Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. In many terrestrial ecosystems, plant and microbial production is primarily limited by nitrogen (N) availability. Thus, understanding microbial taxa involved in the cycling and plant uptake of N is crucial for agricultural production and sustainability. In this study, we sought to better understand how N fertilization alters soil rhizosphere and root endosphere microbial communities during early colonization for two cottonwood species, Populus deltoides and Populus trichocarpa, which are of broad interest for agricultural fiber and biofuel production. Eighty plants representing either species were grown in a greenhouse for a period of three months with and without nitrogen fertilizer using historical agriculture soils from Oregon and West Virginia, which had distinct chemical properties and initial soil microbial communities. Rhizosphere and root endosphere communities of select plants at destructive sampling as well as field soils representing initial conditions were investigated using shotgun metagenomics (~20 Gbp per sample), as well as 16S rRNA gene and ITS2 amplicon sequencing for assessment of prokaryotic and fungal community composition.
Results/Conclusions
Nitrogen fertilization had pronounced effects on several plant growth factors, e.g., plant height, chlorophyll density, plant N content, and root vs. aboveground biomass allocation. A significant proportion of the variation in plant factors within N treatments was correlated with microbial indicators of plant-microbe symbiosis. For instance, lower relative abundances of the N fixation gene nifH and symbiotic fungal taxa were associated with greater allocation of biomass to root structures and reduced overall plant growth. Additionally, patterns of plant-microbe associations were observed for the different soils and Populus species evaluated, demonstrating critical differences between host species as well as initial soil communities. For instance, through assembly and binning techniques, 109 unique metagenome-assembled genomes (MAGs) representing several dominant rhizosphere microorganisms were recovered, and most of these taxa were found to be highly host-specific. MAG abundances also positively correlated with measured plant growth factors, particularly in the case of P. deltoides, and were also disfavored by nitrogen fertilization, further indicating a reduced importance of plant-microbe symbiosis when nutrient constraints are alleviated.