Draft Genome Sequence of Paenibacillus etheri sp. nov. SH7T, a Methyl Tert-Butyl Ether Degrader.

We report here the draft genome sequence of Paenibacillus etheri sp. nov. SH7(T) (= CECT 8558(T) = DSM 29760(T)), isolated from a hydrocarbon-contaminated soil pilot plant in Granada, Spain. The bacterium was isolated and sequenced due to its methyl tert-butyl ether (MTBE)-degrading properties.

GENOME ANNOUNCEMENT

The genus Paenibacillus encompasses approximately 200 species to date (available in the GenBank database), with a diversity of niches, including soil, freshwater, human, and plant rhizosphere habitats. Paenibacillus etheri sp. nov. SH7T (1) was isolated from a hydrocarbon-contaminated soil pilot plant in Spain (2, 3), using enrichment techniques with methyl tert-butyl ether (MTBE) (4), a gasoline additive and common groundwater pollutant. P. etheri has great potential for being used in MTBE bioremediation technologies, due to its MTBE-degrading capabilities (80 mg/liter MTBE in 7 days) (2). There are very few MTBE-degrading microorganisms with published bacterial genomes; hence, a greater scope of unique or diverse metabolic pathways can be found by sequencing MTBE-tolerant/-degrading microorganisms.

Whole-genome sequencing of P. etheri SH7T was performed using short-read (approximately 200- to 300-bp) and long-read (approximately 1-kbp) libraries with the Nextera XT kit (Illumina), and sequenced using 150-bp paired-end reads in the MiSeq Illumina platform. For the long-read library, an initial DNA quantity of 20 ng was used (instead of the default short-read library protocol of 1 ng). A total of 3.1 million reads were generated and reached a genome coverage of >50-fold. Genome assembly was performed with Velvet (k-mer, 99), resulting in 112 contigs, with an N50 of 534,899 bp and genome size of 6,634,505 bp. The sequences were ordered using genome alignment software (Mauve 2.3.1), using Paenibacillus sp. Y412MC10 as a reference. Four contigs of <200 bp were removed.

The resulting assembled and ordered sequences were annotated by the NCBI Prokaryotic Annotation Pipeline, generating a genome size of 6,633,655 bp, with a mean G+C content of 43.1%. NCBI annotation found 5,640 coding sequences (CDSs) and 136 RNA molecules. A Blast comparison of the SH7T 16S RNA gene (accession no. KC625558) with type strains returned the following % identities for Paenibacillus species (query coverage of 100%, unless stated): P. odorifer, 98%; P. borealis, 97%; P. typhae, 97% (query coverage, 97%); P. wynnii, 96%; and P. graminis, 95%. A genome comparison of P. etheri SH7T revealed that its genome size is within the range of its genus; however, the G+C content is lower, as P. graminis RSA19 (accession no. PRJNA202950), Paenibacillus sp. Y412MC10 (accession no. NC_013406), and P. polymyxa (accession no. NC_014483.1) have genome sizes of 6.9, 7.1, and 5.4Mbp and G+C contents of 50.3, 51.2, and 45.8%, respectively.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LCZJ00000000. The version described in this paper is the second version, LCZJ02000000.