Bacterial Microbiomes Associated with the Rhizosphere, Root Interior, and Aboveground Plant Organs of Wheat and Canola at Different Growth Stages

Abstract

Beneficial bacteria associated with agricultural crops may potentially increase crop productivity and health. However, during various plant developmental processes, shifts in the diversity and function of bacterial communities often occur. This study investigated the diversity of bacterial communities associated with the rhizosphere, roots, and aboveground plant organs of wheat and canola at stem elongation, flowering, and ripening stages. The growth-chamber experiment consisted of wheat and canola grown in Orthic Brown Chernozem Calcic Kastanozem and Orthic Black Calcic Chernozem soils from agricultural fields in Saskatchewan, Canada. Rhizosphere bacterial communities of wheat and canola were mainly influenced by soil characteristics, whereas a specific root endophytic community was associated with each crop species. These results suggest that each crop may select distinct root bacterial endophytes from the rhizosphere. Bacteria associated with aboveground plant organs exhibited high variability among crop species and soils. The most abundant bacterial genera associated with the rhizosphere of the crops included Gemmatimonas, Solirubrobacter, and Nocardioides, as well as unclassified genera of families Commamonadaceae, Chitinophagaceae, and Sphingomonadaceae. Other genera (e.g., Stenotrophomonas, Streptomyces, and Variovorax) were predominant in wheat roots, whereas species of Lentzea and Pantoea were the most abundant root endophytes detected in canola. Bacterial communities associated with aboveground organs consisted mostly of species of Corynebacterium and Pseudomonas, and unclassified members of the family Enterobacteriacaeae. This study also revealed that plant growth stages can modulate the diversity of rhizosphere and endophytic bacteria. The influence of plant growth stages on the bacterial microbiome associated with wheat and canola was crop and organ specific.