Open Access

Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China

  • Xiao-Yang Gao1, 11,
  • Xiao-Yang Zhi2,
  • Hong-Wei Li2, 9,
  • Yu Zhou10,
  • Alla Lapidus3, 4,
  • James Han5,
  • Matthew Haynes5,
  • Elizabeth Lobos5,
  • Marcel Huntemann5,
  • Amrita Pati5,
  • Natalia N Ivanova5,
  • Konstantinos Mavromatis5,
  • Brian J Tindall7,
  • Victor Markowitz6,
  • Tanja Woyke5,
  • Hans-Peter Klenk7, 12,
  • Nikos C Kyrpides5, 8 and
  • Wen-Jun Li1, 2Email author
Standards in Genomic Sciences201510:1

https://doi.org/10.1186/1944-3277-10-1

Received: 28 July 2014

Accepted: 6 November 2014

Published: 20 January 2015

Abstract

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125T was isolated from a hypersaline lake in China. The genome of strain YIM 91125T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.

Keywords

Halomonas lutea Aerobic Gram-negative Chemoorganotrophic Moderately halophilic Lake Ebinur

Introduction

Strain YIM 91125T (= DSM 23508T = KCTC 12847T = CCTCC AB 206093T) is the type strain of Halomonas lutea[1]. Currently, there are 83 validly named species in the genus Halomonas on the basis of most recent released from LPSN [2] and EzTaxon-e [3]. Halomonadaceae comprises the largest number of halophilic and halotolerant bacteria described to date, and Halomonas is the largest genus in this family. However, most of the taxa in Halomonadaceae have been reclassified in the past due to their heterogeneous features [47]. In Halomonas, a small group of species has been formally re-located to Chromohalobacter, Cobetia and Kushneria by further taxonomic studies. Members of the genus Halomonas were usually isolated from saline environments [812]. Strain YIM 91125T was originally isolated from soil sample of Ebinur Lake, which has been a long-term target for the studies of element cycling and microbial biota under extremely high-saline conditions in Xinjiang, Northwest China. As a type strain, it’s the original isolate used in species description, which exhibits the relevant phenotypic and genotypic properties cited in the original published taxonomic circumscriptions [13]. This organism grows well across a wide range of salinity and temperature and also participates in nitrogen reduction. In this context, strain YIM 91125T has been sequenced as a halophilic representative, and becomes a part of Genomic Encylopedia of Type Strains, Phase I: the one thousand microbial genomes project.

Here, we present a summary classification and a set of features for H. lutea strain YIM 91125T, together with the description of the genomic sequencing and annotation, and provide brief findings of its genome sequence as compared to genomes of other Halomonas species. The genomic data will provide insights into its new biotechnological applications, such as sewage treatment. The comprehensive genomes of this genus will facilitate our understanding of the ecological roles that Halomonas species play in those hypersaline habitats and their relationships with other halophilic and nonhalophilic microorganisms.

Classification and features

H. lutea YIM 91125T is a Gram-negative-staining, motile, aerobic and moderately halophilic bacterium, which can reduce nitrate (Table 1). Cells of the strain are short rods, 0.4 to 0.7 μm in diameter and 0.6 to 1.0 μm in length (Figure 1). They are motile by means of single polar flagellum and their colonies are orange, flat, opaque and mucoid with slightly irregular edges (Figure 1). The predominant respiratory quinone found in H. lutea YIM 91125T is Q-9, similar to other members of the genus Halomonas. The predominant fatty acids are C18:1 ω7c (25.1%), C16:0 (17.0%), C19:0 cyclo ω8c (13.6%), C12:0 3-OH (10.7%), C12:0 (7.9%), C10:0 (6.0%) and C17:0 cyclo (4.6%) [1]. The profile of major fatty acids in strain YIM 91125T is also similar to other members of the genus Halomonas[1417].
Table 1

Classification and general features of H. lutea YIM 91125 T [18]

MIGS ID

Property

Term

Evidence code a

 

Classification

Domain Bacteria

TAS [19]

Phylum Proteobacteria

TAS [20]

Class Gammaproteobacteria

TAS [21, 22]

Order Oceanospirillales

TAS [21, 23]

Family Halomonadaceae

TAS [4]

Genus Halomonas

TAS [24]

Species Halomonas lutea

TAS [1]

