Abstract
Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N2-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation compared to roots inoculated with WT strain. The noeI mutant-inoculated roots exhibited strong changes in microbiome assembly in the rhizosphere and rhizoplane, including reduced diversity, changed co-occurrence interactions and a substantial depletion of root microbes. Root exudates and soil physiochemical properties were significantly correlated with microbial community shift in the rhizosphere between different rhizobial treatments. These results illustrate that rhizobial symbiotic capacity dramatically alters root-associated microbiomes, in which root exudation and edaphic patterns play a vital role. This study has important implications for understanding the evolution of plant-microbiome interactions.
Highlights
The interactions between plants and microbial communities impact host health, fitness and biogeochemical cycling (PankeBuisse et al, 2015)
As plants were well-fertilized, plant height, leaf chlorophyll content and shoot and root dry weights did not differ among treatments (Figures 1F–I), allowing us to assess the impact of noeI gene-dependent symbiosis on microbial communities independently of plant performance
The nodulation tests in the present study show that the mutation of noeI in rhizobia significantly reduced nodule nitrogenase activity, as reported previously (Liu et al, 2018), and reduced nodulation efficiency of B. diazoefficiens with soybean as the soybean plants inoculated with mutant B. diazoefficiens had fewer but bigger nodules compared to plants inoculated with wild type (WT) strain (Figure 1)
Summary
The interactions between plants and microbial communities (including archaea, bacteria, fungi, oomycetes, and protists) impact host health, fitness and biogeochemical cycling (PankeBuisse et al, 2015). The highly dynamic microbial communities that colonize the root-soil interface, so-called rhizosphere, are important in this context (Lundberg et al, 2012). Apart from plant chemistry, several other factors like soil type, host genotype, developmental stage, nutrient status and rhizosphere-compartmentalization are important determinants of root-associated microbiome assemblages (Cordovez et al, 2019; Brown et al, 2020). The impact of plant genetic variation on root-associated microbiomes is becoming more and more studied (Hu et al, 2018), while much less is known about the importance of microbial genetic variation. High-throughput sequencing studies often investigate the taxonomic or functional compositions of root-associated microbiomes, but do not approach the functional consequences of microbial genetic variation on the host plant (Bai et al, 2015). Genetic manipulation of individual strains can help to assess the importance of selected heritable traits in determining the composition and function of microbiomes in the context of root-microbiome interactions
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