Rhizosphere microbiome dataset of Robusta coffee (Coffea canephora L.) grown in the Central Highlands, Vietnam, based on 16S rRNA metagenomics analysis

Vietnam is the second-largest coffee producer in the world after Brazil. Of the two main coffee production species, namely, Arabica and Robusta, Vietnam is the largest producer of Robusta worldwide [1]. Based on previous reports, the planted coffee area in Vietnam was 695.600 ha and its production was 1.76 million tons in 2020, in which the Central Highlands region accounts for approximately 73% of the planted area and production [2]. Hence, this region is known as the capital of coffee plantations and production in Vietnam. Previous studies have focused on the diversity of rhizospheric bacteria from this plant species cultivated in this region based on cultivation methods [3], [4], [5], [6], [7], [8]. However, no report has been found on the rhizospheric microbial diversity of this important plant in Vietnam. To our knowledge, a dataset of rhizospheric microbial communities of the coffee plant grown in the Central Highlands is still unclear. This report presents a dataset of the rhizosphere microbiome from a representative sample obtained by mixing five rhizospheric soil samples of Coffea canephora L. cultivated in the Central Highlands region using metagenomic next-generation sequencing. This dataset provides information on the rhizospheric microbial diversity of Robusta coffee, particularly its functionality. Therefore, cultivation techniques for sustainable Robusta coffee production in the region could be developed by applying indigenous rhizospheric microbial resources.


Value of the Data
• Data provide information on the rhizospheric microbial diversity of Coffea canephora L. and its functionality in the Central Highlands and other regions in Vietnam. • Data could be used for the comparative analysis of the rhizospheric and endophytic microbiome profiles of Coffea canephora L. cultivated in the Central Highlands and other regions in Vietnam. • Data will be useful for subsequent studies on the conservation of rhizospheric microbial genetic resources and the development of cultivation techniques for applying them for sustainable Robusta coffee production in the Central Highlands to achieve the nutrients required for various stages of development and growth.

Rhizospheric soil sampling
Five rhizospheric soil samples (approximately 100 g each, 5-30 cm in depth) of Coffea canephora L. were collected from five different sites of a 6-year-old coffee field in Khanh Xuan Ward, Buon Ma Thuot City, Dak Lak Province, on October 30, 2021. The samples were mixed well, combined into one representative sample, kept at 4 °C in an ice box, and brought to the laboratory within 1 h after sampling. The sample was stored at −80 °C until analysis.

Isolation of microbial genomic DNA
Microbial genomic DNA was extracted from 300 mg of soil sample using the DNeasy Power-Soil kit (Qiagen, Germany) in accordance with the supplier's instructions.

Library preparation and 16S rRNA metagenomic sequencing
The 16S rRNA gene (regions V1-V9) was amplified using primers [9] , and then libraries of 16S rRNA gene amplicons were prepared using the Swift amplicon 16S plus ITS (internal transcribed spacer) panel kit (Swift Biosciences, USA) in accordance with the supplier's instructions. Finally, the Illumina MiSeq platform (2 × 150 bp paired ends) was used to perform the library 16S rRNA gene amplicon sequencing.

Taxonomic and functional analyses
Taxonomic and functional profiles of rhizospheric microbes were analyzed in accordance with the method of Tran et al. [9] . In brief, bcl2fastq was used to demultiplex raw basecall files. Adapters, primers, and low-quality sequences (average score of < 20 and read length of < 100 bp) were removed using Trimmomatic (version 0.39) [10] and Cutadapt (version 2.10) [11] . The q2-dada2 plugin and denoise-single method within the QIIME2 pipeline (version 2020.8) [12] were used to cluster and dereplicate the reads into amplicon sequence variants. QIIME2 aligned with the SILVA SSURef reference database (version 138) [13] was used for taxonomic analysis of amplicon sequence variants in accordance with the classify-consensus-blast method [14] . Finally, PICRUSt2 (version 2.3.0-b) [15] and MetaCyc databases [16] were used to deduce the functional profiles of rhizospheric microorganisms from the sample based on the results of 16S rRNA gene amplicon sequencing.

Declaration of Competing Interest
The author declares that it has no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data Availability
Rhizosphere microbiome dataset of the Robusta coffee (Coffea canephora L.) grown in the Central Highlands, Vietnam, based on analysis using 16S rRNA metagenomics (Original data).