Modifying the rhizosphere microbiome through targeted plant breeding is key to harnessing positive plant-microbial interrelationships in cropping agroecosystems. Here, we examine the composition of ...rhizosphere bacterial communities of diverse
genotypes to identify: (1) taxa that preferentially associate with genotypes, (2) core bacterial microbiota associated with
, (3) heritable alpha diversity measures at flowering and whole growing season, and (4) correlation between microbial and plant genetic distance among canola genotypes at different growth stages. Our aim is to identify and describe signature microbiota with potential positive benefits that could be integrated in
breeding and management strategies. Rhizosphere soils of 16 diverse genotypes sampled weekly over a 10-week period at single location as well as at three time points at two additional locations were analyzed using 16S rRNA gene amplicon sequencing. The
rhizosphere microbiome was characterized by diverse bacterial communities with 32 named bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, and Acidobacteria. Overall microbial and plant genetic distances were highly correlated (
= 0.65). Alpha diversity heritability estimates were between 0.16 and 0.41 when evaluated across growth stage and between 0.24 and 0.59 at flowering. Compared with a reference
genotype, a total of 81 genera were significantly more abundant and 71 were significantly less abundant in at least one
genotype out of the total 558 bacterial genera. Most differentially abundant genera were Proteobacteria and Actinobacteria followed by Bacteroidetes and Firmicutes. Here, we also show that
genotypes select an overall core bacterial microbiome with growth-stage-related patterns as to how taxa joined the core membership. In addition, we report that sets of
core taxa were consistent across our three sites and 2 years. Both differential abundance and core analysis implicate numerous bacteria that have been reported to have beneficial effects on plant growth including disease suppression, antifungal properties, and plant growth promotion. Using a multi-site year, temporally intensive field sampling approach, we showed that small plant genetic differences cause predictable changes in canola microbiome and are potential target for direct and indirect selection within breeding programs.
Background
The plant root-rhizosphere microbial community interactions play important roles in crop production as those interactions can be beneficial, detrimental, or neutral for the plant. In
...Brassica napus
, our current understanding of root growth dynamics and dominance of bacterial taxa and their dynamics across growth stages is insufficient. In addition, the association of root traits with dominant and potential growth promoting bacteria across growth stages under field conditions has not been well studied.
Methods
:
Here, we use temporally intensive weekly sampling of
B. napus
over a ten-week period to characterize root growth dynamics, dominant rhizosphere bacterial taxa, and association between the two. We characterized the rhizosphere bacteria using high throughput sequencing of the 16S rRNA genes.
Results
:
B. napus
root length showed distinct growth stage patterns with an increase in root length at early stages followed by s and/or gradual increase at flowering followed by reduction at maturity. Fine root length at the two-three leaf stage and seed yield were significantly positively correlated. The dominant microbial community composition was positively correlated with root traits and environmental variables, with the strongest correlation at the vegetative stage. Positive and significant correlations between individual bacterial genera and root traits were observed during vegetative stage, suggesting possible causal linkage between the two.
Conclusions
The observed significant positive correlations between the bacterial genera and root traits and between root length and seed yield under field conditions suggest the potential for designing root development and beneficial microbial interaction-based canola breeding and management strategies.
The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used ...effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.
The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used ...effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of bacterial and fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. We sequenced the bacterial 16S ribosomal RNA gene generating a total of 127.7 million reads and the fungal internal transcribed spacer (ITS) region generating 113.4 million reads. 14,944 unique fungal amplicon sequence variants (ASV) were detected, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. We detected 10,882 unique bacterial ASVs with an average of 249 ASVs per sample. Temporal, site-to-site, and line-driven variability were key determinants of microbial community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.
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