Understanding canola root morphology and microbiomes in response to soil phosphorus fertility
Term: 5 years, ending April 2024
Status: Complete
Researcher(s): Bobbi Helgason, U of S; Leon Kochian, GIFS; David Schneider, SENS; Isobel Parkin, AAFC
SaskCanola Investment: $244,950
Total Project Cost: $439,950
Funding Partners: Global Institute for Food Security
Grower Benefits
We did not find that high rates of phosphorus (P) fertilizer (applied with either 1” or 4” openers) affected crop yield and had only a minimal impact on the overall canola microbiome community structure. In our study, the intermediate-rate P supplied in a narrow opener (35 lb ac in 1” opener) was the most cost-effective fertilization method which generated equivalent canola yield to the high P rate. Our rhizobox studies showed that early canola growth was higher in plants where half of the root system was exposed to fertilized soil and the other half to unfertilized soil. Each half of the root system had a distinct root microbiome indicating that the root-microbiome system may confer the best advantage in soil where P availability is heterogenous as would be found in most field soils.
Project Summary
Canola recruits microbial partners from the soil to its rhizosphere and roots. These microorganisms, known as the root-associated microbiome, enhance plant nutrient uptake, health and can contribute to improved yield. The root-associated microbiome is especially important for soil P cycling and plant P uptake because despite the relatively high total P in our soils, only a small fraction is plant available. The root-associated microbiome transforms organic and sorbed P to soluble, plant available P. In the field and in controlled conditions we identified P-responsive bacteria and fungi under different forms, rates and placements of P application. The root Chitinophaga and Variovorax bacteria as well as Agrocybe fungi were consistently detected in relatively low P soils. When P fertilizer was added, Mucilaginibacter, Burkholderia, and Massilia bacteria in the root, as well as fungi Amaurodon, Penicillium, and Motierella showed higher relative abundance.
We used a variety of approaches to interrogate the canola root microbiome composition and canola growth response to P fertilizer. Overall, the plant growth response in soils was inconsistent in the field reflecting the complex factors contributing to soil P availability and canola uptake. Although broad shifts in bacterial and community structure in response to P fertilizer were not observed, the root microbiome contained P-responsive bacteria and fungi under both low and high P. In controlled condition rhizoboxes, we saw distinctive root-associated microbial communities in soils of high vs. no P, soluble vs. insoluble P, and P-exposed vs. non-exposed regions.
We conducted two field studies: one at the AAFC Scott Research Farm and other at the Conservation Learning Centre as well as three experiments in rhizoboxes in plant growth rooms. Background levels of soil available P were considered minimally sufficient which may have contributed to inconsistent response to P fertilizer in the field and under controlled conditions (where Scott farm soil was also used). Root growth was assessed in rhizoboxes using WinRhizo Tron software and bacterial and fungal communities in the soil and roots were profiled using DNA amplicon sequencing.
This work showed that year-to-year differences in growing conditions at Scott had a strong impact on the P-responsiveness of canola and its microbiome to P fertilizer rate and placement where canola only responded to P fertilizer in the first of two years; microbiome responses to P management were likewise greater in year 1. Due to Covid restriction in year 2, fields site access was restricted to sampling days only. Variability in germination was high in year 2, with significantly lower total soil N compared to year 1 however the cause is unknown. Higher than expected background levels of soil available P in the soil at the Scott research farm (25 mg kg Olson P in spring 2019) likely muted canola response to P application in the field and rhizoboxes.
Canola recruited beneficial bacteria and fungi in its rhizosphere and roots under low and high P conditions. Higher levels of P application led to lower root-pathogen abundance, which was correlated with yield, affirming the importance of proper P nutrition to reduce disease susceptibility. In a comparison of larger vs. smaller rooted Brassica napus lines, the larger-rooted line also produced greater aboveground biomass in early growth stages and its root-associated microbiome structure remained more robust in response to soil P form, where great shifts of the microbial communities were observed in the smaller-rooted one. Primary and secondary canola roots had distinct bacterial and fungal community profiles, likely reflecting different function of the microbiome in the rhizosphere in these regions. The whole-root microbiome profiles were overall similar, but these results indicate that root morphology should be considered when designing experiments for microbiome profiling.
In a two-year field study, of the top 10 most abundant bacteria, two bacteria with plant growth promotion (PGP) capacity were more abundant under low P (Pedobacter and Rhizobium spp.) and one under high P (Mucilaginibacter sp.). We also found that six bacteria and four fungi that are known to have PGP capacity were less abundant overall in the community but increased in relative abundance in high vs. low P soils. The abundance of fungal pathogens that cause Blackleg and Sclerotinia were correlated with 0 P application which appeared to make plants more susceptible to these pathogens, although disease symptoms were not assessed. Positive correlation was observed between canola yield and specific P-responsive root endophytes, including Burkholderia and Chaetothyriaceae. In rhizoboxes, canola growth was highest and root microbiomes differed when half of the roots were supplied with sufficient P and the other half grew in soil where no P was added, showing the important influence of localized soil P availability on microbiome assembly and plant growth. Further development of microbial-based biofertilizers may need to be tailored to inherent soil P fertility and P fertilizer management systems to optimize root-microbiome interactions for P cycling in the root zone.