Assembling Soil Microbiomes To Enhance Plant Traits Relevant To Nitrogen Use Efficiency.

Fertilizer nitrogen use efficiency (NUE) in crops has been well studied for many decades, but few researchers have focused on the role of a plant’s microbiome in inducing greater fertilizer NUE plant phenotypes. In this study, we define a microbiome as a community of microorganisms found within a distinct section of a plant. We hypothesized that root-associated microbiomes can assemble through selective pressure to induce greater fertilizer NUE in plants through delayed flowering in the annual dicot Arabidopsis thaliana. The microbiomes were assembled over generations of selection for early vs. late flowering plant hosts. Rhizosphere samples were collected from plants exhibiting the earlier or delayed flowering phenotypes, and were subsequently inoculated into a new generation of replicated plants with seeds from a static pool. After nine generations, the assembled microbiomes were examined for host-selectivity in inducing the contrasting plant flowering phenotypes across three additional A. thaliana genotypes (Landsberg Erecta, Bensheim, RLD) and a related crucifer (Brassica rapa). We used soil extracellular enzyme activities, ¹⁵N natural abundance of plant tissues, C:N ratios of plant tissues, and 16S Illumina paired-end reads for microbial community analysis to uncover the potential mechanisms underlying the microbial-based induction of the flowering phenotypes. We found that the inoculation of these distinct microbiomes into the soils of four A. thaliana genotypes and B. rapa induced the divergence in flowering time phenotypes. Initial results indicate greater inflorescence biomass in three A. thaliana genotypes and greater total biomass in B. rapa with delayed flowering. Activity levels of soil extracellular enzymes associated with nitrogen mineralization increased two- to five-fold in the delayed flowering phenotype. Analysis of plant tissue ¹⁵N natural abundance additionally indicated microbial-based changes in N transformations between the early and late flowering treatments. Microbial community profiling indicated patterns distinguishing the early and late flowering treatments and the control. Major phyla differentially represented between treatments include Acidobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and class Gammaproteobacteria. The study results suggest that rhizosphere microbiomes can modify plant traits through coordinated modification of soil resource pools. The greater accessibility to mineralized nitrogen from soil organic matter could have enhanced plant biomass found in the delayed flowering phenotypes. The research findings should stimulate future experimental attempts to uncover the role of soil microbial communities in modulating plant traits relevant to NUE in natural and managed ecosystems.