Open Access

Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment

Standards in Genomic Sciences201712:3

DOI: 10.1186/s40793-016-0214-2

Received: 17 September 2015

Accepted: 10 December 2016

Published: 5 January 2017

Abstract

Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K. olearia 7.02% and K. shengliensis 7.83%), with dissimilarity percentages close to the threshold generally described for genus delineation. Nevertheless, the percentage of conserved proteins (POCP), which is much higher than 50% (around 70%), together with phenotypic features of the isolates, confirm the affiliation all Kosmotoga species described so far to the same genus.

Keywords

Marine Hydrothermal vent Thermotogales Chemoorganoheterotroph Thermophile

Introduction

The phylum Thermotogae is currently composed of 50 species spread across 13 genera, distinguishable mainly by their characteristic outer membrane known as the ‘toga’. These genera are named Athalassotoga , Defluviitoga , Fervidobacterium , Geotoga , Kosmotoga , Marinitoga , Mesoaciditoga , Mesotoga , Oceanotoga , Petrotoga , Pseudothermotoga , Thermosipho and Thermotoga [112]. They are grouped into 5 families [1, 10]: (i) Thermotogaceae , comprising the genera Thermotoga and Pseudothermotoga ; (ii) Fervidobacteraceae, comprising the genera Fervidobacterium and Thermosipho ; (iii) Petrotogaceae , comprising the genera Petrotoga , Defluviitoga , Geotoga , Marinitoga and Oceanotoga ; (iv) Kosmotogaceae , comprising the genera Kosmotoga and Mesotoga ; and (v) Mesoaciditogaceae , comprising the genera Mesoaciditoga and Athalassotoga . The first representatives of this phylum described from the mid-1990s were all neutrophilic, thermophilic or hyperthermophilic fermentative bacteria from a range of hot anaerobic microbial environments such as deep-sea and terrestrial vents, anaerobic digesters or oil reservoirs. They are relatively homogeneous in terms of physiology. In the last few years, the description of the genera Mesotoga , Mesoaciditoga and Athalassotoga , corresponding to three divergent lineages among the Thermotogae , showed that there are also representatives of this order that grow under mesophilic or slightly acidic conditions [1, 7, 8]. The different genera of Thermotogae display different tolerances to oxygen and salts, and can produce L-alanine or reduce different sulfur species to prevent the toxic effect of H2 produced during fermentation. Phylogenetic analyses of the 16S rRNA gene and of concatenated ribosomal proteins place Thermotogae as a sister group to Aquificales , representing a deeply-branching lineage of the bacterial tree that emerges close to the first delineation between bacterial and archaeal branches [13]. However, the evolutionary history of these bacteria is also characterized by numerous lateral gene transfer events with Firmicutes and with Thermococcales [13, 14].

The genus Kosmotoga was proposed by DiPippo et al. in 2009 [5] and belongs to the family Kosmotogaceae , one of the five families of the phylum Thermotogae . The genus is currently composed of four type species, K. olearia [5], K. arenicorallina [15], K. shengliensis [15] and K. pacifica [16]. Kosmotoga species have been isolated from oil reservoirs as well as shallow and deep-sea hydrothermal vents. Strain SLHLJ1T (=DSM 26965T = JCM 19180T = UBOCC 3254T =MCCC 1A00641T ) is the type strain of the species K. pacifica , which was isolated from sediments of an active hydrothermal vent on the East Pacific Rise (102°55′W, 3°58′S) [16]. Here, we present a summary of the physiological features of K. pacifica SLHLJ1T, together with a description of the complete genomic sequence and annotation. A brief genomic comparison was made between K. pacifica SLHLJ1T and K. olearia TBF 19.5.1T and we also calculated (i) ANI and (ii) POCP values among pairs of genomes of Thermotogae for which complete genomic sequences were available.

