Soil 16S DNA sequence data and corresponding soil property and wheat yield data from a 72-plot field experiment involving pulses and wheat crops grown in rotations in the semiarid prairie

The soil bacteria diversity and corresponding environmental data made available here are from a 72-field plot experiment testing the effect of pulse frequency in nine wheat-based rotation systems, in the semiarid prairie. The data include sequences of the V6–V8 regions of bacterial 16S rDNA from soil and root extracts, generated using Roche GS FLX Titanium technology, and associated environmental data, specifically levels of soil organic carbon, total carbon, total nitrogen, total phosphorus, pH, electrical conductivity, and extractible sulfate sulfur, copper, iron, manganese, zinc, potassium, nitrate nitrogen, phosphate phosphorus, calcium, and magnesium in the 0–15 cm soil layer, and mineral nitrogen and phosphate in the 0–120 cm soil layer. The grain yield of wheat in the last (4th) phase of the crop rotation systems is also given. The data can be used in meta-analyses of the effect of pea, lentil and chickpea in wheat-based cropping systems on soil bacterial diversity or for monitoring the evolution of soil bacteria communities in cultivated prairie soils in the context of climate change. Samples were collected between 2012 and 2014.


a b s t r a c t
The soil bacteria diversity and corresponding environmental data made available here are from a 72-field plot experiment testing the effect of pulse frequency in nine wheat-based rotation systems, in the semiarid prairie. The data include sequences of the V6eV8 regions of bacterial 16S rDNA from soil and root extracts, generated using Roche GS FLX Titanium technology, and associated environmental data, specifically levels of soil organic carbon, total carbon, total nitrogen, total phosphorus, pH, electrical conductivity, and extractible sulfate sulfur, copper, iron, manganese, zinc, potassium, nitrate nitrogen, phosphate phosphorus, calcium, and magnesium in the 0e15 cm soil layer, and mineral nitrogen and phosphate in the 0e120 cm soil layer. The grain yield of wheat in the last (4th) phase of the crop rotation systems is also given. The data can be used in meta-analyses of the effect of pea, lentil and chickpea in wheat-based cropping systems on soil bacterial diversity or for monitoring the evolution of soil bacteria communities in cultivated prairie soils in the context of climate change.

Data
The data are from a 72-plot field experiment testing the influence of pulse crop frequency on root and rhizosphere bacteria, which was conducted in the semiarid prairie between 2010 and 2014; the data are from 2012 to 2014. They consist of sequences of amplicons of the V6eV8 regions of bacterial 16S rDNA from soil and root extracts obtained by pyrosequencing (Table 1), and levels of soil organic carbon, total carbon, pH, electrical conductivity, and extractible sulfate sulfur, copper, iron, manganese, zinc, potassium, mineral nitrogen (NH 4 -N and NO 3 -N), phosphate phosphorus, calcium, and magnesium in the 0e15 cm soil layer and mineral nitrogen and phosphate in the 0e120 cm soil layer ( Table 2). Treatments impacted the yield of the wheat crop grown in the last (4th) phase of the rotations. This wheat grain yield data are also given below (Table 3).

