Agricultural over-fertilization may adversely impact plant−microbial interactions affecting crop yield. It is unclear if soil microbiomes respond quickly to changes in fertilizer inputs once conditioned to specific nutrient regimes. We conducted a growth chamber study assessing the compositional and functional resilience of root-associated microbiomes of Medicago sativa to nutrient regime changes, and consequences for plant growth. Plants were grown with a common starting soil microbiome under four nutrient treatments: control (no fertilizer), organic phosphorus (compost added), low inorganic P (low triple superphosphate, TSP) and high inorganic P (high TSP). After several conditioning generations, in which microbiomes from rhizospheres of high biomass plants were transferred forward, microbiome composition was distinct across the four treatments. The resulting microbiomes were then transplanted into each of the nutrient treatments, leading generally to functional changes in hydrolytic enzyme activity and taxonomic convergence with other microbiomes transplanted into the same nutrient regime. However, high inorganic P-conditioned microbiomes were resistant to compositional change. Correspondingly, M. sativa grown with high inorganic P-conditioned microbiomes had lower biomass, fewer nodules, and lower %N than plants grown under the same nutrient regime with other microbiomes. These findings suggest that excessive inorganic P fertilization may change microbiomes such that they negatively affect plant growth.
Summary
Climate change‐related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so diverse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants.
In both salt‐amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high‐biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add‐back control (re‐adding initial frozen soil microbiome) as a within‐generation reference for microbiome and plant phenotype selection.
We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently diverged from the add‐back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued.
These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.
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