- Short genome report
- Open Access
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus
Standards in Genomic Sciencesvolume 13, Article number: 19 (2018)
Kushneria konosiri X49T is a member of the Halomonadaceae family within the order Oceanospirillales and can be isolated from salt-fermented larval gizzard shad. The genome of K. konosiri X49T reported here provides a genetic basis for its halophilic character. Diverse genes were involved in salt-in and -out strategies enabling adaptation of X49T to hypersaline environments. Due to resistance to high salt concentrations, genome research of K. konosiri X49T will contribute to the improvement of environmental and biotechnological usage by enhancing understanding of the osmotic equilibrium in the cytoplasm. Its genome consists of 3,584,631 bp, with an average G + C content of 59.1%, and 3261 coding sequences, 12 rRNAs, 66 tRNAs, and 8 miscRNAs.
The gizzard shad, Konosirus punctatus , is a popular marine fish used as a food source in Northeast Asia and is usually consumed as a grilled dish, sushi, or jeotgal (or jeot). Jeotgal is a traditional Korean fermented food made by adding a substantial amount of solar salt to seafood such as fish, shrimp, or shellfish. During fermentation, jeotgal gains an extra flavor that may be caused by a microorganism derived from the environment, solar salt, or sea organisms. In an analysis of the microbiota of salt-fermented seafood, the strain X49T (= KACC 14623T = JCM 16805T) was isolated from the salt-fermented larval gizzard shad, known as Daemi-jeot in Korean . Blast analysis and phylogenetic analysis using the 16S rRNA sequence revealed that the strain X49T belongs to the genus Kushneria .
The genus Kushneria was first proposed as a novel genus by Sanchez-Porro in 2009, on the basis of phylogenetic analyses of 16S and 23S rRNA gene sequences . It comprises a group of related Gram-negative, aerobic, motile, and rod- or oval-shaped bacteria. Most Kushneria strains have been isolated from saline environments and possess hypersaline resistance [2,3,4,5,6,7]. Strain X49T also has a halophilic character . At present, there are four sequenced Kushneria strains, but only the genome of Kushneria marisflavi KCCM 80003T has been reported . Thus, the genomic analysis of strain X49T should help us to understand the genetic basis of adaptation to a hypersaline environment. The present study determined the classification and features of strain X49T, as well as its genome sequence and gene annotations.
Classification and features
Serially diluted suspensions of Daemi-jeot were plated directly on Marine agar medium and maintained under aerobic condition at 25 ± 1 °C for 14 days. To obtain pure isolates, a single colony was repeatedly transferred to new agar plates. Comparison between the 16S rRNA gene sequence of strain X49T (Accession number: GU198748) and those obtained using NCBI BLASTN  with the settings for highly similar sequences produced 100 hits: 47, 36, 1, and 1 from the genera Kushneria , Halomonas , Halomonadaceae , and Chromohalobacter , respectively, and the remaining 15 from uncultured bacteria. The validated species with the maximum sequence similarity was K. marisflavi SW32T (NR_025094), which shared a sequence identity of 98.63%. Phylogenetic analysis using MEGA6  based on 16S rRNA gene sequences of the Kushneria members and related taxa showed that strain X49T was within the cluster comprising the genus Kushneria (Fig. 1). Strain X49T is classified as Proteobacteria , Oceanospirillales , Halomonadaceae , and Kushneria , and is named Kushneria konosiri . Characteristics of K. konosiri X49T are presented in Table 1. The cells were aerobic, Gram-negative, rod- or oval-shaped, and 1.2–3.2 μm in length and 0.5–1.0 μm in width. A flagellum was observed (Fig. 2). The colonies were orange-colored and circular with entire margins on marine agar medium. Growth was observed at 10–37 °C, at pH 4.5–8.5, and in the presence of 0–26% (w/v) NaCl. The physiological characteristics, such as the growth substrates of K. konosiri X49T, have been described in detail previously .
The predominant cellular fatty acids (> 10% of the total) in K. konosiri X49T were C16:0, C18:1 ω7c, Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and C12:0 3OH. The respiratory quinone was ubiquinone Q9, and minor quinones were ubiquinone Q8 and Q10. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unidentified aminophospholipids, two unidentified phospholipids, and two unidentified lipids.
