Open Access

Draft genome sequence of Rubidibacter lacunae strain KORDI 51-2T, a cyanobacterium isolated from seawater of Chuuk lagoon

  • Dong Han Choi
  • , Jee-Youn Ryu
  • , Kae-Kyoung Kwon
  • , Jung-Hyun Lee
  • , Changhoon Kim
  • , Charity M. Lee
  • and Jae Hoon Noh

DOI: 10.4056/sigs.4398180

Received: 16 October 2013

Accepted: 16 October 2013

Published: 16 October 2013

Abstract

A photoautotrophic cyanobacterium, Rubidibacter lacunae was reported in 2008 for the first time. The type strain, KORDI 51-2T, was isolated from seawater of Chuuk lagoon located in a tropical area. Although it belonged to a clade exclusively comprised of extremely halotolerant strains by phylogenetic analyses, R. lacunae is known to be incapable of growth at high salt concentration over 10%. Here we report the main features of the genome of R. lacunae strain KORDI 51-2T. The genome of R. lacunae contains a gene cluster for phosphonate utilization encoding three transporters, one regulator and eight C-P lyase subunits.

Keywords:

Cyanobacteriaphosphonate utilizationphotoautotrophyRubidibacter lacunaeseawater

Introduction

Rubidibacter lacunae type strain KORDI 51-2T (=KCTC 40015T=UTEX L2944T) is a photoautotrophic cyanobacterium isolated from lagoon seawater of Chuuk, Micronesia [1]. At this time, the genus Rubidibacter is comprised of a single isolate. Further, only three environmental 16S rRNA gene sequences in the NCBI showed relatively high sequence similarity of ca. 96% to 16S rRNA gene of the strain. Thus, the genus seems either to be a numerically rare cyanobacterium or, to exploit specific environments such as microbial mats. Actually, the most similar sequences (accession no. of DQ861063 and DQ861117 in GenBank) to Rubidibacter were obtained in microbial mats of a coastal hypersaline pool. Nonetheless, the strain KORDI 51-2T is a non-extreme halotolerant member in the Halothece cluster, exclusively composed of extremely halophilic/halotolerant bacteria. Considering this contrasting phenotypic trait, genomic information of KORDI 51-2T could provide a good clue to understand genomic adaptation of cyanobacteria at extreme salt condition. Here we present a summary of the genomic features of R. lacunae strain KORDI 51-2T.

Classification and features

By phylogenetic analysis of 16S ribosomal RNA genes (Figure 1), R. lacunae KORDI 51-2T was clustered into the Halothece cluster. Four Euhalothece strains belonging to the cluster were isolated from a hypersaline pond (strains MPI 96N303 and MPI 96N304) or a solar evaporation pond (strains MPI95AH10 and MPI95AH13) in Mexico [2]. These strains showed sustained growth between 6-16% salinity, and several strains could grow even in NaCl saturated brine, suggesting that they are at least extremely halotolerant cyanobacteria [2]. Dactylococcopsis salina and other Halothece strains belonging to the cluster were also isolated from various hypersaline environments, such as a solar lake in Egypt, a solar evaporation pond in Spain and hypersaline lagoon in Australia [2,3]. On the contrary, R. lacunae KORDI 51-2T was isolated from natural seawater and able to grow at a salinity between 2 and 7% (Table 1). In addition, R. lacunae KORDI 51-2T contains phycoerythrin, which differentiated it from the other strains belonging to the ‘Halothece’ cluster [1]. The epifluorescence micrograph of the cells and other classification and general features were shown in Figure 2 and Table 1, respectively.

Figure 1

Neighbor-joining tree showing the phylogenetic position of Rubidibacter lacunae KORDI 51-2T relative to other close cyanobacterial strains. GenBank accession numbers for each strain are shown in parenthesis. The tree uses the Jukes-Cantor corrected distance model to construct a distance matrix. Bootstrap values above 60%, based on 1,000 resamplings, are shown at the branching points. Strains with genome sequence are underlined.