Type strain YIM 91125T

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

short rods

TAS [1]

 

Motility

motile

TAS [1]

 

Sporulation

non-sporulating

TAS [1]

 

Temperature range

4-45°C

TAS [1]

 

Optimum temperature

37°C

TAS [1]

 

pH range; Optimum

5.0-9.0

TAS [1]

 

Carbon source

mono- and polysaccarides

TAS [1]

MIGS-6

Habitat

aquatic, fresh water, lake, salinewater

TAS [1]

MIGS-6.3

Salinity

1-20% NaCl (w/v)

TAS [1]

MIGS-22

Oxygen requirement

aerobe

TAS [1]

MIGS-15

Biotic relationship

free living

TAS [1]

MIGS-14

Pathogenicity

none

NAS

MIGS-4

Geographic location

Ebinur Lake (China)

TAS [1]

MIGS-5

Sample collection

2008 or before

NAS

MIGS-4.1

Latitude

45.05

TAS [1]

MIGS-4.2

Longitude

82.977

TAS [1]

MIGS-4.4

Altitude

not reported

 

aEvidence codes – 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 [25].

Figure 1

Transmission electron micrograph of H. lutea YIM 91125 T .

16S rRNA gene sequence of strain YIM 91125T was compared with the newly released database from the Greengenes [26], using NCBI BLAST [27, 28] under default settings (e.g., considering only HSPs from the best 250 hits) and the relative frequencies of taxa were determined, weighted by BLAST scores. The most frequently occurring genera were Halomonas (71.4%), Chromohalobacter (17.8%), Bacillus (3.6%), Haererehalobacter (3.6%) and Modicisalibacter (3.6%) (228 hits in total). Regarding 186 hits to sequences from members of the genus Halomonas, the average identity within HSPs was 95.5%, whereas the average coverage by HSPs was 98.3%. Among all other species, the one yielding the highest score was Halomonas xinjiangensis, which corresponded to identity of 99.9% and HSP coverage of 98.0%. (Note that the Greengenes database uses the INSDC (=EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest scoring environmental sequences were EF157249 and EF157230 (Greengenes short name ‘tar pits clone 101–11 k’ and ‘tar pits clone 101–120 k’), which showed identity of 96.3% and an HSP coverage of 99.6%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were soil like ‘soil’, ‘seafloor’, ‘drilling deep-earth’; water like ‘groundwater’, ‘aquatic’, ‘lake’, ‘marine’; oil and plant. Environmental samples yielded hits of a higher score than the highest scoring species were not found.

Phylogenetic analyses were carried out with two different algorithms, i.e., neighbor-joining (NJ) and maximum-likelihood (ML). The phylogenetic tree was shown in Figure 2 and Additional file 1: Figure S1, which provides an interesting insight into the nomenclature and classification of members of the genus Halomonas, and also indicates the phylogenetic neighborhood of H. lutea. The phylogenetic relationships indicate that H. lutea YIM 91125T is most closely to H. xianhensis A-1T with 99% similarity and the sequence of the sole 16S rRNA gene in the genome differs by 10 nucleotides from the previously published 16S rRNA sequence (EF674852).
Figure 2

Phylogenetic tree highlighting the position of H. lutea relative to the type strains of the other species within Halomonas . According to the most recent release of the EzTaxon-e database, all the 16S rRNA gene sequences of the type strains within genus Halomonas were retained. The tree was inferred from 1,383 aligned bases [29] under the neighbor-joining (NJ) [30] and maximum-likelihood (ML) [31] methods with 1,000 randomly selected bootstrap replicates using MEGA version 5.2 [32]. The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 NJ bootstrap (left) and from 1,000 ML bootstrap (right) replicates [33] if they are larger than 50%. Lineages with type strain genome sequencing projects registered in Genomes OnLine Database (GOLD) [34] are labeled with one asterisk, and those have available genomic data are labeled with two asterisks. Non-type strain LS21of H. campaniensis and H. elongata DSM 2581T listed ‘Complete and Published’ are also labeled with two asterisks.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position and biological application importance [35, 36], and for a better understand the mechanism of its halophilic adaptation. Sequencing of H. lutea YIM 91125T is part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project [37], a follow-up of the GEBA project [38], which aims for increasing the sequencing coverage of key reference microbial genomes. The genome project is deposited in the Genomes OnLine Database (GOLD), and the high quality draft genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE JGI using state of the art sequencing technology [39]. A summary of the project information is shown in Table 2. It presents the project information and in compliance with MIGS version 2.0 compliance [18].
Table 2

