Rice plant-soil microbiome interactions driven by root and shoot biomass

Authors: FERNANDEZ-BACA, CRISTINA - U.S. DEPARTMENT OF AGRICULTURE (USDA); Rivers, Adam; Maul, Jude; KIM, WOOJAE - RURAL DEVELOPMENT ADMINISTRATION - KOREA; MCCLUNG, ANNA; Roberts, Daniel; Reddy, Vangimalla; Barnaby, Jinyoung

Submitted to: Diversity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2021
Publication Date: 3/15/2021
Citation: Fernandez-Baca, C.P., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Reddy, V., Barnaby, J.Y. 2021. Rice plant-soil microbiome interactions driven by root and shoot biomass. Diversity. https://doi.org/10.3390/d13030125.
DOI: https://doi.org/10.3390/d13030125

Interpretive Summary: The interactions between plant host and rhizosphere soil microbial communities play an important role in plant productivity, health and growth. Understanding how plant traits, such as root and shoot biomass, and plant developmental stage impact the structure of the soil microbial community is essential for selecting plant-beneficial microbes through trait-driven breeding. In this study, we used nine rice recombinant inbred lines, and their parents, segregating for root and shoot biomass at two developmental stages, i.e. heading and grain fill, to identify corresponding changes in microbial species, functions, and genes.

Technical Abstract: Plant-soil microbe interactions are complex and affected by many factors including; soil type, edaphic conditions, plant genotype, developmental stage, and plant phenotypic traits. Metagenomic sequencing of rice rhizosphere soil was used to examine how root and shoot biomass influence soil microbial community composition in the rhizospheres of nine recombinant inbred lines (RILs) and their parents, Francis and Rondo. Two plant developmental stages were chosen, i.e. heading and grain fill, based on root and shoot biomass growth patterns across the nine selected RILs and their parents. We used partial least squares (PLS) regression analysis to examine plant trait-driven microbial populations and identify microbial species, functions, and genes corresponding to root and shoot biomass as well as developmental stage patterns. Species identified as correlated with either root or shoot biomass are widely present in soil and include species involved in nitrogen cycling (Anaeromyxobacter spp.) and methane production (Methanocella avoryzae.), as well as known endophytes (Bradyrhizobium spp.). Additionally, PLS analysis allowed us to explore the relationship of developmental stage with species, microbial functions, and genes. Many of the community functions and genes observed during the heading stage were representative of cell growth (e.g. carbohydrate and nitrogen metabolism), while functions identified as correlated with grain fill were indicative of cell decay. These results provide evidence that there exist some microbial communities whose metabolic and gene expressions correspond to plant biomass traits.