Genome sequencing information
Genome project history
K. konosiri X49T was selected for genome sequencing based on its environmental potential and this genome sequencing was part of the Agricultural Microbiome R&D Program (grant number: 914006–4) at the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry (IPET) funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA). The genome sequence was deposited in DDBJ/EMBL/GenBank under accession number CP021323, and the genome project was deposited in the GOLD  under Gp0223024. The sequencing and annotation were performed by Macrogen (Seoul, Korea). The details of the project information and the associations with MIGS  are shown in Table 2.
Growth conditions and genomic DNA preparation
K. konosiri X49T (lab stored, = KACC 14623T = JCM 16805T) was cultured aerobically in LB broth (BD, USA) containing NaCl (4% w/v) at 30 ± 1 °C for 3 days. The genomic DNA of K. konosiri X49T was extracted using a MG™ Genomic DNA Purification kit (Macrogen, Korea) according to the manufacturer’s instructions.
Genome sequencing and assembly
For library preparation, gDNA was sheared with g-TUBE (Covaris Inc., USA) and then used for library preparation by ligating SMRTbell adaptors (20 kb SMRTbell library). The sequences of the generated library were sequenced using the PacBio RSII system, SMRT sequencing with DNA Sequencing Reagent Kit P6 and SMRT Cells 8Pac V3 (Pacific Biosciences). The sequencing generated 1,199,776,790 bp with 160,304 reads. After filtering of sequences that were shorter than 50 bp, 1,199,771,927 bp sequences with 160,189 subreads remained. Assembly was performed using software RS HGAP v3, which consists of pre-assembly, de novo assembly with Celera® Assembler, and assembly polishing with Quiver. Assembly resulted in one scaffold with the complete genome in circular form and 244-fold coverage.
Annotation of the assembled genome was performed using the DOE-JGI Microbial Genome Annotation Pipeline v.4.15.1 . The gene prediction was carried out using the IMG-ER platform. Comparisons of the predicted ORFs using the KEGG , NCBI COG , Pfam , TIGRfam , and InterPro  databases were conducted during gene annotation. Additional gene prediction analyses and functional assignment were carried out using the NCBI PGAP  and the RAST with the gene caller classicRAST  based on the SEED . CRISPR system analysis was carried out using the web-based interface CRISPRFinder (http://crispr.i2bc.paris-saclay.fr/). The chromosome map of K. konosiri X49T was obtained from the output of the IMG pipeline (Fig. 3).
The genome of K. konosiri X49T comprised a single circular chromosome with a length of 3,584,631 bp and a G + C content of 59.1% (Fig. 3 and Table 3). Of the 3347 predicted genes, 3261 were protein-coding. According to tRNAscan-SE and RNAmmer 1.2, 66 tRNA, 12 rRNA (four 5S rRNA, four 16S rRNA, and four 23S rRNA genes), and 8 miscRNA genes were found in the genome. The genome contained one CRISPR structure with 25 spacers of 28 bp and two putative CRISPRs. The number of CDSs including signal peptides was 239 (7.14%). The majority of the protein-coding genes (2815 genes; 84.1%) were assigned to functional categories, while the remainder were annotated as hypothetical proteins (446 genes). The properties and statistics of the genome are summarized in Table 3, and the distributions of genes among the functional categories of COG are shown in Table 4.
Insights from the genome sequence
To determine the genomic relatedness between K. konosiri X49T and closest relative strain K. marisflavi SW32T, the ANI value was calculated using an online calculator (https://www.ezbiocloud.net/tools/ani). The ANI value between two whole genome sequences was 89.32%. This value was well below the threshold of 95%; this suggested that two strains represent genotypically distinct species.
Kushneria members possess hypersaline resistance and K. konosiri X49T can grow optimally at 11–19% (w/v) NaCl and survive in the presence of 26% (w/v) NaCl . To balance the osmotic pressure between the inside and outside of the cell in the hypersaline habitat, theses halophile microorganisms increase the internal osmolarity of the cytoplasm using inorganic ions (mostly potassium ions) or organic compounds (mainly ectoine, choline, glycine betaine, and proline betaine, etc.), which are known as compatible solutes for the exclusion of salt ions. Genome analysis through the IMG pipeline revealed that K. konosiri X49T can adapt its salt tolerance using several functional genes (Fig. 4). In response to changes in the external osmolality, potassium is accumulated in the cytoplasm by transport via the Trk-type transport systems, KUP system, or Kdp two-component system [22,23,24]. With increasing potassium levels, osmoprotective compounds are accumulated by synthesis and/or uptake in the cytoplasm as a bi-phasic response . Also, expression of membrane proteins such as OMPs and of MDOs is affected by environmental osmolarity [25, 26].
