Habitat and tree species identity shape aboveground and belowground fungal communities in Central European forests

This repository contains the data and pre-processing pipeline, as well as the R script for the analysis accompanying our paper:

Hofmann B, Dreyling L, Dal Grande F, Otte J & Schmitt I 2023. Habitat and tree species identity shape aboveground and belowground fungal communities in Central European forests. Frontiers in Microbiology doi: 10.3389/fmicb.2023.1067906.

Contacts

Lukas Dreyling
Doctoral Candidate
E-Mail

Imke Schmitt
Principal Investigator
E-Mail

Francesco Dal Grande
Principal Investigator
E-Mail

Contents

1. Pre-Processing Pipeline
2. Data
3. Analysis Script

Additionally you need to download the raw reads here.

If you lack the computing power to process the raw reads, the resulting ASV tables, FASTA files, taxonomy table and metadata are located here.
An archived version of this repository can be found at Zenodo.

Before starting

You will need to have the following software installed.

Pre-Processing

• fastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• Cutadapt https://cutadapt.readthedocs.io/
• R https://www.r-project.org/
  • dada2 https://benjjneb.github.io/dada2/index.html
  • ShortRead https://kasperdanielhansen.github.io/genbioconductor/html/ShortRead.html
  • Biostrings https://bioconductor.org/packages/release/bioc/html/Biostrings.html
• BLASTn https://www.ncbi.nlm.nih.gov/books/NBK279690/

Analysis

• R https://www.r-project.org/
• Rstudio https://www.rstudio.com/
  • here https://here.r-lib.org/
  • tidyverse https://www.tidyverse.org/
  • decontam https://benjjneb.github.io/decontam/
  • phyloseq https://joey711.github.io/phyloseq/
  • LULU https://github.com/tobiasgf/lulu
  • Biostrings https://bioconductor.org/packages/release/bioc/html/Biostrings.html
  • microbiome https://github.com/microbiome/microbiome
  • fantaxtic https://github.com/gmteunisse/Fantaxtic
  • igraph https://igraph.org/
  • SpiecEasi https://github.com/zdk123/SpiecEasi
  • ranacapa https://github.com/gauravsk/ranacapa
  • rgexf https://github.com/gvegayon/rgexf
  • vegan https://rdrr.io/cran/vegan/man/vegan-package.html
  • MicEco https://github.com/Russel88/MicEco