DOI: 10.5061/dryad.r2280gbnc
title: Picky eaters: selective microbial diet of avian ectosymbionts

description: 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. 
description: # Pcitrea\_fm\_microbes 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.