Assesing the Impact on Soybean Root Gene Expression of Inoculation with Hub microbes

ABSTRACT: Drought is an increasing threat to soybean (Glycine max) production worldwide. In addition to methods such as breeding and genetic modification, inoculation of plants or soils with single microbes and microbial consortia are being explored to mitigate the impacts of drought stress on crop plants. One criterion for selecting microbes within a consortium is to select hub taxa, which are those whose abundances appear to be highly correlated with abundances of other taxa in the microbiome. To assess the impact of microbial inoculations with hub taxa on soybean, I identified five hub taxa from soybean roots which were then used to inoculate soybeans grown in 75% sand and 25% no-till soil from the KBS LTER. No-till soil was used to match the environment from which hub taxa were identified and isolated, and because no-till soils are known to confer resilience to low-moisture stress. Inoculated and control plants were then exposed to low-moisture stress as seedlings. Selected hub taxa included two fungi (Humicola sp., and Gibellulopsis sp.) and three bacteria (Streptomyces sp., Massilia sp., and Caulobacter segnis). The impact of inoculation on plant hosts was assessed with phenotype measures (aboveground and belowground) and plant functional measures (transcriptomics and non-target metabolomics of roots). The impact on the microbiome was assessed using amplicon sequencing of DNA as well as cDNA created from RNA extracted from roots. Inoculation had a minor impact on the microbiome that was most apparent when a more active fraction of the microbiome was analyzed using cDNA. cDNA amplicon sequencing demonstrated that Bradyrhizobium was enriched earlier in inoculated samples compared to control samples and that Glomus was enriched earlier in control samples. Transcriptomics of soybean roots demonstrated that genes related to nodulation were upregulated in inoculated samples, and non-targeted metabolomics appeared to show a possible signal of increased nodulation related metabolites in inoculated samples. Molecular and metabolomics data agreed with phenotypic data which showed increases in nodulation as well as increased aboveground growth, likely related to increased nitrogen fixation activity. Experiments using field soils and enriching individual hub taxa revealed that this effect of increased resilience to drought and nodulation was reproducible with both Caulobacter segnis and Streptomyces treatments. Overall, these results support the hypothesis that hub taxa can be used as inocula to improve the performance and resilience of the host plants.

ORGANISM(S): Glycine max

PROVIDER: GSE200609 | GEO | 2026/06/01

REPOSITORIES: GEO