Picky eaters: selective microbial diet of avian ectosymbionts
Data files
Nov 12, 2024 version files 2.61 MB
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Pcitrea_fm_microbes-main-dryad.zip
2.61 MB
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README.md
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Abstract
Individual organisms can function as ecosystems inhabited by symbionts. Symbionts may interact with each other in ways that subsequently influence their hosts positively or negatively, although the details of how these interactions operate collectively are usually not well understood.
Vane-dwelling feather mites are common ectosymbionts of birds and are proposed to confer benefits to hosts by consuming feather-degrading microbes. However, it is unknown whether these mites exhibit generalist or selective diets, or how their dietary selection could potentially impact their symbiotic functional nature.
In this study, we conducted 16S rDNA and ITS1 amplicon sequencing to examine the microbial diet of feather mites. We characterized and compared the diversity and composition of bacteria and fungi in the bodies of mites living on feathers of the Prothonotary Warbler, Protonotaria citrea, to microbial assemblages present on the same feathers.
We found less diverse, more compositionally similar microbial assemblages within mites than on feathers. We also found that mites were resource selective. Based on the identity and known functions of microbes found within and presumably preferred by mites, our results suggest that these mites selectively consume feather-degrading microbes. Therefore, our results support the proposition that mites confer benefits to their hosts.
This study provides insight into symbioses operating at multiple biological levels, highlights the ecological and evolutionary importance of the synergistic interactions between species, and greatly expands our understanding of feather mite biology.
This repo includes all the code necessary to reproduce results presented in the associated manuscript. Below, you will find an overview of the repo's contents, along with guidance on individual README files that provide detailed instructions and descriptions for specific sections.
Associated manuscript: Matthews, A.E., B.K. Trevelline, A.J. Wijeratne, and T.J. Boves. 2024. Picky eaters: selective
microbial diet of avian ectosymbionts. Journal of Animal Ecology. DOI: 10.1111/1365-2656.14215
The purpose of this study was to understand the dietary selection of vane-dwelling feather mites found on Prothonotary Warblers (Protonotaria citrea) and how their dietary selection impacts their functional nature with hosts (i.e., are they parasites, mutualists, or commensals?). We found that feather mites exhibit a selective diet of feather microbes, many of which have known feather-degrading functions. Our findings support the idea that mites act as mutualistic feather “cleaners” and highlight the synergistic interactions between co-occurring symbionts in animal ecosystems.
Contents overview
This repo is organized into two main sections:
16S_qiime_20221004
- Contains analyses for 16S (bacteria) sequences of feathers and mite data
- This directory is divided into several subdirectories that are numbered in order of operation:
- 01_batch_effects: test for sequencing batch effects
- 02_Run1Run2_combo: combine data from two sequencing runs, run initial analyses (e.g., trim primers, DADA2, taxonomy/SILVA)
- 03_decontam: decontaminate reads (i.e., leave only bacteria)
- 04_SeparateSamples: separate biological samples from control samples
- 05_AlphaBetaDiversity: analyze alpha and beta diversity stats
- 06_RPCA: run RPCA analyses
- 07_TaxaBarplots: create taxa barplots
- 08_R: plotting and analyses run in R (e.g., 'pretty plots,' dietR)
- 09_Maaslin: differential abundance analyses
- 11_picrust: predictive metagenomic analyses (removed, but available upon request)
ITS_qiime_20230220
- Contains analyses for ITS (fungi) sequences of feathers and mite data
- This directory is divided into several subdirectories that are numbered in order of operation:
- 01_ForwardData: trim adapters
- 02_dada2: run DADA2
- 03_taxonomy: run taxonomy/UNITE
- 04_decontam: decontaminate reads (i.e., leave only fungi)
- 05_SeparateSamples: separate biological samples from control samples
- 06_AlphaBetaDiversity: analyze alpha and beta diversity stats
- 07_TaxaBarplots: create taxa barplots
- 08_RPCA: run RPCA analyses
- 09_R: plotting and analyses run in R (e.g., 'pretty plots,' dietR)
- 10_Maaslin: differential abundance analyses
- 11_FUNguild: predictive functional analyses (removed, but available upon request)
Individual subdirectory READMEs
Each subdirectory has a dedicated README file providing more detailed information, such as the scripts used to generate results/output files, analysis guidelines, data formats, as well as variable definitions. Please consult these individual READMEs for specific instructions related to each component of this repo.
NOTE: This repo has been "cleaned up" from a private repo for the public.