Open Access

Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8T

  • Ji-Hyun Yun1,
  • Yong-Joon Cho2,
  • Jongsik Chun2,
  • Dong-Wook Hyun1 and
  • Jin-Woo Bae1Email author
Standards in Genomic Sciences20149:9030495

https://doi.org/10.4056/sigs.4708537

Published: 15 June 2014

Abstract

Leucobacter salsicius M1-8T is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8T, as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.

Keywords

chromate resistance Leucobacter salsicius Microbacteriaceae

Introduction

The strain M1-8T (= KACC 21127T = JCM 16362T) is the type strain of the species Leucobacter salsicius [1], which was isolated from a Korean salt-fermented seafood known as “jeotgal” in Korean. The species epithet was derived from the Latin word salsicius, which means salty [1]. The genus Leucobacter was proposed in 1996 [2] and comprises a group of related Gram-positive, aerobic, non-motile, rod-shaped bacteria. Leucobacter strains have been recovered from a variety of ecological niches, including activated sludge from soil [3], wastewater [46], river sediments containing chromium [5], nematodes [7,8], food [1,9], potato plant phyllosphere [10], chironomid egg masses [11], air [12], soil [13], and feces [14]. Several Leucobacter strains have been reported to possess chromate resistance [1,4,11]. At present, there are 18 validly named Leucobacter species, but the only sequenced genomes in this genus were Leucobacter sp. UCD-THU [15] and L. chromiiresistens [16]. Among them, the highest resistance to chromate (up to 300 mM K2CrO4) was observed in L. chromiiresistens, in vivo [13]. However, no information has been generated on genes related to the mechanism of chromate resistance.

L. salsicius strain M1-8T has lower chromate resistance than L. chromiiresistens but it still exhibits moderate resistance (up to 10.0 mM Cr(VI)). Thus, the genomic analysis of L. salsicius M1-8T should help us to understand the molecular basis of adaptation to a chromium-contaminated environment. The present study determined the classification and features of Leucobacter salsicius strain M1-8T, as well as its genome sequence and gene annotations.

Classification and features

16S rRNA analysis

A representative genomic 16S rRNA gene of strain M1-8T was compared with those obtained using NCBI BLAST [17] with the default settings (only highly similar sequences). The most frequently occurring genera were Leucobacter (65.0%), unidentified bacteria (20.0%), Curtobacterium (6.0%), Microbacterium (5.0%), Leifsonia (2.0%), Subtercola (1.0%), and Zimmermannella (1.0%) (100 hits in total). The species with the Max score was Leucobacter exalbidus (AB514037), which had a shared identity of 99.0%.

The multiple sequence alignment program CLUSTALW [18] was used to align the 16S rRNA gene sequences from M1-8T and related taxa. Phylogenetic trees were constructed based on the aligned gene sequences using the maximum-likelihood, maximum-parsimony, and neighbor-joining methods based on 1,000 randomly selected bootstrap replicates using MEGA version 5 [19]. Strain M1-8T shared 99.1% nucleotide sequence similarity with L. aerolatus Sj10T, the closest validated Leucobacter species according to the phylogeny (Figure 1). Figure 1 shows the phylogenetic position of L. salsicius in the 16S rRNA-based tree. The sequence of the single 16S rRNA gene copy found in the genome did not differ from the previously published 16S rRNA sequence (GQ352403).
Figure 1.

Phylogenetic tree showing the position of Leucobacter salsicius relative to the type strains of other species within the genus Leucobacter, using Glaciibacter superstes AHU1791T as the outgroup. The sequences were aligned using CLUSTALW [18] and the phylogenetic tree was inferred from 1,390 aligned characteristics of the 16S rRNA gene sequence using the maximum-likelihood (ML) algorithm [20] with MEGA5 [19]. The branches are scaled in terms of the expected number of substitutions per site. The numbers adjacent to the branches are the support values based on 1,000 ML bootstrap replicates [20] (left), 1,000 maximum-parsimony bootstrap replicates [21] (middle), and 1,000 neighbor-joining bootstrap replicates [22] (right), for values >50%.

