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Benckiser and Schnell, 2007), and of the importance of these below-ground systems
to global nutrient cycling (Lynch et al., 2004). Hollister et al. (2010) recently
demonstrated the linkages between above- and below-ground communities, and
showed that soil microbial communities could be altered by changes in the above-
ground plant cover. Globally, research has suggested that a strong interdependence
exists between the soil biota and plants, with soil microbial communities being
important drivers of terrestrial ecosystem productivity (Cai et al., 2010).
The classical ecological approach to describe an ecosystem is firstly to characterize
community composition by identifying and enumerating the species present, and then
to assign roles in ecosystem function to species or groups. Although this is
appropriate for different above-ground ecosystems, it is not practical for microbial
ecology because of the vast numbers of microorganisms involved (Kent and Triplett,
2002). It is now accepted that the great microbial variation responsible for a number
of soil processes far exceeds previous estimates (Kelly, 2003). How this large
genotypic diversity affects functional diversity and microbial ecology is still being
established (Upchurch et al., 2008). Consequently, accurate, reliable mechanisms to
study soil microbes are required (Kirk et al., 2004; Mitchell and Zuccaro, 2006).
The ultimate goal of the soil microbial ecologist is to understand the interactions of
the microbiota with the environment so that predictions of the impact of change can
be made, leading to better management of soil functions (Hirsch et al., 2010).
Traditional methods of soil analysis that involve measuring and modelling the
distribution of chemical compounds and determining their transformation rates, have
hitherto provided the basis for understanding soil biogeochemical processes. While
this approach also demonstrates the regulatory role of microbes in these processes, it
does not indicate their complex contribution to soil function (Kelly, 2003). Of
necessity, therefore, new directions have evolved in soil microbiological research to
provide information on both taxonomic and functional diversity within the resident
microbial communities (Kennedy and Gewin, 1997; Nannipieri et al., 2003; Hollister
et al., 2010).
There is a close relationship between ecosystem function and soil health, which may
be defined as “the continued capacity of soil to function as a vital living system,
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