Organism information

Classification and features

Strain SLHLJ1T was isolated by repeated streaking on plates as described elsewhere [16]. In this study, a whole-genome phylogeny of the Thermotogae lineage was constructed based on the core genome (499 core genes) from 20 complete genomes. The core genes were chosen based on identified orthologous genes, which were also single-copy genes from 20 genomes (Additional file 1: Table S1). The result indicated that K. pacifica SLHLJ1T was affiliated to the genus Kosmotoga , which formed a deep branch in the phylogenetic tree constructed with the neighbor-joining algorithm (Fig. 1). K. pacifica SLHLJ1T was closely related to K. arenicorallina , sharing 97.93% 16S rRNA gene sequence similarity, and was distantly related (<93%) to the other species of the genus Kosmotoga . Phylogenetic comparison of 16S rRNA gene sequences of K. pacifica SLHLJ1T and other Thermotogae also supported the result that K. pacifica SLHLJ1T clusters with other Kosmotoga species (Additional file 2: Figure S1) [16].
Fig. 1

Phylogenetic tree indicating the position of K. pacifica strain SLHLJ1T relative to other type and non-type strains with complete genome sequences within the phylum Thermotogae. The tree was constructed by the neighbor-joining method using 499 core genes (approximately 163,000 amino acid sequences). Bootstrap values (in %) are based on 500 replicates and are shown at the nodes with >50% bootstrap support. The scale bar represents 5% sequence divergence

K. pacifica SLHLJ1T cells are Gram-negative non-motile short rods or ovoid cocci (~1 μm long by ~0.6 μm wide) surrounded by a typical toga. They appear singly or occasionally in chains of 3–4 cells within the sheath (Fig. 2). Spores were never observed. Strain SLHLJ1T grows between 33 and 78 °C, but the optimal growth temperature is 70 °C. Growth occurs under strictly anaerobic and obligate chemoorganoheterotrophic conditions. A small amount of yeast extract is required for growth. The following substrates support growth in the presence of 0.02% yeast extract: peptone, brain–heart infusion, tryptone, glycerol, maltose, xylose, glucose, fructose, cellobiose, trehalose, lactate, propionate and glutamate. The strain can reduce L-cystine and elemental sulfur [16]. A summary of the classification and general features of K. pacifica SLHLJ1T is presented in Table 1.
Fig. 2

Transmission electron micrograph of K. pacifica strain SLHLJ1T, showing the toga

Table 1

Classification and general features of K. pacifica SLHLJ1T [12]

MIGS ID

Property

Term

Evidence codea

  

Domain Bacteria

TAS [17]

  

Phylum Thermotogae

TAS [18, 19]

  

Class Thermotogae

TAS [18, 20]

 

Current classification

Order Kosmotogales

TAS [18, 21]

  

Family Kosmotogaceae

TAS [18, 22]

  

Genus Kosmotoga

TAS [12, 23]

  

Species Kosmotoga pacifica

TAS [16]

  

Type strain SLHLJ1T

TAS [16]

 

Gram stain

Negative

TAS [16]

 

Cell shape

Coccobacilli with a ‘toga’ (a sheath-like structure)

TAS [16]

 

Motility

non-motile

TAS [16]

 

Sporulation

Non-sporulating

TAS [16]

 

Temperature range

33-78 °C

TAS [16]

 

Optimum temperature

70 °C

TAS [16]

 

pH range; Optimum

5.5-8.5;7

 
 

Carbon source

Yeast extract, peptone, brain–heart infusion, tryptone, glycerol, maltose, xylose, glucose, fructose, cellobiose, trehalose, lactate, propionate and glutamate

TAS [16]

 

Energy metabolism

Chemoorganoheterotrophic

TAS [16]

MIGS-6

Habitat

Hydrothermal vent environment

TAS [16]

MIGS-6.3

Salinity

0.5-6% NaCl (w/v)

TAS [16]

MIGS-22

Oxygen requirement

Anaerobic

TAS [16]

MIGS-15

Biotic relationship

Free living

TAS [16]

