Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition

Piper CL, Siciliano SD, Winsley T, Lamb EG

Date Published: December 10, 2014

DOI: http://dx.doi.org/10.5061/dryad.5sn8m

 

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Title Piper_plotdata
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Description File Piper_plotdata This file includes all aboveground plant community measurements.
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Title Piper_soildata
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Description File Piper_soilsdata This file includes all soil variables measured in both the A and B soil horizons at each plot.
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Title Piper_plantcommunity
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Description File Piper_plantcommunity This file includes estimates of percent cover for all vascular plant species encountered in the plots.
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Title Piper_Ahorizon_bacteria_phylum
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Description File Piper_Ahorizon_bacteria_phylum This file includes abundance estimates for bacterial OTUs in A-horizon soil samples clustered at the phylum level. Taxonomic assignment according to the Greengenes 2011 taxonomy
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Title Piper_Ahorizon_bacteria_order
Downloaded 21 times
Description File Piper_Ahorizon_bacteria_order This file includes abundance estimates for bacterial OTUs in A-horizon soil samples clustered at the order level. Taxonomic assignment according to the Greengenes 2011 taxonomy
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Title Piper_Bhorizon_bacteria_phylum
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Description File Piper_Bhorizon_bacteria_phylum This file includes abundance estimates for bacterial OTUs in B-horizon soil samples clustered at the phylum level. Taxonomic assignment according to the Greengenes 2011 taxonomy
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Title Piper_Bhorizon_bacteria_order
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Description File Piper_Bhorizon_bacteria_order This file includes abundance estimates for bacterial OTUs in B-horizon soil samples clustered at the order level. Taxonomic assignment according to the Greengenes 2011 taxonomy
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Title Piper_BacterialOTU_taxonomy
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Description File Piper_bacterialOTU_taxonomy This file summarizes the taxonomy of bacterial OTUs observed in this study. Taxonomic assignment of OTUs was achieved by BLAST comparison of the seed sequences against the Greengenes 2011 database (McDonald et al., 2012) by trimming the Greengenes sequences to the same region as the seed sequences to improve assignment (Werner et al., 2012). Numbers in brackets indicate the confidence in which a particular name was assigned e.g. (100) is 100% confidence that the correct name was assigned Some OTUs are unnamed at some level of classification (e.g. f__(100) indicates that an OTU belongs to a certain unnamed family). Alternatively, an OTU may be "unclassified" denoting that the species could not be fit with any known bacterial groups.
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Title Piper_BacterialOTU_by_sample_matrix
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Description File Piper_bacterial_OTU_sample_matrix This file contains the raw OTU by sample matrix for all soil samples. OTU_names are explained in the file Piper_bacterial_OTU_taxonomy The samples were analysed as a subsampled dataset in which a total of 114 samples were analysed, standardised to 2550 reads each (singleton OTUs were removed from the dataset, therefore the abundance totals don't all add up to 2550) This is a matrix of each OTU at species level (0.03 dissimilarity) and its standardised (to 2550 reads) occurrence in each sample.
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When using this data, please cite the original publication:

Piper CL, Siciliano SD, Winsley T, Lamb EG (2015) Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition. Journal of Ecology 103(2): 386-396. http://dx.doi.org/10.1111/1365-2745.12356

Additionally, please cite the Dryad data package:

Piper CL, Siciliano SD, Winsley T, Lamb EG (2014) Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5sn8m
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