Glyphosate affects the rhizobacterial communities in glyphosate-tolerant cotton

► Glyphosate effects on the rhizobacteria of glyphosate-tolerant cotton were analysed in two fields. ► Soil textures were clayey (field 1) or clayey-loam (field 2). ► The effect has been assessed by DNA pyrosequencing of rhizobacterial DNA. ► Structure and diversity of rhizobacteria have been analysed by two different methods. ► Rhizobacterial communities of field 1 recovered better from glyphosate than those of field 2.