Complete genome sequence of Halomonas sp. R5-57

The marine Arctic isolate Halomonas sp. R5-57 was sequenced as part of a bioprospecting project which aims to discover novel enzymes and organisms from low-temperature environments, with potential uses in biotechnological applications. Phenotypically, Halomonas sp. R5-57 exhibits high salt tolerance over a wide range of temperatures and has extra-cellular hydrolytic activities with several substrates, indicating it secretes enzymes which may function in high salinity conditions. Genome sequencing identified the genes involved in the biosynthesis of the osmoprotectant ectoine, which has applications in food processing and pharmacy, as well as those involved in production of polyhydroxyalkanoates, which can serve as precursors to bioplastics. The percentage identity of these biosynthetic genes from Halomonas sp. R5-57 and current production strains varies between 99 % for some to 69 % for others, thus it is plausible that R5-57 may have a different production capacity to currently used strains, or that in the case of PHAs, the properties of the final product may vary. Here we present the finished genome sequence (LN813019) of Halomonas sp. R5-57 which will facilitate exploitation of this bacterium; either as a whole-cell production host, or by recombinant expression of its individual enzymes. Electronic supplementary material The online version of this article (doi:10.1186/s40793-016-0192-4) contains supplementary material, which is available to authorized users.


Introduction
Halomonas sp. R5-57 is a marine member of the Halomonadaceae, a family of Gram-negative chemoorganotrophic bacteria that display moderate to high salt tolerance. Members of this genus have been isolated from diverse saline environments such as ocean water [1,2], salterns [3], marine hydrothermal vents [4], hypersaline lakes [5,6] and salted fermented food [7]. Several species of Halomonas have also been identified as human pathogens [1,8,9] Halomonas species have a number of technologically exploitable features. Both compatible solutes, which the bacteria accumulate as part of their adaptation to saline environments, and extracellular polymers, which protect the cells from environmental stresses and aid in biofilm formation, are used in pharmaceutical, food-processing and biotechnological industries [10,11]. Additionally, polyhydroxyalkanoates which are accumulated by the bacterium as energy storage compounds can be used to produce biodegradable plastic materials [12]. Finally, the high solubility of Halomonas proteins, both in their folded and unfolded states have led to their use as fusion tags for improving the solubility of recombinantly expressed proteins [13].
The isolation, characterization and genome sequencing of Halomonas sp. R5-57 was undertaken as part of the MARZymes project which aims to identify novel coldadapted enzymes and organisms from marine sources. Here we present the complete genome sequence of Halomonas sp. R5-57 together with its temperature and salinity growth optima and functional screening for various activities.

