Application of glyphosate or paraquat before the emergence of maize plants (Zea mays L.) had no detectable effect on the rhizosphere or endophyte bacterial community structure under the tested field conditions.

Herbicides are applied in agricultural practices to manage weeds. How these herbicides applied before maize emergence (Zea mays L.) might affect the rhizosphere and endophytic bacterial community is still largely unknown. In this study, plots were treated with 400 g paraquat ha-1 (Gramoxone®, paraquat ion 20% w/w), 1,089 g glyphosate ha-1 (Faena®, potassium salt of glyphosate 446 g/L) or weeds were hand removed before maize emerged and the bacterial community was determined in the bulk soil at the start of the experiment, in the bulk soil, rhizosphere, roots and stem at flowering (after 101 days), in the rhizosphere, roots, stem and grains at flowering (after 166 days) and in harvested grains dried for 24 days. Application of paraquat or glyphosate had no significant effect on the bacterial community structures and its putative metabolic functions compared to those in the manual weed-removed control plots. Haliangium_463188 was enriched in soil when glyphosate was applied and Flavobacterium in plots treated with paraquat. The bacterial community and its metabolic functions was different between the bulk soil, rhizosphere, root and stem, while it was similar in the stem and grains. Two phylotypes, i.e., an unidentified Alphaproteobacteria and uncultured member of the Marinilabiliaceae (JC017), dominated in the stem and grains of the maize plants (relative abundance > 95%). Many putative biosynthesis pathways were strongly enriched in the maize stem compared to the roots. It was found that application of glyphosate or paraquat before maize emergence had no significant effect on the soil, rhizosphere, root, stem or grain bacterial community structure. However, there was a clear change in the bacterial community from the rhizosphere to the roots, stem and grains of the maize plants and an unidentified Alphaproteobacteria and uncultured member of the Marinilabiliaceae, i.e., JC017, became highly dominant.