Open Access

Draft genome sequence of Halopiger salifodinae KCY07-B2T, an extremly halophilic archaeon isolated from a salt mine

Standards in Genomic Sciences201510:124

https://doi.org/10.1186/s40793-015-0113-y

Received: 20 April 2015

Accepted: 24 November 2015

Published: 10 December 2015

Abstract

Halopiger salifodinae strain KCY07-B2T, isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic archaeon. In this work, we report the features of the type strain KCY07-B2T, together with the draft genome sequence and annotation. The draft genome sequence is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and contains 4204 protein-coding genes and 50 rRNA genes.

Keywords

Halopiger salifodinae ArchaeaExtreme halophileGenomeSalt mine

Introduction

The genus Halopiger , which belongs to the family Halobacteriaceae , was originally established in 2007 by Gutiérrez et al. [1]. The type species of the genus Halopiger is Halopiger xanaduensis SH-6T. To date, the genus is comprised of three validly published species and two effectively but not validly published species: H. xanaduensis [1], Halopiger aswanensis [2], Halopiger salifodinae [3], Halopiger djelfamassiliensis [4] and Halopiger goleamassiliensis [5]. The species of the genus were reported to be isolated from hypersaline environments such as salt lake sediment [1, 4, 5], hypersaline soil [2] and salt mine [3]. All are Gram-negative, strictly aerobic and extremely halophilic [15]. In this genus, three genome sequences, including one finished genome sequence H. xanaduensis SH-6T, and two draft genome sequences H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T, are available in Standards in Genomic Sciences [46], except H. aswanensis 56T which showed highest 16S rRNA gene similarity to H. xanaduensis SH-6T (99.1 %). Here we present a summary of the classification and a set of features of strain H. salifodinae KCY07-B2T, together with a description of the non-contiguous finished genomic sequencing and annotation.

Organism Information

Classification and features

A representative genomic 16S rRNA gene sequence of H. salifodinae KCY07-B2T was compared with sequences deposited in the GenBank database using BLASTN [7]. The 16S rRNA gene sequence analysis showed that H. salifodinae KCY07-B2T shared the highest sequence identities to H. xanaduensis SH-6T (95.8 %), followed by H. aswanensis 56T (95.5 %), H. djelfamassiliensis IIH2T (94.9 %) and H. goleamassiliensis IIH3T (94.8 %), and shared low sequence similarities (<94.8 %) to species of other genera. The phylogenetic tree was reconstructed by the neighbor-joining method using MEGA 5 and Kimura’s 2-parameter model for distance calculation [8, 9]. The phylogenetic tree was assessed by boot-strapping for 1000 replications, and the consensus tree was shown in Fig. 1.
Fig. 1

Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showed the relationship of H. salifodinae KCY07-B2T and other related haloarchaeal species. GenBank accession numbers were indicated in parentheses. Bootstrap values based on 1000 replicates were shown for branches with more than 60 % support. Bar, 0.02 substitutions per nucleotide positions. Methanospirillum hungatei JF-1T [30] was used as outgroup

H. salifodinae KCY07-B2T can tolerant high salinity (5.4 M NaCl ) and high temperature (50 °C) [3]. Cells lyse in distilled water. The optimal growth condition of strain KCY07-B2T occured in medium NOM-3 with 2.9–3.4 M NaCl [3]. The optimum temperature was 37–45 °C. The optimum pH was 7.0, with a growth range of pH 6.0–8.0 [3]. Cells of strain KCY07-B2T are strictly aerobic, non-motile and pleomorphic rod-shaped (Fig. 2). Several sugars, organic acids and amino acids can serve as sole carbon and energy sources, and amino acids are not required in the growth medium [3]. The features of H. salifodinae KCY07-B2T are listed in Table 1.
Fig. 2

Electron micrographs of cells of strain KCY07-B2T grown in liquid medium under optimum condition. a Transmission electron micrographs of strain KCY07-B2T revealing rod-shaped, bar, 0.2 μm, b Showing a mixture of pleomorphic cells including short and long rod-shaped, bar, 2 μm

Table 1

Classification and general features of H. salifodinae KCY07-B2T according to the MIGS recommendations [10]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Archaea

TAS [31]

Phylum Euryarchaeota

TAS [32]

Class Halobacteria

TAS [33, 34]

