Bacterial tag-encoded FLX amplicon pyrosequencing of the 16S rDNA gene was used to evaluate bacterial diversity of a clay loam soil (fine, mixed, thermic Torrertic Paleustolls) after 10 years under an integrated livestock (beef)-cotton ( Gossypium hirsutum L.) production system compared to continuous cotton in a semiarid region. In the integrated system, cattle alternatively grazed a perennial warm-season grass [ Bothriochloa bladhii (Retz) S.T. Blake] paddock and small grains grown in two paddocks of a wheat ( Triticum aestivum L.)-fallow-rye ( Secale cereal L.)-cotton rotation. Areas excluded from grazing in the integrated system were also evaluated. Maximum observed number of unique sequences operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the species level) corresponded to 1200 and 1100 at 0-5 and 5-15 cm depths, respectively. Predominant phyla (up to 65% of abundance) at 0-5 and 5-15 cm in this soil were Proteobacteria, Actinobacteria and Gemmatimonadetes. Proteobacteria were predominant in soil under all components of the integrated livestock-cotton system compared to continuous cotton whereas Bacteroidetes were predominant under continuous cotton. Firmicutes (i.e., Clostridia) and Chlorofexi (i.e., Thermomicrobia) were more abundant in soil under fallow periods of the rotation compared to under cotton (Rye- Cotton-Wheat-Fallow or continuous cotton) or grass (i.e., pasture). The lowest OTUs were detected in soil under fallow periods of the rotation (Wheat- Fallow-Rye-Cotton) compared to the other treatments. Grazing effects were significant for Actinobacteria, Proteobacteria and Chlorofexi. Compared to the continuous cotton system, this study revealed significant changes in bacterial phyla distribution under integrated livestock-cotton systems for a semiarid soil after 10 years. Positive correlations were found between certain bacteria ( Proteobacteria, Firmicutes, Chloroflexi, Verrucomicrobiae and Fibrobacteres) and the activities of alkaline phosphatase and beta-glucosidase or beta-glucosaminidase.
