The aim of doctoral thesis was to examine the effects of organic matter inputs and different tillage intensities on the content and distribution of soil organic carbon (Corg) and nutrients, and on the size and composition of microbial communities, in particular in terms of the microbially mediated processes (eg. N cycle). In the long-term experiment (>20 years) in Moškanjci with different tillage intensities, the Corg content in the top 10 cm of the soil increased significantly over the five years after the transition from conventional to organic farming, but only under minimum tillage (MT), which also had higher inputs of organic matter in the form of weed and crop root biomass, than under conventional tillage (CT). The higher Corg stocks as well as Corg and nutrient content in the upper 10 cm of MT was also reflected in higher microbial biomass, abundance of soil microbial communities (bacteria, archaea, fungi and N cycle functional genes) and altered diversity and composition of bacteria and fungi (Illumina sequencing). The latter responded to tillage differently in rhizosphere soils and crop roots. We also studied the short-term effects of the transition from MT to direct sowing or no tillage (NT). Changes in microbial biomass and the abundance of bacteria, archaea and fungi were already evident after two years, but limited to the top cm of the soil. The rapid response of the microbial communities to the addition of labile organic matter, and less to the different straw management (incorporation to the top 10 cm vs. left on surface vs. no added), was also shown in the pot experiment. Straw incorporation, where the contact of the straw with the soil was closer, significantly increased fungal abundance in the top 10 cm of soil, which was also reflected in higher microbial respiration (CO2 efflux) in the initial phase of straw decomposition. The slurry increased availability of labile C and N forms, thereby indirectly affecting the higher abundance of bacteria and fungi in the top 10 cm of soil, and significantly higher microbial respiration compared to no-slurry treatments. The combination of straw incorporation and slurry addition had a positive effect on the abundance of the nosZII gene in the top 10 cm of soil. In conclusion, different agricultural practices (tillage, organic fertilisation, crop residue management) have a specific impact on soil microenvironmental conditions, which is reflected in the altered microbial size (biomass, abundance) and composition.
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