GENOME ANNOUNCEMENT
The genus
Micrococcus, a member of the phylum
Actinobacteria, currently consists of 17 taxonomically valid species (
http://www.bacterio.net ). Members of the genus
Micrococcus are found in a wide range of diverse environments, including the type species
Micrococcus luteus, a known commensal that is found in humans and can contribute to food spoilage (
1).
Micrococcus sp. strain NDB3Y10 was isolated from a water sample collected from a newly drilled (65 h) gas bore well located in the upper Surat Basin, Roma, Queensland, Australia. Strain NDB3Y10 grew optimally under aerobic conditions at 37°C and pH 8 in basal PL medium (
2) supplemented with 0.2% yeast extract, glucose, and tryptone. The strain was also able to grow on PL medium supplemented with 0.01% yeast extract and 10 mM 1,2-dichloroethane (1,2-DCE), a highly toxic environmental pollutant. Partial 16S rRNA gene sequencing analysis revealed that
Micrococcus luteus DSM 20030
T was the nearest phylogenetic neighbor with a sequence identity of 96.44%. Further analysis using Biolog plates (GN2 Micro Plate, Biolog, USA) showed that the strain metabolized several different carboxylic acids, saccharides, pyruvic acid methyl ester, and succinic acid mono-methyl-ester. We report here the first genome sequence of the 1,2-DCE-utilizing
Micrococcus sp. strain NDB3Y10, isolated from a water sample collected from a newly drilled bore well producing coal seam gas.
High-molecular-weight DNA was extracted from a late log phase culture of strain NDB3Y10 using a modification of Marmur’s method (
3). The DNA was sent to the Australian Genome Research Facility (AGRF) for TruSeq library prep and sequencing on the Illumina MiSeq platform. The sequencing run produced a total of 1,306,503 paired-end reads (250 bp), which were reduced to 1,296,434 reads after quality filtering.
De novo assembly was performed using SPAdes version 3.5.0, which produced a high-quality draft genome consisting of 84 contigs (≥500 bp in length) with an
N50 of 64,137 bp and an average genome coverage of 247×. The contigs had a G+C content of 72.97% and a combined length of 2,497,512 bp, which is estimated to cover 99.85% of the total genome length.
Annotation of the draft genome of strain NDB3Y10 using Prokka version 1.12b (
4) revealed the presence of 2,274 protein-coding and 55 RNA gene sequences. Average nucleotide identity using BLAST (ANIb) analysis showed that strain NDB3Y10 shared the highest ANIb value (>98%) with
M. luteus strains SK58 and 773_MLUT, which were isolated from human hosts. A comparative analysis using Roary (
5) identified genes involved in the uptake of molybdenum and in the biosynthesis of molybdopterin, as well as a methane monoxygenase in strain NDB3Y10, thus excluding the other 11 genomes of
M. luteus strains (SK85, modasa, NCTC 2665, trpE16, RIT304, RIT305, RIT324W, SUBG006, 773_MLUT, 1058_MLUT, and SEN31). RAST (
6) annotations of the genome of strain NDB3Y10 identified haloacid dehalogenase and haloalkane dehydrogenase-like genes, a class of hydrolytic dehalogenases involved in the degradation of halogenated hydrocarbons such as 1, 2-DCE (
7). This constitutes the first report of the 1,2-DCE-utilizing
Micrococcus sp. strain NDB3Y10 in which potential hydrolytic dehalogenases have been identified.
Accession number(s).
This whole-genome shotgun project has been deposited in GenBank under the accession number
LQAC00000000 . The version described in this paper is the first version, LQAC00000000.1.