Data from: Effects of live yeasts and their metabolic products on bumble bee microcolony development
Data files
Apr 02, 2026 version files 392.73 KB
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final_MC_info.csv
10.65 KB
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metabo_data_nectar_md.csv
860 B
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metabo_data_nectar.csv
51.29 KB
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metabo_data_pollen_md.csv
860 B
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metabo_data_pollen.csv
64.36 KB
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nectar_data_normalized.csv
122.70 KB
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pollen_data_normalized.csv
123.17 KB
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README.md
10.83 KB
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survival_d_sharedfrail_total.csv
8 KB
Abstract
Bumble bees can benefit from fungi, though the mechanisms underlying these benefits remain unknown and could include nutrition, resource supplementation, or pathogen protection. We tested how adding living yeasts or their metabolic products to Bombus impatiens diets in a factorial experiment affects microcolony performance, including survival, reproduction, and pathogen presence. We additionally assessed the effects of yeast treatments on diet (nectar and pollen) chemical composition using untargeted metabolomics. Yeasts impacted microcolony reproduction and survival, but effects depended on the source colony. Colonies containing the putative pathogen Aspergillus showed reduced reproduction, but yeast treatments reduced Aspergillus prevalence. Yeast treatments altered the chemical composition of nectar and pollen, but most distinguishing compounds were unidentified. Our results suggest limited direct effects of yeasts via nutrition, resource supplementation, or modification of diets, instead suggesting that yeasts may benefit bees through interactions with the pathogens, including Aspergillus. Overall, the effects of yeast supplementation are context-dependent, and more research is necessary to better understand the factors important in determining their impacts on bee hosts.
https://doi.org/10.5061/dryad.f1vhhmh5t
Description of the data and file structure
This dataset contains all data and code associated with Effects of live yeasts and their metabolic products on bumble bee microcolony development. This data tests possible nutritional mechanisms through which symbiotic yeasts may benefit bumble bees by factorially manipulating the presence of 1) living yeast cells and 2) yeast metabolites in the diet (nectar and pollen) provided to microcolonies of the bumble bee Bombus impatiens. Data consists of performance and behavior metrics for 76 microcolonies (n = 19/treatment), including nectar consumption, worker survival, reproductive output (total and separated by life stage), and pathogen presence and abundance (for pathogens Aspergillus, Aspergillus flavus, and Ascosphaera apis). Additionally, to test the impact of yeast treatments on nectar and pollen chemical composition, primary untargeted metabolomics using GC-TOF MS was performed on nectar and pollen from 20 microcolonies (n = 5 nectar and pollen samples/treatment). This resulted in datasets containing 564 chemical compounds, which were then filtered and normalized using MetaboAnalyst 6.0, resulting in final datasets containing 423 compounds, which were used for downstream diversity and composition analyses.
Files and variables
File: final_MC_info.csv
Description: Spreadsheet containing information on experimental microcolonies, including yeast treatments, nectar consumption, offspring production, and pathogen presence and abundance. Missing values are denoted as "NA".
