The data are provided as supplemental material to the following article:
Louca, S., Jacques, S. M. S., Pires, A. P. F., Leal, J. S., Srivastava, D. S., Parfrey, L. W., Farjalla, V. F., Doebeli, M. (2016). High taxonomic variability despite stable functional structure across microbial communities
. Nature Ecology & Evolution 1:0015
Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists.
Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics.
The relative importance of these processes and their effects on community function remain largely unknown.
To address this uncertainty, here we examined bacterial and archaeal communities in replicate "miniature" aquatic ecosystems contained within the foliage of wild bromeliads.
We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups.
We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable.
Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift.
Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.
Popular science summaries of this study
Blog post on Nature Ecology & Evolution website.
Commentary paper in Nature Ecology & Evolution.
The data provided below for download include standard downstream products derived from the 16S rRNA amplicon sequences and shotgun metagenomic sequences,
such as OTU tables and KEGG gene tables, for the 22 bromeliad samples considered in this study. Only sequence data identified as prokaryotic are included.
The raw sequence data are available on the NCBI SRA under project accession PRJNA321235.
In particular, raw 16S rRNA amplicon sequences are available under SRA run accessions SRR3498561-SRR3498582, and raw metagenomic sequences are available under SRA run accessions SRR3498952-SRR3498973.
Accession details are also available for download below.
|Representative 16S rRNA amplicon sequences of detected OTUs.|
|Phylogenetic tree of OTU representative sequences, in Newick format.|
|Coordinates of sampled bromeliads.|
|Geodesic distances between bromeliads.|
|OTU table, listing absolute read counts per bromeliad and per OTU.|
|Sample metadata, NCBI accession numbers and download links for raw sequences.|
|Table listing OTU-function annotations, predicted with FAPROTAX.|
|Function table (relative function abundances) predicted from OTUs with FAPROTAX.|
|OTU subtables within each functional group, predicted with FAPROTAX.|
|KEGG gene table, listing metagenomic reads per gene ortholog and per sample.|
|Normalized KEGG gene table, i.e. listing relative abundances of gene orthologs.|
|Metagenomic function table, listing read counts per sample for broad functional categories.|
|Normalized metagenomic function table.||