Order Halobacteriales

TAS [3537]

Family Halobacteriaceae

TAS [38, 39]

Genus Halopiger

TAS [1]

Species Halopiger salifodinae

TAS [3]

Type strain: strain KCY07-B2T = JCM 18547T = CGMCC 1.12284T

TAS [3]

 

Gram stain

negative

TAS [3]

 

Cell shape

pleomorphic rods

TAS [3]

 

Motility

non-motile

TAS [3]

 

Sporulation

non-sporulating

NAS

 

Temperature range

25–50 °C

TAS [3]

 

Optimum temperature

37–45 °C

TAS [3]

 

pH range; Optimum

6.0–8.0; 7.0

TAS [3]

 

Carbon source

acetate, L-asparagine, citrate, fumarate, D-glucose, L-glutamate, glycine, isoleucine, L-lysine, L-malate, D-mannose, L-serine, D-sorbitol, starch, succinate and L-threonine

TAS [3]

 

Energy metabolish

heterotrophic

IDA

MIGS-6

Habitat

salt mine

TAS [3]

MIGS-6.3

Salinity

1.9–5.4 M NaCl (optimum 2.9–3.4 M)

TAS [3]

MIGS-22

Oxygen requirement

aerobic

TAS [3]

MIGS-15

Biotic relationship

free-living

IDA

MIGS-14

Pathogenicity

non-pathogenic

NAS

 

Biosafety

1

NAS

MIGS-4

Geographic location

Kuche county, Akesu area in Xinjiang province, P.R. China

TAS [3]

MIGS-5

Sample collection time

2009

IDA

MIGS-4.1

Latitude

not reported

 

MIGS-4.2

Longitude

not reported

 

MIGS-4.4

Altitude

not reported

 

aEvidence 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 [40, 41]

Genome sequencing information

Genome project history

This genome was selected for sequencing on the basis of its phylogenetic position and 16S rRNA sequence similarity to other members of the genus Halopiger . This whole genome shotgun project of strain H. salifodinae KCY07-B2T was deposited at DDBJ/EMBL/GenBank under the accession number JROF00000000 and the sequence consisted of 83 contigs (further assembling constructed these contigs into 81 scaffolds). Table 2 shows the project information and its association with MIGS version 2.0 compliance [10].
Table 2

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

High-quality draft

MIGS-28

Libraries used

One pair-end 500 bp library and one pair-end 2 Kb library

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Fold coverage

130 × (based on 500 bp library), 65 × (based on 2 Kb library)

MIGS-30

Assemblers

SOAP denovo

MIGS-32

Gene calling method

RAST

 

Locus Tag

LT39

 

Genbank ID

JROF00000000

 

Genbank Date of Release

November 17, 2014

 

GOLD ID

Gi0079167

 

NCBI Project ID

261874

 

BIOPROJECT

PRJNA261874

MIGS 13

Source Material Identifier

JCM 18547

 

Project relevance

Phyloenetic diversity, Study of the archaeal diversity in a salt mine

Growth conditions and genomic DNA preparation

H. salifodinae KCY07-B2T was cultivated aerobically on 37 °C for 4 days in NOM-3 medium, which contains (per liter distilled water) 5.4 g KCl, 0.3 g K2HPO4, 0.25 g CaCl2, 0.25 g NH4Cl, 26.8 g MgSO4 · 7H2O, 23.0 g MgCl2 · 6H2O, 184.0 g NaCl, 1.0 g yeast extract, 0.25 g fish peptone, 0.25 g sodium formate, 0.25 g sodium acetate, 0.25 g sodium lactate and 0.25 g sodium pyruvate (adjusted to pH 7.0 with 1 M NaOH) [3]. Genomic DNA was extracted using the method described by Marmur [11]. The purity, quality and the concentration of genomic DNA preparation were analyzed by 0.7 % agarose gel electrophoresis with λ-Hind III digest DNA Marker (TaKaRa, Dalian, China) and measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., USA).

