Open Access

Complete genome sequence of Kangiella koreensis type strain (SW-125T)

  • Cliff Han1, 2,
  • Johannes Sikorski3,
  • Alla Lapidus1,
  • Matt Nolan1,
  • Tijana Glavina Del Rio1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Susan Lucas1,
  • Feng Chen1,
  • Alex Copeland1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Galina Ovchinnikova1,
  • Amrita Pati1,
  • David Bruce1, 2,
  • Lynne Goodwin1, 2,
  • Sam Pitluck1,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land1, 5,
  • Loren Hauser1, 5,
  • Yun-Juan Chang1, 5,
  • Cynthia D. Jeffries1, 5,
  • Patrick Chain1, 6,
  • Elizabeth Saunders1, 2,
  • Thomas Brettin1, 2,
  • Markus Göker3,
  • Brian J. Tindall3,
  • Jim Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz1,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk3 and
  • John C. Detter1, 2
Standards in Genomic Sciences20091:1030226

DOI: 10.4056/sigs.36635

Published: 31 December 2009

Abstract

Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125T is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

mesophile non-pathogenic aerobic and anaerobic growth Oceanospirillales

Introduction

Strain SW-125T (= DSM 16069 = KCTC 12182 = JCM 12317) is the type strain of the species Kangiella koreensis, which is the type species of the tiny (two species containing) genus Kangiella [1]. This genus was only recently identified (2004) in the course of screening microorganisms from a tidal flat of the Yellow Sea in Korea. The genus is named Kangiella in order to honor Professor Kook Hee Kang, a Korean microbiologist, for his contribution to microbial research. The species name pertains to Korea, from where the strain was isolated [1]. Although many moderately halophilic or halotolerant bacteria have been isolated and characterized taxonomically from this habitat [1], literature on Kangiella is very limited. Presently, the organism appears to be of interest solely for its position in the tree of life. Here we present a summary classification and a set of features for K. koreensis SW-125T together with the description of the complete genomic sequencing and annotation.

Classification and features

It is not evident from the taxonomic description of K. koreensis if any other strains beside SW-125T have been isolated from this species. Uncultured clones with high 16S rRNA gene sequence similarity to the sequence of strain SW-125T (AY520560) have been obtained from moderate saline crude oil contaminated soil in China (clone B109, 99%, EU328030). The highest degree of similarity to sequences from environmental metagenomic libraries [2] was only 91% (As of June 2009).

Figure 1 shows the phylogenetic neighborhood of K. koreensis strain SW-125T in a 16S rRNA based tree. Analysis of the two identical 16S rRNA gene sequences in the genome of strain SW-125T differed by two nucleotides from the previously published 16S rRNA sequence generated from DSM 16069 (AY520560). The slight difference between the genome data and the reported 16S rRNA gene sequence is most likely due to sequencing errors in the previously reported sequence data.
Figure 1.

Phylogenetic tree highlighting the position of K. koreensis SW-125T relative to the other type strains in the phylogenetic neighborhood.. The tree was inferred from 1,476 aligned characters [3,4] of the 16S rRNA gene sequence under the maximum likelihood criterion [5], and rooted with the type strain of the order Oceanospirillales. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates, if larger than 60%. Strains with a genome sequencing project registered in GOLD [6] are printed in blue; published genomes in bold.

K. koreensis cells are rods of 0.2–0.5 × 1.5–4.5 µm in size (Table 1 and Figure 2). The colonies are smooth, raised, circular to irregular, light yellowish-brown in color and 2.0–3.0 mm in diameter after seven days incubation at 30°C on marine agar 2216 (MA) (Difco) [1]. The following physiological features are from Yoon et al. [1]. The growth conditions have been explored in quite detail. The growth at various temperatures was determined after incubation for at least 15 days on marine agar 2216 (Difco). The optimal growth temperature was at 30–37°C, with a minimum temperature of 4°C and a maximum temperature of 43°C [1]. The conditions of growth in dependence of pH were determined in marine broth 2216 (Difco). The optimal pH is 7.0–8.0. Growth is still possible at pH 5.5, but not at pH 5.0 [1]. Growth at various NaCl concentrations (1–15 %) was investigated in MB or trypticase soy broth (TSB, Difco). The optimal growth occurs in the presence of 2–3% NaCl (MB), growth still occurs in the presence of 12% NaCl (MB), but not without NaCl (TSB) or in the presence of more than 13% NaCl (MB) [1]. Growth under anaerobic conditions occurs on MA supplemented with nitrate. Strain SW-125T hydrolyses casein, tyrosine, Tween 20, Tween 40 and Tween 60, but not Hypoxanthine and xanthine [1]. Furthermore, H2S is not produced, and nitrate is not reduced under aerobic conditions but to nitrogen gas under anaerobic conditions [1]. Acid is not produced from the following sugars: adonitol, L-arabinose, D-cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, D-mannitol, D-mannose, D-melezitose, melibiose, myo-inositol, D-raffinose, L-rhamnose, D-ribose, D-sorbitol, sucrose, D-trehalose or D-xylose [1]. Unfortunately, a list of carbon sources from which acid is produced is not delivered [1]. When assayed with the API ZYM system, alkaline phosphatase, esterase (C4), esterase lipase (C8), leucine arylamidase, valine arylamidase, trypsin and naphthol-AS-BI-phosphohydrolase are present, but lipase (C14), cystine arylamidase, α-chymotrypsin, acid phosphatase, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase are absent [1]. Strain SW-125T was found to be susceptible to polymyxin (50 U), streptomycin (50 µg), penicillin (20 U), chloramphenicol (50 µg), ampicillin (10 µg), cephalothin (30 µg) and erythromycin (15 µg), and to be resistant to novobiocin (5 µg) and tetracycline (30 µg) [1].
Figure 2.

