Information about microbial functionality in agricultural soils is still scarce, and in this study we used a shotgun metagenomic approach to compare different soil [conventional tillage (CT) with plowing and disking, and no-tillage (NT) with direct sowing into the residues of previous crops], and crop [crop succession (CS, soybean-summer/wheat-winter) or rotation (CR, soybean/maize-summer)/wheat/ lupine/oat-winter)] managements in a 13-year-old field experiment in southern Brazil. Differences were detected between NT and CT in some functional subsystems, e.g., NT had more sequences associated with the metabolism of aromatic compounds, which might be related to higher capacity to degrade pesticides, more sequences of the adenylate cyclase (cAMP) pathway, which might confer stability to the microbial community, among others. On the other hand, CT showed more sequences related to carbohydrate metabolism, what could be related with a lower content of organic matter and need to metabolize a broader range of carbon sources. Also, we detected differences related to crop management, e.g., crop rotation showed more sequences in the metabolism of amino acids and derivatives and carbohydrate subsystems, what might result from higher diversity of crop-residues added to the soil. However, it was notable that the differences in the diversity of taxa previously shown in the same experiment was far greater than the functional diversity reported now, emphasizing a high level of microbial functional redundancy. ã 2014 Elsevier B.V. All rights reserved.