contains many species which cannot be cultured by conventional means. Furthermore, given the heterogeneity of soil, information obtained from pure cultures may not be readily translated to the soil environment.

However the increasing use of new molecular tools, looking at genes in the environment and using stable isotopes (¹³C and ¹⁵N) help solving many of the problems associated with research on soil biodiversity.
Some recommendations for research on soil biodiversity can be made:

• Better understanding of the taxonomy of soil organisms – away from indicator species
• Better understanding of the function of soil organisms in the context of nutrient webs
• Application of ecological theory to soil (microbial) ecosystems
• Role of soil organisms in high input agroecosystems (Barrios, 2007)
• Use of soil biodiversity for in bio-prospecting (link to AM doc 279)
• Linking ecosystem scales: small to large
• Environmental and temporal gradients
• Sequencing of soil metagenome