Nitrifying bacteria and archaea withstanding glyphosate in fertilized soil microcosms

•Fertilized soils had higher nitrate content than control.•Fertilized soils had higher bacterial amoA and AOB: bacteria ratio than control.•AOA to AOB was generally lower in fertilized soils than in control.•DGGE profiles of amoA showed low diversity and no short-term effect of amendments.•Glyphosate+N fertilizer amendment had no effect compared to fertilizer alone.