Interactions between the diversity of primary producers (plants) and of decomposers (microbes and mesofaunal communities), the two key functional groups that form the basis of all ecosystems have major consequences on the functioning of agricultural ecosystems. Soil microorganisms control the transformation and mineralization of natural compounds and xenobiotics. The soil microbiota, existing in extremely high density and diversity, rapidly modify the energetic performance and activity rates to changing environmental conditions. Thus, the microbial consortium possesses the ability to accommodate environmental constraints by adjusting (i) activity rates, (ii) biomass, and (iii) community structure. These parameters are particularly important to take into consideration when evaluating soil quality. The present paper gives an overview about the possibilities to use bacterial and fungal populations as an indicator for soil quality. Furthermore also the applicability of nematodes for the determination of soil health will be discussed.

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Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.