Data from: Acquisition of an obligate environmental symbiont may be limited in the arboreal environment
Data files
May 14, 2025 version files 48.80 KB
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Dryad_data.zip
42.52 KB
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README.md
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Abstract
Many eukaryotic organisms have environmentally acquired microbial symbionts. In animals, microbes commonly occupy the gut and may supply critical nutrients. The leaf-footed bug, Leptoglossus zonatus (Coreidae), is a true bug that is dependent upon ingestion of the free-living, soilborne bacterium Caballeronia early in development for growth and reproduction. In 2019 and 2020, we tested the ability of second instar L. zonatus to acquire Caballeronia in the canopy of pomegranate trees where L. zonatus are often found. We compared the acquisition rate of Caballeronia in nymphs left to forage for the symbiont to bugs fed Caballeronia in advance. Additionally, we aimed to determine whether the microhabitat of potential symbiont sources influenced acquisition success. We hypothesized that the acquisition rate would be heterogeneous among treatments. In 2019, ∼30% of experimental bugs acquired Caballeronia, compared to 75% of those fed the symbiont. In 2020, only about 4% of experimental bugs acquired any symbiont. The symbiont composition of caged bugs differed, and strain diversity was reduced relative to wild bugs. We concluded that Caballeronia is present in the canopy environment, but nymphs may fail to acquire it in the fragments of habitat represented by caged branches, suggesting a cost to host dependency on environmentally acquired symbionts.
Journal: FEMS Microbiology Ecology
Authors: Liam Sullivan, Suzanne Kelly, Alison Ravenscraft, Martha Hunter
Description: This README file describes the open-format and R-formatted data packages accompanying the above publication.
Files in Open_format_data/bug_data:
1. Sullivan_infection_data.csv:
The counts of Caballeronia infected individuals from each replicate. Variables: Year represents year the data was collected. Trt is the treatment applied. Tree is synonymous with replicate number. Num_pos is the number of bugs tested that were positive for Caballeronia. Num_neg is number of bugs tested that were negative for Caballeronia. Num_tested is the total number of bugs in each replicate.
2. Sullivan_lifestage_clean.csv
Census data from each cage at the end of the experiment. Variables: Tree_num is the replicate number. Trt is the treatment applied. Second, third, fourth, fifth, total adult reflect the number of individuals at each life stage. Total_alive is the sum of live bugs in each cage at the end of the experiment. Early summarizes bugs in the 2nd through 4th instars. Late summarizes bugs in the 5th instar and adult stages. Prop_old is the proportion of the live bugs in the “late” category. Year is the year when the experiment was run.
3. Sullivan_mortality.csv
The summary of mortality for each replicate in each year. Tree_num is replicate number. Trt is the treatment applied. Total_alive is the number of live insects in each replicate at take down. Year is the year when the experiment was run. Tot.dead is the total dead bugs in each cage at the end of the experiment. Tot.dead.log is the log(x+1) transformation of tot.dead. Initial is the number of bugs in each replicate at the start of the experiment.
4. Sullivan_daily_highs.csv
Data used to compare conditions between 2019 and 2020 blocks. Date.Time. is the day the data was collected from. Year is the block. High.temps is the max temperature achieved each day in °C. High.rh is the max relative humidity recorded each day.
Files in R_Files:
1. Sullivan_FEMSME_analysis+figs.R
This script reproduces the analysis and figures for the paper cited above.
2. Sullivan_infection_data.Rdata:
The counts of Caballeronia infected individuals from each replicate. Variables: Year represents year the data was collected. Trt is the treatment applied. Tree is synonymous with replicate number. Num_pos is the number of bugs tested that were positive for Caballeronia. Num_neg is number of bugs tested that were negative for Caballeronia. Num_tested is the total number of bugs in each replicate.
3. Sullivan_lifestage_clean.Rdata
Census data from each cage at the end of the experiment. Variables: Tree_num is the replicate number. Trt is the treatment applied. Second, third, fourth, fifth, total adult reflect the number of individuals at each life stage. Total_alive is the sum of live bugs in each cage at the end of the experiment. Early summarizes bugs in the 2nd through 4th instars. Late summarizes bugs in the 5th instar and adult stages. Prop_old is the proportion of the live bugs in the “late” category. Year is the year when the experiment was run.
4. Sullivan_mortality.Rdata
The summary of mortality for each replicate in each year. Tree_num is replicate number. Trt is the treatment applied. Total_alive is the number of live insects in each replicate at take down. Year is the year when the experiment was run. Tot.dead is the total dead bugs in each cage at the end of the experiment. Tot.dead.log is the log(x+1) transformation of tot.dead. Initial is the number of bugs in each replicate at the start of the experiment.
5. Sullivan_daily_highs.Rdata
Data used to compare conditions between 2019 and 2020 blocks. Date.Time. is the day the data was collected from. Year is the block. High.temps is the max temperature achieved each day in °C. High.rh is the max relative humidity recorded each day.
6. Sullivan_Proportion_infected+late_stage.Rdata
Data was used to generate 3a and b. Data is a long-formatted summary of the proportion of bugs in each replicate that are *Caballeronia *positive and the proportion of bugs that are 5th instar or adult. Year is the block. TRT is the treatment applied. Tree is the replicate number. Prop defines which proportion is used in value, either 5th instar or adult, or Caballeronia positive. Value is the proportion of the replicate meeting the criteria from the category prop.
7. Sullivan_prop_infect_by_stage.Rdata
Data used to generate figure 2b. Data consists of both the number of and calculated proportion of bugs within each replicate that are positive for *Caballeronia *and the age “group” which they were sorted into. Year is the block. TRT is the treatment applied. Tree is the replicate number. Num_pos is the number of *Caballeronia *positive bugs. Num_neg is the number of *Caballeronia *negative bugs. Num_tested is total bugs that underwent diagnostic PCR in each replicate. Prop_pos is the portion of *Caballeronia *positive bugs in the replicate. Prop_neg is the portion of *Caballeronia *positive bugs in the replicate. Group is the age group that bugs were sorted into, either early (3rd or 4th instar) or late (5th instar or adult).
8. Sullivan_Proportion_infect_fig.Rdata
Data used to generate figure 2a. Data consists of both the number of and calculated proportion of bugs within each replicate that are positive for *Caballeronia *and the age “group” which they were sorted into. Year is the block. Trt is the treatment applied. Tree is the replicate number. Num_pos is the number of *Caballeronia *positive bugs. Num_tested is total bugs that underwent diagnostic PCR in each replicate. Prop_pos is the portion of *Caballeronia *positive bugs in the replicate.
9. caged bugs analysis.R
This script reproduces the analysis of *Caballeronia *community composition and the associated figure.
10. Caged_wildFall.Rdata
Phyloseq object necessary to reproduce the analysis in caged bugs analysis.R