The Draft Genome Sequence of Burkholderia sp. Strain Nafp2/4-1b Confirms Its Ability To Produce the Plant Growth-Promoting Traits Pyoverdine Siderophores, 1-Aminocyclopropane-1-Carboxylate Deaminase, and the Phytohormone Auxin

Burkholderia sp. strain Nafp2/4-1b is a rhizobacterium isolated from the rhizosphere of grassland in South Africa.

M embers of the genus Burkholderia are Gram-negative bacteria belonging to the beta subclass of Proteobacteria and are part of a larger group of rhizobacteria that can establish a positive interaction within plant roots. Several strains within the genus are known to colonize the rhizosphere and play key roles in crop yield, plant health, and soil fertility (1,2). They are therefore often referred to as plant growth-promoting rhizobacteria (PGPR) due to their ability to improve the growth and health of several economically important crops (3,4).
The Burkholderia sp. strain presented here, Nafp2/4-1b, was initially isolated from the rhizosphere of grassland in South Africa. For isolation, a 100-l aliquot of serially diluted rhizosphere soil suspension was plated on solid nutrient agar (NA) medium and was incubated at 28°C for 24 h. Selected pure colonies of the bacteria were evaluated for their growth-promoting activity in maize (Zea mays L.) and in vitro detection of major PGPR traits.
Based on the growth-promoting traits exhibited in both the gnotobiotic test and the in vitro characterization, the genome of this strain was sequenced to confirm and increase our understanding of its PGPR properties for possible use as a biofertilizer inoculant in crop production. For DNA extraction, a single pure colony of the bacterium was grown in Luria Bertani (LB) broth for 24 h on a rotary shaker at 28°C. One milliliter of the culture suspension was used to extract total DNA using the Wizard genomic DNA purification kit and protocol (Promega, Madison, WI, USA). Paired-end DNA libraries were prepared using the Nextera protocol (Illumina, USA) for sequencing on a HiSeq 2500 instrument (Illumina, USA) at the Agricultural Research Council's Biotechnology Platform in Onderstpoort, South Africa. About 13,542,806 paired-end sequences (125 bp each) were obtained prior to adaptor quality trimming and the merging of overlapped reads. CLC Genomics Workbench 8.5.1 was used for the trimming and genome assembly, with the default setting of 20 bp used. This resulted in a final number of merged and unmerged reads of 8,610,493 being used to produce the final assembly. The draft genome consists of 92 scaffolds (i.e., 110 contigs), with an N 50 value of 322,407 bp and a maximum scaffold size of 1,302,675 bp. The total draft genome size is estimated at 7,786,570 bp (i.e., 123ϫ coverage), with a GC content of 66.2%. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) was used for genome annotation (5,6), which identified 7,223 putative coding regions.
Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PXXL00000000. The version described in this paper is version PXXL01000000. The SRA accession number for the raw data is PRJNA438206.

ACKNOWLEDGMENTS
Due acknowledgment goes to the National Research Foundation (NRF) of South Africa for the financial support to A. I. Hassen under the project for development of microbial inoculants for enhanced legume production.
Opinions expressed, and conclusions arrived at, are those of the authors and are not necessarily to be attributed to the NRF.