Draft Genome Sequence of Halomonas smyrnensis AAD6 ^T

Abstract

Turkey b Halomonas smyrnensis AAD6T is a Gram-negative, aerobic, exopolysaccharide-producing, and moderately halophilic bacterium that produces levan, a fructose homopolymer with many potential uses in various industries. We report the draft genome sequence of H. smyrnensis AAD6 T , which will accelerate research on the rational design and optimization of microbial levan production. H alomonas smyrnensis AAD6T was isolated from soil samples taken from the Çamaltı Saltern area (Turkey) and was found to excrete high levels of levan exopolysaccharide (5). Further research on the potential uses of levan produced by Halomonas sp. as a bioflocculating agent (7), its nanostructured thin films (9), its suitability for peptide-based drug nanocarrier systems (8), and a scheme for economical production from waste (4) have been reported. Moreover, the first genome scale metabolic model of Chromohalobacter salexigens DSM 3043 was reported, which in turn formed the basis for the reconstruction of a generic in silico metabolic model of levan-producing Halomonas sp. (1). Recently, H. smyrnensis strain AAD6T was identified as a Gram-negative, nonmotile, dark-yellow-pigmented, aerobic, moderately halophilic bacterium (6).In this study, whole-genome sequencing of H. smyrnensis AAD6 T was performed by using a combination of 454 GS FLXϩ (454 Life Sciences, Branford, CT) and Ion Proton (Ion Torrent Systems, Inc., Guilford, CT) sequencers. The shotgun sequence data generated consisted of 1,082,564 reads (mean length of 498.36 bp) and 359,877 reads (mean length of 122.42 bp), respectively, providing 140-fold coverage. The duplicates in the sequence data were eliminated with CLC Genomics Workbench (v5.0.1). De novo assembly of the whole sequencing reads was carried out with Newbler Assembler (v2.3). One hundred ninetytwo contigs, with a minimum length of 500 bp, were obtained. Alignment of these contigs and elimination of the overlaps using Sequencher 5.0 (3) resulted in 81 high-quality contigs. These contigs were mapped to the raw data with CLC Genomics Workbench (v5.0.1) to estimate the terminals, and using overlapping terminal regions, the contigs were assembled into 34 supercontigs via Geneious Pro (v5.5.6) software. The draft genome of H. smyrnensis AAD6T was structured with 34 supercontigs (total assembly size of 3,561,919 bp). Gene prediction and annotation were carried out using the RAST server (2).The draft genome that resulted had a mean GC content of 67.9%, 3,237 coding sequences, 1,756 subsystems, and 64 RNA genes. Putative functions could be assigned to 2,436 protein-coding genes, whereas 801 hypothetical proteins had no match to any known proteins. Genome analysis revealed a number of genes related to exopolysaccharide biosynthesis, including the genes for levansucrase and ExoD.Phylogenetic analysis of the draft genome revealed a rather close relationship to other species of the genus Halomonas, where Halomonas salina (99.5%) and Halomonas halophila (99.5%) were found to be the closest species on the basis of 16S rRNA sequ...

Effective stimulating factors for microbial levan production by Halomonas smyrnensis AAD6T

“…Moreover, the generic metabolic model of Halomonas smyrnensis AAD6 T was reconstructed to elucidate the relationship between levan biosynthesis and other metabolic processes (16). Recently, the producer strain has been identified as a novel species of the genus Halomonas and named as H. smyrnensis AAD6 T (17) and its whole genome sequence has been announced (18).…”

Systems biology solutions to challenges in marine biotechnology

“…These marine projects include genomes of marine haloarchaea and halobacteria, microorganisms from marine oxygen minimum zones, bacterioplankton clades, dark ocean microorganisms, marine red alga, marine protista, carbon monoxide oxidizing thermophiles, marine microbial communities from multiple species of wood-boring bivalves, hydrocarbon-degrading bacteria (including glucose-oxidizing and sulfate-reducing bacteria), ammonia-oxidizing bacteria, bacterial symbionts of gutless marine worms, actinomycetes, flavobacteria, and other marine bacterial strains. The recent years have clearly shown that these genome studies gave important clues on the marine life in terms of symbiosis (Müller et al, 2004), defense mechanisms (Thakur et al, 2005) and biopolymer production (Sogutcu et al, 2012), and expected to accelerate marine biotechnology especially via better understanding of the organisms' genetics and metabolism, improvement of cultivation techniques for these marine organisms, discovery of novel pathways for energy and carbon use, development of efficient and profitable production schemes by use of different hydrocarbons for energy sources, and discovery of novel commercial applications of marine organisms, in near future.…”

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“…Mannitol as an effective stimulatory factor for levan production has also been analyzed systematically. 89 Draft genome sequence analysis by Sogutcu et al 90 identified several genes related to EPS biosynthesis, including the genes for levansucrase and ExoD. More recently, whole-genome analysis of H. smyrnensis AAD6T by Diken et al 91 revealed Hs_SacB gene encoding the extracellular levan sucrase which catalyzes levan synthesis from sucrose-based substrates by transfructosylation 86 and bear striking similarities with levansucrases from Pseudomonas strains.…”