Intraspecific plant-soil feedback in four tropical tree species is inconsistent in a field experiment

Eck, Jenalle L.1 ; Hernández Hassan, Lourdes2; Comita, Liza S.3

Published Apr 23, 2024 on Dryad. https://doi.org/10.5061/dryad.0cfxpnw8p

Data files

Apr 23, 2024 version files 147.52 KB

Abstract

Soil microbes can influence patterns of diversity in plant communities via plant-soil feedbacks. Intraspecific plant-soil feedbacks occur when plant genotype causes variation in soil microbial composition, resulting in differences in the performance of seedlings growing near their maternal plants versus seedlings growing near non-maternal conspecific plants. How consistently such intraspecific plant-soil feedbacks occur in natural plant communities is unclear, especially under variable field conditions. We conducted an in situ experiment with four native tree species on Barro Colorado Island (BCI), Panama. Seedlings of each species were transplanted beneath their maternal tree or another conspecific tree in the BCI forest. Mortality and growth were assessed at the end of the wet season (~4 months post-transplant) and at the end of the experiment (~7 months post-transplant). Differences in seedling performance among field treatments were inconsistent among species and eroded over time. Effects of field environment were detected at the end of the wet season in two of the species: Virola surinamensis seedlings had higher survival beneath their maternal tree than other conspecific trees, while the opposite pattern was found in Ormosia macrocalyx. However, these differences disappeared by the end of the experiment. Our results suggest that intraspecific plant-soil feedbacks may not occur consistently under field conditions in tropical tree species and may have a limited role in determining seedling performance in tropical tree communities. Future studies are needed to elucidate the environmental and genetic factors that determine the incidence and direction of intraspecific plant-soil feedbacks in plant communities.

README: Intraspecific plant-soil feedback in four tropical tree species is inconsistent in a field experiment

Here we present the data and R script used to produce the results described in our manuscript of the same name. This includes three elements: 1) data collected on seedlings of four tropical tree species during a field experiment conducted on Barro Colorado Island (BCI), Panama, 2) summary data formatted to enable easy plotting of the survival of seedlings in that same experiment, and 3) the R script that supported analysis of the experimental data.

In brief, to test whether conspecific seedling performance was reduced near maternal conspecific trees relative to non-parent conspecific trees, we conducted an in situ experiment with four native tree species on Barro Colorado Island (BCI), Panama. Seedlings of each species were transplanted beneath their maternal tree or another conspecific tree in the BCI forest. Mortality and growth were assessed at the end of the wet season (~4 months post-transplant) and at the end of the experiment (~7 months post-transplant).

Differences in seedling performance among field treatments were inconsistent among species and eroded over time. Effects of field environment were detected at the end of the wet season in two of the four species: Virola surinamensis seedlings had higher survival beneath their maternal tree than other conspecific trees, while the opposite pattern was found in Ormosia macrocalyx. However, these differences disappeared by the end of the experiment.

Description of the data and file structure

There are three relevant files: one data file containing data from the field experiment (field_experiment_data.txt), one data file containining data in a format for easy plotting of seedling survival (survival_plot_data.txt), and one code file containing script used for data analysis in R (R_code_for_analysis.R). More information about the data files and the variables it contains can be found below. More information about the code file and explanation can be found at the end of this README.

Throughout the data file, NA cells represent either a) missing data for the variable or b) the variable is not applicable to the row.

field_experiment_data.txt

In this dataset, each row is one seedling individual from the field experiment. This dataset is tab-delimited and contains headers. All dates are reported in the format MM/DD/YYYY.

Column explanations:

ID: The unique identifier for the seedling individual in the experiment.
species: The species of the seedling individual in the experiment.
seed.Acode: The unique identifier for the seed source adult individual.
soil.Acode: The unique identifier for the focal adult the seedling was planted near in the field.
mother.othercon: Which of the two field experimental treatments the seedling was grown in (maternal conspeecific tree or other conspecific tree).
plot: The ID of the specific plot beneath the focal adult the seedling was grown in.
n.seedlings.plot: The number of seedlings planted in that plot at the beginning of the experiment.
date.anyspecies.0: The date the first experimental seedling was transplanted into the field experiment. Used for calculating days since the beginning of the experiment.
date.0: The date the given experimental seedling was transplanted into the field experiment. Used for calculating days since transplant of the seedling.
exp.day: The number of days that had elapsed since the beginning of the experiment when the given seedling was transplanted.
ht.0: The stem height (in centimeters) of the seedling at the time of transplant.
lnum.0: The number of leaves on the seedling at the time of transplant.
la.0.ov: The estimated leaf area of the seedling (in centimeters squared) at the time of transplant. Calculated using species-specific allometric equations produced using measurements of the stem height, leaf number, leaf area, and dry biomass of a subset of potential experimental seedlings at the beginning of the experiment.
dry.wt.est.0.ht.lnum: The estimated dry biomass (in grams) of the seedling at the time of transplant based on it's ht.0 and lnum.0. Calculated using the allometric equation mentioned above.
dry.wt.est.0.ht.la: The estimated dry biomass (in grams) of the seedling at the time of transplant based on ht.0 and dry.wt.est.0.ht.lnum. Calculated using the allometric equation mentioned above.

