Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi
Data files
Jan 23, 2024 version files 623.04 KB
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ap.qs_Hardcode0s.csv
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KingFungiTablewithTax_AnimalPathogens_DummyCode.csv
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KingFungiTablewithTax_AnimalPathogens_Remove0s.csv
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KingFungiTablewithTax_PlantPathogens_DummyCode.csv
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KingFungiTablewithTax_PlantPathogens_Remove0s.csv
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KingFungiTablewithTax.csv
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mpbg.qs_Hardcode0s.csv
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Myr_Paths_by_Genus_DummyCode.csv
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Myr_Paths_by_Genus_Remove0s.csv
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pp.qs_Hardcode0s.csv
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README.md
Abstract
The putative benefits to seeds in myrmecochory (ant-mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harbored different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant-handled seeds and seeds with manually-removed elaiosomes were less dissimilar. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction of the seed coat pathogenic community, which may be driven by elaiosome removal or as a byproduct of ant cleaning behaviors and chemical secretions.
README: Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi
https://doi.org/10.5061/dryad.2ngf1vhwv
The following are associated with this manuscript:
Alpha Diversity R Scripts (for all fungi, animal pathogens, plant pathogens, and myrmecochore pathogens)
AlphaDiveristy_All_Fungi.R
- This is the R script for analyzing the Alpha Diversity (using Hill numbers via HillR) for all fungal taxa associated with seed washes
AlphaDiveristy_Myrmecochore_Paths.R
- This is the R script for analyzing the Alpha Diversity (using Hill numbers via HillR) for all fungal taxa identified as pathogenic to myrmecochores associated with seed washes
AlphaDiveristy_Plant_Paths.R
- This is the R script for analyzing the Alpha Diversity (using Hill numbers via HillR) for all fungal taxa identified as pathogenic to plants associated with seed washes
AlphaDiversity_Animal_Paths.R
- This is the R script for analyzing the Alpha Diversity (using Hill numbers via HillR) for all fungal taxa identified as pathogenic to animals associated with seed washes
Beta Diversity R Scripts (for all fungi, animal pathogens, plant pathogens, and myrmecochore pathogens)
BetaDiveristy_AnimalPaths.R
- This is the R script for analyzing the Beta Diversity (calculated as community turnover using Hill numbers via HillR) for all fungal taxa identified as pathogenic to animals associated with seed washes
BetaDiversity_AllFungi.R
- This is the R script for analyzing the Beta Diversity (calculated as community turnover using Hill numbers via HillR) for all fungal taxa associated with seed washes
BetaDiversity_MyrmecochorePaths.R
- This is the R script for analyzing the Beta Diversity (calculated as community turnover using Hill numbers via HillR) for all fungal taxa identified as pathogenic to myrmecochores associated with seed washes
BetaDiversity_PlantPaths.R
- This is the R script for analyzing the Beta Diversity (calculated as community turnover using Hill numbers via HillR) for all fungal taxa identified as pathogenic to plants associated with seed washes
RDA R Scripts (for all fungi, animal pathogens, plant pathogens, and myrmecochore pathogens)
RDA_AllFungi.R
- This is the R script for analyzing the Beta Diversity (as a distance-based redundancy analysis using vegan) for all fungal taxa associated with seed washes while controlling for seed type
RDA_AnimalPathogens.R
- This is the R script for analyzing the Beta Diversity (as a distance-based redundancy analysis using vegan) for all fungal taxa identified as pathogenic to animals associated with seed washes while controlling for seed type
RDA_MyrmeochorePathogens.R
- This is the R script for analyzing the Beta Diversity (as a distance-based redundancy analysis using vegan) for all fungal taxa identified as pathogenic to myrmecochores associated with seed washes while controlling for seed type
RDA_PlantPathogens.R
- This is the R script for analyzing the Beta Diversity (as a distance-based redundancy analysis using vegan) for all fungal taxa identified as pathogenic to plants associated with seed washes while controlling for seed type