Classification and features
Halomonas sp. R5-57 was isolated from the skin of the red sea squirt Halocynthia papillosa collected from the Barents Sea in Spring 2009. The animal was dissected and the skin homogenized in an equal volume of sterile sea water and 50 μl was plated onto IM8 media [14]. An individual colony was picked from this raw plate after incubation at 4°C for two weeks, and was subsequently re-streaked two times and grown at 4°C for 1 week.
Liquid cultures for DNA isolation and growth curves were prepared by inoculating Luria-Bertani media with 3.5 % NaCl from these pure isolates. A summary of the isolation and phenotypic characteristics of Halomonas sp. R5-57 are given in Table 1. PCR product of the partial 16s rRNA gene was generated using the 27F and 1492R universal primers [15], and then sequenced with the BigDye terminator kit version 3.1 (Applied Biosystems) using the 515 FD primer. This placed isolate R5-57 with other psychrotolerant species of Halomonas, having 99 % identity to H. glaciei DD 39T (MTCC 4321; JCM 11692), isolated from fast ice in Antarctica [16]. Neighbor-joining analysis of the full-length 16S rRNA gene shown in Fig. 1 Evidence codes -IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [44] Scanning electron micrographs show that this bacterium is rod-shaped and has a number of flagella with a peritrichous arrangement (Fig. 2). Cells for microscopy were taken from colonies after 24 h growth and fixed with 5 % glutaraldehyde for 1 h, then 2.5 % glutaraldehyde overnight. Fixed suspensions were applied to Poly-L-Lysine coated slides for 2-5 min and post-fixed with 1 % osmium tetroxide for 30 min followed by dehydration with increasing concentrations of ethanol (30 %, 60 %, 90 %, 96 %, 5 min each, 99 % 5 min twice) hexamethyldisilazine (2 min, two times), and finally incubation in a dessicator with silica gel for approximately 2 h. Dried specimens were sputter-coated with gold and observed with a ZEISS MERLIN Scanning Electron Microscope with an accelerating voltage of 2.0 kV.
Members of the Halomonadaceae are characterized by having high salt tolerance, and as the 16S rRNA sequence of Halomonas sp. R5-57 clusters with other psychrotolerant strains H. titanicae, H. variabilis and H. boliviensis, we investigated both the salinity and temperature optimum of this isolate. Growth rates measured on LB medium containing 0.5 -12 % NaCl at temperatures between 4 -41°C show Halomonas sp. R5-57 has an optimum of 20°C in 3.5 % NaCl, the salinity of seawater, and requires minimum salt concentration of 1.0 % for any significant growth to occur. The salinity of the medium also had a marked effect on the temperature tolerance of Halomonas sp. R5-57 as below 7 % NaCl growth rates peaked at 20°C then decreased rapidly; but at 10 -12 % NaCl the temperature optimum increased to 30°C and growth was observed at up to 41°C (Additional file 1: Figure S1).
Metabolic activities of Halomonas sp. R5-57 were determined with the API® system, using tests NE and E (bioMérieux). Tests were conducted at 25°C, all media was supplemented with 3.5 % NaCl and final results were scored after 5 days. Halomonas sp. R5-57 is oxidase positive, reduced nitrate to nitrite, was able to utilize citrate, ferment or oxidize glucose, manitol, inositol, sorbitol, melbiose, sacharose, melibiose amygdaline arabinose, and assimilate N-acetyl glucosamine, potassium gluconate, capric acid and adipic acid. Additionally this strain displayed beta galactosidase, arginine dehydrolase gelatinase activities, and hydrolysed esculin.

Growth conditions and genomic DNA preparation
Pure cultures of Halomonas sp. R5-57 were grown for two days at 20°C to stationary phase. Growth media was in LB supplemented with 3.5 % NaCl. High molecular weight DNA was isolated using the GenElute Bacterial Genomic Kit (Sigma) following the manufacturer's instructions for Gram negative strains. Briefly, cells were harvested by centrifugation from 1.5 ml culture, lysed in 'Lysis solution T' containing RNase A followed by treatment with Protinase K. All subsequent steps involving binding to, and elution from spin columns were carried out according to the kit protocol, and the final genomic DNA sample was eluted in distilled water. Where mixing was required, gentle inversion of the sample was used in lieu of vortexing or pipetting to avoid shearing of the sample DNA. The DNA concentration was estimated by the absorbance at 260 nm, and purity was assessed by the ratio of absorbance at 260 to 280 nm measured on a Nanodrop spectrophotometer (Thermo scientific).
Genomic DNA was further prepared for Illumina sequencing by sonication using a Covaris sonicator down to~700 bp, and the library was produced with Solid Phase Reversible Immobilization works technology (Beckman Coulter). The sample was then separated on a 2 % agarose gel (120V, 40 min) and DNA of 750-850 bp was retrieved. Afterwards PCR was performed to amplify the library.   MIRA hybrid assembly [20] which allowed mapping of the Illumina reads onto the PacBio scaffold for correction of indels, resulting in a single circular chromosome with no plasmids.

Genome annotation
Genes were identified using Glimmer 3 [21] and annotated using an in-house annotation pipeline where protein-coding sequences were searched against the COG database [22] and assigned with COG numbers, signal peptides were predicted using Phobius [23], and tRNA genes were identified using the tRNAscan-SE tool [24].

