Input data and Supplementary Results for "Community-level signatures of ecological succession in natural bacterial communities"

<p>&nbsp;</p> <p><strong>README<br> ======</strong></p> <p><br> This file describes the content of the different files included in this repository to<br> reproduce results from [1] and some of its supplementary results.</p> <p>&nbsp;</p> <p><strong>## Input files ##</strong></p> <p><strong>* 20151016_Functions_remainder.csv</strong></p> <p>&nbsp;&nbsp; &nbsp;Functions measured in [2]. The relevant quantities used in [1] are labelled with &quot;7&quot;, and include:<br> &nbsp;&nbsp; &nbsp;<br> &nbsp;&nbsp; &nbsp;* Community: Id of the sample<br> &nbsp;&nbsp; &nbsp;* Replicate<br> &nbsp;&nbsp; &nbsp;* Plate<br> &nbsp;&nbsp; &nbsp;* mgCO2.7: CO2 measured along 7 days of experiment<br> &nbsp;&nbsp; &nbsp;* CPM7: Cell counts at the end of the experiment<br> &nbsp;&nbsp; &nbsp;* pgRPC.7: CO2 per cell<br> &nbsp;&nbsp; &nbsp;* ATP7: ATP measured (nM)<br> &nbsp;&nbsp; &nbsp;* mG7: beta glucosidase (mM)<br> &nbsp;&nbsp; &nbsp;* mN7: beta chitinase (mM)<br> &nbsp;&nbsp; &nbsp;* mX7: xylosidase (mM)<br> &nbsp;&nbsp; &nbsp;* mP7: phosphatase (mM)<br> &nbsp;<br> <strong>* samples_metadata_time0.tsv</strong></p> <p>&nbsp;&nbsp; &nbsp;* Samples: Id of the sample&nbsp;&nbsp; &nbsp;<br> &nbsp;&nbsp; &nbsp;* Part.dates: Date of sampling<br> &nbsp;&nbsp; &nbsp;* Part.GPS.PAM: Optimal sampling sites&nbsp;&nbsp; &nbsp;<br> &nbsp;&nbsp; &nbsp;* Part.SparCC.PAM.t0: Optimal partition using SparCC<br> &nbsp;&nbsp; &nbsp;* Part.SJD.PAM.t0: Optimal partition using Jensen-Shannon Divergence<br> &nbsp;&nbsp; &nbsp;* Part.Dir.t0: Optimal partition using Dirichlet mixtures<br> &nbsp;&nbsp; &nbsp;* Part.month: Month in which the community was sampled<br> <strong>* Dist_GPS-Haversine.dat</strong></p> <p>&nbsp;&nbsp; &nbsp;Haversine (spatial) distances between samples</p> <p><strong>* corMat-SparCC_20151016_OTU_remainder.clean.samples.txt</strong></p> <p>&nbsp;&nbsp; &nbsp;Matrix of correlations between samples computed with SparCC<br> &nbsp;&nbsp; &nbsp;<br> <strong>* distMat_ShannonJensen_Samples_Time0.clean.dat</strong></p> <p>&nbsp;&nbsp; &nbsp;Distance matrix computed with Jensen-Shannon divergence.</p> <p>&nbsp;</p> <p><br> <strong>## Supplementary results ##</strong></p> <p><strong>* SEMmodels.zip</strong></p> <p>&nbsp;&nbsp; &nbsp;Results for the Structural Equation Models analysed. The structure of the folders follows the one<br> &nbsp;&nbsp; &nbsp;available at the repository of the [project ](https://github.com/apascualgarcia/TreeHoles_descriptive).<br> &nbsp;&nbsp; &nbsp;<br> <strong>* TaxaSummaries.zip</strong></p> <p>&nbsp; The file contains one folder for each community-class, with matrices in different formats (biom and txt)&nbsp; computing the relative abundances of the OTUs at different taxonomic levels (labelled L2 being the proxy for&nbsp; Phylum to L6, the proxy of species). These matrices can be visualized interactively opening with a web&nbsp; browser the files area_charts.html.</p> <p><strong>#### References ####</strong></p> <blockquote> <p>&nbsp;[1] Pascual-Garc&iacute;a, A., &amp; Bell, T. (2019). Community-level signatures of ecological succession in natural bacterial communities. Nature Communications (In press)</p> </blockquote> <blockquote> <p>&nbsp;[2] Rivett, Damian W., and Thomas Bell. Abundance determines the functional role of bacterial phylotypes in complex communities.&quot; Nature microbiology 3.7 (2018): 767.</p> </blockquote> <p>&nbsp;</p>