Canola Root–Associated Microbiomes in the Canadian Prairies

Abstract

Canola is one of the most economically important crops in Canada, and the root and rhizosphere microbiomes of a canola plant likely impact its growth and nutrient uptake. The aim of this study was to determine whether canola has a core root microbiome (i.e., set of microbes that are consistently selected in the root environment), and whether this is distinct from the core microbiomes of other crops that are commonly grown in the Canadian Prairies, pea, and wheat. We also assessed whether selected agronomic treatments can modify the canola microbiome, and whether this was associated to enhanced yield. We used a field experiment with a randomized complete block design, which was repeated at three locations across the canola-growing zone of Canada. Roots and rhizosphere soil were harvested at the flowering stage of canola. We separately isolated total extractable DNA from plant roots and from adjacent rhizosphere soil, and constructed MiSeq amplicon libraries for each of 60 samples, targeting bacterial, and archaeal 16S rRNA genes and the fungal ITS region. We determined that the microbiome of the roots and rhizosphere of canola was consistently different from those of wheat and pea. These microbiomes comprise several putative plant-growth-promoting rhizobacteria, including Amycolatopsis sp., Serratia proteamaculans, Pedobacter sp., Arthrobacter sp., Stenotrophomonas sp., Fusarium merismoides, and Fusicolla sp., which correlated positively with canola yield. Crop species had a significant influence on bacterial and fungal assemblages, especially within the roots, while higher nutrient input or seeding density did not significantly alter the global composition of bacterial, fungal, or archaeal assemblages associated with canola roots. However, the relative abundance of Olpidium brassicae, a known pathogen of members of the Brassicaceae, was significantly reduced in the roots of canola planted at higher seeding density. Our results suggest that seeding density and plant nutrition management modified the abundance of other bacterial and fungal taxa forming the core microbiomes of canola that are expected to impact crop growth. This work helps us to understand the microbial assemblages associated with canola grown under common agronomic practices and indicates microorganisms that can potentially benefit or reduce the yield of canola.

Gut Mycobiome Dysbiosis is Linked to Hypertriglyceridemia Among Home Dwelling Elderly Danes

“…The matrices were Hellinger-transformed using the “decostand” function followed by the “rda” function of the “vegan” package in R [34]. Significance levels determined by ANOVA and the R 2 values were generated by the “RsquareAdj” function in R [35], [36]. Correlation of anthropometric/body-composition data, fecal and plasma metabolome, and gut mycobiome associations were investigated by sparse Partial Least Squares (sPLS) performed using the R package mixOmics [37].…”

Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding

“…including Stenotrophomonas rhizophila have antagonistic activity against fungal pathogens including V. dahlia in oil seed rape (Alström, 2001;Wolf et al, 2002). Arthrobacter and Stenotrophomonas are likely broadly present in the core microbiome of canola, having been identified in other surveys of the core rhizosphere microbiome of field grown canola (Lay et al, 2018) and in related Brassica rapa (Germida et al, 1998;Siciliano and Germida, 1999;Larcher et al, 2008;Croes et al, 2013;Tkacz et al, 2015). Positive correlations between Arthrobacter and Stenotrophomonas with canola yield (Lay et al, 2018) suggest an important beneficial influence of these bacteria on canola.…”

“…Strains of Klebsiella isolated from wheat rhizosphere produce indole acetic acid (IAA) with demonstrated promotion of root growth (Sachdev et al, 2009). Serratia is a plant growth-promoting bacteria and is positively correlated with canola yield (Lay et al, 2018) and promotes growth in rapeseed (Alström, 2001;Neupane et al, 2013). Finally, Pseudomonas, a well-studied plant growth-promoting bacterium enhances root elongation of canola and is characterized by its ability to produce phytohormones, IAA, and cytokinin (Pallai et al, 2012).…”

“…For example, a study on 27 maize inbred lines indicated the presence of a small but significant proportion of heritable variation in total bacterial diversity across field environments and substantially more heritable variation between replicates of lines within each field . A study of Brassica napus root-associated microbiomes in the Canadian Prairies identified bacterial taxa which were positively correlated with canola yield (Lay et al, 2018). Identifying genetically controlled positive plant-microbial interactions by comparing lines within breeding programs and across diversity panels is the first step in determining if plant breeders could develop varieties by selecting for genetic factors controlling beneficial plant-microbial interrelationships.…”

“…The rhizosphere microbiome has commonly been targeted to identify positive plant-microbial relationships. Past microbiome studies using culture dependent and independent approaches have shed light on the structure and composition of the plant microbiota in many crops (Garland, 1996;Germida et al, 1998;Bulgarelli et al, 2012;Lundberg et al, 2012;Schlaeppi et al, 2013;Edwards et al, 2015;Lay et al, 2018). Continuing advances in biotechnology and bioinformatics are enabling researchers to evaluate the microbiome to a greater depth, incorporating more replications and to account for variables such as genotype, time, and space.…”