DOI: 10.5061/dryad.xd2547dpw
title: Tree seedling functional traits mediate plant-soil feedback survival responses across a gradient of light availability

description: Though not often examined together, both plant-soil feedbacks (PSFs) and
 functional traits have important influences on plant community dynamics
 and could interact. For example, seedling functional traits could impact
 seedling survivorship responses to soils cultured by conspecific versus
 heterospecific adults. Furthermore, levels of functional traits could vary
 with soil culturing source. In addition, these relationships might shift
 with light availability, which can affect trait values, microbe abundance,
 and whether mycorrhizal colonization is mutualistic or parasitic to
 seedlings. To determine the extent to which functional traits mediate PSFs
 via seedling survival, we conducted a field experiment. We planted
 seedlings of four temperate tree species across a gradient of light
 availability and into soil cores collected beneath conspecific (sterilized
 and live) and heterospecific adults. We monitored seedling survival twice
 per week over one growing season, and we randomly selected subsets of
 seedlings to measure mycorrhizal colonization and phenolics, lignin, and
 NSC levels at three weeks. Though evidence for PSFs was limited, Acer
 saccharum seedlings exhibited positive PSFs (i.e., higher survival in
 conspecific than heterospecific soils). In addition, soil microbes had a
 negative effect on A. saccharum and Prunus serotina seedling survival,
 with reduced survival in live versus sterilized conspecific soil. In
 general, we found higher trait values (measured amounts of a given trait)
 in conspecific than heterospecific soils and higher light availability.
 Additionally, A. saccharum survival increased with higher levels of
 phenolics, which were higher in conspecific soils and high light. Quercus
 alba survival decreased with higher AMF colonization. We demonstrate that
 functional trait values in seedlings as young as three weeks vary in
 response to soil source and light availability. Moreover, seedling
 survivorship was associated with trait values for two species, despite
 both drought and heavy rainfall during the growing season that may have
 obscured survivorship-trait relationships. These results suggest that
 seedling traits could have an important role in mediating the effects of
 local soil source and light levels on seedling survivorship and thus plant
 traits could have an important role in PSFs.
description: We conducted a factorial blocked design field experiment,
 consisting of four tree species, seven soil sources (sterilized
 conspecific, live conspecific, and five heterospecific), and a gradient of
 forest understory light levels (low, medium, and high), for a total of
 3,024 seedlings. We monitored seedling survival twice per week over one
 growing season, and we randomly selected subsets of seedlings to measure
 mycorrhizal colonization and phenolics, lignin, and NSC measurements at
 three weeks. We used Cox proportional hazards survival models to evaluate
 survival and linear mixed effects models to test how light availability
 and soil source influence traits. 
description: # Tree seedling functional traits mediate plant-soil feedback survival
 responses across a gradient of light availability
 [https://doi.org/10.5061/dryad.xd2547dpw](https://doi.org/10.5061/dryad.xd2547dpw) Give a brief summary of dataset contents, contextualized in experimental procedures and results. ## Description of the data and file structure There is one included file a .csv containing the data used for analyses in this manuscript. In the .csv file, we include measured trait, survival, and imputated trait data for the field experiment. Detailed information about each column follows: * No: Seedling unique ID number. * Plot: Number of the field plot the seedling was planted in. (1-18) * Subplot: Subplot within the main plot the seedling was planted in. Broken into 5 subplots (1 per corner, plus 1 in the middle). (A-E) * Species: Includes Acer saccharum, Prunus serotina, Quercus alba, and Quercus rubra. * Light ISF: Light level quantified with HemiView software. Represents the amount of light reaching each subplot at a height of 1m. * Light Cat: Categorical light level created by splitting the range of Light\_ISF values into three bins (low, med, high). * Core: Year the soil core was removed from the field. * Soil: Species from which the soil core was taken. Includes all species, plus Acer rubrum, Populus grandidentata, and a sterilized conspecific for each species. * Adult: Individual tree that soil was taken from. Up to 6 adults per species. Used as a random effect in analyses. * Sterile: Whether the soil was sterilized or not. * Conspecific: Whether the soil was conspecific, heterospecific, or sterilized conspecific. * Myco: Mycorrhizal type of the seedling species (AMF or EMF). * SoilMyco: Mycorrhizal type of the species culturing the soil (AMF or EMF). * PlantDate: The date that seedlings were planted in the field pots. * AMF: Percent arbuscular mycorrhizal fungi colonization on the fine roots of harvested seedlings. * EMF: Percent ectomycorrhizal fungi colonization on the root tips of harvested seedlings. * Phenolics: Calculated as nmol Gallic acid equivalents per mg dry extract (see manuscript for detailed methods) * NSC: Calculated as percent dry mass nonstructural carbohydrates (see manuscript for detailed methods) * Lignin: Calculated as percent dry mass lignin (see manuscript for detailed methods) * Census: The census number at which time the seedling died or was harvested. * Time: The number of days at which time the seedling died or was harvested. * Event: Used for survival analysis to indicate status of each individual seedling at a given time (above) * 0 = harvested or experiment ended * 1 = dead * Harvest: Indicates whether the seedling was harvested for trait measurement. * Alive: Indicates if the seedling was alive at the end of the second growing season. "X" in this field indicates alive status. Missing data is coded as NA. ## Sharing/Access information There are no licenses or restrictions placed on the data (public domain). All data was collected from this single experiment and is presented in the associated manuscript: Wood KEA, Kobe RK, Ibáñez I, McCarthy-Neumann S. 2023\*Tree seedling functional traits mediate plant-soil feedback responses across a gradient of light availability. \*Plos One.\*​ For any questions about the manuscript or dataset, including methodology and availability, please contact the corresponding author: Katherine EA Wood, woodkat7@msu.edu. ## Code/Software All analyses were performed with R version 3.5.1 (R Core Team, 2020). We used the “coxph” function in the survival package (Therneau & Grambsch, 2000) to fit Cox proportional hazards regression models. We tested the significance of main effects using a likelihood ratio test with the “Anova” function. We tested for multicollinearity variance inflation factors using the “vif” function in the car package (Fox & Weisberg, 2019). Post-hoc Tukey pairwise comparisons of significant main effects and Bonferonni corrections for multiple comparisons were made using the “emmeans” function in the multcomp package (Hothorn et al., 2008; Lenth, 2020). We used the missForest package (Stekhoven & Buehlmann, 2012) to impute trait data for seedlings monitored for survival.