Draft Genome Sequence of Pantoea ananatis GB1, a Plant-Growth-Promoting Hydrocarbonoclastic Root Endophyte, Isolated at a Diesel Fuel Phytoremediation Site Planted with Populus.

We report the 4.76-Mb draft genome of Pantoea ananatis GB1, a Gram-negative bacterium of the family Enterobacteriaceae, isolated from the roots of poplars planted for phytoremediation of a diesel-contaminated plume at the Ford Motor Company site in Genk, Belgium. Strain GB1 promotes plant growth in various hosts and metabolizes hydrocarbons.

GENOME ANNOUNCEMENT

The genus Pantoea is known for its metabolic versatility (1), and P. ananatis has been globally implicated as a pathogen in significant agricultural crops and forest tree species (2). More recently, P. ananatis strains have been reported to exhibit a range of host interactions including beneficial, weakly pathogenic, commensal, and mutualistic (3, 4). We found that P. ananatis GB1 promotes the growth of hybrid poplar cuttings (Populus deltoides × [trichocarpa × deltoides] cv. Grimminge), as well as Lupinus luteus and Cytisus striatus, even though 16S rRNA gene sequence data along with phenotypic profiling indicate that GB1 is closely related to the rice pathogen Pantoea ananatis PA13 (5).

An Ion Torrent PGM (Life Technologies, Inc., Carlsbad, CA) was used for sequencing after extracting DNA from stationary-phase cells of GB1 using standard techniques as described by Thijs et al. (6). In total, 1.52 million reads (mean length 265 bases) generated 403 Mb of data (>362 M Q20 bases) in Torrent Suite 4.2.1. These were assembled using SPAdes 3.1.0 (7, 8) (uniform coverage mode; k-mers 21, 33, 55, 77, 99) into 33 contigs greater than 500 bp, giving a consensus length of 4,765,050 bp at 51.0× coverage (largest contig 780,856 bp; N50 = 363,336 bp). The Rapid Annotations using Subsystems Technology (RAST) server (9) was used to identify closely related organisms with complete genomes in NCBI RefSeq. Pantoea ananatis PA13 (GenBank accession no. CP003085) was used as a reference to reorder the GB1 contigs in Mauve (10).

Genome annotation was completed in the PGAP (NCBI) pipeline (11). The P. ananatis GB1 genome is 4.76 Mb and consists of one chromosome (55.2 % G+C) which includes 4,433 coding genes that were arranged into pathways using Pathway Tools (12, 13), 273 pseudogenes, 13 rRNAs (5S, 16S, 23S), 53 tRNAs, and 6 noncoding RNAs (ncRNAs).

Homologues of genes related to plant growth promoting traits such as inorganic phosphorus solubilization, nitrogen fixation, and siderophore production were found, along with multiple copies of genes for alkanes utilization such as: alkane monooxygenase genes (alkB), medium-chain acyl-CoA dehydrogenase (acdA) genes, and long-chain acyl-CoA dehydrogenase (acdB) genes. Interestingly, GB1 carries a bacterial laccase gene, in agreement with reports of a novel bacterial laccase, Lac4, produced by P. ananatis Sd-1, a strain that is able to oxidize nonphenolic and phenolic compounds (14).

The use of P. ananatis GB1 plant-growth-promoting inoculant for improving phytoremediation of diesel-contaminated sites is being explored.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JYGW00000000. The version described in this paper is version JYGW01000000.