The following columns repeat for each census of the data. The census can be identified by .0, .1, .2, ... .h after the variable name. .0 Is the transplant/initial census. .h is the harvest census. Here it is written as .X to indicate repetition.

date.X: The date of the census.
time.X: The number of days that had elapsed since the first seedling of the seedling's species was transplanted.
time.in.trt.X: The number of days that had elapsed since the seedling was placed in the field treatment at the time of the census. Could be NA if the seedling died.
exp.day.X: The number of days that had elapsed since any seedling of any species was placed in the field experiment.
plot.ht.X: The height of the seedling (in cm), as measured once planted in the plot.
lnum.X: The number of leaves the seedling had at the census.
surv.X.01: Whether or not a seedling survived until the given census (binary variable, 0 = mortality, 1 = survival).
clipping.0.X.yn: Whether or not signs of clipping were present in the seedling at the given census (binary variable, y = yes, n = no).
dry.wt.est.X.ht.lnum: Estimated total dry biomass (in grams) of the seedling at the census, based on plot.ht.X and lnum.X. Calculated using the allometric equation mentioned above.

The following harvest census data columns are unique (do not repeat for each census).

ht.h: The stem height (in centimeters) of the seedling at harvest (measured outside of the plot, so true height).
la.h: The measured total leaf area (in centimeters squared) of the seedling (measured using a leaf area scanner).
clipping.0.h.yn: Whether or not signs of clipping had ever been observed in the seeling during the experiment (binary variable, y = yes, n = no).
tot.dry.wt: The total dry biomass (in grams) of the seedling at harvest.
rgr.0.1.est.ht.lnum: The relative growth rate (i.e., rate of growth, in grams, per day) of the seedling between census 0 and 1, based on height and leaf number.
rgr.1.2.est.ht.lnum: The relative growth rate of the seedling (i.e., rate of growth, in grams, per day) between census 1 and 2, based on height and leaf number.
rgr.2.3.est.ht.lnum: The relative growth rate of the seedling (i.e., rate of growth, in grams, per day) between census 2 and 3, based on height and leaf number.
rgr.3.4.est.ht.lnum: The relative growth rate of the seedling (i.e., rate of growth, in grams, per day) between census 3 and 4, based on height and leaf number.
rgr.4.harvest.est.ht.lnum: The relative growth rate of the seedling (i.e., rate of growth, in grams, per day) between census 4 and harvest, based on height and leaf number.

survival_plot_data.txt

In this dataset, each row is one census of one field treatment x species treatment combination. This summary data is intended for easy plotting of survival over time in the field experiment. It is derived from data included in field_experiment_data. This dataset is tab-delimited and contains headers.

Column explanations:

survey: The census the data corresponds to. 0 = transplant, then 1, 2, ... 5 = harvest.
date.avg: The average date that the seedlings in each treatment combination were surveyed during this census.
exp.day.avg: The average number of days that had elapsed since the beginning of the experiment during this census for this combination of species and treatment.
time.in.trt.avg: The average number of days that had elapsed since the first seedling of this species was transplanted during this census for this combination of species and treatment.
species: The species that the census data corresponds to.
field.environment: The field treatment that the census data corresponds to.
alive: The number of seedlings that were alive in this species x field treatent combination during this census.
dead: The number of seedlings that had died in this species x field treatent combination during this census.
tot: The total number of seedlings that had been transplanted in this species x field treatent combination.
surv.rate: The survival rate (i.e., proportion) of the seedlings in the given species x field treatment combination during the given census.

Sharing/Access information

There are no other publicly accessible locations of the data.

Data was derived only from first-hand collection by the listed authors.

Code/Software

The code file containing the R script used for data analysis is included (R_code_for_analysis.R). It is formatted for use with the R Statistical Software, which is freely available online.

R_code_for_analysis.R

The R code file requires the data files (field_experiment_data.txt and survival_plot_data.txt) to run. Please make sure to set your working directory in R to a location that includes these files.

The file contains all of the code used to produce the results and figures that appear in the relevant manuscript. Data analysis components (e.g., survival analysis versus growth analysis) are labelled using hierarchical subsection notation and headings.

Data analysis was run with R version 4.2.2. The code requires installation and usage of the following packages: lme4, lmerTest, ggplot2, car, performance, interactions, tidyr.