Table 1

Classification and general features of R. lacunae strain KORDI 51-2T according to the MIGS recommendations [4]

MIGS ID

     Property

     Term

      Evidence codea

     Domain Bacteria

      TAS [5]

     Phylum Cyanobacteria

      TAS [6-8]

     Class Cyanobacteria

      TAS [8,9]

     Current classification

     Order Unknown

     Family 1.1

      TAS [7]

     Genus Rubidibacter

      TAS [1]

     Species Rubidibacter lacunae

      TAS [1]

     Type strain KORDI 51-2

      TAS [1]

     Gram stain

     Not reported

     Cell shape

     Rods

      TAS [1]

     Motility

     None

      TAS [1]

     Sporulation

     None

      IDA

     Temperature range

     25-35oC

      TAS [1]

     Optimum temperature

     30oC

      TAS [1]

MIGS-6

     Habitat

     Seawater

      TAS [1]

MIGS-6.3

     Salinity

     2-7% (optimum: 5)

      TAS [1]

MIGS-22

     Oxygen     Carbon source     Energy source

     Aerobic     Autotroph     Phototroph

      TAS [1]      TAS [1]      TAS [1]

MIGS-15

     Biotic relationship

     Free living

      TAS [1]

MIGS-14

     Pathogenicity

     None

      NAS

MIGS-4

     Geographic location

     Chuuk state, Micronesia

      TAS [1]

MIGS-5

     Sample collection time

     July, 2004

      IDA

MIGS-4.1

     Latitude

     7o 13’ N

      IDA

MIGS-4.2

     Longitude

     151o 58’ E

      IDA

MIGS-4.3

     Depth

     40 m

      IDA

MIGS-4.4

     Altitude

     Not applicable

      NAS

a) 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 [9].

Figure 2

Epifluorescence micrograph of R. lacunae KORDI 51-2T. The picture was taken under green excitation and then converted to gray scale. Bar, 3 μm.

Genome sequencing and annotation

Genome project history

The organism was selected for sequencing on the basis of its phylogenetic position. The genome project was deposited in the Genomes On Line Database [10] and draft genome sequence was deposited in GenBank database (accession number ASSJ00000000). The genome sequencing was carried out in Macrogen Inc. (Seoul, Korea) using GS-FLX Titanium sequencing technology. Table 2 presents the project information and its association with MIGS version 2.0 compliance [4].

Table 2

Genome sequencing project information

MIGS ID

     Property

     Term

MIGS-31

     Finishing quality

     Draft

MIGS-28

     Libraries used

     Shotgun library

MIGS-29

     Sequencing platforms

     454 GS-FLX Titanium

MIGS-31.2

     Sequencing coverage

     30×

MIGS-30

     Assemblers

     Newbler version 2.3

MIGS-32

     Gene calling method

     Prodigal, GenePRIMP

     Genbank ID

     ASSJ00000000

     Genbank Date of Release

     October 7, 2013

     GOLD ID

     Gi22154

     Project relevance

     Cyanobacterial ecology

Growth conditions and DNA isolation

R. lacunae KORDI 51-2T was grown in a 50 ml culture flask filled with 50 ml of modified f/2 medium in which silicate was omitted and ammonium chloride was supplemented (final conc. of 100 μM). The culture flask with inoculum was incubated at 25oC at about 20 μE m-2 s-1 (light:dark=14:10) for 3 weeks. Genomic DNA was isolated using Qiagen Genomic-tip 100/G (Qiagen) according to the manufacturer’s instruction.

Genome sequencing and assembly

The genome was sequenced by pyrosequencing (GS-FLX Titanium). A shotgun library was constructed according to GS FLX Titanium Sequencing Method Manual. The 291,414 pyrosequencing reads obtained has an average length of 442.12 bp and were assembled using the Newbler assembler (version, 2.3; Roche) with default options. The final assembly resulted in 126 contigs longer than or equal to 500 bp with the contigs sum of 4,215,105 bp. After removing 27 short contigs with low coverage in order to minimize possible contamination, the remaining 99 contigs were used for further analyses (Table 3).

Table 3

Genome statistics

Attribute

    Value

      % of totala

Genome size (bp)

    4,153,658

DNA Coding region (bp)

    3,323,928

      80.02

DNA G+C content (bp)

    2,335,216

      56.22

No. of contigs

    99

Total genesb

    3,790

RNA genes

    50

      1.32

Protein-coding genes

    3,740

      98.68

Genes with functional prediction

    2411

      63.61

Genes with enzymes

    775

      20.45

Genes with transporter classification

    343

      9.05

Genes assigned to COGs

    2,228

      58.79

Genes assigned to Pfam

    2,511

      66.25

Genes assigned to TIGRFam

    976

      25.75

Genes assigned in paralog clusters

    2427

      64.04

Genes with signal peptides

    137

      3.61

Genes with transmembrane helices

    810

      21.37

a) The total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome.

b) Also includes 283 pseudogenes.

