Data processing and analysis
The obtained raw sequencing reads were processed using the AmpProc
pipeline (v5.1) (https://github.com/eyashiro/AmpProc). Due to
variable amplicon length between domains (the eukaryotic amplicons are
too long to merge), the data was processed in single read mode without
taxonomy assignment to generate a complete biome dataset of the reverse
read (R1), and to extract the eukaryotic ZOTUs for individual domain
analyses. A paired end treatment of the raw sequences was also performed
to retrieve the highest possible taxonomic resolution forBacteria and Archaea . Taxonomic classification was
performed manually using SILVA S138 (Quast et al., 2013).
Data analysis was performed using R version 3.6.1 (R Development Core
Team, 2020) wrapped by RStudio version 1.2.5001
(http://www.rstudio.com/). Visualisation of the obtained data and
ordination analysis were performed using the packages ampvis2 (Andersen,
Kirkegaard, Karst, & Albertsen, 2018) and ggplot2 (Wickham, 2016).