To regulate the osmolarity between cytoplasm and environment, the genome of K. konosiri X49T encodes potassium uptake-related loci: the Trk system (low-affinity potassium transport; two TrkA and two TrkH genes), KUP system (two potassium uptake permeases), and Kdp two-component system (one sensor histidine kinase KdpD and one operon response regulator KdpE). The X49T genome also encodes a variety of organic compound regulation systems including ectoine biosynthesis-related genes (one EctA, L-2,4-diaminobutyric acid acetyltransferase; one EctC, L-ectoine synthase; and two EctD, ectoine hydrolases), betaine uptake-related genes (ten members of the betaine-carnitine-choline transport family; two BetPT, proline-betaine transporters; and six OsmC, F, V, and Y, glycine-betaine transporters), betaine biosynthesis-related genes (one BetA, choline dehydrogenase; two BetB, betaine aldehyde dehydrogenases; and one BetC, choline sulfatase), and one glycerol uptake facilitator protein. The osmoregulated membrane protein-related genes (three OmpA-OmpF Porin Family and osmoregulated periplasmic glucan biosynthesis) and osmoregulated periplasmic glucan-related genes (two MdoC, glucan biosynthesis proteins; one MdoB, phosphoglycerol transferase MdoB-like AlkP superfamily enzyme) were also found in the genome (Fig. 4).
Carotenoids are naturally occurring pigments that not only act as antioxidants but also enhance salt stress tolerance . The first step of carotenoid biosynthesis starts by formation of one phytoene from two molecules of GGPP, and phytoene is converted to α- or β-carotene along the biosynthesis pathway. α- or β-carotene is transformed into xanthophyll by obtaining an oxygen atom (Fig. 5). The colonies of K. konosiri X49T were orange. The genome of K. konosiri X49T encodes genes related to carotenoid biosynthesis: two GGPP synthases, one phytoene synthase, two phytoene desaturases, one lycopene β-cyclase, one β-carotene hydroxylase, and one enhancing lycopene biosynthesis protein 2. However, there is no xanthophyll cycle-related gene, ZEP, which is key for conversion of zeaxanthin to violaxanthin, suggesting that the orange color of the colony of K. konosiri is derived from β-carotene or β-cryptoxanthin. These carotenoids may act also as the potential osmoprotectants (Fig. 5).
The orange pigmented K. konosiri X49T was isolated from a salt-fermented food, Daemi-jeot, and was resistant to a hypersaline environment. Whole genome sequence analysis and physiological observations leads us to conclude that K. konosiri X49T is a orange-coloured halophile and its capabilities of a cellular response are enabled by a variety of genes determining the ‘carotenoid biosynthesis’ and ‘inorganic or organic transport and metabolism’. The presence of ectoine and betaine biosynthesis genes or transport system related genes demonstrates the possibility of a cellular response to high osmolarity through biosynthesis of ectoine and betaine to protect the cell from stress. As ectoine or betaine can play as a protectant under stress condition, the genome sequence of K. konosiri X49T may provide the molecular basis for its hypersaline tolerance and may lead to new development in its diverse biotechnological applications comprising environmental, medical and biofuel industries.
Clusters of orthologous groups
Clustered regularly interspaced short palindromic repeat
Department of energy
- GOLD :
Genomes on line database
Joint genome Institute
Kyoto encyclopedia of genes and genomes
Minimum information about a genome sequence
Outer membrane proteins
Prokaryotic genome annotation pipeline
Rapid annotation using subsystem technology
Yun JH, Park SK, Lee JY, Jung MJ, Bae JW. Kushneria konosiri sp. nov., isolated from the Korean salt-fermented seafood Daemi-jeot. Int J Syst Evol Microbiol. 2017;67:3576–82.
Sanchez-Porro C, de la Haba RR, Soto-Ramirez N, Marquez MC, Montalvo-Rodriguez R, Ventosa A. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Int J Syst Evol Microbiol. 2009;59:397–405.
Soto-Ramirez N, Sanchez-Porro C, Rosas S, Gonzalez W, Quinones M, Ventosa A, Montalvo-Rodriguez R. Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico. Int J Syst Evol Microbiol. 2007;57:900–5.
