DOI: 10.5061/dryad.g4f4qrg0b
title: Data from: Acquisition of an obligate environmental symbiont may be limited in the arboreal environment

description: 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.
description: # Acquisition of an obligate environmental symbiont may be constrained in
 the arboreal environment of a leaf-footed bug 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