Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits

Shade tolerance is a central concept in forest ecology and strongly influences forest community dynamics. However, the plant traits and conditions conferring shade tolerance are yet to be resolved. We propose that shade tolerance is shaped not only by responses to light but also by a species’ defense and recovery functional traits, soil microbial communities, and interactions of these factors with light availability. We conducted a greenhouse experiment for three temperate species in the genus Acer that vary in shade tolerance. We grew newly germinated seedlings in two light levels (2% and 30% sun) and controlled additions of microbial filtrates using a wet-sieving technique. Microbial filtrate treatments included: <20 µm, likely dominated by pathogenic microbes; 40-250 µm, containing arbuscular mycorrhizal fungi (AMF); combination, including both filtrate sizes; and sterilized combination. We monitored survival for nine weeks and measured fine root AMF colonization, hypocotyl phenolics, stem lignin, and stem+root nonstructural carbohydrates (NSC) at three-week intervals. We found that differences in seedling survival between low and high light only occurred when microbes were present. AMF colonization, phenolics, and NSC generally increased with light. Phenolics were greater with <20 µm microbial filtrate, suggesting that soil-borne pathogens may induce phenolic production and NSC was greater with 40-250 µm filtrate, suggesting that mycorrhizal fungi may induce NSC production. Across species, microbe treatments, and light availability, survival increased as phenolics and NSC increased. Therefore, shade tolerance can be explained by interactions among soil-borne microbes, seedling traits, and light availability, providing a more mechanistic and trait-based explanation of shade tolerance and thus forest community dynamics.

Methods
We conducted a fully factorial greenhouse experiment, including: 3 temperate tree species (Acer negundo, A. rubrum, and A. saccharum) X 4 soil microbial filtrate treatments (none/control, pathogens in <20µm filtrate, arbuscular mycorrhizal fungi in 40-250µm filtrate, and a combination of the <20µm and 40-250µm filtrates) X 2 light levels (2% and 30% full sun). We monitored survival for 9 weeks and harvested a subset of seedlings at 3, 6, and 9 weeks to measure phenolics, lignin, nonstructural carbohydrates, and root colonization by arbuscular mycorrhizal fungi. Detailed methods for each step can be found in the methods section of the manuscript.

Provided data include: species, light level, microbial filtrate, adult tree from which soil was collected, bench in the greenhouse, when the seedling was harvested for trait measurement, the time that the seedling was no longer monitored, event (0 = harvested or no longer monitored after experiment ended, 1 = dead), the amount of arbuscular mycorrhizal fungi observed, phenolics, lignin, nonstructural carbohydrates, and imputed values for each trait (used for trait ~ survival analysis).

An additional file provides the model used for analyzing seedling survival.