Variables
- ID: Microcolony ID
- source col: Queenright colony microcolonies were sourced from
- treatment: 4 level factor including both live yeast and metabolite treatment information
- cell_treat: presence of living yeast cells
- met_treat: presence of yeast metabolites
- survival_term_total: Average number of workers alive throughout the duration of the microcolony's lifespan
- weightdiff_total: Weight difference between nectar cups when they were first given to colonies and after 3 days of feeding (in g)
- survival_term_feeding: Average number of workers alive during the 3-day nectar feeding assay
- perbee_consumption*: *The total weight difference of nectar cups divided by the average number of workers alive during the 3-day nectar feeding assay - the total amount of nectar consumed per surviving bee
- male_days: The number of days to emergence of the first adult male
- number males: The number of emerged males produced throughout the microcolony's lifespan
- male_mass_g: The weight of all males in a microcolony (in g)
- avg_malemass: The average mass of males within a microcolony (in g)
- eggnum: The number of eggs at the end of the microcolony's lifespan
- eggmass_g: The weight of all eggs in a microcolony (in g)
- avg_eggmass: The average mass of eggs within a microcolony (in g)
- larvnum: The number of larvae at the end of the microcolony's lifespan
- larvmass_g: The weight of all larvae in a microcolony (in g)
- avg_larvmass: The average mass of larvae within a microcolony (in g)
- pupnum: The number of pupae at the end of the microcolony's lifespan
- pupmass_g: The weight of all pupae in a microcolony (in g)
- avg_pupmass: The average mass of pupae within a microcolony (in g)
- ueadultnum: The number of un-emerged adults at the end of the microcolony's lifespan
- ueadultmass_g: The weight of all un-emerged adults in a microcolony (in g)
- avg_ueadultmass: The average mass of un-emerged adults within a microcolony (in g)
- total_offspring: Total count of all offspring produced by a microcolony (including eggs, larvae, pupae, un-emerged adults, and adult males)
- offspring_pres: Binary variable indicating whether a microcolony produced at least one offspring (1) or produced no offspring (0)
- Aspergillus_pres: Presence of the genus Aspergillus within a microcolony, as determined by PCR
- Aflav_pres: Presence of Aspergillus flavus within a microcolony, as determined by PCR
- Aflav_logcopynum: Total copy number of Aspergillus flavus in a microcolony, as determined by qPCR (log scale)
- Aflav_rawcopynum: Total copy number of Aspergillus flavus in a microcolony, as determined by qPCR
File: metabo_data_nectar.csv
Description: Results of primary untargeted metabolomics performed on microcolony nectar samples. Values are raw, unfiltered data. Each column (excluding column 1) represents a metabolite detected using GC-TOF MS. Unidentified compounds are denoted by numerical strings, representing the compound ID in the BinBase database. Values for each metabolite indicate peak height for the associated mass spectra.
Variables
- Sample: Identifier for samples, with the first number representing the microcolony ID, the second value representing the provision (n for nectar, p for pollen), and the third value representing sample number at the West Coast Metabolomics Center.
File: metabo_data_nectar_md.csv
Description: Associated metadata for nectar samples used for primary untargeted metabolomics.
Variables
- Sample: Identifier for samples, with the first number representing the microcolony ID, the second value representing the provision (n for nectar, p for pollen), and the third value representing sample number at the West Coast Metabolomics Center.
- cell_treat: presence of living yeast cells
- met_treat: presence of yeast metabolites
- com_treat: 4 level factor including both live yeast and metabolite treatment information
- source_col: Queenright colony microcolonies were sourced from
- total_offspring: Total count of all offspring produced by a microcolony (including eggs, larvae, pupae, un-emerged adults, and adult males)
- offspring_pres: Binary variable indicating whether a microcolony produced at least one offspring (1) or produced no offspring (0)
- survival_term: Average number of workers alive throughout the duration of the microcolony's lifespan
File: metabo_data_pollen.csv
Description: Results of primary untargeted metabolomics performed on microcolony pollen samples. Values are raw, unfiltered data. Each column (excluding column 1) represents a metabolite detected using GC-TOF MS. Unidentified compounds are denoted by numerical strings, representing the compound ID in the BinBase database. Values for each metabolite indicate peak height for the associated mass spectra.
Variables
- Sample: Identifier for samples, with the first number representing the microcolony ID, the second value representing the provision (n for nectar, p for pollen), and the third value representing sample number at the West Coast Metabolomics Center.
File: metabo_data_pollen_md.csv
Description: Associated metadata for pollen samples used for primary untargeted metabolomics.
Variables
- Sample: Identifier for samples, with the first number representing the microcolony ID, the second value representing the provision (n for nectar, p for pollen), and the third value representing sample number at the West Coast Metabolomics Center.