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Improved-High-Quality Draft

MIGS-28

Libraries used

Illumina standard shotgun library

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Fold coverage

119 ×

MIGS-30

Assemblers

Velvet v. 1.1.04; ALLPATHS v. r41043

MIGS-32

Gene calling method

Prodigal 1.4

 

Locus Tag

NZ_ARKK01000000

 

Genbank ID

ARKK00000000

 

Genbank Date of Release

April 23, 2013

 

GOLD ID

Gi11553

 

BIOPROJECT

PRJNA199405

 

Project relevance

Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project

MIGS-13

Source Material Identifier

Halomonas lutea DSM 23508

Growth conditions and DNA isolation

H. lutea strain YIM 91125T (DSM 23508T), was grown in DSMZ medium 514b (Medium 514 plus additional salt) at 37°C [40]. DNA was isolated from 0.5-1.0 g of cell pasted using Jetflex Genomic DNA Purification Kit (Qiagen, Hilden, Germany), following the standard protocol as recommended by the manufacturer, but with an additional incubation (60 min, 37°C) with 50 μl proteinase K and finally adding 200 μl protein precipitation buffer (PPT). DNA is available through the DNA Bank Network [41].

Genome sequencing and assembly

The draft genome of strain YIM 91125T was generated at JGI using Illumina technology [42]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform which generated 9,251,032 reads totaling 1,387.7 Mb. All general aspects of library construction and sequencing performed at the JGI. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts. The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet version 1.1.04 [43]; (2) 1–3 Kb simulated paired end reads were created from Velvet contigs using Wgsim [44]; (3) Illumina reads were assembled with simulated read pairs using Allpaths-LG [45]. The final draft assembly contained 49 contigs in 42 scaffolds. The total size of the genome is 4.5 Mbp and the final assembly is based on 538.9 Mbp of Illumina data, which provides an average 119.0 × coverage of the genome.

Genome annotation

Genes were identified using Prodigal [46] as part of the DOE JGI genome annotation pipeline [47], following by a round of manual curation using the JGI GenePRIMP pipeline [48]. The predicted CDSs were translated and used to search the NCBI non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro database. These data sources were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) platform [49].

Genome properties

The assembly of the draft genome sequence consists of 42 scaffolds (Figure 3) amounting to 4,533,090 bp, and G+C content is 59.1%. The majority of the protein-coding genes (83.0%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. 3,325 protein coding genes belong to 422 paralogous families in this genome. 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 map of the largest scaffold in Halomonas lutea YIM 91125 T . From bottom to the top: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG catergories), RNA genes (tRNA green, rRNA red, other RNAs black), GC content, GC skew (purpele/olive).

Table 3

Genome statistics

Attribute

Value

Genome size (bp)

4,533,090

DNA coding (bp)

3.982.279

DNA G + C (bp)