Cabrera A, Aguilera M, Fuentes S, Incerti C, Russell NJ, Ramos-Cormenzana A, Monteoliva-Sanchez M. Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almeria, southern Spain. Int J Syst Evol Microbiol. 2007;57:376–80.
Yoon JH, Choi SH, Lee KC, Kho YH, Kang KH, Park YH. Halomonas marisflavae sp. nov., a halophilic bacterium isolated from the Yellow Sea in Korea. Int J Syst Evol Microbiol. 2001;51:1171–7.
Bangash A, Ahmed I, Abbas S, Kudo T, Shahzad A, Fujiwara T, Ohkuma M. Kushneria pakistanensis sp. nov., a novel moderately halophilic bacterium isolated from rhizosphere of a plant (Saccharum spontaneum) growing in salt mines of the Karak area in Pakistan. Antonie Van Leeuwenhoek. 2015;107:991–1000.
Zou Z, Wang G. Kushneria sinocarnis sp. nov., a moderately halophilic bacterium isolated from a Chinese traditional cured meat. Int J Syst Evol Microbiol. 2010;60:1881–6.
Yun JH, Bae JW. Complete genome sequence of the halophile bacterium Kushneria marisflavi KCCM 80003T, isolated from seawater in Korea. Mar Genom. 2018;37:35-8.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The genomes on line database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2010;38:D346–54.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8.
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109–14.
Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43:D261–9.
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res. 2010;38:D211–22.
Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. TIGRFAMs and genome properties in 2013. Nucleic Acids Res. 2013;41:D387–95.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37:D211–5.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44:6614–24.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005;33:5691–702.
Ly A, Henderson J, Lu A, Culham DE, Wood JM. Osmoregulatory systems of Escherichia coli: identification of betaine-carnitine-choline transporter family member BetU and distributions of betU and trkG among pathogenic and nonpathogenic isolates. J Bacteriol. 2004;186:296–306.
Xue T, You Y, Hong D, Sun H, Sun B. The Staphylococcus aureu KdpDE two-component system couples extracellular K+ sensing and Agr signaling to infection programming. Infect Immun. 2011;79:2154–67.
Dominguez-Ferreras A, Munoz S, Olivares J, Soto MJ, Sanjuan J. Role of potassium uptake systems in Sinorhizobium melilot osmoadaptation and symbiotic performance. J Bacteriol. 2009;191:2133–43.
Csonka LN, Hanson AD. Prokaryotic osmoregulation: genetics and physiology. Annu Rev Microbiol. 1991;45:569–606.
Kennedy EP. Osmotic regulation and the biosynthesis of membrane-derived oligosaccharides in Escherichia coli. Proc Natl Acad Sci U S A. 1982;79:1092–5.
Kang L, Ji CY, Kim SH, Ke Q, Park SC, Kim HS, Lee HU, Lee JS, Park WS, Ahn MJ, et al. Suppression of the beta-carotene hydroxylase gene increases beta-carotene content and tolerance to abiotic stress in transgenic sweetpotato plants. Plant Physiol Biochem. 2017;117:24–33.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.
Garrity GM, Bell JA, Lilburn T, Phylum XIV. Proteobacteria. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s manual of systematic bacteriology, volume 2, the Proteobacteria, part B: the Gammaproteobacteria 2nd ed. New York: Springer; 2005. p. 1.
Garrity GM, Bell JA, Lilburn T, Class III. Gammaproteobacteria. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s manual of systematic bacteriology, volume 2, the Proteobacteria, part B: the Gammaproteobacteria, 2 edn. New York: Springer; 2005. p. 1.
Garrity GM, Bell JA, Lilburn T, Order VIII. Oceanospirillales. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s manual of systematic bacteriology, volume 2, the Proteobacteria, part B: the Gammaproteobacteria 2nd ed. New York: Springer; 2005. p. 270–323.
Garrity GM, Bell JA, Lilburn T, Family IV. Halomonadaceae. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM, editors. Bergey’s manual of systematic bacteriology, volume 2, the Proteobacteria, part B: the Gammaproteobacteria 2nd ed. New York: Springer; 2005. p. 300–23.
This study was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry (IPET) through the Agricultural Microbiome R&D Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (grant number: 914006–4).
The authors declare that they have no competing interests.
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