Does European-introduced Phragmites australis experience below-ground microbial enemy release in North America?

# Does European-introduced *Phragmites australis* experience below-ground microbial enemy release in North America? [https://doi.org/10.5061/dryad.3ffbg79rn](https://doi.org/10.5061/dryad.3ffbg79rn) This repository contains all the datasets and R code needed to analyze the study, "Does European introduced *Phragmites australis* experience below-ground microbial enemy-release in North America?". Datasets are presented in .csv format and titles will correspond to the analysis performed. The detailed annotated code used to analyze each of the datasets is included in the Ecosphere Models.R file. The code used to reproduce the figures found in the study is also included in the Ecosphere Figures 2.R file. For any additional information please contact the corresponding author Sean Lee at ([[e-mail])](mailto:slee38@tulane.e) ## Description of the data and file structure ### *Biomass analysis* We explored the effects of soil inocula on *Phragmites* seedling biomass sourced from different habitats across both North America (invasive range) and Europe (native range). *Phragmites* seedlings were sourced from the same corresponding habitats across the two ranges as well and used to populate a fully factorially crossed seedling growth experiment. These datasets described below were used to create the stacked barplot representing the total, aboveground, and belowground biomass of *Phragmites* seedlings (Fig. 2) and also create the linear mixed effect models used to analyze the effects of seed and soil inocula range on explaining the variation in observed biomass. 1. ER_BIOMASS_FIGS_2.csv * Contains aboveground, belowground, and total biomass of *Phragmites* seedlings at harvest in grams as well as variables such as seed and soil range of the seeds used in the experiment and the soil inocula used to inoculate each pot. * These data were used to create the stacked barplot representing total, aboveground, and belowground biomass of *Phragmites* seedlings (Fig. 2). * "SEED_RANGE": Describes which continent the seed originated from (US_SDR: seed collected from North America, and DE_SDR: seed collected from Europe) * "SOIL_RANGE": Describes the continent the soil inoculum was sourced from (US_SOR: North American soil, DE_SOR: European soil, and STER_SOR: sterilized inoculum). * "AGB": Aboveground biomass of the seedling in grams. * "BGB": Belowground biomass of the seedling in grams. * "TOT_BM": Total biomass of the seedling in grams. 2. "ER_BIOMASS_new_2.csv" * Contains aboveground, belowground, and total biomass of *Phragmites* seedlings at harvest in grams as well as variables such as seed range and soil range which were used as fixed effects in our linear mixed effects models, as well as soil habitat which was used as a random effect in the total biomass model. * These data were used to create the linear mixed effects models to analyze the effects of seed and soil range on total, aboveground, and belowground biomass. * "SEED_RANGE": Describes the continent the seeds were sourced from (US_SER: North American seeds, and DE_SER: European seeds). * "SOIL_RANGE": Describes the continent the soil inoculum was sourced from (US_SOR: North American soil, DE_SOR: European soil, and STER_SOR: sterilized inoculum). * "SOIL_HAB_TYPE": Describes the habitat type the soil inoculum was sourced from (URB_SOH: soil taken from an urban environment, TID_SOH: soil taken from a tidal environment, FRESH_SOH: soil taken from a freshwater environment, and STER_SOH: sterilized soil inoculum). * "AGB": Aboveground biomass of the seedling in grams. * "BGB": Belowground biomass of the seedling in grams. * "TOT_BM": Total biomass of the seedling in grams. ### *Soil microbial community analysis* To explore the composition and structuring of soil bacteria and fungi communities in *Phragmites* associated soils we performed 16S and ITS rRNA sequencing. These datasets were generated from the sequencing data and used to create NMDS plots, perform indicator analyses, perform PERMANOVA, and for fungal communities, analyze the proportion of fungi belonging to different guilds according to FUNGuild. 1. SIXTEEN_GENUS_ORD_NO_STER.csv * Contains OTU counts for bacterial 16S rRNA on the genus level, without the incorporation of samples taken from sterilized treatments. * This dataset is used to create NMDS plots for Fig. 3, and code for this figure can be found in the *Ecosphere Figures.R* file. 2. ITS_GENUS_ORD_NO_STER.csv * Contains OTU counts for fungal ITS rRNA on the genus level, without the incorporation from samples taken from sterilized treatments. * This dataset is used to create NMDS plots for Fig. 3, and code for this figure can be found in the *Ecosphere Figures.R* file. 3. SIXTEEN_GENUS_AGGREGATE.csv * Contains OTU counts for bacterial 16S rRNA on the genus level, without the incorporation of samples taken from sterilized treatments. * This dataset is used to perform the bacterial indicator analysis based on soil range, hence the first three columns represent different geographic and environmental variables. * "SOURCE": Describes the soil source of the inoculum (USU: North American soil taken from