The considerable intensification of agricultural practices during last decades caused diverse problems for soils. A better understanding of how agricultural management strategies affect soil microbial communities, that are key player of many soil processes, is needed in order to promote sustainable farming strategies. Prokaryotic communities were studied based on 16S rRNA gene amplicon sequencing in soil samples obtained from the long-term field trial in Bernburg (Germany) at two contrasting seasonal time points. The long-term field trial allows to compare between different tillage managements (plough vs. cultivator) and fertilization intensities (intensive vs. extensive).