Genome annotation

The gene prediction and functional annotation of the genome sequence was basically performed within the Integrated Microbial Genomes – Expert Review (IMG-ER) platform [11]. The tRNAScan-SE was used to find tRNA genes [12]. Ribosomal RNA genes and ncRNA were predicted using RNAmmer [13] and Infernal [14] using the Rfam model [15], respectively. Identification of protein coding genes was performed using Prodigal [16], followed by a round of manual curation using the JGI GenePRIMP pipeline [17]. The predicted CDS were searched using the TIGR-fam, Pfam and COG databases implemented in the IMG systems.

Genome properties

The draft genome of R. lacunae KORDI 51-2T, with a total of 4.15 Mbp from 99 contigs, contains 56.22% G+C contents (Figure 3 and Table 3). A total of 3,790 genes were predicted. Of these, 283 pseudogenes. The remaining 3,457 were annotated as protein-coding genes and 50 for RNA genes (3 for rRNA, 41 for tRNA and 6 other nc RNA). The properties and the statistics of the genome are summarized in Table 3. 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: color by COG categories and RNAs on forward strand, genes on forward strand, genes on reverse strand, color by COG categories and RNAs on reverse strand, GC content, GC skew.

Table 4

Number of genes associated with the 25 general COG functional categories

Code

     Value

      % age

      Description

J

     149

      6.08

      Translation

A

     1

      0.04

      RNA processing and modification

K

     109

      4.45

      Transcription

L

     127

      5.18

      Replication, recombination and repair

B

     1

      0.04

      Chromatin structure and dynamics

D

     24

      0.98

      Cell cycle control, mitosis and meiosis

Y

     0

      -

      Nuclear structure

V

     43

      1.75

      Defense mechanisms

T

     105

      4.28

      Signal transduction mechanisms

M

     166

      6.77

      Cell wall/membrane biogenesis

N

     25

      1.02

      Cell motility

Z

     1

      0.04

      Cytoskeleton

W

     0

      -

      Extracellular structures

U

     62

      2.53

      Intracellular trafficking and secretion

O

     118

      4.81

      Posttranslational modification, protein turnover, chaperones

C

     149

      6.08

      Energy production and conversion

G

     126

      5.14

      Carbohydrate transport and metabolism

E

     172

      7.01

      Amino acid transport and metabolism

F

     58

      2.37

      Nucleotide transport and metabolism

H

     157

      6.4

      Coenzyme transport and metabolism

I

     51

      2.08

      Lipid transport and metabolism

P

     158

      6.44

      Inorganic ion transport and metabolism

Q

     75

      3.06

      Secondary metabolites biosynthesis, transport and catabolism

R

     331

      13.5

      General function prediction only

S

     244

      9.95

      Function unknown

-

     1562

      41.21

      Not in COGs

Insights from the genome sequence

A genome analysis of R. lacunae KORID 51-2T, revealed that it contains a gene cluster participating in organic phosphonate utilization. Likewise with a marine nitrogen-fixing cyanobacterium, Trichodesmium erythraeum IMS101 [18], the strain KORDI 51-2T has orthologs to phnC-E (transporters) and phnG-M (C-P lyase complex) (Figure 4A). Additionally, an ortholog to phnF (transcriptional regulator) is found in strain KORDI 51-2T, but not in T. erythraeum IMS101. Phylogenetic analysis of PhnJ proteins found in various bacterial strains, showed that PhnJ proteins of cyanobacteria form polyphyletic lineages (Figure 4B), suggesting that the phn gene cluster of cyanobacteria might be acquired by horizontal gene transfer. As KORDI 51-2T can grow in media supplemented with variety of organic phosphonate substrates (2-aminoethylphosphonate, methylphosphonate, phosphonoacetic acid and phosphonoformic acid) as a sole P-source (data not shown), the strain must be able to cleave C-P bonds of organic phosphonate by C-P lyase pathways and utilize them as a P-source.

Figure 4

DNA topology of the phn cluster (A) and phylogenetic analysis of the PhnJ protein (B). A, Genes encoding phosphonate transport (gray), regulation (light gray), and the C-P lyase subunits (dark gray) are shown. Additional two sets of transporters were not shown. B, Phylogenetic relationship of the PhnJ protein from a variety of bacteria determined by maximum-likelihood analysis. Bootstrap values >70 are shown at the nodes. The scale bar represents amino-acid substitution per site.

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Dr. EC Yang for sequence submission. This study was supported by the Ministry of Oceans and Fisheries of Korea and the Korea Institute of Ocean Science and Technology (KIOST) research programs (PM57371, PE99161, PE98962).


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