DOI: 10.5061/dryad.fj6q5742p
title: Data from: Plant, insect, and soil microbial communities vary across brome invasion gradients in northern mixed-grass prairies

description: Species interactions shape native plant communities, influencing both
 composition and ecosystem processes, with invasion by non-native species
 threatening these dynamic relationships, native species, and function. The
 consequences of invasive plants in particular may stretch across taxa to
 impact plant, insect, and soil microbial communities directly and
 indirectly, with consequences for ecological functioning. In northern
 mixed-grass prairies in the United States, invasion by two annual brome
 grasses, Bromus arvensis and B. tectorum, negatively impacts rangeland
 plants; however, the simultaneous effects on insects and soil microbes
 (bacteria and archaea), and the implications for ecological function, have
 received less attention. Here, using observational field studies conducted
 at two mixed-grass prairie sites in Montana and Wyoming, we assessed the
 relationships between plants, insects, and soil microbes across gradients
 of invasion by B. arvensis and B. tectorum. Overall, we found differences
 in plant and insect communities and functional groups with increasing
 invasion abundance for both brome species. However, associations between
 invasion and the soil microbial community were species specific, as we
 only saw these relationships under B. tectorum invasion, implying B.
 tectorum may have more substantial consequences for rangeland management.
 While invasion by annual bromes may cause changes in certain plant and
 insect functional groups, such as C4 perennial grasses and certain insect
 herbivores, soil microbial functional groups may be less impacted,
 especially under B. arvensis invasion. This work sheds light on the need
 to explore changes in natural communities across taxa and to all invasive
 species, as ecosystem effects are likely to be contingent upon both.
description: These datsets were collected from the Thunder Basin (TB)
 Ecoregion in Wyoming and Fort Keogh (FK) Livestock and Range Research
 Laboratory in Montana. 
description: # Plant, insect, and soil microbial communities vary across brome invasion
 gradients in northern mixed-grass prairies
 Contains datasets
 associated with plant, insect, and soil microbial community analyses in R
 -Date of data collection: 2019-2022 -Geographic location: Thunder Basin
 Ecoregion, Wyoming, and Fort Keogh Livestock and Range Research
 Laboratory, Montana. Below, Thunder Basin Ecoregion is abbreviated TB and
 Fort Keogh Livestock and Range Research Laboratory is abbreviated FK. Note
 also that BRAR = Bromus arvensis and BRTE = Bromus tectorum throughout.
 Many variables are repeated throughout datasets, so for readability, we
 define each variable once. ### **Datasets included:** **-File
 list:** **1) TB_FK_fieldwork_v5.R** Description: R script containing
 workflow for this project. Imports subsequent datasets. **2)
 TB_plotinfo.csv** Description: Contains specific plot information for the
 study conducted in TB. Exact plot coordinates is replaced with
 "null" to protect the privacy of the landowners who allowed us
 to conduct this work. Variable list: -location: TB -plot: unique plot
 number (1-50) -plot_type: O = observational study -invasion_percent:
 invasion levels, later replaced by 1-5 -plot_name: unique plot identifier
 -invasive_type: which invasive species gradient we were considering (BRAR
 = Bromus arvensis and BRTE = Bromus tectorum) -grad_num: unique gradient
 number assigned to each block -phone_lat, phone_long, garmin_lat,
 garmin_long: specific GPS coordinates for plots, replaced with null **3)
 FK_plotinfo.csv** Description: Contains specific plot information for the
 study conducted in FK. Exact plot coordinates is replaced with
 "null" to protect the privacy of the landowners who allowed us
 to conduct this work. Variable list: -location: FK -grad_num: unique
 gradient number assigned to each block -plot: unique plot number (1-48)
 -plot_type: C or R is inconsequential for 2020 for this study, but was
 later used for another study to designate control versus treatment plots.
 We removed those treatment plots in subsequent analyses.
 -invasion_percent: invasion levels, later replaced by 1-5 -plot_name:
 unique plot identifier -invasive_type: which invasive species gradient we
 were considering (BRAR = Bromus arvensis) -latitude and longitude:
 specific GPS coordinates for plots, replaced with null **4)
 speciesinfo_TB.csv** Description: specific information on the plant
 species found at TB, as well as the functional groups we assigned. In our
 analyses, we used "funct2" as our assignments. Variable list:
 -symbol: 4 digit code (first two letters of genus name, first two letters
 of species name) as used by the USDA to abbreviate each plant species
 -scientific_name: scientific name of each plant species -functional_group:
 broad plant functional group -perennial_annual: whether each species is a
 perennial or annual species -native_invasive: whether each species is
 native or invasive in this region (note invasive also refers to introduced
 species) -spec_funct_group: specific plant functional group -family:
 Family for each plant species -funct2: plant functional group as used in
 these analyses **5) speciesinfo_FK.csv** Description: specific information
 on the plant species found at FK, as well as the functional groups we
 assigned. In our analyses, we used "funct2" as our assignments.
