Functional diversity and taxonomic diversity are often two vastly different measurements. Functional diversity includes the magnitude and capacity of soil inhabitants that are involved in key roles. These processes are selected to represent biologically meaningful processes, such as carbon or nitrogen cycling, decomposition of various compounds, and other transformations (Zak et al., 1994). Taxonomic diversity is determined by culturability and isolation of species, and may represent 20% or less of the microbes present and active in soil. Speciation relies on characterization of known phenotypic or genetic characterizations that may not be present in soil and possibly have no bearing on soil processes (Lee and Pankhurst, 1992).
Microbial diversity indexes have been used to describe the status of microbial communities and their response to natural or human disturbances. Microbial diversity indexes can function as bioindicators of the stability of a community and can be used to describe the ecological dynamics of a community and the impact of stress on that community (Mills and Wassel, 1980; Atlas, 1984). Chemically stressed or heavy metal-stressed soils were found to decrease in microbial diversity depending on the type of chemical applied (Atlas, 1984; Reber, 1992). A factor limiting the greater use of these indexes is the absence of detailed information on the microbial species composition of soil environments (Torsvik et al., 1990).
The ability of an ecosystem to buffer the effects of extreme disturbances may depend in part on the diversity of the system (Elliott and Lynch, 1994). It may be important to monitor diversity as an indicator of change or in response to a stress. The extinction rate of species within a system may be an important indicator of the status of the system and critical in determining the level of diversity necessary to maintain an agroecosystem. The actual numbers of species and species composition may not be as important as the flux of species within a system and the functioning of those individuals within that system.
Diversity indexes can be used to indicate the effect of disturbance; however, greater diversity may not always be desirable. Greater diversity should not be equated with a more stable system; rather, the changes in diversity with management may be more informative of the status of a soil microbial community. Diversity issues in understanding quality of soil may not be enlightening unless the functions of the system are taken into account. Basic shifts in large groups in an ecosystem may indicate a change, but may not be able to address functioning of that altered system. Microbial communities and their processes need to be examined, not only in relation to the individuals that make up the community, but also with regard to the effect of perturbations or environmental stresses on those communities.
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