Scanning electron micrograph of K. koreensis SW-125T (Manfred Rohde, Helmholz Centre for Infection Research, Braunschweig).

Table 1.

Classification and general features of K. koreensis SW-125T according to the MIGS recommendations [7].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [8]

 

Phylum Proteobacteria

TAS [9]

 

Class Gammaproteobacteria

TAS [10,11]

 

Order Oceanospirillales

TAS [12,11

 

Family Incertae sedis

NAS

 

Genus Kangiella

TAS [1]

 

Species Kangiella koreensis

TAS [1]

 

Type strain SW-125

 
 

Gram stain

negative

TAS [1]

 

Cell shape

rods, 0.2–0.5 × 1.5–4.5 µm

TAS [1]

 

Motility

nonmotile

TAS [1]

 

Sporulation

non-sporulating

TAS [1]

 

Temperature range

4–43°C

TAS [1]

 

Optimum temperature

30–37°C

TAS [1]

 

Salinity

requires 2–3% (w/v) NaCl, growth at 12% but not 13% NaCl

TAS [1]

MIGS-22

Oxygen requirement

aerobic and anaerobic growth

TAS [1]

 

Carbon source

no specific information available

 
 

Energy source

peptone

TAS [1]

MIGS-6

Habitat

tidal flats

TAS [1]

MIGS-15

Biotic relationship

free living

NAS

MIGS-14

Pathogenicity

unknown

 
 

Biosafety level

1

TAS [13]

 

Isolation

tidal flat sediment

TAS [1]

MIGS-4

Geographic location

Daepo Beach, Yellow Sea, Korea

TAS [1]

MIGS-5

Sample collection time

2004 or before

TAS [1]

MIGS-4.1

Latitude, Longitude

33.245, 126.409

NAS

MIGS-4.2

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); 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 [14]. If the evidence code is IDA, then the property was observed for a living isolate by one of the authors or an expert mentioned in the acknowledgements.

Information on the composition of the peptidoglycan composition is unavailable. The predominant respiratory lipoquinone of K. koreensis SW-125T is the ubiquinone Q-8 (comprising approximately 84–88%) [1]. The fatty acids comprise iso-C11:0 (5.6%), iso-C13:0 (0.4%), iso-C15:1 F (1.2%), iso-C15:0 (57.6%), iso-C16:0 (0.7%), C16:0 (1.1%), iso-C17:0 (7.2%), iso-C17:1 ω 9c (8.6%), iso-C11:0 3-OH (10.5%), iso-C17:1 ω9c (8.6%), iso-C11:0 3-OH(10.5%), iso-C15:0 3-OH (0.9%), iso-C17:0 3-OH (1.0%) and summed feature 1 (iso-C15:1 and/or C13:0 3-OH) (3.2%) [1]. The predominance of iso-branched chain fatty acids indicates that the initial step in fatty acid synthesis is determined by an enzyme with a high degree of specificity for branched chain precursors (rather than acetate). The polar lipids of neither members of this species nor members of this genus have been investigated.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genomes OnLine Database [12] and the complete genome sequence in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Two genomic libraries: one 8 kb pMCL200 Sanger library and one 454 pyrosequence standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX

MIGS-31.2

Sequencing coverage

8.6× Sanger; 41× pyrosequence

MIGS-30

Assemblers

Newbler version 1.1.02.15, phrap

MIGS-32

Gene calling method

Prodigal

 

INSDC ID

CP001707

 

INSCD date of release

August 28, 2009

 

GOLD ID

Gc01097

 

INSDC project ID

29443

 

Database: IMG-GEBA

2501533215

MIGS-13

Source material identifier

DSM 16069

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

K. koreensis SW-125T, DSM 16069, was grown in DSMZ medium 514 (BACTO Marine Broth) [15] at 28°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol, but with a modification ‘L’ for cell lysis, as described in Wu et al. [16].

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website (http://www.jgi.doe.gov/). 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 3,167 overlapping fragments of 1,000 bp and entered into the assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [17]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. 329 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The final assembly consists of 24,350 Sanger and 478,372 pyrosequence (454) reads. Together all sequence types provided 49.6x coverage of the genome. The error rate of the completed genome sequence is less than 1 in 100,000.

