Community structures and substrate utilization of bacteria in soils from organic and conventional farming systems of the DOK long-term field experiment

Preservation or improvement of soil quality and productivity is of major importance for sustainable agriculture. Microorganisms strongly influence these soil characteristics as they are involved in nutrient cycling, transformation processes and soil aggregate formation, as well as in plant pathology or plant growth promotion. A profound understanding of structure, dynamics and functions of soil microbial populations represents one key to the understanding and description of soil quality. Therefore, we analyzed long-term effects of three farmyard manure (FYM)-based farming systems, i.e. bio-dynamic (BIODYN), bio-organic (BIOORG) and conventional (CONFYM), on microbiological soil characteristics and compared them to long-term effects of minerally fertilized (CONMIN) and unfertilized (NOFERT) control systems. Furthermore, we compared these long-term effects of farming systems to short-term effects of the crops winter wheat and grass-clover ley. The DOK field experiment in Therwil, Switzerland, which was established in 1978, represents in a unique long-term comparison, allowing to approach these questions. Effects on microbiological soil characteristics were assessed with a polyphasic approach by analyzing soil microbial biomass, soil DNA content, colony forming unit (CFU) counts, community level substrate utilization (CLSU) patterns with Biolog™ EcoPlates, and terminal restriction fragment length polymorphism (T-RFLP) profiles of bacterial 16S rRNA genes. The soil biomass parameters, i.e. microbial biomass, DNA content and CFU, were all strongly influenced by the farming systems, whereas only CFUs were significantly affected by the two crops analyzed. Differences among the FYM-based farming systems BIODYN, BIOORG and CONFYM were only significant for microbial biomass and DNA content. CLSU and T-RFLP profiling, on the other hand, allowed for consistent differentiation of soil bacterial community structure in relation to the influence of farming systems and crops. The analyses revealed that the main and highly significant effect on microbiological soil characteristics was related to FYM applications. Less strong but significant effects were caused by the two crops, i.e. winter wheat and grass-clover. Effects of the farming systems BIODYN, BIOORG and CONFYM on soil bacterial community structure were relatively weak and not significant. These results suggest that for successful soil quality management fertilization regime and crop rotation are of major importance and that polyphasic approaches are needed to describe and assess microbiological soil characteristics.