Qiime2 Pipeline for sequence processing and rarefaction
Qiime2_ITS_To_Taxonomy_Pipeline
- This is the Qiime2 Pipeline from real sequence reads through the processing of those reads
Qiime2_RarefiedTable_Pipeline_toFunGuild
- This is the Qiime2 Pipeline from processed and trimmed reads to rarefied samples to taxonomic assignment of ASVs though FunGuild
Associated Excel datafiles for above scripts
For all excel files, the following abbreviations are true:
- For Samples- BR indicates a bloodroot seed wash; WG indicates a wild ginger seed wash; JD indicates a twinleaf seed wash; A indicates an ant-handled seed wash; C indicates a control seed wash; CE indicates a no elaiosome seed wash (in which the elaiosome was sterilely, manually removed; numbers indicate replicates (1-16)
- For Seed_Type- Bloodroot indicates a bloodroot seed wash (Sanguinaria canadensis); WildGinger indicates a wild ginger seed wash (Asarum canadense); Twinleaf indicates a twinleaf seed wash (*Jeffersonia diphylla) *
- Treatment- Ant indicates an ant-handled seed wash; Control indicates a control seed wash; ControlNoElaiosome indicates a no elaiosome seed wash (in which the elaiosome was sterilely, manually removed)
- For Ant samples only: ColonyCode indicates the individual colony that handled the seeds; ColonySize indicates the number of worker ants in that colony; ColonyLocation indicates where that colony was collected from; HandlingScore is a numerical scale from 1 (no ant handling of seeds) to 5 (all seeds were handled by ants and all elaiosomes were removed by ants).
- All other columns without clear names (i.e., random letters and numbers) indicate Amplicon Sequence Variants (ASVs) and thus are a unique fungal species
KingFungiTablewithTax
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is the complete fungal data
KingFungiTablewithTax_AnimalPathogens_DummyCode
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Animal Pathogens. There is an additional column (Dummy_OTU) with an abundance of 1 for all samples to deal with zero data (no animal pathogens in some samples) in dbRDA analyses.
KingFungiTablewithTax_AnimalPathogens_Remove0s
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Animal Pathogens. In this dataset used for beta diversity, samples with no animal pathogens were removed for analysis
KingFungiTablewithTax_PlantPathogens_DummyCode
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Plant Pathogens. There is an additional column (Dummy_OTU) with an abundance of 1 for all samples to deal with zero data (no plant pathogens in some samples) in dbRDA analyses.
KingFungiTablewithTax_PlantPathogens_Remove0s
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Plant Pathogens. In this dataset used for beta diversity, samples with no plant pathogens were removed for analysis
mpbg.qs_Hardcode0s
- See above for some column descriptors. q0, q1, q2, q3, q4, q5, q6 columns are all Hill number calculations (order q) for that sample. This is only the fungi ASVs that were identified as Myrmecochore Pathogens. In this dataset used for alpha diversity, samples with no myrmecochore pathogens were hardcoded to 0 (i.e., having no myrmecochore pathogens)
Myr_Paths_by_Genus_DummyCode
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Myrmecochore Pathogens. There is an additional column (Dummy_OTU) with an abundance of 1 for all samples to deal with zero data (no myrmecochore pathogens in some samples) in dbRDA analyses.
Myr_Paths_by_Genus_Remove0s
- See above for column descriptors. Numbers in each row under each ASVs indicate the abundance of that ASV in that sample. Rows indicate a sample. This is only the fungi ASVs that were identified as Myremecochore Pathogens. In this dataset used for beta diversity, samples with no mrymecochore pathogens were removed for analysis
pp.qs_Hardcode0s
- See above for some column descriptors. q0, q1, q2, q3, q4, q5, q6 columns are all Hill number calculations (order q) for that sample. This is only the fungi ASVs that were identified as Plant Pathogens. In this dataset used for alpha diversity, samples with no plant pathogens were hardcoded to 0 (i.e., having no plant pathogens)
ap.qs_Hardcode0s
- See above for some column descriptors. q0, q1, q2, q3, q4, q5, q6 columns are all Hill number calculations (order q) for that sample. This is only the fungi ASVs that were identified as Animal Pathogens. In this dataset used for alpha diversity, samples with no animal pathogens were hardcoded to 0 (i.e., having no animal pathogens)
Sharing/Access information
N/A
Code/Software
All statistics were run in R version 3.6.0
All sequence processing was done in Qiime2