DOI: 10.5061/dryad.5sn8m
title: Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition

description: Plant and soil communities are tightly linked, but the mechanisms by which
 the invasion of an exotic plant and the resulting shifts in plant
 diversity and productivity influence soil bacterial community structure
 remain poorly understood. We investigated the effects of invasive smooth
 brome (Bromus inermis) on grassland soil bacterial community structure
 using massively-parallel sequencing of the 16S rRNA gene to determine
 bacterial community richness, evenness, composition, and beta diversity
 (UniFrac indices) of soils collected along a gradient of smooth brome
 abundance. We evaluated several hypotheses including: a) that the declines
 in native plant diversity associated with smooth brome invasion would
 cause declines in bacterial community diversity, and b) that mechanisms
 driving smooth brome effects on bacterial community structure involved
 altered soil edaphic properties rather than preferential invasion in areas
 of high soil nitrogen and distinct soil microbial communities. Smooth
 brome invasion led to increased soil nitrogen, soil carbon and root
 biomass. Bacterial evenness and bacterial richness increased with
 increasing smooth brome cover, while bacterial beta diversity declined. We
 found no evidence of a dominant direct link between the alteration of soil
 edaphic properties by brome and the changes in the soil bacterial
 community. Rather, the main controls on the soil bacterial community were
 direct effects of pH and smooth brome that could not be linked to the
 edaphic changes. The most important effect of brome on the bacterial
 community was the selective suppression of dominant bacterial species,
 which allowed rarer bacteria to increase in relative abundance. Synthesis:
 Here we show that plant community composition influences bacterial
 community structure at a very fine scale, but that these changes are not
 due to altered soil total nitrogen or carbon content. The dominant direct
 effect of smooth brome invasion on soil communities suggests non-edaphic,
 i.e. inter and intra-trophic, interactions among smooth brome and
 non-bacterial components of the soil ecosystem are key drivers of soil
 community structure. Some of the data in this repository were also
 reported in the following paper: Piper, C.L., Lamb, E.G. &
 Siciliano, S.D. (In Press) Smooth brome changes gross soil nitrogen
 cycling processes during invasion of a rough fescue grassland. Plant
 Ecology. doi:10.1007/s11258-014-0431-y
description: Piper_plotdataFile Piper_plotdata This file includes all aboveground plant community measurements.Piper_soildataFile Piper_soilsdata This file includes all soil variables measured in both the A and B soil horizons at each plot.Piper_plantcommunityFile Piper_plantcommunity This file includes estimates of percent cover for all vascular plant species encountered in the plots.Piper_Ahorizon_bacteria_phylumFile 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 taxonomyPiper_Ahorizon_bacteria_orderFile 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 taxonomyPiper_Bhorizon_bacteria_phylumFile 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 taxonomyPiper_Bhorizon_bacteria_phylym.csvPiper_Bhorizon_bacteria_orderFile 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 taxonomyPiper_BacterialOTU_taxonomyFile 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.Piper_BacterialOTU_by_sample_matrixFile 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.