MIGS-14

Pathogenicity

None

NAS

MIGS-23.1

Isolation

Sediment

TAS [16]

MIGS-4

Geographic location

East Pacific Rise

TAS [16]

MIGS-5

Sample collection time

July 2011

TAS [16]

MIGS-4.1

Latitude

3°58′S

TAS [16]

MIGS-4.2

Longitude

102o55′W

TAS [16]

MIGS-4.3

Altitude

-2891 m

TAS [16]

a Evidence 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 on anecdotal evidence). These evidence codes are from the Gene Ontology project [24]. * The rank of phylum is not covered by the Rules of the International Code of Nomenclature of Prokaryotes

Genome sequencing information

Genome project history

This organism was selected for sequencing based on its phylogenetic position. The complete genome sequence was deposited in GenBank under the accession number CP011232. Sequencing, finishing and annotation of the K. pacifica SLHLJ1T genome were performed by the Shanghai Majorbio Bio-pharm Technology Co., Ltd (Shanghai, China). Table 2 presents the main project information and its association with MIGS version 2.0 compliance [25].
Table 2

Project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Two genomic libraries: one 454 PE library (3 kb insert size) and one Illumina PE library (500 bp insert size)

MIGS-29

Sequencing platforms

Illumina Miseq, 454 GS FLX Titanium

MIGS-31.2

Fold coverage

564 × Illumina; 112 × 454 3 K-PE

MIGS-30

Assemblers

Newbler version 2.8

MIGS-32

Gene calling method

NCBI PGAP pipeline

 

Locus Tag

IX53

 

Genbank ID

CP011232.1

 

GenBank Date of Release

June 3, 2015

 

GOLD Project ID

Gp0119521

 

BIOPROJECT

PRJNA256122

MIGS-13

Source material identifier

UBOCC 3254 and MCCC 1A00641

 

Project relevance

Thermophile, GEBA

Growth conditions and DNA isolation

Strain SLHLJ1T was grown anaerobically for 24 h at 70 °C in 50 mL DSMZ medium 282 (with yeast extract as a carbon and energy source), supplemented with 12 g/L L-cystine. DNA was isolated from the liquid phase without L-cystine, using a standard phenol/chloroform/isoamyl alcohol extraction protocol [26]. The quality and quantity of the extracted DNA were analyzed using agarose gel electrophoresis and NanoDrop. A total of around 20 μg DNA was obtained.

Genome sequencing and assembly

The genome was sequenced using a combination of an Illumina MiSeq (2 × 300 bp) and 454 sequencing platforms. Libraries were prepared in accordance with manufacturer’s instructions. The Newbler V2.8 software package was used for sequence assembly and quality assessment [27]. The draft genome sequence was generated using 454 data. The 454 draft assembly was based on 243,758,031 bp 454 draft data. Newbler parameters were -consed, -a 50, -l 350, -g, -m, and -ml 20. The Phred/Phrap/Consed software package [28] was used for sequence assembly and quality assessment in the subsequent finishing process. Illumina reads were used for gap-filling, correcting potential base errors and increasing consensus quality. Gaps were then filled in by sequencing the PCR products using an ABI 3730xl capillary sequencer. A total of four additional reactions were necessary to close gaps and to improve the quality of the finished sequence. Together, the combination of the Illumina and 454 sequencing platforms provided 676 × coverage of the genome. The final assembly contained 637,426 pyrosequences and 4,870,336 Illumina reads.

Genome annotation

The protein-coding genes, structural RNAs (5S, 16S, and 23S), tRNAs and small non-coding RNAs were predicted using the NCBI PGAP server online [29]. The functional annotation of predicted ORFs was performed using RPS-BLAST [30] against the COG database [31] and Pfam database [32]. The TMHMM program was used for gene prediction with transmembrane helices [33] and the signalP program for gene prediction from peptide signals [34]. ANI values were calculated using JSpecies software [35] and the ANI tool of the Integrated Microbial Genome (IMG) system [36]. POCP indexes were calculated as described elsewhere [37].

