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Little is known about the composition and diversity of the bacterial community associated with plant roots. The purpose of this study was to investigate the diversity of bacteria associated with the roots of canola plants grown at three field locations in Saskatchewan, Canada. Over 300 rhizoplane and 220 endophytic bacteria were randomly selected from agar‐solidified trypticase soy broth, and identified using fatty acid methyl ester (FAME) profiles. Based on FAME profiles, 18 bacterial genera were identified with a similarity index >0.3, but 73% of the identified isolates belonged to four genera: Bacillus (29%), Flavobacterium (12%), Micrococcus (20%) and Rathayibacter (12%). The endophytic community had a lower Shannon‐Weaver diversity index (1.35) compared to the rhizoplane (2.15), and a higher proportion of Bacillus, Flavobacterium, Micrococcus and Rathayibacter genera compared to rhizoplane populations. Genera identified in the endophytic isolates were also found in the rhizoplane isolates. Furthermore, principal component analysis indicated three clusters of bacteria regardless of their site of origin, i.e., rhizoplane or endophytic. In addition, the rhizoplane communities of canola and wheat grown at the same site differed significantly. These results indicate that diverse groups of bacteria are associated with field‐grown plants and that endophytes are a subset of the rhizoplane community.

Plant characteristics are known to alter endophytic and rhizosphere microbial communities; however, the effect of crop breeding programs on the microbial endophytic and rhizosphere communities is not clear. The purpose of this study was to determine if root-associated microbial communities differed between three cultivars of canola (Brassica spp.) and wheat (Triticum spp.). BiologTM analysis was used to characterize the microbial communities associated with the root interior and rhizosphere soil of field grown canola (Parkland, Excel, and Quest cultivars) as well as wheat (PI 167549, Red Fife, and CDC Teal cultivars). Fatty acid methyl ester (FAME) profiles of roots and rhizosphere soil of the cultivars were also compared. These crop cultivars represent a continuum from older to the most recent crop cultivars, with Quest being a transgenic canola variety tolerant of the herbicide glyphosate. To the best of our knowledge, Quest is not directly related to Parkland or Excel. The endophytic community of Quest used the BiologTM polymer, carbohydrate, amino acid, and miscellaneous functional guilds at a slower rate than the endophytic community of Excel or Parkland. Furthermore, there were lower levels of the microbial FAMEs, 18:0, 18:3 w6c (6,9,12), 16:0 2OH, and 15:0 2OH in the roots of Quest compared with Excel or Parkland. In contrast, there were no differences in the utilization rate of BiologTM functional guilds or the microbial FAMEs in the roots of the three wheat cultivars studied. The correlation between the ability of endophytic and rhizosphere communities to utilize BiologTM substrates was lower in Quest and CDC Teal compared with earlier crop cultivars. Our results indicate that endophytic and rhizosphere microbial communities of the transgenic cultivar Quest were different from nontransgenic cultivars grown at the same field site.Key words: Brassica spp., Triticum spp., rhizosphere, endophytes, FAME, BiologTM, transgenic.