Dataset of amplicon metagenomic assessment of barley rhizosphere bacteria under different fertilization regimes

The metagenomic dataset profiled in this research is built on bacterial 16S rRNA gene amplicon of DNA mined from barley rhizosphere under chemical (CB) and organic (OB) fertilization. Amplicon-based sequencing was prepared by the Illumina platform, and the raw sequence dataset was examined using Metagenomic Rast Server (MG-RAST). The metagenome comprised sixteen samples that include CB1 (494,583 bp), CB2 (586,532 bp), CB3 (706,685 bp), CB4 (574,606 bp), CB5 (395,460 bp), CB6 (520,822 bp), CB7 (511,729 bp), CB8 (548,074 bp), OB1 (642,794 bp), OB2 (513,767 bp), OB3 (461,293 bp), OB4 (498,241 bp), OB5 (689,497 bp), OB6 (423,436 bp), OB7 (478,657 bp) and OB8 (279,186 bp). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA827679 (CB1), PRJNA827686 (CB2), PRJNA827693 (CB3), PRJNA827699 (CB4), PRJNA827706 (CB5), PRJNA827761 (CB6), PRJNA827780 (CB7), PRJNA827786 (CB8), PRJNA826806 (OB1), PRJNA826824 (OB2), PRJNA826834 (OB3), PRJNA826841 (OB4), PRJNA826853 (OB5), PRJNA827254 (OB6), PRJNA827256 (OB7), and PRJNA827257 (OB8) at NCBI. Actinobacteria dominated the soil samples at the phylum level.


Value of the Data
• The dataset gives understanding on the influence of different fertilizer regimes on the structure, composition and diversity of microbiome from soils obtained from barley rhizosphere.• Microbial communities residing in soils obtained from barley rhizosphere may possibly function as a pool of biological-active molecules and unique genes necessary for biotechnological, ecological and industrial purposes.• Barley rhizosphere emerges as one of the factors of yield potential in crops, as well as plays a significant function in improving plant fitness.
• The knowledge of the influence of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere bacteria will assist in engineering soil to increase microbial diversity in the agroecosystem.

Table 1
The sequence information of barley rhizosphere under chemical and organic fertilization.

Samples
Base

Experimental Design, Materials and Methods
In this experiment, we collected sixteen soil samples of 20 g each from barley rhizosphere (the barley plants are 6 weeks old) under chemical fertilization (CB1-8) (25 °39 32.2 S 27 °39 49.8 E) and barley rhizosphere under organic fertilization (OB1-8) (25 °39 04.9 S, 27 °40 46.6 E) at a depth of 0-15 cm [1] .For the inorganic field, 75 kg ha −1 K 2 O, 75 kg ha −1 P 2 O 5 , and150 kg ha −1 N were the quantities of inorganic fertilizer which had been in use.Urea, potassium sulphate and calcium superphosphate were the sources of N fertilizer, K fertilizer, and P fertilizer respectively.The organic fertilizer field has been undergoing the use of cow dung of 10,625 kg ha −1 amount for more than a decade.The fertilization regimes employed in this study was in line with the United State Department of Agriculture (USDA, 2014).10 × 4 m was the measurement for the respective planting field for this research and the cultivar planted on both field is barley seeds (Puma).Each of the research fields (that is CB and OB) were 10 m away.Sterile plastic bags were used to temporarily store the soil samples and then moved to cooler boxes filled with ice.On getting to the laboratory, the soil samples (after removal of debris) were stored in the refrigerator at -20 °C for further analysis.We used the Nucleospin Soil kit (Macherey-Negel, Germany) to extract the DNA of the entire barley rhizosphere microbiome by using the kit's manual as a guide.
The mined DNA was later sent to Molecular Research Laboratory, Clovis road, Texas, United States.Libraries of the 16S rRNA were arranged from the QC-passed DNA samples via the universal primers 515F (5 -GTGCCAGCMGCCGCGGTAA-3 ) and 806R (5 -GGACTACHVGGGTWTCTAAT-3 ) with standard Illumina barcodes and adapters.The Ampure XP beads were further used to purify the amplicons.Agilent DNA 10 0 0 Bioanalyser was used to validate the barcoded libraries, while the quantification was done with the Qubit DNA BR reagent assay.After that, the MiSeq was used to sequence the quantified libraries that were later processed and analysed via the MG-RAST server v4.0.3 ( http://metagenomics.anl.gov/ ) [ 2 , 3 ].Raw data were uploaded as FASTQ files after demultiplexing of pairedend reads.Reads generated after quality processing and deduplication (by eliminating sequences that are: (a) greater than 5 ambiguous base pairs with 15 phred score cutoff (b) artificial sequences made by sequencing artifacts (c) have a length of greater than 2 standard deviations from the average value) by MG-RAST pipeline analysis, were subjected to annotation by using a BLAST-like alignment device called BLAT against a database that offers a nonredundant integration of numerous databases called M5NR database.Taxonomic analysis was done using RDP database under the following conditions: a maximum alignment length of 15 base pairs, an e-value of 1e -5 and a minimum identity of 60%.MG-RAST pipeline made available estimation of microbial abundances present in barley rhizosphere under chemical fertilization (CB) and barley rhizosphere under organic fertilization (OB).
After the MG-RAST analysis on the sequences, we visualized them by plugging them with a stacked bar chart in Excel (version 2010) to appraise the taxonomic abundance.An evaluation of the species richness was done with rarefaction curves from the MG-RAST tool.

Limitations
Not applicable.

Ethics Statement
The current work follows the ethical requirements for publication in Data in Brief.It does not involve human subjects, animal experiments, or any data collected from social media platforms.

Fig 2 .
Fig 2. The rarefaction curves showing the species richness computation among barley rhizosphere under chemical (CB) and organic (OB) fertilization.