Genome properties

The properties and statistics about the genome are summarized in Table 3. The genome is organized in one circular chromosome of 2,169,170 bp (42.52% GC content). In total, 2074 genes were predicted, 1897 of which were protein-coding genes, and 177 of which were RNA genes; 124 pseudogenes were also identified. Most protein-coding genes (83.75%) were assigned putative functions and the remaining ones were annotated as hypothetical proteins. The distribution of genes between COG functional categories is presented in Table 4 and Fig. 3.
Table 3

Genome statistics

Attribute

Value

% of Total

Genome size (bp)

2,169,170

100.0

DNA coding (bp)

1,814,445

83.65

DNA G + C (bp)

922,242

42.52

DNA scaffolds

1

 

Total genes

2074

100.00

Protein coding genes

1897

91.47

RNA genes

177

8.53

Pseudo genes

124

5.98

Genes in internal clusters

ND

ND

Genes with function prediction

1737

83.75

Genes assigned to COGs

1124

54.19

Genes assigned Pfam domains

1770

85.34

Genes with signal peptides

37

1.78

Genes with transmembrane helices

538

25.94

CRISPR repeats

0

0

ND not determined

Table 4

Number of genes associated with the general COG functional categories

Code

Value

% a

Description

J

129

6.80

Translation, ribosomal structure and biogenesis

A

0

0.00

RNA processing and modification

K

53

2.79

Transcription

L

53

2.79

Replication, recombination and repair

B

2

0.11

Chromatin structure and dynamics

D

13

0.69

Cell cycle control, cell division, chromosome partitioning

Y

0

0.00

Nuclear structure

V

20

1.05

Defense mechanisms

T

24

1.27

Signal transduction mechanisms

M

45

2.37

Cell wall/membrane biogenesis

N

2

0.11

Cell motility

Z

0

0.00

Cytoskeleton

W

0

0.00

Extracellular structures

U

17

0.90

Intracellular trafficking and secretion, and vesicular transport

O

49

2.58

Posttranslational modification, protein turnover, chaperones

C

109

5.75

Energy production and conversion

G

128

6.75

Carbohydrate transport and metabolism

E

105

5.54

Amino acid transport and metabolism

F

40

2.11

Nucleotide transport and metabolism

H

34

1.79

Coenzyme transport and metabolism

I

26

1.37

Lipid transport and metabolism

P

80

4.22

Inorganic ion transport and metabolism

Q

14

0.74

Secondary metabolites biosynthesis, transport and catabolism

R

96

5.06

General function prediction only

S

85

4.48

Function unknown

-

773

40.75

Not in COGs

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

Fig. 3

Graphical map of the chromosome of K. pacifica strain SLHLJ1T. From the edge to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs purple and rRNAs red), GC content and GC skew

Insights from the genome sequence

In the genome sequence of K. pacifica SLHLJ1T, a relatively large number of genes were observed to be assigned to the COG functional categories for transport and metabolism of carbohydrates (6.75%), amino acids (5.54%), translation, ribosomal structure and biogenesis (6.8%), and energy production and conversion (5.75%). Further genome analysis of K. pacifica SLHLJ1T revealed it contained genes for the Embden-Meyerhof-Parnas pathway to convert glucose into pyruvate, but not for the complete pentose phosphate pathway and Entner-Doudoroff pathway due to the lack of several key genes (such as glucose 6-phosphate dehydrogenase and 2-keto-3-deoxy-6-phospho-gluconate aldolase). In addition, the tricarboxylic acid cycle was also found to be incomplete in K. pacifica SLHLJ1T. The strain is capable of breaking down substrates such as xylose, cellobiose or trehalose, which is not surprising since an abundance of genes coding for carbohydrate breakdown has been predicted in its genome.

