Data from: Plant, insect, and soil microbial communities vary across brome invasion gradients in northern mixed-grass prairies
Data files
Feb 22, 2024 version files 503.63 KB
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FK_2020_insectbiomass.csv
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FK_2020_insectID.csv
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FK_2020_microbe_richness.csv
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FK_2020_speciescomp.csv
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FK_2021_herbivory.csv
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FK_2021_insectbiomass.csv
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FK_2022_herbivory.csv
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FK_2022_insectbiomass.csv
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FK_insect_feeding_guilds.csv
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FK_plotinfo.csv
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FKdistance-matrix.tsv
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func_table3.tsv
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mapping.csv
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README.md
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speciesinfo_FK.csv
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speciesinfo_TB.csv
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TB_2019_insectbiomass.csv
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TB_2019_insectID.csv
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TB_2019_speciescomp.csv
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TB_insect_feeding_guilds.csv
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TB_microbe_richness.csv
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TB_plotinfo.csv
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TBdistance-matrix.tsv
Abstract
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.
README: Plant, insect, and soil microbial communities vary across brome invasion gradients in northern mixed-grass prairies
https://doi.org/10.5061/dryad.fj6q5742p
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 >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.
Methods
These datsets were collected from the Thunder Basin (TB) Ecoregion in Wyoming and Fort Keogh (FK) Livestock and Range Research Laboratory in Montana.