Morphology and physiology

Strain M1-8T is classified as class Actinobacteria, order Actinomycetales, family Microbacteriaceae, genus Leucobacter (Table 1) [1]. The strain L. salsicius M1-8T was isolated from a Korean salt-fermented food that contains tiny shrimp (shrimp jeotgal). The cells of strain M1-8T were rod-shaped, 1.0–1.5 µm in length, and 0.4–0.5 µm in diameter (Figure 2). No flagella were observed. The colonies were cream in color and circular with entire margins on marine agar medium. Strain M1-8T was aerobic and Gram-positive (Table 1). Optimum growth was observed at 25–30°C, at pH 7.0–8.0, and in the presence of 0–4% (w/v) NaCl. The tolerance of Cr (VI) was observed at up to 10.0 mM K2CrO4. The physiological characteristics, such as the growth substrates of M1-8T, were described in detail in a previous study [1].
Figure 2.

Scanning electron micrograph of Leucobacter salsicius M1-8T, which was obtained using a SUPRA VP55 (Carl Zeiss) at an operating voltage of 15 kV. The scale bar represents 1 µm.

Table 1.

Classification and general features of L. salsicius M1-8T according to the Minimum Information about a Genome Sequence (MIGS) recommendations [23]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [24]

 

Phylum Actinobacteria

TAS [25]

 

Class Actinobacteria

TAS [26]

 

Order Actinomycetales

TAS [2629]

 

Family Microbacteriaceae

TAS [26,27,30,31]

 

Genus Leucobacter

TAS [2]

 

Species Leucobacter salsicius

TAS [1]

 

Type strain M1-8T

TAS [1]

 

Gram stain

Positive

TAS [1]

 

Cell shape

Rod-shaped

TAS [1]

 

Motility

Non-motile

TAS [1]

 

Sporulation

Not reported

 
 

Temperature range

Mesophile

TAS [1]

 

Optimum temperature

25–30°C

TAS [1]

 

pH

pH 7–8

TAS [1]

MIGS-22

Oxygen requirement

Aerobic

TAS [1]

 

Carbon source

Heterotroph

TAS [1]

 

Energy metabolism

Not reported

 

MIGS-6

Habitat

Fermented food

TAS [1]

MIGS-6.3

Salinity

Halotolerant

TAS [1]

MIGS-15

Biotic relationship

Free-living

NAS

MIGS-14

Pathogenicity

Not reported

NAS

 

Isolation

Fermented food (Shrimp jeotgal, a Korean salt-fermented food)

TAS [1]

MIGS-4

Geographic location

South Korea

TAS [1]

MIGS-5

Sample collection date

May 2009

NAS

MIGS-4.1

Latitude

Not reported

 

MIGS-4.1

Longitude

Not reported

 

MIGS-4.3

Depth

Not reported

 

MIGS-4.4

Altitude

Not reported

 

The evidence codes are as follows. TAS: traceable author statement (i.e., a direct report exists in the literature). NAS: non-traceable author statement (i.e., not observed directly in a living, isolated sample, but based on a generally accepted property of the species, or anecdotal evidence). These evidence codes are derived from the Gene Ontology project [32].

Figure 2 Scanning electron micrograph of Leucobacter salsicius M1-8T, which was obtained using a SUPRA VP55 (Carl Zeiss) at an operating voltage of 15 kV. The scale bar represents 1 µm.

Chemotaxonomy

The peptidoglycan hydrolysate from strain M1-8T contained alanine, 2,4-diaminobutyric acid (DAB), γ-aminobutyric acid (GABA), glutamic acid, and glycine. The predominant fatty acids (>10% of the total) in M1-8T were anteiso-C15:0 (63.6%), anteiso-C17:0 (16.7%), and iso-C16:0 (14.2%). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and an unknown glycolipid. The major menaquinone in M1-8T was MK-11 and the minor menaquinones were MK-10 and MK-7.

