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).