Genome properties
The genome comprises one circular chromosome of 5031571 bp which is graphically represented in Fig. 3a indicating the GC distribution (55.75 % overall) and GC skew. The properties and statistics of the genome are summarized in Tables 3 and 4. Four thousand six hundred seventy seven genes were predicted, 4599 of which are protein coding genes. Four thousand two hundred twenty five (91.87 %) of the protein coding genes were assigned to a putative function with the remaining genes annotated as hypothetical proteins.
Insights from the genome sequence BRIG [25] was used to generate the comparison between the fully-genome sequenced species H. elongata DSM 2581 ASM19687v1 (4.06 Mb, 63.6 % G + C) and H. campaniensis ASM69648v1 (4.07 Mb, 52.6 % G + C), and the draft sequence of the type strain H. boliviensis LC1 (4.2 Mb, 54.7 % GC). The comparison was performed on the nucleotide sequences with a lower cut off identity threshold of 50 %. The genome comparison reveals several unique regions in the Halomonas sp. R5-57 genome. Most of these include mobile genetic elements, and some contain genes for membrane transporters, secretion proteins and restriction-modification systems (Fig. 3a). Halomonas sp. R5-57 has the highest overall similarity to the recently deposited High-Quality Draft sequence of Halomonas sp. TG39a (ASM74439v1; 4.9 Mb, 55.0 % G + C). A pairwise comparison using the nucleotide sequences of these two genomes and visualization in ACT [26] identified eight regions which differ between the two genomes: two of these appear to be translocations and correspond to parts of the Halomonas sp. R5-57 which are not found in H. elongata, H. campaniensis, or H. boliviensis, five others are insertions which are unique to Halomonas sp. R5-57 and one is an insertion in Halomonas sp. TG39a Fig. 3b.

Extended insights
Species of Halomonas, like other halotolerant chemorganotrophic bacteria, produce compatible solutes to  The total is based on the total number of protein coding genes in the genome maintain the osmotic balance inside their cells. An example is ectoine which is produced by cultivation of strains H. boliviensis and H. elongata [27]. The genes of Halomonas sp. R5-57 involved in ectoine biosynthesis, hydroxylation and transportation, as well as for the production of PHAs are listed in Table 5 together with their predicted properties and locus tags. The approximate position of these genes is shown on the graphical representation of the Halomonas sp. R5-57 chromosome (Fig. 3a). High homology is found between the two EctD protein products of Halomonas sp. PHAs are cellular energy-storage molecules that can serve as precursors for bioplastic production by humans, [12,28]. Halomonas sp. R5-57 carries three genes annotated as polyhydroxyalkanoate synthases (PHA Cs); the enzymes responsible for carrying out the final polymerization step in PHA biosynthesis [28]. The product of phaC HALO1802 has high homology with PHA C1sequences of H. boliviensis (91 %) and H. campaniensis (86 %) and with enzymes from Halomonas spp.O-1 (86 %) and H. elongata (77 %) which have recently been heterologously produced and characterized [29]. The putative PHA C (HALO2716) of Halomonas sp. R5-57 differs from the PHA C1 sequences, but has 75 % homology with another PHA C from H. boliviensis. A third possible PHA C comprising loci HALO3139 and HALO3140 contains a frameshift generating a stop codon after 67 amino acids, and is found within the phage-containing poorly-conserved 3367-3491 kbp region of the Halomonas sp. R5-57 genome (Fig. 3a). The phaC genes of Halomonas sp. R5-57 have been cloned, and their recombinant expression and structural elucidation is part of ongoing studies by our group to more fully understand the biochemical properties and catalytic mechanism of these enzymes.
Given its ability to tolerate salt concentrations up to 12 %, extracellular enzymes from Halomonas sp. R5-57 are expected to be functional under moderate-to-high salt conditions and thus could be employed in highsalinity reaction conditions. Functional screening of Halomonas sp. R5-57 using the API® system and platebased assays revealed several secreted enzyme activities that could be of interest in industrial and biotechnological settings. Subsequent to genome sequencing, the genes annotated with enzyme classes that could impart these functions were identified together with putative signal peptides for secretion (Table 6).
A further possible application for Halomonas sp. R5-57 would be manipulation of its cellular machinery for use as a protein-expression host. The low-temperature and high-salinity growth optima could be potentially advantageous for recombinant production of psychrophilic or halophilic enzymes, which can suffer from poor solubility in commonly-used E. coli-based expression systems. Additionally, as osmolyte compounds are known to be potent protein stabilizers [30], their induction simultaneously with intracellular heterologous protein expression in Halomonas could present a further strategy to improve solubility of 'difficult' recombinant protein targets. The in-depth sequence information of halophilic bacterial strains, such as we have provided in this project will be key to engineering of such organisms in realization of this goal.