Genome sequencing and annotation

Genome project history

L. salsicius strain M1-8T was selected for genome sequencing based on its environmental potential and is part of the Next-Generation BioGreen 21 Program (No.PJ008208). The genome sequence was deposited in DDBJ/EMBL/GenBank under accession number AOCN00000000 and the genome project was deposited in the Genomes On Line Database [33] under Gi21829. The sequencing and annotation were performed by ChunLab Inc., South Korea. A summary of the project information and the associations with “Minimum Information about a Genome Sequence” (MIGS) [34] are shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved high-quality draft

MIGS-28

Libraries used

454 PE library (8 kb insert size), Illumina PE library (150 bp)

MIGS-28.2

Number of reads

4,157,212 sequencing reads

MIGS-29

Sequencing platforms

PacBio RS, Illumina GAii, 454-GS-FLX-Titanium

MIGS-31.2

Sequencing coverage

189.78 × Illumina; 7.96 × pyrosequence; 15.88 × PacBio

MIGS-30

Assemblers

Roche gsAssembler version 2.6, CLCbio CLC Genomics Workbench version 5.0

MIGS-32

Gene-calling method

Prodigal 2.5

 

INSDC ID

AOCN01000000

 

GenBank Date of Release

April 3, 2013

 

GOLD ID

Gi21829

 

NCBI project ID

175945

 

Database: IMG

2526164546

MIGS-13

Source material identifier

KACC 21127T, JCM 16362T

 

Project relevance

Environmental and biotechnological

Growth conditions and DNA isolation

L. salsicius strain M1-8T was cultured aerobically in marine agar medium at 30°C. Genomic DNA was extracted using a G-spin DNA extraction kit (iNtRON Biotechnology), according to the standard protocol recommended by the manufacturer.

Genome sequencing and assembly

The genome was sequenced using a combination of an Illumina Hiseq system with a 150 base pair (bp) paired-end library, a 454 Genome Sequencer FLX Titanium system (Roche) with an 8 kb paired-end library, and a PacBio RS system (Pacific Biosciences). The Illumina reads were assembled using CLC Genomics Workbench ver. 5.0. The initial assembly was converted for the CLC Genomics Workbench by constructing fake reads from the consensus to collect the read pairs in the Illumina paired-end library. The 454 paired-end reads were assembled with Illumina data using gsAssembler ver. 2.6 (Roche) and the PacBio sequences were clustered into overlapping assembled data. CodonCode Aligner and CLC Genomics Workbench 5.0 were used for sequence assembly and quality assessment in the subsequent finishing process. The Illumina (189.78-fold coverage; 4,003,590 reads), PacBio (88-fold coverage; 23,441 reads), and 454 sequencing (7.96-fold coverage; 130,181 reads) platforms provided 213.62 × coverage (total 4,157,212 sequencing reads) of the genome. The final assembly identified one scaffold that included 28 contigs.

Genome annotation

The genes in the assembled genome were predicted using Integrated Microbial Genomes - Expert Review (IMG-ER) platform as part of the DOE-JGI genome annotation pipeline [35], followed by a round of manual curation using the JGI GenePRIMP pipeline. Comparisons of the predicted ORFs using the SEED [36], NCBI COG [37], Ez-Taxon-e [38], and Pfam [39] databases were conducted during gene annotation. Additional gene prediction analyses and functional annotation were performed with the Rapid Annotation using Subsystem Technology (RAST) server databases [40] and the gene-caller GLIMMER 3.02. RNAmer 1.2 [41] and tRNAscan-SE 1.23 [42] were used to identify rRNA genes and tRNA genes, respectively. The CLgenomicsTM 1.06 (ChunLab) was used to visualize the genomic features.