2.676.712

DNA scaffolds

42

Total genes

4,368

Protein-coding genes

4,284

RNA genes

84

Pseudo genes

51

Genes in internal clusters

3,325

Genes with function prediction

3,625

Genes assigned to COGs

3,497

Genes with Pfam domains

3,674

Genes with signal peptides

326

Genes with transmembrane helices

1,033

CRISPR repeats

1

Table 4

Number of genes associated with general COG functional categories

Code

Value

% age

Description

J

183

4.66

Translation, ribosomal structure and biogenesis

A

1

0.03

RNA processing and modification

K

278

7.08

Transcription

L

168

4.28

Replication, recombination and repair

B

6

0.15

Chromatin structure and dynamics

D

37

0.94

Cell cycle control, Cell division, chromosome partitioning

V

36

0.92

Defense mechanisms

T

208

5.30

Signal transduction mechanisms

M

210

5.35

Cell wall/membrane biogenesis

N

92

2.34

Cell motility

U

80

2.04

Intracellular trafficking and secretion

O

158

4.02

Posttranslational modification, protein turnover, chaperones

C

291

7.41

Energy production and conversion

G

273

6.95

Carbohydrate transport and metabolism

E

352

8.96

Amino acid transport and metabolism

F

85

2.16

Nucleotide transport and metabolism

H

186

4.74

Coenzyme transport and metabolism

I

133

3.39

Lipid transport and metabolism

P

218

5.55

Inorganic ion transport and metabolism

Q

126

3.21

Secondary metabolites biosynthesis, transport and catabolism

R

467

11.89

General function prediction only

S

339

8.63

Function unknown

-

871

19.94

Not in COGs

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

Insights from the genome sequence

The genomic sequences of twelve Halomonas species are available, including H. lutea YIM 91125T. Genome properties of those Halomonas species are shown in Table 5, but only H. elongate and H. campaniensis have complete genome sequences. These Halomonas genome sequences exhibit dramatic interspecies variations in size, ranging from 5.34 Mb (H. titanicae) to 2.85 Mb (H. jeotgali); and the size of H. lutea is larger than the average size, suggesting acquisition of functions may allow better adaption to its environment, e.g., genes coding for tripartite ATP-independent periplasmic (TRAP) transporters for substrate uptake or nitrate degradation [50]. Also, GC contents of those species vary from 52.65% (H. campaniensis) to 67.86% (H. smyrnensis), and of H. lutea (59.05%) is around the average GC content, close to H. anticariensis (58.54%). In addition, the distribution of genes into COG categories was not entirely similar in all twelve compared genomes (Figure 4). And H. lutea has more specific genes, since proteins with COG only account for 71.18% which is lower than other members. Compared with other Halomonas species, the proportions of genes with signal peptide and transmembrane helices of H. lutea are respectively 7.46% and 23.65%, close to the corresponding averages. The abundance of transmembrane helices related genes indicates the important role in metabolism process of Halomonas.
Table 5

Comparison of genome features of Halomonas species

Species

Genome size (Mb)

GC content (%)

Gene count

H. anticariensis FP35T

5.07

58.54

4817

H. boliviensis LC1T

4.14

54.68

3915

H. campaniensis LS21

4.07

52.65

3665

H. elongata DSM 2581T

4.06

63.61

3556

H. halocynthiae DSM 14573T

2.88

53.80

2773

H. halodenitrificans DSM 735T

3.47

63.95

3256

H. jeotgali HwaT

2.85

62.92

2636

H. lutea YIM 91125T

4.53

59.05

4368

H. smyrnensis AAD6T

3.56

67.86

3326

H. stevensiss S18214T

3.69

60.25

3523

H. titanicae BH1T

5.34

54.58

2908

H. zhanjiangensis DSM 21076T

4.06

54.48

3739

Figure 4

Distribution of functional classes of predicted genes in Halomonas species chromosomes accordingf to the clusters of orthologous groups of proteins.

DNA-DNA hybridization is considered as a gold-standard of distinguishing species [51]. Digital DDH similarities between genome of H. lutea and those of other Halomonas species were calculated using GGDC web server version 2.0 under recommend setting [52, 53]. The probabilities of DDH value > 70% assessed via logistic regression under three formulae indicate that H. lutea is different from other species of the genus (Table 6). The inter-genome distances under formula 2 between H. lutea and H. anticariensis, H. boliviensi, H. campaniensis, H. elongata, H. halocynthiae, H. halodenitrificans, H. jeotgali, H. smyrnensis, H. stevensii, H. titanicae and H. zhanjiangensis are about 0.22, the corresponding DDH estimates below the 70% threshold under formula 2 are: 19.5% (± 2.29), 20.2% (± 2.31), 21.1% (± 2.33), 20.1% (± 2.31), 19.2% (± 2.29), 19.4% (± 2.29), 19.9% (± 2.30), 20.3% (± 2.32), 20.4% (± 2.32), 20.5% (± 2.32), 18.9% (± 2.28), respectively. The standard deviations indicate the inherent uncertainty in estimating DDH values from intergenomic distances based on models derived from empirical test data sets. Given that the low degree of DNA-DNA similarity among Halomonas species, it appears justified to assume that these strains represent different species. For better understanding of the relationships between H. lutea and other Halomonas members, availability of more genome sequences of representatives are needed to implement phylogenomic inference.
Table 6

Digital DDH similarities between H. lutea DSM 23529 T and the other Halomonas s pecies

