DOI: 10.5061/dryad.tb2rbp0b3
title: Data from: Competition and soil-microbe mediated interactions following dieback of a dominant wetland plant

description: Plant invasions can have important consequences for the soil ecosystem
 which, in turn, can affect interactions with other plant species and
 impose serious constraints on restoration efforts. In the Mississippi
 River Delta (MRD), USA, widespread dieback of the dominant wetland plant,
 Phragmites australis, was followed by the colonization of invasive
 Colocasia esculenta (taro) in many areas. We conducted a common-garden
 experiment to investigate the competitive interactions among taro and two
 P. australis lineages prevalent in the MRD, Delta and European invasive
 (EU), and the role of taro soil microbes in mediating those interactions.
 Plant types were grown alone or together and crossed with a microbial
 treatment (sterilized or live taro-soil biota). After one growing season,
 we measured plant above- and belowground biomass. In the absence of taro
 microbes, Delta and EU had equivalently strong negative effects on each
 other’s biomass and the biomass of taro; whereas, taro had only a small
 negative effect on the biomass of P. australis. However, taro-soil
 microbes had a strong legacy effect, reducing Delta and EU biomasses by
 30-33% and taro by 66% when plants were grown without a competitor.
 Interestingly, when Delta and EU were in competition, the soil legacy
 resulted in EU being a better competitor – total biomass of Delta and EU
 were reduced by 90% and 68%, respectively, in comparison to
 no-microbe/no-competitor controls. Overall, the effects of competition and
 the taro-soil legacy on Delta and EU were determined to be additive. In
 contrast, taro microbes and P. australis competitors acted
 antagonistically to affect taro’s biomass, resulting in only a 67% (with
 Delta) or 48% (with EU) reduction in taro biomass relative to experimental
 controls. We conclude that restoration of P. australis in the MRD may
 require manipulating the soil community to mitigate taro-legacy effects
 and choosing the P. australis lineage that is the best competitor in the
 presence of plant-soil feedbacks.
description: # Competition and soil-microbe mediated interactions following dieback of
 Phragmites australis in the Mississippi River Delta
 [https://doi.org/10.5061/dryad.tb2rbp0b3](https://doi.org/10.5061/dryad.tb2rbp0b3) ## Description of the data and file structure Data for all analyses are provided as *.csv files. Each csv file has an associated R code that was used for the analysis of these data. R version 4.3.1. The R code, Delta Total Biomass.R is written to analyze total biomass for the Delta lineage. However, the response variable can be changed to analyze above and belowground biomass and for the other two plant species/lineages. The R code proportional effects plots.R creates all proportional effect size plots and the additive-effects plots. Data for those plots is generated using the Delta Total Biomass.R code and are summarized in all of the other *.csv files. ### Files and variables #### File: Taro_competition_raw.csv **Description:** This dataset contains aboveground, belowground and total biomass for Delta and EU lineages of *P. australis* and taro for each bucket and for each competition and taro-microbe treatment. Cells reporting "NA" denote missing values. The effects of taro-microbe treatment and presence of a competitor on the biomass of each focal species was analyzed using the R-code: Delta Total Biomass - JTC.R ##### Variables * Species: the combination of species present in each bucket (EU, Delta, Taro, Taro and Delta, Taro and EU or EU and Delta Microbe: taro microbes present (YES) or absent (NO) POP: source population (see Table S1) POT: identifies the bucket, ranging from 201 to 344 TARO: Taro present (YES) or absent (NO) from the bucket DELTA: Delta present (YES) or absent (NO) from the bucket EU: EU present (YES) or absent (NO) from the bucket TARAPOP: identifies the source population of taro (if any) in the bucket DELTAPOP: identifies the source population of Delta (if any) in the bucket EUPOP: identifies the source population of EU (if any) in the bucket EUABOVEWT: aboveground dry mass of EU in grams EUBELOWWT: belowground dry mass of EU in grams EUTOTALWT: total dry mass of EU in grams (sum of EUABOVEWT and EUBELOWWT) DABOVEWT: aboveground dry mass of Delta in grams DBELOWWT: belowground dry mass of Delta in grams DTOTALWT: total dry mass of Delta in grams (sum of DABOVEWT and DBELOWWT) TABOVEWT: aboveground dry mass of Taro in grams TBELOWWT: belowground dry mass of Taro in grams TTOTALWT: total dry mass of Taro in grams (sum of TABOVEWT and TBELOWWT) #### File: Delta_Total_Biomass_-_JTC.R **Description:** This R code was used to analyze the effects of taro-microbe treatment and presence of a competitor on the biomass of each focal species. The source of the data used in this analysis is Taro_competition_raw.csv #### File: Proportional_comp-microbe_effects-abovegroundX.csv **Description:** This dataset summarizes the mean proportional reduction in plant aboveground biomass in response to the competition and taro-microbe treatment. It also includes bootstrapped 95% confidence intervals computed with the dataset Taro_competition_raw.csv and code Delta_Total_Biomass - JTC.R. This table was used to construct a figure depicting the proportional reduction in aboveground biomass in response to our experimental treatments. The figure was constructed using the R-code: Proportional effects plots.R ##### Variables * Species: this is the focal species (either Delta, EU or Taro) whose proportional reduction in biomass is reported in this table Competitor: the species/lineage of competitor present with the focal species Microbe: taro-microbes present (Yes) or absent (No) Prop: the proportional reduction in biomass, relative the control situation (no competitor, no microbes), in response to the presence of a competitor and presence or absence of taro microbes Lower_CI: bootstrap estimates for the lower end of the 