Genome properties

The genome comprised a circular chromosome with a length of 3,185,418 bp and a G+C content of 64.5% (Figure 3 and Table 3). Of the 2,933 predicted genes, 2,865 were protein-coding genes and 68 were RNA genes (three 5S rRNA genes, three 16S rRNA genes, three 23S rRNA genes, 51 predicted tRNA genes, and eight miscRNA genes). The majority of the protein-coding genes (2,275 genes; 77.6%) was assigned putative functions, while the remainder was annotated as hypothetical proteins (182 genes). The genome properties and statistics are summarized in Table 3. The distributions of genes among the COGs functional categories are shown in Table 4.
Figure 3.

Graphical map of the largest scaffold. From the outside to the center: genes on the reverse strand (colored according to the COGs categories), genes on the forward strand (colored according to the COGs categories), and RNA genes (tRNAs in red and rRNAs in blue). The inner circle shows the GC skew, where yellow indicates positive values and blue indicates negative values. The GC ratio is shown in red/green, which indicates positive/negative, respectively.

Table 3.

Genome statistics

Attribute

Value

% of totala

Genome size (bp)

3,185,418

100

DNA coding region (bp)

2,905,046

91.20

DNA G+C content (bp)

2,054,445

64.5

Total genes

2,933

100

RNA genes

68

2.32

rRNA operons

3

0.31

Protein-coding genes

2,865

97.68

Genes with predicted functions

2,275

77.57

Genes in paralog clusters

2,357

80.36

Genes assigned to COGs

2,210

75.35

Genes assigned Pfam domains

2331

79.47

Genes with signal peptides

195

6.65

Genes with transmembrane helices

784

26.73

aThe totals are 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 general COGs functional categories

Code

Value

% agea

Description

J

156

6.38

Translation, ribosomal structure, and biogenesis

A

4

0.16

RNA processing and modification

K

218

8.91

Transcription

L

167

6.83

Replication, recombination, and repair

B

1

0.04

Chromatin structure and dynamics

D

21

0.86

Cell cycle control, cell division, and chromosome partitioning

Y

0

0.00

Nuclear structure

V

40

1.64

Defense mechanisms

T

100

4.09

Signal transduction mechanisms

M

112

4.58

Cell wall/membrane/envelope biogenesis

N

0

0.00

Cell motility

Z

1

0.04

Cytoskeleton

W

0

0.00

Extracellular structures

U

32

1.31

Intracellular trafficking, secretion, and vesicular transport

O

69

2.82

Posttranslational modification, protein turnover, and chaperones

C

131

5.36

Energy production and conversion

G

129

5.27

Carbohydrate transport and metabolism

E

315

12.88

Amino acid transport and metabolism

F

74

3.03

Nucleotide transport and metabolism

H

101

4.13

Coenzyme transport and metabolism

I

81

3.31

Lipid transport and metabolism

P

154

6.30

Inorganic ion transport and metabolism

Q

51

2.09

Secondary metabolites biosynthesis, transport, and catabolism

R

307

12.55

General function prediction only

S

182

7.42

Function unknown

-

723

24.65

Not in COGs

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

Insights from the genome sequence

Leucobacter salsicius M1-8T and Leucobacter members, such as L. chromiireducens, L. aridicollis, L. luti, and L. alluvii, have been shown to possess chromate resistance in previous studies, while Zhu et al. reported the reduction of chromate by Leucobacter sp. [43]. In the present study, the genome analysis of Leucobacter salsicius M1-8T detected two copies of chromate transport protein A (ChrA), which is a membrane protein that confers heavy metal tolerance via chromate ion efflux from the cytoplasm. Potentially, this gene is a key feature that allows Leucobacter to adapt to chromate-contaminated environments. The genome sequence of L. salsicius M1-8T should provide deeper insights into the molecular mechanisms that underlie chromium tolerance and it may facilitate the development of biotechnological applications to improve chromium-contaminated field sites.

Declarations

Acknowledgements

We would like to thank Seong Woon Roh and his team members for help with SEM analysis (Jeju Center, Korea Basic Science Institute, Korea). This study was supported by a grant from the Next-Generation BioGreen 21 Program under No. PJ008208, Rural Development Administration, Republic of Korea.

Authors’ Affiliations

(1)
Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University
(2)
ChunLab Inc., Seoul National University

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