Reference species

Formula 1

Formula 2

Formula 3

H. anticariensis

14.9 ± 3.14

19.5 ± 2.29

15.0 ± 2.67

H. boliviensis

13.0 ± 2.99

20.2 ± 2.31

13.4 ± 2.56

H. campaniensis

13.0 ± 2.99

21.1 ± 2.33

13.3 ± 2.56

H. elongata

15.6 ± 3.19

20.1 ± 2.31

15.6 ± 2.70

H. halocynthiae

13.0 ± 2.99

19.2 ± 2.29

13.3 ± 2.56

H. halodenitrificans

14.5 ± 3.11

19.4 ± 2.29

14.6 ± 2.65

H. jeotgali

13.5 ± 3.03

19.9 ± 2.30

13.8 ± 2.59

H. smyrnensis

15.5 ± 3.18

20.3 ± 2.32

15.5 ± 2.70

H. stevensiss

13.5 ± 3.04

20.4 ± 2.32

13.8 ± 2.59

H. titanicae

13.0 ± 2.99

20.5 ± 2.32

13.3 ± 2.56

H. zhanjiangensis

13.2 ± 3.01

18.9 ± 2.28

13.5 ± 2.57

GenBank accession numbers for the reference genomes: H. anticariensis (NZ_ASTJ00000000), H. boliviensi (NZ_AGQZ00000000), H. campaniensis (CP007757), H. elongata (NC_014532), H. halocynthiae (AUDZ00000000), H. halodenitrificans (JHVH00000000), H. jeotgali (NZ_AMQY00000000), H. smyrnensis (NZ_AJKS00000000), H. stevensii (NZ_AJTS00000000), H. titanicae (NZ_AOPO00000000), H. zhanjiangensis (NZ_ARIT00000000).

As a halophilic bacterium, the genome of H. lutea also shows properties related to solute and ion transport, 203 genes related ion transport and metablism, 60 genes related TRAP-type C4-dicarboxylate transport system which is a crucial family of solute transporters. Moreover, nitrate reduction was tested using API 20NE system and 57 genes were predicted to participate in the nitrogen metabolism. PTS IIA-like nitrogen-regulatory protein, nitrate and sulfonate transport systems related genes were also detected in its genome.

Conclusions

The genome sequence and annotation of H. lutea YIM 91125T were presented. The genome comprises 42 scaffolds which together represent the organism of approximately 4.53 Mb. It encodes for key genes and pathways involved in the compatible solutes production and nitrogen degradation. This provides clues to discover novel genes and functions, and leads to an improved understanding of halophilic microbial evolution and function in the extremely salty conditions. YIM 91125T participates in nitrogen cycling, although the process of reducing nitrogen needs further studies to fully understand the related pathways. The genome sequencing of H. lutea marks an important step toward a comprehensive genomic catalog and the metabolic diversity of halophilic bacteria. It may contribute to further studies on important process for Halomonas, such as quorum-sensing regulatory and osmoadaption. Combining with genomes of other members in Halomonas, will make an important advance in understanding of the ecological roles that Halomonas species play in those hypersaline environments and their relationships with other halophilic and nonhalophilic microorganisms.

Abbreviations

DDH: 

DNA-DNA hybridization

HSP: 

High-scoring segment pair.

Declarations

Acknowledgements

Susanne Schneider is gratefully acknowledged the assistance for growing H. lutea cultures. We also thank Evelyne-Marie Brambilla for DNA extraction and quality control (both at the DSMZ). This work was performed under the auspices of the US Department of Energy's 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. A. L. was supported in part by Russian Ministry of Science Mega-grant no. 11.G34.31.0068 (Dr. Stephen J O'Brien Principal Investigator). W.-J. Li was supported by ‘Hundred Talents Program’ of the Chinese Academy of Sciences.

Authors’ Affiliations

(1)
Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences
(2)
Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University
(3)
Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University
(4)
Algorithmic Biology Lab, St. Petersburg Academic University
(5)
DOE Joint Genome Institute
(6)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(7)
Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(8)
Department of Biological Sciences, King Abdulaziz University
(9)
The First Hospital of Qujing City, Qujing Affiliated Hospital of Kunming Medical University
(10)
State Key Laboratory Breeding Base for Zhejiang Sustainable Plant Pest Control, Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences
(11)
University of Chinese Academy of Sciences
(12)
School of Biology, Newcastle University

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