Genome sequencing and assembly

The genome of H. salifodinae KCY07-B2T was sequenced using Solexa paired-end sequencing technology (HiSeq2000 system, Illumina, Inc., USA) [12]. A shotgun library was constructed with a 500 bp-span paired-end library (~500 Mb available reads, ~130-fold genome coverage) and a 2000 bp-span paired-end library (~250 Mb available reads, ~65-fold genome coverage). The sequence data from an Illumina HiSeq 2000 were assembled with SOAPdenovo v.1.05 [1315]. The final assembly identified 83 contigs and 81 scaffolds (the minimum length is 523 bp) generating a genome size of 4.35 Mb. The quality of the sequencing reads data was estimated by G + C content and sequencing depth correlation analysis.

Genome annotation

The tRNAs and rRNAs were identified using tRNAscan-SE [16], RNAmmer [17] and Rfam database [18]; The open reading frames and the functional annotation of translated ORFs were predicted and achieved by using the RAST server online [19, 20]. Classification of some predicted genes and pathways were analyzed using COGs [21, 22] and KEGG [2325] databases. Meanwhile, we used CRISPRs web server [26] to predict CRISPRs and InterPro [27, 28] to obtain the GO annotation with the database of Pfam [29].

To estimate the mean level of nucleotide sequence similarity at the genome level between e KCY07-B2T and the genus Halopier genomes available to date ( H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T), we compared the ORFs only using comparison sequence based in the server RAST [19] at a query coverage of ≥60 % and a minimum nucleotide length of 100 bp.

Genome properties

The draft genome sequence of H. salifodinae KCY07-B2T revealed a genome size of 4,350,718 bp (scaffold length) with a 65.41 % G + C content. Of the 4254 predicted genes, 4204 were protein-coding genes, and 50 were rRNA genes. There were one 16S rRNA gene, two 23S rRNA genes and two 5S rRNA genes. A total of 2887 genes (68.67 %) were assigned a putative function (Table 3). Table 4 showed the distribution of genes into COG functional categories.
Table 3

Genome statistics of Halopiger salifodinae KCY07-B2T, including nucleotide content and gene count levels

Attribute

Value

% of totala

Genome size (bp)

4,350,718

100.00

DNA coding (bp)

3,567,421

82.00

DNA G + C (bp)

2,845,805

65.41

DNA scaffolds

81

 