an urban environment, UST: North American soil taken from a tidal environment, USF: North American soil taken from a freshwater environment: DEU: European soil taken from an urban environment, DET: European soil taken from a tidal environment, and DEF: European soil taken from a freshwater environment). * "HAB_TYPE": Describes the habitat type the soil inoculum was sourced from (URBAN: soil taken from an urban environment, TIDAL: soil taken from a tidal environment, FRESHWATER: soil taken from a freshwater environment). * "RANGE": Describes the continent the soil inoculum was sourced from (US: North American soil, and EU: European soil). * The code for performing the bacterial indicator analysis is located in the *Ecosphere Models.R* file. 4. ITS_GENUS_AGGREGATE.csv * Contains OTU counts for fungal ITS rRNA on the genus level, without the incorporation from samples taken from sterilized treatments. * This dataset is used to perform the fungal indicator analysis and the PERMANOVA based on soil range, hence the first three columns representing different geographic and environmental variables. * "SOURCE": Describes the soil source of the inoculum (USU: North American soil taken from an urban environment, UST: North American soil taken from a tidal environment, USF: North American soil taken from a freshwater environment: DEU: European soil taken from an urban environment, DET: European soil taken from a tidal environment, and DEF: European soil taken from a freshwater environment). * "HAB_TYPE": Describes the habitat type the soil inoculum was sourced from (URBAN: soil taken from an urban environment, TIDAL: soil taken from a tidal environment, FRESHWATER: soil taken from a freshwater environment). * "RANGE": Describes the continent the soil inoculum was sourced from (US: North American soil, and EU: European soil). * The code for performing the fungal indicator analysis is located in the *Ecosphere Models.R* file. 5. PERMANOVA_16S_GENUS * Contains OTU counts for bacterial 16S rRNA on the genus level, with the incorporation of samples taken from sterilized treatments. * These sterilized samples were omitted from the PERMANOVA during the analysis (see the *Ecosphere Models.R* file). * This dataset is used to perform the PERMANOVA based on soil range, hence the first three columns represent sample ID, geographic, and environmental variables. * "SAMPLE_ID": Sample ID code, describes the soil source (see naming convention above) and the replicate number. * "SOIL_RANGE": Describes the continent the soil inoculum was sourced from (US: North American soil, DE: European soil, and STER: sterilized inoculum). * "HAB_TYPE": Describes the habitat type the soil inoculum was sourced from (URBAN: soil taken from an urban environment, TIDAL: soil taken from a tidal environment, FRESHWATER: soil taken from a freshwater environment). 6. ER_FUNGAL_GUILD_MODEL.csv * Contains proportion of fungal OTUs that are categorized into different guilds according to the FUNGuild database using OTUs collected from our ITS rRNA data, without the incorporation of samples taken from sterilized treatments. * These data were used to calculate the relative proportions of guilds based on soil range and whether or not North American soil fungal communities significantly differed in proportions of fungi belonging to different guilds compared to communities found in Europe (see the *Ecosphere Models.R* file). * "TRT": Sample ID code, describes the soil source (see naming convention above). * "HAB_TYPE": Describes the habitat type the soil inoculum was sourced from (URBAN: soil taken from an urban environment, TIDAL: soil taken from a tidal environment, FRESHWATER: soil taken from a freshwater environment). * "SOIL_RANGE": Describes the continent the soil inoculum was sourced from (US: North American soil, and EU: European soil). * "ENDOPHYTE": Proportion of fungal OTU counts classified as potential endophytic fungi. * "PATHOGEN_PARASITE": Proportion of fungal OTU counts classified as potential plant pathogens and parasites. * "MYCORRHIZAE": Proportion of fungal OTU counts classified as potential mycorrhizae. * "SAPROTROPH": Proportion of fungal OTU counts classified as potential plant saprotrophs. ### **.R Files** 1. Ecosphere Figures 2.R * Contains R code to reproduce the figures in the manuscript. * Each section of code will correspond to the figure within the manuscript (i.e., Fig. 2, and Fig. 3) 2. Ecosphere Models.R * Contains R code for models used to analyze the data for this study including the models for biomass, FUNGuild guild classification proportions, distance-to-centroid of NMDS for 16S and ITS communities by soil range, bacterial and fungal indicators by soil range, and PERMANOVA of bacterial and fungal communities. 3. Ecosphere supplemental.R * Contains R code to reproduce the figures and models described in the supplemental materials. * Each section of code will correspond to the figure or analysis within the supplemental materials (i.e., Fig. S1, and Fig. S2) ## Sharing/Access information All data used in this study is contained here in this DRYAD page. A README associated with the supplemental materials can be found in the README (supplemental material) docx. file uploaded to Zenodo.