- cell_treat: presence of living yeast cells
- met_treat: presence of yeast metabolites
- com_treat: 4 level factor including both live yeast and metabolite treatment information
- source_col: Queenright colony microcolonies were sourced from
- total_offspring: Total count of all offspring produced by a microcolony (including eggs, larvae, pupae, un-emerged adults, and adult males)
- offspring_pres: Binary variable indicating whether a microcolony produced at least one offspring (1) or produced no offspring (0)
- survival_term: Average number of workers alive throughout the duration of the microcolony's lifespan
File: pollen_data_normalized.csv
Description: Results of primary untargeted metabolomics performed on microcolony pollen samples. Values are filtered, normalized data produced by MetaboAnalyst. Column 1 represents metabolites detected using GC-TOF MS. Unidentified compounds are denoted by numerical strings, representing the compound ID in the BinBase database. Each column represents a pollen sample, with the first row representing sample ID. Values for each metabolite indicate normalized peak height for the associated mass spectra.
File: survival_d_sharedfrail_total.csv
Description: Survival results for workers in experimental microcolonies exposed to different yeast treatments. Microcolonies may have multiple rows associated with them, with each row representing a successive worker death.
Variables
- ID: Microcolony ID
- source col: Queenright colony microcolonies were sourced from
- treatment: 4 level factor including both live yeast and metabolite treatment information
- cell_treat: presence of living yeast cells
- met_treat: presence of yeast metabolites
- time.start: Number denoting the beginning of survival measurements. All values are 0, as all worker survival was recorded starting at the beginning of the experiment.
- time.stop: The time (in days) at which a worker death in a microcolony was recorded.
- time: Total time (in days) that each worker lived
- event: Binary variable denoting whether a worker death was observed (1) or was right-censored due to the end of the experiment (0)
- Aspergillus_pres: Presence of the genus Aspergillus within a microcolony, as determined by PCR
File: nectar_data_normalized.csv
Description: Results of primary untargeted metabolomics performed on microcolony pollen samples. Values are filtered, normalized data produced by MetaboAnalyst. Column 1 represents metabolites detected using GC-TOF MS. Unidentified compounds are denoted by numerical strings, representing the compound ID in the BinBase database. Each column represents a pollen sample, with the first row representing sample ID. Values for each metabolite indicate normalized peak height for the associated mass spectra.
Code/software
All data was analyzed using R version 4.2 and MetaboAnalyst 6.0
R packages required for this script are:
- 'dplyr' (version 1.0.10)
- 'ggplot2' (version 3.5.0)
- 'ggbeeswarm' (version 0.7.2)
- 'ggpubr' (version 0.6.0)
- 'MASS' (version 7.3-60)
- 'randomForest' (version 4.7-1.1)
- 'survival' (version 3.4-0)
- 'tidyverse' (version 2.0.0)
- 'vegan' (version 2.6-4)
- 'viridis' (version 0.6.3)
The attached code files include:
- yeastfunctions.Rmd: An R Markdown file containing all code used for analysis of survival, reproduction, nectar consumption, pathogen presence and abundance, and metabolomic data (excluding the analyses performed in MetaboAnalyst)
- yeastfunctions.html: a knitted version of the R Markdown code
Microcolonies of B. impatiens (5 workers per microcolony) were created from Koppert queenright colonies and reared on one of four different diets (nectar and pollen), manipulating the presence of 1) live yeast cells and 2) yeast metabolites in a factorial manner. Over four weeks, worker survival was measured daily in each microcolony, and time to emergence of the first adult offspring was tracked. Nectar consumption of a subset of microcolonies was measured over a three day period. After four weeks, all surviving microcolonies were frozen and dissected to remove, count, and weigh developing offspring (eggs, larvae, pupae, adult males). Each microcolony was screened for the presence of the pathogens Aspergillus, Aspergillus flavus, and Ascosphaera apis by dissecting out guts from three workers per microcolony, pooling them, and extracting DNA for PCR (all pathogens) and qPCR (A. flavus only).
To measure impacts of yeast treatments on chemical composition of diet (nectar and pollen), a subset of microcolony provisions (n = 5 nectar and pollen samples per treatment) were collected three days after treatment application and sent to the UC Davis West Coast Metabolomics Center for primary untargeted metabolomics using GC-TOF MS. Metabolomics datasets here include raw data, data normalized using MetaboAnalyst, and associated metadata.