95% confidence interval Upper_CI: bootstrap estimates for the upper end of the 95% confidence interval #### File: Proportional_comp-microbe_effects-belowgroundX.csv **Description:** This dataset summarizes the mean proportional reduction in plant belowground biomass in response to the competition and taro-microbe treatment. It also includes bootstrapped 95% confidence intervals computed with the dataset Taro_competition_raw.csv and code Delta_Total_Biomass - JTC.R. This table was used to construct a figure depicting the proportional reduction in aboveground biomass in response to our experimental treatments. The figure was constructed using the R-code: Proportional effects plots.R ##### Variables * Species: this is the focal species (either Delta, EU or Taro) whose proportional reduction in biomass is reported in this table Competitor: the species/lineage of competitor present with the focal species Microbe: taro-microbes present (Yes) or absent (No) Prop: the proportional reduction in biomass, relative the control situation (no competitor, no microbes), in response to the presence of a competitor and presence or absence of taro microbes Lower_CI: bootstrap estimates for the lower end of the 95% confidence interval Upper_CI: bootstrap estimates for the upper end of the 95% confidence interval #### File: Proportional_comp-microbe_effectsX.csv **Description:** This dataset summarizes the mean proportional reduction in plant total biomass in response to the competition and taro-microbe treatment. It also includes bootstrapped 95% confidence intervals computed with the dataset Taro_competition_raw.csv and code Delta_Total_Biomass - JTC.R. This table was used to construct a figure depicting the proportional reduction in total biomass in response to our experimental treatments. The figure was constructed using the R-code: Proportional effects plots.R ##### Variables * Species: this is the focal species (either Delta, EU or Taro) whose proportional reduction in biomass is reported in this table Competitor: the species/lineage of competitor present with the focal species Microbe: taro-microbes present (Yes) or absent (No) Prop: the proportional reduction in biomass, relative the control situation (no competitor, no microbes), in response to the presence of a competitor and presence or absence of taro microbes Lower_CI: bootstrap estimates for the lower end of the 95% confidence interval Upper_CI: bootstrap estimates for the upper end of the 95% confidence interval #### File: Additive_effect.csv **Description:** This dataset summarizes the observed (Comp-M) and additive expectation (Merge) for the mean proportional reduction in plant total biomass in response to the presence of a competitor and taro-microbe. It also includes bootstrapped 95% confidence intervals computed with the dataset Taro_competition_raw.csv and code Delta_Total_Biomass - JTC.R. This table was used to construct a figure depicting the observed and additive expectation for the reduction in total biomass for cases where a competitor and taro microbes are present. The figure was constructed using the R-code: Proportional effects plots.R ##### Variables * Species: this is the focal species (either Delta, EU or Taro) whose proportional reduction in biomass is reported in this table Competitor: the species/lineage of competitor present with the focal species Condition: Comp-M = the observed mean effect size derived directly from the experimental treatments for the presence of a competitor and presence of taro microbes. Merge = the estimated mean effect size when we add the proportional reduction in biomass due to the competitor alone and due to the microbe alone. Prop: the proportional reduction in biomass based on either the observed or additive expectation. Lower_CI: bootstrap estimates for the lower end of the 95% confidence interval Upper_CI: bootstrap estimates for the upper end of the 95% confidence interval #### File: Proportional_effects_plot.R **Description:** This R code is used to construct plots that depict the proportional reduction in biomass (Total, Aboveground or Belowground) for each focal species/lineage when grown in the presence/absence of a competitor and presence/absence of taro microbes. The R code also constructs a plot of the observed and expected additive effects of the presence of a competitor and taro microbes. ## Code/software The analyses were conducted using R version 4.3.1. The packages used include:  ade4 kableExtra knitr psych ggplot2 car emmeans lmerTest plotly rlang grid rlist gdata Rmisc tidyr blmeco rcompanion dplyr #### File: Soil_chemistry.csv **Description:** This dataset summarizes the soil chemistry for three replicates of three soil types used in the experiment: River silt (replicates RS1, RS2, RS3), live taro soil (replicates TS1, TS2, TS3) and autoclaved taro soil (ATS1, ATS2, ATS3). Analysis of these chemistry data is provided in Soil chemical analysis.R. ##### Variables * Chemical Profile: type of chemical analyzed and units reported in table * Code: abbreviated code for each chemical compound * RS1: River silt, replicate 1 * RS2: River silt, replicate 2 * RS3: River silt, replicate 3 * TS1: Live taro soil, replicate 1 * TS2: Live taro soil, replicate 2 * TS3: Live taro soil, replicate 3 * ATS1: autoclaved taro soil, replicate 1 * ATS2: autoclaved taro soil, replicate 2 * ATS3: autoclaved taro soil, replicate 3 #### File: Soil_chemical_analysis.R **Description:** This R code is used to analyze soil chemistry in spreadsheet Soil chemistry.xlsx. First, means, SD and SE are computed for each of the three soil types (RS, TS and ATS). Next, a principal component analysis is conducted using the chemical profiles for the three soil types. A bi-plot is constructed for principal components 1 and 2. Finally, a PERMANOVA is conducted to test for differences between Live taro soil (TS) and autoclaved taro soils (ATS), and between River silt (RS) and Live taro soils (TS). ## Code/software The analyses were conducted using R version 4.3.1. The packages used include:  openxlsx readxl writexl dplyr ggplot2 tidyr vegan