Total genes

4254

100.00

Protein coding genes

4204

98.82

RNA genes

50

1.18

Pseudo genes

not determined

not determined

Genes in internal clusters

not determined

not determined

Genes with function prediction

2561

60.20

Genes assigned to COGs

2887

67.87

Genes assigned Pfam domains

2694

63.33

Genes with signal peptides

122

2.9

Genes with transmembrane helices

910

21.39

CRISPR repeats

3

0.07

aThe 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

Table 4

Number of genes associated with the 25 general COG functional categories

Code

value

% agea

Description

J

175

4.16

Translation, ribosomal structure and biogenesis

A

1

0.02

RNA processing and modification

K

175

4.16

Transcription

L

120

2.85

Replication, recombination and repair

B

6

0.14

Chromatin structure and dynamics

D

25

0.59

Cell cycle control, Cell division, chromosome partitioning

V

35

0.83

Defense mechanisms

T

131

3.12

Signal transduction mechanisms

M

118

2.81

Cell wall/membrane biogenesis

N

16

0.38

Cell motility

U

19

0.45

Intracellular trafficking and secretion

O

131

3.12

Posttranslational modification, protein turnover, chaperones

C

255

6.07

Energy production and conversion

G

200

4.76

Carbohydrate transport and metabolism

E

306

7.28

Amino acid transport and metabolism

F

77

1.83

Nucleotide transport and metabolism

H

159

3.78

Coenzyme transport and metabolism

I

115

2.74

Lipid transport and metabolism

P

215

5.11

Inorganic ion transport and metabolism

Q

60

1.43

Secondary metabolites biosynthesis, transport and catabolism

R

550

13.08

General function prediction only

S

299

5.45

Function unknown

-

1317

31.33

Not in COGs

aThe total is based on the total number of protein coding genes in the genome

Insights from the genome sequence

Strain H. salifodinae KCY07-B2T was isolated from a salt mine sample. The experiments showed this strain could grow at 2.9–3.4 M NaCl for optimal growth, and the cells lysed in distilled water. So the analysis of the genome sequence focused on the adaption mechanism of the halophilic archaea in hypersaline-environments. Strain H. salifodinae KCY07-B2T mainly utilized “the salt-in strategy” to maintain osmotic balance. According to the annotation of genome sequence, Trk system potassium uptake protein were found, which were responsible for K+ uptake and transport, including 9 copies TrkH genes and 5 copies TrkA genes. Five copies of Kef-type K+ transport proteins, one copy glutathione-regulated potassium-efflux protein KefB and 8 pH adaptation potassium efflux system proteins were found that were related to K+ efflux. And there also existed 8 copies of potassium channel proteins. In addition, the genome contains 13 copies of Na+/ H+ antiporter proteins related to Na+ efflux. The genome of strain H. salifodinae KCY07-B2T contains 12 genes related to the synthesis and transport of the compatible-solute glycine betaine for resistance to osmotic stress including: 7 choline-sulfatases, 2 high-affinity choline uptake protein BetTs, 2 glucose-methanol-choline oxidoreductase and 1 glycine betaine transporter OpuD coding genes. These proteins were also related to the metabolic pathway converting choline sulfate to glycine betaine. All these proteins and systems mentioned played an important role in the adaption of osmotic stress in high salt environment.

Currently, three genomes from Halopiger species are available. Here, we compare the genome of strain H. salifodinae KCY07-B2T with strains H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T (Table 5). The size of genome of H. salifodinae KCY07-B2T (4.35 Mb) is similar to H. xanaduensis SH-6T (4.35 Mb) but larger than that of H. djelfamassiliensis IIH2T (3.77 Mb) and H. goleamassiliensis IIH3T (3.90 Mb). The G + C content of H. salifodinae KCY07-B2T (65.41 %) is similar to H. xanaduensis SH-6T (65.18 %) and higher than that of H. djelfamassiliensis IIH2T (64.30 %) but lower than that of H. goleamassiliensis IIH3T (66.06 %). In addition, H. salifodinae KCY07-B2T shares a mean genomic sequence similarity of 79.74 %, 80.16 % and 79.17 % with strains H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T, respectively.
Table 5

Genomic comparison of H. salifodinae KCY07-B2T with three other Halopiger speciesa

Species

Strain

Genome accession number

Genome size (Mb)

G + C content

H. salifodinae

KCY07-B2T

JROF00000000

4.35

65.41

H. xanaduensis,

SH-6T

NC_015666

4.35

65.18

H. djelfamassiliensis

IIH2T

PRJEB1777

3.77

64.30

H. goleamassiliensis

IIH3T

PRJEB1780

3.90

66.06

aSpecies and strain names, genome accession numbers, sizes and G + C contents

Conclusions

Strain KCY07-B2T is the third member of the genus Halopiger to be described and the fourth whose genome sequence report is available. These data will provide a new perspective of how microorganisms adapt to halophilic environments, and may also provide a pool of functional enzymes that work at higher salty.

Abbreviations

NCBI: 

National Center for Biotechnology Information

EMBL: 

European Molecular Biology Laboratory

DDBJ: 

DNA Data Bank of Japan

BLASTN: 

Basic Local Alignment Search Tool for Nucleotide

MIGS: 

Minimum Information about a Genome Sequence

RAST: 

Rapid Annotations using Subsystems Technology

COG: 

Cluster of Orthologous Groups of proteins

KEGG: 

Kyoto Encyclopedia of Genes and Genomes

CRISPR: 

Clustered Regularly Interspaced Short Palindromic repeat sequences

GO: 

Gene Ontology

DNA: 

Deoxyribonucleic Acid

16S rRNA: 

ribosomal Ribonucleic Acid

JCM: 

Japan Collection of Microorganisms

CGMCC: 

China General Microbiological Culture Collection Center

H. salifodinae KCY07-B2T

Halopiger salifodinae KCY07-B2T

H. xanaduensis SH-6T

Halopiger xanaduensis SH-6T

H. aswanensis 56T

Halopiger aswanensis 56T

H. djelfamassiliensis IIH2T

Halopiger djelfamassiliensis IIH2T

H. goleamassiliensis IIH3T

Halopiger goleamassiliensis IIH3T

Declarations

Acknowledgements

We thank Hong Cheng for her help on offering some websites for data analysis. This work was supported by the China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (grant no. DY125-14-E-02) and the Chinese Natural Science Foundation (grant no. 31170001).

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
College of Life Sciences, Zhejiang University
(2)
Second Institute of Oceanography, State Oceanic Administration

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© Zhang et al. 2015