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 phenol..., 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 arbuscula..., We performed all analyses in R 3.5.1 (R Core Team, 2020). We used the rjags package (Plummer, 2019) to fit survival models and to run predicted survival and contrast simulations. We used the built-in “lmer” function to fit linear mixed effects models and tested significance of main effects using the “Anova” function in the car package (Fox & Weisberg, 2019). Model selection for linear mixed effects models was determined with the “step” function in the lmerTest package (Kuznetsova et al., 2017). Post-hoc Tukey pairwise comparisons of significant main effects were made using the “emmeans” and “joint_tests” functions in the multcomp package (Hothorn et al., 2008; Lenth, 2020)., # Dataset for \"Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits\"

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We conducted a fully factorial blocked-design greenhouse experiment at the Michigan State University Tree Research Center in Lansing, Michigan, USA (42.7 ºN, 84.5 ºW). The experiment consisted of three species, four microbial communities (<20 µm, representing pathogenic microbes; 40-250 µm, representing AMF; combined filtrate (both <20 µm and 40-250 µm); and sterilized combined filtrate) and two light levels (2% and 30% full sun, representing shade and light gap environments). Individual pots were set up on six different benches (three per light level), where all treatment combinations were represented. We planted 80 seedlings per treatment combination for a total of 1,920 seedlings. We monitored seedlings every three days for survival, and randomly selected subsets for trait measurements (percent colonization by arbuscular mycorrhizal fungi, phenolics, l...