Because of the fundamental role in mediating soil processes and the responsiveness to soil managements, microbial abundance, diversity, and activity are among the most important soil quality parameters (Andrews and Carroll 2001; Karlen et al. 2001, 2003; Andrews et al. 2003; Anderson and Domsch 2010). In fact, the effect of agricultural management on microbial community is directly related to changes in soil quality (Schloter et al. 2003), that encompass the size and diversity of specific functional microbial groups (Helgason et al. 1998; Chang et al. 2001).
A great number of methods have been developed to determine the presence and activities of microbial communities in soil. Some of them are internationally standardized (Winding et al. 2005), such as measures of population size for either a single organism type, a functional group, or a whole community. The effect of agricultural managements on soil microorganisms can be measured with changes in both community size (cell number) or microbial biomass, and biological activity, such as soil respiration. However, although addition to soil of good quality compost may increase global microbial biomass and enhance enzyme activity (Albiach et al. 2000; Perucci et al. 2000; Debosz et al. 2002), the specific responses of various bacterial groups to changing environment in agricultural soils are poorly known (Buckley and Schmidt 2001; Kiikkila et al. 2001; Chander and Joergensen 2002). Moreover, several studies showed that, in order to assess fertilizers' effects, microbial enumeration methods by plate counts (Sarathchandra et al. 1993) and nematode counts (Parfitt et al. 2005) are possibly more sensitive than measurements of microbial biomass.
Fungal and microbial biomass is thought to be a sensitive indicator of soil quality and an early predictor of changes in SOM dynamics. In fact, the rate of microbial fraction turnover is relatively fast (2-6 years) as compared to more than 20 years of SOM turnover (Jenkinson 1990). Thus, fungal and microbial biomass are SOM living components (Jenkinson and Ladd 1981) representing an active soil carbon that is more sensitive to soil management than total organic carbon (Frey et al. 1999; Bayley et al. 2002; Weil and Magdoff 2004; Six et al. 2006). However, microbial biomass C generally reflects the amount of total organic matter content. Both SOM and microbial biomass decline under agricultural or land disturbance, indicating exploitation of organic resources and impact of differing tillage systems, fertilizers, and crop rotations (Luizao et al. 1992; Sparling 1997; Frey et al. 1999; Vineela et al. 2008). Soil respiration is the best indicator of the whole metabolic activity of soil microorganisms, since it allows comparison of different soils and soil management effects (Machulla 2003; Solaiman 2007). Soil respiration, as referred to SOM content to give a coefficient of organic matter mineralization (CEM), may express the potential capacity of soil to accumulate or mineralize carbon (Diaz-Ravinaa et al. 1988).
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