Study title: Acidic mine pit lakes as natural bioreactors: in-situ attenuation mediated by biosulfidogenesis
Authors: Charlotte van der Graaf1, Javier Sánchez‑España2, Iñaki Yusta3, Andrey Ilin3, Sudarshan Shetty1, Nicole Bale4, Laura Villanueva4, Alfons J.M. Stams1*5*, Irene Sánchez‑Andrea1*
Affiliations:
1 Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
2 Geochemistry and Sustainable Mining Unit, Dept of Geological Resources, Spanish Geological Survey (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain
3 Dept of Mineralogy and Petrology, Basque Country University (UPV/EHU), Apdo. 644, 48080, Bilbao, Spain
4 Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
5 Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Correspondence: Irene Sánchez‑Andrea (irene.sanchezandrea[at]wur.nl) and Charlotte van der Graaf (lot.vandergraaf[at]wur.nl)
For code related queries: Charlotte van der Graaf (lot.vandergraaf[at]wur.nl)
This repository contains the codes for the analysis of 16S rRNA amplicon sequencing data in the research article by van der Graaf C., et al (2020) Biosulfidogenesis mediates natural attenuation in acidic mine pit lakes. Under review. [Link](to be updated).
Structure:
van-der-Graaf-et-al-2020-Acidic-mine-pit-lakes
Structure:
van-der-Graaf-et-al-2020-Acidic-mine-pit-lakes/
|------- input/ # biom and metadata files are located here.
|------- Galaxy22-[NG-Tax__Huelva-library_concat].biom1.zip # unzip this file before running the analysis
|------- FCLZ-mappingfile-metadata-final.csv # metadata file
|------- acid_pit_lakes_v03_NGTax.Rmd # Rmarkdown file with analysis workflow
Clone or download the repository as zipped file, unzip and open the .Rproj file. The open the .rmd file in R to re-run the analysis.