Genome Sequence of Bacillus velezensis S141, a New Strain of Plant Growth-Promoting Rhizobacterium Isolated from Soybean Rhizosphere.

Bacillus velezensis strain S141 is a plant growth-promoting rhizobacterium isolated from soybean (Glycine max) rhizosphere that enhances soybean growth, nodulation, and N2 fixation efficiency by coinoculation with Bradyrhizobium diazoefficiens USDA110. The S141 genome was identified to comprise a 3,974,582-bp-long circular DNA sequence encoding at least 3,817 proteins.

GENOME ANNOUNCEMENT

Plant growth-promoting rhizobacteria (PGPR) are naturally occurring soil bacteria that aggressively colonize plant roots for better plant growth (1). Various bacterial species have been reported as PGPR, including some Bacillus species (2). Several Bacillus strains currently promote plant growth through the suppression of disease and improvement in nutrient acquisition by functioning as biofertilizers or phytohormone producers (1, 3). Bacillus velezensis S141 is a PGPR isolated from soybean rhizosphere soil in Thailand and is closely related to B. subtilis GB03 based on 16S rRNA gene sequencing (4). B. velezensis S141 is capable of increasing soybean growth, nodulation, and N2 fixation efficiency via coinoculation with Bradyrhizobium diazoefficiens USDA110. Therefore, we aimed to determine the whole-genome sequence of B. velezensis S141 to reveal the genetic background of its soybean growth-promoting capacity involving symbiotic N2 fixation with B. diazoefficiens USDA110.

B. velezensis S141 genomic DNA was prepared using the Wizard Genomic DNA purification kit (Promega, USA), and a genomic DNA library was constructed using the NEBNext ultra DNA library prep kit for Illumina (New England BioLabs Inc., USA) according to the manufacturer’s protocol. B. velezensis S141 genome sequencing was performed on an Illumina MiSeq platform. After quality filtering, 11,675,054 high-quality paired-end reads (2 × 300 bp) were assembled using CLC Genomics Workbench version 10.0.1 (Qiagen, USA). Total read coverage was 300-fold. After trimmed (paired) assembly using the CLC Genomics Workbench, a draft genome with 19 scaffolds was obtained. Gaps between scaffolds were closed using PCR and Sanger sequencing to obtain the complete sequence of the circular chromosome. The genome sequence was automatically annotated using the Microbial Genome Annotation Pipeline (MiGAP) (5). Based on 16S rRNA gene analysis using BLAST searches, the highest sequence identities (up to 100%) were identified with B. amyloliquefaciens, B. velezensis, B. subtilis, and B. methylotrophicus. Average nucleotide identity analysis using the Map Reads to Reference tool indicated that among all related Bacillus species, the B. methylotrophicus NAU-B3 (B. amyloliquefaciens subsp. plantarum NAU-B3) genome sequence (6) showed the highest identity (96.44%) to that of strain S141. Strain NAU-B3 was recently reclassified as B. velezensis (7), and thus we decided to name strain S141 B. velezensis S141.

The B. velezensis S141 chromosome was found to be a 3,974,582-bp-long circular DNA without a plasmid. Its genome comprises at least 3,817 protein-coding genes. Compared with another PGPR Bacillus strain, B. velezensis FZB42 (B. amyloliquefaciens subsp. plantarum FZB42) (7), strain S141 contains putative genes involved in indole-3-acetic acid (IAA) production (8), including ipdC and dhaS encoding indole-3-pyruvate decarboxylase and indole-3-acetaldehyde dehydrogenase, respectively, to synthesize IAA from indole-3-pyruvic acid; putative iaaH encoding indole-3-acetamide hydrolase to synthesize IAA from indole-3-acetamide; and yhcX encoding nitrilase to synthesize IAA from indole-3-acetonitrile. Additionally, we found ysnE, which putatively encodes IAA transacetylase involved in the tryptophan-independent IAA biosynthesis pathway. Thus, we suggest that B. velezensis S141 possesses multiple genes that are functionally related to auxin production and play key roles in its ability to promote plant growth.

Accession number(s).

B. velezensis S141 genome sequence was deposited in DDBJ/EMBL/GenBank under accession number AP018402.