DOI: 10.5061/dryad.gmsbcc2zt
title: Metadata from: Rhizosphere bacteria and fungi are differentially structured by host plants, soil mineralogy and ectomycorrhizal communities in the Alaskan tundra

description: The rhizosphere contains a diverse group of bacteria and fungi living near
 plant roots whose composition and function are key drivers of ecosystem
 and biogeochemical processes. Despite rich literature on rhizosphere
 communities, surprisingly few studies have examined the drivers of
 rhizosphere community structures in natural settings. We collected 513
 root samples from 141  individual plants representing six plant
 species and three mycorrhizal association types across four glacial drifts
 in the North Slope of Alaska. Glacial drifts ranged from 11,000 to 4.5
 million years since deglaciation representing a gradient in glacial
 history and mineralogical weathering. We found that glacial history, a
 strong proxy for soil mineralogy, explained most of the captured variation
 in rhizosphere bacterial communities (13.3%) and ectomycorrhizal fungal
 communities (10.2%) while interactions between glacial history and host
 plants explained the most variation in fungal rhizosphere communities
 (11.6%). We analyzed ectomycorrhizal fungal communities from the shrub
 Betula nana across spatial scales and sites and found a large correlation
 between ectomycorrhizal and rhizosphere communities, and that
 ectomycorrhizal composition was most similar among root fragments
 belonging to the same plant, followed by plants at the same site, and were
 most dissimilar for plants at different sites. Here, we have presented the
 metadata associated with rhizosphere and mycorrhizal characterization of
 tundra plants.
description: # Rhizosphere Bacteria and Fungi are Differentially Structured by Host
 Plants, Soil 1 Mineralogy and Ectomycorrhizal Communities in the Alaskan
 Tundra - Metadata
 [https://doi.org/10.5061/dryad.gmsbcc2zt](https://doi.org/10.5061/dryad.gmsbcc2zt) ## Description of the data and file structure Rhizosphere communities were obtained from six common tundra plants (*Betula nana, Eriophorum vaginatum, Salix Pulchra, Salix reticulata, Empetrum nigrum and Vaccinium uliginosum*) and mycorrhizal communities from *B. nana*. We washed 0.5 - 2 grams of plant roots in a 0.9% NaCl solution to obtain rhizosphere slurries, and performed DNA amplification using the bacterial primers 16S, and fungal primers ITS4. Metadata for sample collection is included as well as relevant data processing and analysis scripts as well as figure generation. Raw reads are available on NCBI Sequence Read Archive: BioProject PRJNA1037070. Sequencing data was cleaned using the dada2 pipeline and further analyzed using the R package phyloseq in three separate scripts (16S_pipe_FINAL, ITS_pipe_FINAL, ECM_pipe_FINAL*). *Additional scripts included were used for mantel correlations (mantel_pipe_run4_16S, mantel_pipe_run4_ITSreseqs) and assignment of bacterial functional annotations using FAPROTAX analysis (Faprotax_script). ### Files and variables #### File: Mycorrhizosphere_characterization_metadata.csv **Description:** This dataset contains primarily field relevant information at the time of collection. Samples 1-3, 6-10, 14-16, 23-24, 35-37, 39-41, 44-45 and 50 were discarded from the analysis due to one of the following reasons: 1) contained more than one collected individual, 2) unable to be identified, or 3) contained plants with unbalanced representation across sites (ie. *Equisetum arvense* and *Rhododendron sp.*). Notes were taken as needed and were primarily descriptive. ##### Variables * Plant.no refers to the individual plant which subsamples were taken from * Host.plant refers to the plant species * Common.name is the non-Latin name * Date, time, year and weather refer to when the sample was taken from the tundra * Nearest plot refers to the plot which we were permafrost coring and is relevant to another data set * Glacial drift refers to the glacial history of the site * Vegetation.type is either moist acidic tundra (MAT) or moist non-acidic tundra (MNT) * Air.temperature refers to the temperature at the time of collection in degrees Celsius * Collector refers to the person taking the samples from the field - Notes are any miscellaneous information ### File: Mycorrhizosphere_characterization_metadata_-_subsamples.csv **Description:** This dataset is a companion to the full metadata file and contains information plant.no's 1-50. Due to the exploratory nature of the first field season, the initial goal was to obtain root weights and rhizosphere pH to use as explanatory variables for microbiome composition. Due to the lack of explanatory power of these variables, they were dropped from the protocol and were not conducted for plant.no's 51-141. ##### Variables * Sample_ID is a unique identifier based on the plant.no and Root.id combination * Root.id is the fragment of root subsampled from the individual plant (plant.no) ## Code/software R statistical software was used for statistical analyses, data visualization, and data processing. Various packages were used within these scripts including phyloseq, phylosmith, vegan, tidyverse, pheatmap, MiscMetabar, ggplot2, DEseq2 and powdR. **16S_pipe_FINAL.R 39.83 KB** * Used for all microbial processing and analyses at it relates to rhizosphere bacterial communities. **ITS_pipe_FINAL.R 33.08 KB** * Used for all microbial processing and analyses at it relates to rhizosphere fungal communities. **ECM_pipe_FINAL.R 37.1 KB** * Used for all microbial processing and analyses at it relates to ectomycorrhizal fungal communities belonging to *B. nana*. **Faprotax_script.R 8.56 KB** * Used for generating data inputs to be used in Faprotax annotations as well as complementary analyses. **mantel_pipe_run4_16S.R 6.93 KB** * This code was used as an accompaniment to the 16S_pipe, primarily to examine mantel correlations between rhizosphere bacteria and ectomycorrhizal fungal compositions in *B. nana*.  **mantel_pipe_run4_ITS_reseqs.R 9.6 KB** * This code was used as an accompaniment to the ITS_pipe, primarily to examine mantel correlations between rhizosphere fungal and ectomycorrhizal fungal compositions in *B. nana*.  ## Access information n/a