Abstract
Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.
Highlights
The rhizosphere is a dynamic region of soil immediately surrounding plant roots that emerges through the interaction between plant roots, soil, and microorganisms (Hinsinger et al, 2009; Philippot et al, 2013)
Removal of sequencing reads assigned to non-bacterial operational taxonomic units (OTUs), the remaining 14,662 OTUs were identified at 97% similarity
Alpha diversity of the rhizosphere microbiome of the different wheat genotypes varied across different growth chamber cycling lengths (Supplementary Figure 1; Supplementary Table 1)
Summary
The rhizosphere is a dynamic region of soil immediately surrounding plant roots that emerges through the interaction between plant roots, soil, and microorganisms (Hinsinger et al, 2009; Philippot et al, 2013). Rhizosphere-associated microbes have been documented to be involved in plant health (Berendsen et al, 2012; Pollak and Cordero, 2020). Root-derived carbon makes the rhizosphere a hot spot for numerous microbial activities and interactions, affecting nutrient cycling, plant growth, and tolerance to abiotic and biotic stress (Philippot et al, 2013). Root traits and architecture have been associated with differences in microbiome composition (Pérez-Jaramillo et al, 2017; Saleem et al, 2018)
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