Genome annotation

Genes were identified using Prodigal [18] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline (http://geneprimp.jgi-psf.org/) [19]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes Expert Review platform (http://img.jgi.doe.gov/er) [20].

Genome properties

The genome is 2,852,073 bp long and comprises one main circular chromosome with a 43.7% GC content. (Table 3 and Figure 3). Of the 2,695 genes predicted, 2,647 were protein coding genes, and 48 RNAs; 14 pseudogenes were also identified. The majority of the protein-coding genes (71.7%) were assigned a putative function while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

2,852,073

100.00%

DNA Coding region (bp)

2,585,246

90.64%

DNA G+C content (bp)

1,245,988

43.69%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,695

100.00%

RNA genes

48

1.78%

rRNA operons

2

 

Protein-coding genes

2,647

98.22%

Pseudo genes

14

0.52%

Genes with function prediction

1,932

71.69%

Genes in paralog clusters

163

6.05%

Genes assigned to COGs

2,034

75.47%

Genes assigned Pfam domains

1,995

74.03%

Genes with signal peptides

691

25.64%

Genes with transmembrane helices

727

26.98%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

% age

Description

J

170

6.4

Translation, ribosomal structure and biogenesis

A

1

0.1

RNA processing and modification

K

129

4.9

Transcription

L

106

4.0

Replication, recombination and repair

B

0

0.0

Chromatin structure and dynamics

D

29

1.1

Cell cycle control, mitosis and meiosis

Y

0

0.0

Nuclear structure

V

30

1.1

Defense mechanisms

T

134

5.1

Signal transduction mechanisms

M

139

5.3

Cell wall/membrane biogenesis

N

40

1.5

Cell motility

Z

1

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

81

3.1

Intracellular trafficking and secretion

O

130

4.9

Posttranslational modification, protein turnover, chaperones

C

141

5.3

Energy production and conversion

G

41

1.5

Carbohydrate transport and metabolism

E

197

7.4

Amino acid transport and metabolism

F

54

2.0

Nucleotide transport and metabolism

H

118

4.5

Coenzyme transport and metabolism

I

84

3.2

Lipid transport and metabolism

P

113

4.3

Inorganic ion transport and metabolism

Q

53

5.3

Secondary metabolites biosynthesis, transport and catabolism

R

235

8.9

General function prediction only

S

223

8.4

Function unknown

-

613

23.2

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Helga Pomrenke for growing K. koreensis cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, as well as German Research Foundation (DFG) INST 599/1-1.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
Lawrence Livermore National Laboratory
(7)
University of California Davis Genome Center

References

  1. Yoon JH, Oh TK, Park YH. Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004; 54:1829–1835. PubMed PubMed doi:10.1099/ijs.0.63156-0View ArticlePubMedGoogle Scholar
  2. Venter JC, Remington K, Heidelberg J, Halpern A, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66–74. PubMed doi:10.1126/science.1093857View ArticlePubMedGoogle Scholar
  3. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452View ArticlePubMedGoogle Scholar
  4. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMedView ArticlePubMedGoogle Scholar
  5. Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008; 57:758–771. doi:10.1080/10635150802429642 PubMed doi:10.1080/10635150802429642View ArticlePubMedGoogle Scholar
  6. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed PubMed doi:10.1093/nar/gkm884PubMed CentralView ArticlePubMedGoogle Scholar
  7. 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; 26:541–547. PubMed doi:10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  8. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87: 4576–4579. PubMed doi:10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  9. Woese CR, Stackebrandt E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985; 6: 143–151. PubMedView ArticlePubMedGoogle Scholar
  10. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: edDJ Brenner, NR Krieg, JT Staley, Garrity GM (eds), Bergey’s Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 1.View ArticleGoogle Scholar
  11. List Editor Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol 2005; 55: 2235–2238. doi:10.1099/ijs.0.64108-0Google Scholar
  12. Garrity GM, Bell JA, Lilburn T. Order VIII. Oceanospirillales ord. nov. In: edDJ Brenner, NR Krieg, JT Staley, Garrity GM (eds), Bergey’s Manual of Systematic Bacteriology, second edition, vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 270.View ArticleGoogle Scholar
  13. Anonymous. Biological Agents: Technical rules for biological agents www.baua.de TRBA 466.
  14. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 PubMed doi:10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  15. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
  16. Wu M, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. (In press)Google Scholar
  17. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12–20. doi:10.4056/sigs.761PubMed CentralView ArticlePubMedGoogle Scholar
  18. Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http://compbio.ornl.gov/prodigal/
  19. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted)Google Scholar
  20. Markowitz VM. Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. Expert Review of Functional Annotations for Microbial Genomes. Bioinformatics 2009; 25:2271–2278 PubMed doi:10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar

Copyright

© The Author(s) 2009