 Variable list: -symbol: 4 digit code (first two letters of genus name,
 first two letters of species name) as used by the USDA to abbreviate each
 plant species -scientific_name: scientific name of each plant species
 -functional_group: broad plant functional group -perennial_annual: whether
 each species is a perennial or annual species -native_invasive: whether
 each species is native or invasive in this region (note invasive also
 refers to introduced species) -spec_funct_group: specific plant functional
 group -funct2: plant functional group as used in these analyses **6)
 FK_2022_herbivory.csv** Description: plant herbivory data for FK in 2022
 Variable list: -year: year of data collection -date: collection data for
 this data -plant_rep: 1-12, number assigned to each individual plant
 sampled in each plot -plant_sp: 4 digit code for the plant species studied
 -species: scientific name of the plant species studied -plant stage: R =
 reproductive, V = vegetative plant stage -tot_num_leaves: total number of
 leaves found on the individual -num_herb_leaves: count of leaves that
 experienced herbivory -per_herb_leaf1-10: percent herbivory on leaf 1 up
 to leaf 10 (plant needed to have at least 2 leaves to be sampled, and if
 it had &gt;10 leaves, 10 were randomly sampled) -per_herb_plant: percent
 herbivory on the whole plant **7) FK_2021_herbivory.csv** Description:
 plant herbivory data for FK in 2021 \**8) FK_2020_speciescomp.csv **
 Description: plant species composition data for FK in 2020 Variable list:
 -year: year of data collection -aerial_basal: we collected both aerial and
 basal cover data for all plots -bareground-end of dataset: percent cover
 of each species or category **9) FK_insect_feeding_guilds.csv**
 Description: insect feeding guild assignments used in this study for FK
 -order2: insect Order -family2: insect Family -feeding_guild: feeding
 classification -herbivore_type: if an herbivore, what kind -guild: feeding
 group assignment used in analyses **10) FKdistance-matrix.tsv**
 Description: soil microbial distance matrix as outputted from QIIME2 for
 FK using Bray-Curtis dissimilarities. Letters and numbers (e.g., E10,
 corresponds to a unique plot. It designates the well on the 96-well plate
 used for microbial analyses.) **11) FK_2020_microbe_richness.csv**
 Description: soil microbial richness found in each plot in FK in 2020.
 Variable list: -id: unique plot identifier as assigned when samples were
 put into 96-well plate -residual: residuals as found from QIIME2 analyses
 -observed_features: plot level microbial richness -predicted
 observed_features: predicted richness as simulated by QIIME2 workflow
 **12) TB_insect_feeding_guilds.csv** Description: insect feeding guild
 assignments used in this study for TB **13) func_table3.tsv** Description:
 functional group table output for soil microbial analyses for FK and TB
 Variable list: -OUT_ID: functional group assigned by Faprotax database
 -A1-H9: occurrence data for each microbial functional group within each
 plot (A1-H9 refer to unique plot identifiers) **14)
 TBdistance-matrix.tsv** Description: soil microbial distance matrix as
 outputted from QIIME2 for TB using Bray-Curtis dissimilarities. Letters
 and numbers (e.g., A1, corresponds to a unique plot. It designates the
 well on the 96-well plate used for microbial analyses.) **15)
 TB_microbe_richness.csv** Description: soil microbial richness found in
 each plot in TB in 2019. \**16) mapping.csv ** Description: metadata for
 soil microbial analyses for FK and TB to be used in QIIME2 workflow **17)
 FK_2022_insectbiomass.csv** Description: biomass (weight) data for insect
 groupings for FK in 2022 Variable list: -date: date measurement took place
 in the lab, not data of field collection -weighed_by: initials of
 researcher taking each measurement -order: insect Order or misc for
 unidentifiable insect parts -indiv_orthoptera_biomass: individual
 orthoptera biomass -order_biomass: biomass as weighed by Order
 -total_biomass: plot level biomass of all insects and insect pieces
 -notes: any applicable commentary **18) TB_2019_speciescomp.csv**
 Description: plant species composition data for TB in 2019 **19)
 TB_2019_insectID.csv** Description: insect identification for Family for
 TB in 2019 Variable list: -sample: unique sample number for each insect
 within a plot **20) FK_2020_insectID.csv** Description: insect
 identification for Family for FK in 2020 Variable list: -name: initials of
 researcher doing identification **21) TB_2019_insectbiomass.csv**
 Description: biomass (weight) data for insect groupings for TB in 2019.
 Note we dropped plot 8 from analyses due to missing data. **22)
 FK_2020_insectbiomass.csv** Description: biomass (weight) data for insect
 groupings for FK in 2020. **23) FK_2021_insectbiomass.csv** Description:
 biomass (weight) data for insect groupings for FK in 2021. ##
 Sharing/Access information Links to other publicly accessible locations of
 the data: *
 
 ## Code/Software All analyses done in R version 3.6.2. Packages needed
 include vegan, tidyverse, codyn, ggplot2, nlme, lme4, and lmerTest. Script
 is annotated within. All data and code is available publicly on Github.