Application of organic matter temporarily shifts the carrot prokaryotic communities in the endosphere but not in the rhizosphere

The objective of this study was to evaluate the effect of organic matter application on the formation of root endophytic prokaryotic communities associated with carrot (Daucus carota subsp. sativus). Carrots were grown in a planter under five fertilizer treatments (weed compost, bark compost, cattle manure, chemical fertilizer, and no-fertilizer control) and the compositions of rhizosphere and root endosphere prokaryotic communities were determined by amplicon sequencing analysis targeting the 16S rRNA gene at 60 and 108 days after sowing.