||Agricultural practices and changes in soil conditions, such as water content, inorganic N content, temperature, pH and organic material availability, affect the bacterial community structure. Soil characteristics and the bacterial community structure were monitored in soil with maize (Zea mays L.) and wheat (Triticum aestivum L.) rotation, zero tillage and crop residue kept (ZTRK) or removed (ZTRR), and conventional tillage with monoculture maize (CTMR) or maize-wheat rotation and crop residue removed (CTRR) or kept in the field and ploughed in (CTRK). The soil organic C was significantly affected by tillage practices and decreased ZTRK > CTRK > CTRR = ZTRR > CTMR, while water content and NO3− concentration showed large fluctuations over the crop cycle, but were not affected significantly by agricultural practices. The bacterial community structure showed large changes over the crop cycle determined by varying soil characteristics, most importantly water content and NO3− concentration and six bacterial genera, i.e. Achromobacter, Bacillus, Halomonas, Kaistobacter, Pseudomonas and Serratia, while changes due to agricultural practices were much smaller. It was found that the bacterial community structure was affected significantly by time, tillage (zero tillage versus conventional tillage), crop residue management (kept versus removed) and crop rotation (CTMR versus CTRR treatment).