Repository for the paper: Biodiversity and niche partitioning in an anaerobic benzene degrading culture
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and free energy source and nitrate as the electron acceptor. We demonstrate that only a few community members are able to degrade benzene, and that most of the others feed on the metabolic left-overs or on the contents of dead cells making up a food web with different trophic levels. As a result of niche partitioning, a high species richness is maintained and the complexity of a natural community is stabilized in a relatively simple environment. This view highlights the importance of species interactions and interdependencies, which drive microbial community structure and function. These mechanisms may well be conserved across ecosystems.
In the bioreactor folder you can find Analysis_MAGs.Rmd code and the corresponding data (in the Data folder) to reproduce most if not all of the analysis and figures. The Data folder contains files of mRNA samples mapped to each MAG, ORFs DNA sequnaces per MAG, KEGG selections for benzene degradation, tables of presence and absece of KOs/MAGs and KOs-mRNAs/MAGs, DNA abundaces (Anvi'o result), Summary per MAG, taxonomy assignments and total mapped mRNA count per sample.
Metagenome-assembled genomes can be found in an Anvi'o result at zenodo open-access repository under http://doi.org/10.5281/zenodo.3939224. To obtain the data, use anvi-summarize command.
In the succesion experiment folder you can find Analysis_succession.Rmd code and the corresponding data (in the Data folder) to reproduce most if not all of the analysis and figures. The Data folder contains the raw and normilized OTUs tables, taxonomy assignments and metabolomics results in a table formats.
Metagenomics shotgun & 16S rRNA gene amplicon sequencing are available in the European Nucleotide Archive under primary accession PRJEB39357.
The data and code in this repository is released under a Creative Commons Attribution-ShareAlike 4.0 International Public License