DOI: 10.25829/bexis.31349-9
title: Soil bacterial (16S) communities from 10 grassland plots in Germany (2015-2018; Illumina MiSeq) - OTU abundances (subset of dataset 25346)

description: Cooperation between the BE projects SADE, Scalemic, Microorganisms (core): Plant-soil feedbacks (PSFs) underlying grassland plant richness and productivity are typically coupled with nutrient availability; however, we lack understanding of how restoration measures to increase plant diversity might affect PSFs. We examined the roles of sward disturbance, seed addition and land-use intensity (LUI) on PSFs. We conducted a disturbance and seed addition experiment in ten grasslands along a LUI gradient and characterized plant biomass and richness, soil microbial biomass, community composition and enzyme activities. This dataset contains OTU abundances for bacterial community composition of the years 2015, 2016, 2017 and 2018 on 10 selected SADE plots in the Schwäbische Alb. This is a subset of dataset 25346 made as accompanying data for the article "Microbial drivers of plant richness and productivity in a grassland restoration experiment along a gradient of land-use intensity" published in New Phytologist.
description: Detailed description of study design: In each of 10 grasslands we set-up a full-factorial experiment consisting of disturbance and seed addition treatments. This resulted in four 7 m × 7 m subplots per grassland, which contained one of four combinations: control, disturbed, seeds added and both disturbed and seeds added. In most cases the four subplots were grouped together with a 2 m margin between the subplots. In few cases, subplots were more scattered because of site heterogeneity or requirements by farmers owning the grasslands. For the disturbance treatment, the top 10 cm of the grassland sward was destroyed using a rotary harrow. Thereby, the sward was broken up and turned over, creating open patches with bare soil while fragments of the former sward, were left on the disturbed subplots. Disturbance was applied once in October 2014. The seed addition treatment consisted of adding a highly diverse, region-specific seed mixture of plant species to each subplot. While the same seed mixture was added to each plot within a region, different species pools were used for different regions. Seeds were purchased from commercial seed suppliers which guaranteed regional origin from geographically defined zones. The mixture consisted of 66 species and in the Schwäbische Alb. The number of seeds added depended on seed mass and was targeted to 100 seeds × m−2 (for seeds 1 mg), 34 (for seeds 1mg − 10 mg) and 17 (for seeds &gt; 10 mg). In few cases, the final number was slightly lower due to limited seed availability. Seeds were added twice, with two thirds of the mixtures added in November 2014 and one third in March 2015. For an even distribution of the seeds, they were mixed with sand or crushed soybean, which was also added to the control plots. We recorded the species and their cover to analyse different stability measures, community assembly with disturbance and/or seed addition effect depending on the land-use intensity and initial species richness.br/Sampling design: We collected soil samples each year in May from 2015 to 2018 on each treatment plot with a soil auger of 5.4 cm diameter, 10 cm depth. We recorded the precise core depth to calculate soil bulk density. Four soil cores per plot in the first year and two cores per plot in the following years were mixed and a subsample was frozen in dry ice for molecular analyses (DNA isolation and amplicon sequencing) and transported to a -80°C freezer.br/Sample preparation: From each sample a pooled soil sample was sieved: soil aliquots were afterwards stored at -20 °C and DNA was extracted from soil samples of each sampled plot. DNA was extracted from 0.4 g of each soil compartment sample, using PowerSoil® DNA Isolation Kit (MO BIO Laboratories Inc., Carlsbad, CA, USA). The bacterial 16S rDNA V4 region was targeted while DNA amplification using a PCR approach (Primer set PCR: 515f-806r).br/Equipment: Illumina MiSeqbr/Data analysis: The bacterial raw sequences from the soil samples were processed using a customized bioinformaitc pipeline following the MOTHUR SOP. The obtained bacterial sequences were clustered into operational taxonomic units (OTUs) based on 97% similarity and taxonomy was assigned those OTUs against SILVA database.br/Literature references: Abrahão A., Marhan S., Boeddinghaus R. S., Nawaz A., Wubet T., Hölzel N., Klaus V. H., Kleinebecker T., Freitag M., Hamer U., Oliveira R. S., Lambers H., Kandeler E. (2022): Microbial drivers of plant richness and productivity in a grassland restoration experiment along a gradient of land use intensity. New Phytologist.br/Data references: BExIS dataset 25346 Version 2 and 31350. Silva Database Version 128: https://www.arb-silva.de/. MOTHUR SOP Version 1.43.0: https://mothur.org/wiki/miseq_sop/