Rice plant biomass traits influencing rhizosphere soil microbial community composition

Authors: FERNANDEZ-BACA, CRISTINA - US Department Of Agriculture (USDA); Rivers, Adam; Maul, Jude; KIM, WOOJAE - Korean Rural Development Administration; McClung, Anna; Roberts, Daniel; Barnaby, Jinyoung

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/15/2020
Publication Date: 1/6/2021
Citation: Fernandez-Baca, C., Rivers, A.R., Maul, J.E., Kim, W., McClung, A.M., Roberts, D.P., Barnaby, J.Y. 2020. Rice plant biomass traits influencing rhizosphere soil microbial community composition. Proceedings of Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 65. Electronic Publication.

Interpretive Summary:

Technical Abstract: Soil microbial communities can increase nutrient availability to plants and influence plant growth and overall health. Likewise, soil microorganisms in the plant rhizosphere rely on root exudates, such as carbon metabolites and nutrients, as growth substrates. Plant species directly influence soil microbial communities through root exudates which change as the plant matures. Even within plant species, the rhizosphere soil microbial community can be altered by plant genotype differences. Plant breeding efforts have the potential to make use of beneficial plant-soil microbiome interactions. Specifically, understanding how changes in growth patterns of plant traits, such as root and shoot biomass, during developmental transition (e.g. from vegetative to reproductive stages) may shed light on plant trait–driven shifts in microbial community structure. Furthermore, studying the dynamic relationship between plant host and soil microbial populations could inform future plant breeding efforts to optimize beneficial microbial populations that influence soil health and plant nutrition. To examine a temporal profile of microbial composition that are associated with changes in plant biomass (i.e. root and shoot), nine recombinant inbred lines (RILs) from a Francis/Rondo (FR) mapping population segregating for shoot biomass (SB) and root biomass (RB) were selected along with two parent lines, Rondo, with high RB/SB, and Francis, with low RB/SB. Plant and soil samples were collected at two developmental stages, i.e. heading and grain fill, and were evaluated for RB and SB dry weights and rhizosphere microbial community profiles, respectively. These two developmental stages were selected for displaying contrasting RB and SB growth patterns across the 11 inbred lines as well as representing the changes that occur during reproduction. Shotgun metagenomic sequencing was used to examine the temporal relationship between rice cultivar-specific root and shoot biomass traits and the rhizosphere soil microbial community. Libraries were constructed with DNA extracted from rhizosphere soil samples for metagenomic sequencing on the NextSeq platform. Microbial taxa that were associated with changes in biomass included species from the Actinobacteria, Chloroflexi, Planctomycetes, Proteobacteria, and Verrucomicrobia phyla. Within the Proteobacteria, several Alphaproteobacteria species were identified and correlated with shoot and root biomass. Within this phylum, a Phenylobacterium sp., aerobic or facultatively anaerobic non-spore forming bacteria, was negatively correlated with RB, SB, and grain fill. Perhaps unsurprisingly, a Bradyrhizobium sp., which is a known rice root endophyte capable of nitrogen-fixation, was identified as positively associated with root biomass, but, interestingly, also with shoot biomass and during grain fill. Several taxa showed a significant positive correlation with rice shoot biomass and this pattern was well-presented during grain fill. Especially interesting, Anaeromyxobacter spp. are gram negative facultative anaerobes that are known to perform dissimilatory iron reduction and have been shown to use nitrate as an electron acceptor making it an important species for biogeochemical cycling of nutrients. A methanogen, Methanocella avoryzae, was also positively correlated with increased shoot biomass and during grain fill stage. Generally, many of the community functions and genes observed during the heading stage were representative of cell growth, while functions identified as correlated with grain fill were indicative of cell decay indicating that some microbial communities exist whose metabolic functions correspond positively to plant shoot and root biomass. Understanding how plant traits, such as root and shoot biomass, and plant developmental stage impact the structure and function of rhizosphere soil microbial communiti