The effects of phytoplankton deposition on water-sediment interface bacterial communities

A repository for R code, scripts from the manuscript "Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface"

by Dandan Izabel-Shen, Séréna Albert, Monika Winder, Hanna Farnelid and Francisco J. A. Nascimento

Corresponding author: Dandan Izabel-Shen, Department of Ecology, Environment and Plant Sciences, Stockholm University; email: dand.shen@gmail.com

_This work has been published in Molecular Ecology. https://doi.org/10.1111/mec.15984

The script and computing notes provided in this Github repository are also published in Zenodo https://doi.org/10.5281/zenodo.4743185 or this publication of this study.

To cite this work or code

Dandan Izabel-Shen, Séréna Albert, Monika Winder, Hanna Farnelid and Francisco J. A. Nascimento. (2021). Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface. Molecular Ecology. https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15984

Data

The FASTQ files and associated metadata are available in the European Nucleotide Archive under the accession number PRJEB39288.

Installation

The following packages (and their dependencies) are required to run the whole analysis

library("vegan"); packageVersion("vegan") # 2.5.6
library("phyloseq"); packageVersion("phyloseq")  # 1.30.0
library("DESeq2"); packageVersion("DESeq2") # 1.26.0
library("ggplot2"); packageVersion("ggplot2") # 3.3.2
library("BiocManager"); packageVersion("BiocManager") # 1.30.10"
library("gplots"); packageVersion("gplots") # 3. 1. 0
library("gridExtra");packageVersion("gridExtra") # 2.3
library("picante");packageVersion("picante") # 1.8.2
library("dplyr");packageVersion("dplyr") # 1.0.2
library("stats");packageVersion("stats") # 3.6.2
library("RColorBrewer");packageVersion("RColorBrewer") # 1.1.2
library("VennDiagram"); packageVersion("VennDiagram") # 1.6.20
library("ggpubr"); packageVersion("ggpubr") # 0.4.0
library("tidyverse"); packageVersion("tidyverse") # 1.3.0
library("car"); packageVersion("car") # 3.0.10
library("agricolae"); packageVersion("agricolae") # 1.3.3
library("scales"); packageVersion("scales") # 1.1.1.
library("graphics"); packageVersion("graphics") # 3.6.0

How to run

The R scripts in the base folder should be run interactively (for instance with RStudio).

The folder 'R_analysis' contains scripts and computing notes written for data analysis and visualization.

The folder 'InputFiles' under "R_ananlysis" contains all data files required to run the analysis and plotting.