Draft Genome Sequence of Thermophilic Exiguobacterium sp. Strain JLM-2, Isolated from Deep-Sea Ferromanganese Nodules.

Exiguobacterium sp. strain JLM-2 is a thermophilic bacterium isolated from deep-sea ferromanganese (FeMn) nodules. The estimated genome of this strain is 2.9 Mb, with a G+C content of 48.32%. It has a novel circular 15,570-bp plasmid. The draft genome sequence may provide useful information about Mn-microbe interactions and the genetic basis for tolerance to environment stresses.

GENOME ANNOUNCEMENT

The genus Exiguobacterium was first described in 1983 by Collins et al. (1), and the species formerly described as Brevibacterium acetylicum incertae sedis was included in the genus Exiguobacterium as E. acetylicum in 1994 (2). Exiguobacterium spp. have been isolated from, or molecularly detected in, many extreme environments, such as Antarctic ice (3), Himalayan glaciers (4), Siberian permafrost (5), deep-sea hydrothermal vents (6), and hot/hyperalkaline springs (7, 8).

The isolate Exiguobacterium sp. strain JLM-2 was isolated from deep-sea FeMn nodule samples, which were collected at a water depth of 3,573 m using Jiaolong’s operated submersible loaded on the Xiangyanghong 09 scientific exploration ship from Jiaolong Seamount’s dormant hydrothermal vent, South China Sea, during the first experimental application cruise on 3 July 2013. The concentrations of MnO and Fe2O3 in the FeMn nodules were 40% and 10%, respectively, by inductively coupled plasma-mass spectrometry (ICP-MS).

Exiguobacterium sp. JLM-2 is a Gram-positive extracellular amylase-producing bacterium that can grow at 4 to 53°C and has resistance to Mn2+ (220 mM). Based on 16S rRNA gene phylogeny, the isolate is closely related to group II within the Bacillales family XII incertae sedis, Firmicutes (7).

Genomic DNA was extracted and sequenced using the Illumina HiSeq 2500 platform and assembled using Velvet version 1.0 (9). This assembly generated 23 contigs, with an N50 length of 343,188 bp and an average length of 126,112 bp, which were assembled into 12 scaffolds, with an N50 length of 2,092,945 bp and an average length of 241,796 bp. The draft genome of Exiguobacterium sp. JLM-2 consists of a total 2,998 open reading frames (ORFs). Its genome has a novel circular 15,570-bp plasmid with 19 ORFs. The draft genome is 2.9 Mb, with a G+C content of 48.32%.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LDNY00000000.