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.
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.
Acetylene-reducing bacteria isolated from the setts (stem cuttings used as seed pieces) and roots of two sugar cane varieties propagated aseptically from stem cuttings were identified using a computer-assisted scheme based on 75 biochemical tests. Because 106 to 108 acetylene-reducing bacteria per gram (fresh weight basis) were found in the roots, while 10 to 100 times fewer were present in the sett, we suggest that the root is the site of bacterial multiplication. Sterilization of the sett surface before planting or root sterilization at harvest reduced or completely removed acetylene-reducing bacteria and associated whole plant acetylene-reducing activity. This indicates that most of the active bacteria were on the sett and root exteriors. Setts did not exhibit acetylene-reducing activity until after emergence of the roots. Since shoot emergence was not necessary for acetylene-reducing activity, the extensive carbohydrate supply of the sett itself must have provided the carbon substrate for bacterial N2 fixation. The acetylene-reducing bacteria isolated were facultative anaerobes of the families Enterobacteriaceae and Bacillaceae. Klebsiella pneumoniae, Enterobacter cloacae, Erwinia herbicola, and Bacillus polymyxa were present inside the sett and the roots but E. herbicola was the dominant bacterium on the root exterior. No Beijerinckia spp. or Azotobacter spp. were found associated with the sett or the roots.
Oil sands mining in northern Alberta impacts a large footprint, but the industry is committed to reclaim all disturbed land to an ecologically healthy state in response to environmental regulations. However, these newly reconstructed landscapes may be limited by several factors that include low soil nutrient levels and reduced microbial activity. Rhizosphere microorganisms colonize plant roots providing hosts with nutrients, stimulating growth, suppressing disease and increasing tolerance to abiotic stress. High-throughput sequencing techniques can be used to provide a detailed characterization of microbial community structure. This study used 16S rRNA amplicon sequencing to characterize the bacterial root microbiome associated with annual barley (Hordeum vulgare) and sweet clover (Melilotus albus) growing in an oil sands reclamation area. Our results indicate that Proteobacteria dominated the endosphere, whereas other phyla such as Acidobacteria and Gemmatimonadetes were restricted to the rhizosphere, suggesting that plants have the ability to select for certain soil bacterial consortia. The bacterial community in the endosphere compartments were less rich and diverse compared to the rhizosphere. Furthermore, it was apparent that sweet clover plants were more selective, as the community exhibited a lower richness and diversity compared to barley. Members of the family Rhizobiaceae, such as Sinorhizobium and Rhizobium were mainly associated with clover, whereas Acholeplasma (wall-less bacteria transmitted by insects) was unique to barley. Genera from the Enterobacteriaceae family, such as Yersinia and Lentzea were also mostly detected in barley, while other genera such Pseudomonas and Pantoea were able to successfully colonize both plants. Endophytic bacterial profiles varied within the same plant species at different sampling locations; however, these differences were driven by factors other than slope positions or cover management. Our results suggest that bacterial endophytic communities of plants growing in land reclamation systems are a subset of the rhizosphere community and selection is driven by plant factors.
Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.
The association of winter wheat (Triticum aestivum L. cv. Norstar) with root-colonizing bacteria (rhizobacteria) was studied in potted soil experiments in the growth chamber. Thirty-six known bacteria, some of which have been reported to stimulate plant growth, and 75 isolates obtained from the rhizosphere of winter wheat were tested for their effects on plant growth and development in two different soils. Two known bacteria and 12 isolates stimulated growth of winter wheat. Of these, the most effective were nine isolates that significantly (P < 0.01) increased plant height, root and shoot biomass, and number of tillers. The plant growth promoting effects of isolates were different in the two soils. Three of these strains were tentatively classified as Pseudomonas aeruginosa, and two each as Pseudomonas cepacia, Pseudomonas fluorescens, and Pseudomonas putida. Some isolates induced significant increases in seedling emergence rates and (or) demonstrated antagonism in vitro against Rhizoctonia solani and Leptosphaeria maculans. These results demonstrate the potential use of plant growth promoting rhizobacteria as inoculants for winter wheat. Key words: pseudomonads, plant growth promoting rhizobacteria, winter wheat, rhizosphere, bacterial inoculants.
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