Experimental design, materials, and methods
The 4-year crop rotation experiment was conducted from 2010 to 2013 (cycle-1), and repeated from 2011 to 2014 (cycle-2). The two cycles of the experiment were located side-by-side on the same land, at the Swift Current Research and Development Centre of Agriculture and Agri-Food Canada, in Specifications      southwest Saskatchewan, Canada, a semiarid region. There were nine crop rotation treatments with pulse frequency ranging from zero to three. Treatments were: W-W-W-W, P-W-W-W, C-W-W-W, P-W-P-W, L-W-L-W, C-W-C-W, P-P-P-W, L-L-L-W, and C-C-C-W, where W ¼ wheat, C ¼ chickpea, P ¼ pea, and L ¼ lentil. In each of the two identical experimental cycles, treatments were randomized in four complete blocks. This experiment and the methodology employed are described in detail elsewhere [3].
Rhizosphere soil samples were taken in the fall following harvest of the third year crops (phase-3). Rhizosphere soil samples were collected from 3 to 4 root systems taken to a depth of approximately 30 cm with a shovel, from three randomly selected locations along the third and second rows in each plot. Plant roots were placed in Ziploc™ bags and kept in coolers on ice during sampling operation. Root samples were transported in a van over approximately 3 km and kept in a walk-in cold chamber at 4 C until processing. Rhizosphere soil samples were immediately collected into Ziploc™ bags by brushing the soil remaining attached to roots after shaking, using a soft toothbrush. Rhizosphere soil samples were stored at À80 C prior to molecular analysis.
Root sampling took place at the mid-bloom stage in the fourth year of the rotations. The roots of three plants randomly selected in each plot, were taken with a shovel to a depth of approximately 30 cm, and placed in Ziploc™ bags, in coolers on ice. Samples were momentarily placed in a walk-in cold chamber at 4 C upon return to the crop research building. Roots were then washed in tap water and stored at À80 C prior to molecular analysis.
Genomic DNA was extracted from 100 mg of fresh roots or 1 g of rhizosphere soil using DNeasy Plant Mini Kit (Qiagen) and Ultra Clean Soil DNA Isolation Kit (MoBio), respectively [3]. The V6eV8 regions of bacterial 16S rDNA were amplified using Nübel et al. (1996) [4] 968f/1401r primer set. The reverse primer (1401r) included the B adapter and the forward primer (968f), the A adapter and a 10-bp multiplex identifiers (1 of 12 different Roche MIDs). The PCR reaction volume was 20 ml and the reaction was conducted as described before [3]. Libraries were pooled, and purified using Agencourt AMPure XP (Beckman Coulter) and quality checked on an Agilent 2100 Bioanalyzer. Pools of 12 libraries in equimolar amounts were submitted to Genome Quebec for pyrosequencing with Roche GS FLX Titanium technology.
Sequences were trimmed, filtered, de-replicated, and clustered using the UPARSE pipeline [1] and deposited in NCBI (Table 1). Sequences were clustered into operational taxonomic units (OTUs) based on 97% similarity. The RDP classifier was then used to assign taxonomy to the OTUs using the 16S rRNA training set 16 [2].
The top (0e15 cm) soil layer of each plot was sampled in the fall of phase-3, after harvest. Duplicated samples were taken using a 30-mm-diameter soil corer. Samples were sieved through 2-mm mesh, and stored at 4 C prior to analysis. Total carbon (C) was determined from a 12e15 mg soil sample on an Elemental analyzer (Elementar vario MICRO cube); 5e6 mg samples for organic carbon (C) were analyzed on the same equipment after pretreatment according to M. Baccanti and B. Colombo [5]. Soil extractions were prepared for soil mineral N [6], soil test P [7], potassium (K) [8] and soil extractible sulfur (S) [9]. Nitrogen, phosphorus and sulfur in these soil extracts were measured by colorimetry on the segmented flow auto-analyzer (Technicon, AAII System, Tarrytown, NY); K was measured by AAS on an atomic absorption spectrometer (Hitachi Z-8200). Copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) were extracted with diethylenetriaminepentaacetic acid/triethanolamine [10]; calcium (Ca) and magnesium (Mg) were extracted with ammonium acetate [11]; and all six were measured by ICP-OES (Fisher Scientific iCAP6300 Duo). Soil pH and electrical conductivity were measured using the saturated paste method [12] The N and phosphorus levels in the soil profile of each plot was also measured from duplicated 3-cm soil cores taken from the 0e120 cm top soil layer using the analytical procedures described above. The values presented in Table 2 are averages of the duplicates. Phase-4 wheat grain yield (Table 3) was obtained by harvesting the central six rows of each plot using a plot combine, at harvest maturity.