DOI: 10.5061/dryad.rr4xgxdjj
title: Canopy height and epiphytic bryophytes shape fungal communities in a temperate rainforest

description: Fungal communities contribute to plant ecology and evolution in forested
 ecosystems. Their diverse interactions with associated host plants can
 vary along abiotic and biotic gradients, but these gradients are poorly
 understood in complex natural ecosystems. Given the high diversity of
 epiphytic plants in many ecosystems, forest canopies offer a unique and
 underexplored system for studying plant-associated microbial diversity and
 distribution. We explored both abiotic and biotic factors structuring
 arboreal fungal communities. Specifically, we hypothesized that
 bryophyte-associated fungal communities are structured by the vertical
 height gradient within host trees (from the ground to high in the canopy),
 vary across host plant species, and that living bryophytes host distinct
 fungal communities compared to dead bryophyte matter. To test these
 hypotheses, we sampled living and dead bryophytes (mosses and liverworts)
 across three different bryophyte host species and four heights, ranging
 from the forest floor to 18 meters above the ground. We characterized the
 fungal community composition in each sample using metabarcoding. Fungal
 communities showed significant variation across substrates: bryophytes
 collected from the ground exhibited 17% greater Shannon diversity and 34%
 higher taxonomic richness than epiphytic bryophytes, while living
 bryophytes had 15% higher diversity and 30% greater richness than dead
 tissues. This pattern suggests that the diverse microhabitats within
 living bryophytes may drive microbial diversity. Community analysis
 identified a core fungal community across living bryophyte samples, but
 rare taxa accounted for a majority of reads, driving differences in
 community composition between different heights and bryophyte species.
 Epiphytic bryophyte-associated fungal communities show high heterogeneity
 across different substrates and heights, which provides insight into the
 structuring of the forest microbiome and epiphyte ecology. These results
 demonstrate the importance of exploring canopy-associated microbes to
 better understand microbial diversity and function in forest ecosystems.
description: # Canopy height and epiphytic bryophytes shape fungal communities in a
 temperate rainforest Dataset DOI:
 [https://doi.org/10.5061/dryad.rr4xgxdjj](https://doi.org/10.5061/dryad.rr4xgxdjj) ## Description of the data and file structure The data include fungal ITS sequencing results from bryophyte (moss and liverwort) samples, collected in order to determine how fungal diversity and community composition vary from the ground to the canopy, between bryophyte species, and between living and dead bryophytes. ## Access information Other publicly accessible locations of the data: * None Data was derived from the following sources: * All data was generated by and for this project. ## Code/software All data processing and analysis were performed in R version 4.4.0. Packages are included within the code. All packages are free and easily downloadable. **BryoFung_ITS_Dada2.R** * Load in raw sequencing data * Dereplication: combine identical sequences while retaining quality **BryoFung_MCToolsDecontamPhylo.R** * Use phyloseq to identify and remove contaminants **CanopyMicrobeAnalysis_ToShare.Rmd** * All analysis and figure generation. * Analysis of microbial alpha/beta diversity, community composition, and functional diversity. ### Files and variables #### File: EpiMicrMETAsqueaky.txt **Description:** Metadata for all samples remaining after data was decontaminated. ##### Variables * SAMPLE: Name of sample. TreeID-Plot-SampleType (e.g. 01-V2-PORNAV) * DateCollected * Collector: Person who collected the sample. * TreeID: Numerical ID of tree (1-12) * Site: Site where sample was collected (Hoh Rainforest) * Height: Categorical height within tree (T0=ground, V1/V2/V3 are ascending heights on trunk) * MeasuredHeight: Measured height from ground (m) * SampleType: Bryophyte species (ISOMYO = *Isotheium myosuroides*, PORNAV = *Porella navicularis*, METMEN = *Metaneckera menziesii*, COM = community, NECRO = dead bryophyte tissue) * SampleControl: experimental sample or control * ZYMO BATCH: batch number when extracting microbial DNA * Extraction Date: date of extraction * number in batch: tracking number within extraction batch * Concentration_ngul: DNA concentration (ng/ul) * CollNotes: notes from a collection of samples in the field * LabNotes: notes from DNA extraction #### File: Laurel_Cleaned_NoUnassigned_Mctoolsr.txt **Description:** Community matrix of fungal ASVs in bryophyte samples, after cleaning, containing only fungal ASVs assigned at the phylum level #### File: SamMap.txt **Description:** Mapping file for DNA sequencing ##### Variables * Same variables listed above * Time: Height category in tree (T0/V1/V2/V3) * Type: ISOMYO, PORNAV, METMEN, COM, or NECRO #### File: SamMapClean.txt **Description:** Sample Map after removing contaminants and insufficient samples #### File: ITS_FullTable_McToolsR.txt **Description:** Community matrix before cleaning/rarefaction #### File: IR_taxonomy_loaded.csv **Description:** Taxonomy of fungal ASVs present in samples ##### Variables * taxonomy1: kingdom * taxonomy2: phylum * taxonomy3: class * taxonomy4: order * taxonomy5: family * taxonomy6: genus * taxonomy7: species #### File: IR_map_loaded.csv **Description:** Sample metadata ##### Variables * SampleID * See descriptions in EpiMicrMETAsqueaky.txt #### File: FullITS_seqtab_newlabels.csv **Description:** Community matrix with fungal ASVs as columns and samples as rows #### File: IR_data_loaded.csv **Description:** Community matrix after cleaning and rarefaction, with fungal ASVs as rows and samples as columns #### File: ITS_CleanTable_McToolsR.txt **Description:** Community matrix after cleaning #### File: taxatab.csv **Description:** Taxonomy data for fungal ASVs ##### Variables * SeqID * Taxonomy labels #### File: FullITS_seqtab.csv **Description:** Community matrix with fungal ASVs as columns and samples as rows #### File: SamMap.csv **Description:** Same as other mapping files ##### Variables: * Same as other mapping files #### File: ITS_taxonomy.xlsx **Description:** Taxonomy data for fungal sequences present in samples. #### File: ITS_Sequences.zip **Description:** .zip file containing sequencing data from all samples (see below). ### DNA SEQUENCING DATA Format of file names: SampleID_Read.fastq.gz TreeID-Height-SampleType_Read#.fastq.gz