Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits
Data files
Oct 31, 2023 version files 180.68 KB
Abstract
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.
README: Dataset for "Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits"
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, lignin, and nonstructural carbohydrates) at three, six, and nine weeks. Data were collected 2016-2017.
Description of the data and file structure
There are two included files. A .csv file containing data and a .txt file with the survival model.
In the .csv file, we include measured trait, survival, and imputated trait data for the greenhouse experiment. Detailed information about each column follows:
- No: Seedling unique ID number
- Species: 3 Temperate tree species that co-occur within the same forest, belong to the same genus, but vary in shade tolerance
- Acsa = Acer saccharum
- Acru = Acer rubrum
- Acne = Acer negundo
- Light: Light levels were created using shade cloth over greenhouse benches
- Low = 2% full sunlight
- High = 30% full sunlight
- Microbe: Microbial filtrates were acquired through the wet-sieving method (see manuscript for more details)
- Control = sterilized Combined filtrate, used only in supplementary analyses
- None = deionized water + filter paper
- Small = <20µm filtrate in deionized water + filter paper
- Large = deionized water + 40-250µm filtrate on filter paper
- Combined = both <20µm filtrate in deionized water + 40-250µm filtrate on filter paper
- Adult: Number of the adult tree used for soil collection; used as a random effect in analyses; up to 4 per species
- Bench: Number of the bench each seedling was grown on; used as a random effect in analyses
- Harvest: Time (in weeks) that the seedling was harvested (if at all) for trait measurement
- 3, 6, or 9 weeks
- Time: Number of days into the experiment, at which time the seedling either was harvested, died, or the experiment ended
- Event: Used for survival analysis to indicate status of each individual seedling at a given time (above)
- 0 = harvested or experiment ended
- 1 = dead
- AMF: Calculated as AMF Count / AMF Intersections for percent colonization by AMF (see manuscript for detailed methods)
- 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)
- AMF_Imp: Percent colonization AMF, imputated from measured data for analyses of trait relationships with survival
- PHN_Imp: Phenolic content, imputated from measured data for analyses of trait relationships with survival
- NSC_Imp: Percent dry mass nonstructural carbohydrates, imputated from measured data for analyses of trait relationships with survival
- LIG_Imp: Percent dry mass lignin, imputated from measured data for analyses of trait relationships with survivalSharing/Access information
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, McCarthy-Neumann S. 2023*. Tree seedling shade tolerance arises from interactions with microbes and is mediated by functional traits. *Frontiers in Ecology and Evolution.
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
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).
surv-model.txt includes the survival model to be run through RJags in R. Software and package versions should not matter, since the text file is just the model structure.
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.
Usage notes
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).