Genome Sequence of Herbaspirillum sp. Strain GW103, a Plant Growth-Promoting Bacterium

Abstract

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land. Here we report the 5.05-Mb draft genome sequence of the strain, providing bioinformation about the agronomic benefits of this strain, such as multiple traits relevant to plant root colonization and plant growth promotion.

GENOME ANNOUNCEMENT

Beneficial plant-microbe interactions are of interest in agricultural biotechnology because microorganisms inhabiting the rhizosphere increase agricultural production and suppress plant diseases as biocontrol agents. Plant growth-promoting bacteria are widely distributed in soil and belong to various genera, including Herbaspirillum (4, 5). The genus Herbaspirillum is classified in the family Oxalobacteraceae within the class Betaproteobacteria, and its first reported genome was that of endophytic Herbaspirillum seropedicae strain SmR1 (4).

Herbaspirillum sp. strain GW103 was isolated from rhizosphere soil of the reed Phragmites australis on reclaimed land for the ability to utilize 1-aminocyclopropane-1-carboxylate (ACC), a precursor of the plant hormone ethylene, as a sole nitrogen source. The isolate exhibited a growth-promoting effect on Chinese cabbage under salinity stress. Here we report the whole-genome draft sequence and annotation of strain GW103.

The genome of strain GW103 was sequenced by using a combination of the 454 GS FLX titanium system (Roche Diagnostics, Branford, CT) with a paired-end library (131,707 reads) and an Illumina GA IIx genome analyzer (San Diego, CA) with a paired-end library (62,940,877 reads). The 454 GS FLX and Illumina GA reads were assembled using a Roche GS assembler 2.6 and CLC Genomics Workbench 5.0 (CLCbio, Katrinebjerg, Denmark). Gene annotation was carried out using the automated annotation platform RAST (rapid annotations using subsystems technology) server (1). Genes encoding tRNAs and rRNA operons were determined using the tRNAscan-SE (3) and RNAmmer (2) software programs, respectively.

The resulting sequences were assembled into one scaffold consisting of 52 contigs at 1,266.28-fold coverage. The complete genome of H. seropedicae strain SmR1 (NC_014323) was used as a reference sequence for the genomic assemblage (4). The contig gaps were closed, in part, by sequencing of PCR products, resulting in one scaffold with six contigs. The genome sequence obtained had a total of 5,047,645 bp with a G+C content of 62.46% and 4,655 coding sequences. It did not have a plasmid. Additionally, the predicted draft genome contained 56 tRNA genes and six rRNA genes, including two 5S rRNA genes, two 23S rRNA genes, and two 16S rRNA genes. RAST analysis showed that approximately 87.09% of the nucleotides were predicted as protein-encoding genes, and 73.66% of the open reading frames were annotated.

The genome annotation revealed the presence of the ACC deaminase gene and genes related to the biosynthesis pathways of indole-3-acetic acid and siderophores, which are plant growth-promoting factors. The genome also contained genes that encode factors, such as cellulolytic enzymes, hemagglutinins, and hemolysins, required for the penetration of plant cells, attachment at the surface, and biofilm formation during plant root colonization (4).

The genomic information obtained suggests that plant growth promotion by strain GW103 is achieved by direct interaction between the microbe and the host plant and also indirectly due to its antagonistic activity against plant pathogens via siderophore production.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. AJVC00000000. The version described in this paper is the first version, AJVC01000000.