Prior to this study, the only available genome for the genus Kosmotoga was K. olearia TBF 19.5.1T. Here, we compared the genome of K. pacifica SLHLJ1T with K. olearia TBF 19.5.1T (Table 5). K. olearia and K. pacifica share share 92.98% 16S rRNA gene sequence similarity based on full 16S rRNA sequences. The genome size of strain SLHLJ1T is slightly smaller than that of strain TBF 19.5.1T. These two strains have nearly identical G + C contents: 42.52% for strain SLHLJ1T against 41.5% for strain TBF 19.5.1T. Strain SLHLJ1T has a slightly smaller gene content than strain TBF 19.5.1T (2074 vs 2194). K. pacifica SLHLJ1T shares 1524 orthologous genes with K. olearia TBF 19.5.1T.
Table 5

Comparative genomic characteristics of K.pacifica SLHLJ1T and K. olearia TBF 19.5.1T

Genome Name

Genome size (bp)

%GC

Gene count

Protein coding

Plasmid number

rRNA

tRNAs

Orthologous genes

K. pacifica SLHLJ1T

2,169,170

42.5

2074

1897

0

6

46

1534

K. olearia TBF 19.5.1T

2,302,126

41.5

2194

2116

0

6

46

1579

Furthermore, we wanted to confirm the affiliation of K. pacifica SLHLJ1T to the genus Kosmotoga with genomic data. Indeed, there are two lineages within the Kosmotoga genus ( K. pacifica SLHLJ1T and K. arenicorallina S304T on the one hand, and K. shengliensis 2SM-2T and K. olearia TBF 19.5.1 T on the other) and these are distantly related based on 16S rRNA gene sequence comparisons (they share between 91.7 and 92.4% 16S rRNA gene sequence similarity) [38]. ANI is a useful index for species circumscription [35], and it was recently proposed that a prokaryotic genus could be defined as a group of species with all pairwise POCP values higher than 50% [37]. We therefore performed these two types of analyses to address the issue of the limits of the genus Kosmotoga . The POCP index and ANI value between K. pacifica SLHLJ1T and K. olearia TBF 19.5.1T were respectively 70.2% and 68.5% (with JSpecies) (Fig. 4), or 72.5% (with the IMG system), supporting the assignment of these two isolates to two different species of the same genus.
Fig. 4

Relationships between POCP (a)/ANI (b) and 16S rRNA gene identity for pairs of genomes from different genera and the same genus within Thermotogae. ANI values were calculated using JSpecies software

A total of 20 complete genomic sequences belonging to the phylum Thermotogae are publicly available in the NCBI database, including representatives of the genera Defluviitoga , Fervidobacterium , Kosmotoga , Marinitoga , Mesotoga , Petrotoga , Thermosipho and Thermotoga . To gain a thorough understanding of the evolutionary relationships and phenotypic distances among the different groups in the Thermotogae , a phylogenomic analysis was conducted based on core gene sequences from these 19 genomic sequences and the one of K. pacifica . In addition, POCP and ANI values between pairs of strains were also calculated. Results are shown in Figs. 1 and 4. The interspecies ANI values calculated using JSpecies and IMG system software ranged from 64 to 99% and from 6 to 99%, respectively, while the intergenera ANI values were in the ranges of 60–70% and 65–86%. Thirty six percent of the intergenera ANI values overlapped with the interspecies ANI values; a result showing, in agreement with [37],that ANI cannot be used as a boundary for genus delineation. Interspecies POCP values were between 55.8 and 95.6%, with a large majority above 57%. Intergenera POCP values ranged from 33.7 to 76.6%, with a majority below 57% (Fig. 4, Additional file 3: Table S3). POCP analyses revealed that there were several high percentages of conserved proteins between representatives of different genera, such as Defluviitoga tunisiensis vs Petrotoga mobilis (76.6%), Fervidobacterium nodosum vs Thermosipho africanus (66.1%), Fervidobacterium pennivorans vs Thermosipho africanus (64.3%) or Thermosipho melanesiensis vs Fervidobacterium nodosum (64.6%). This result was surprising for us, knowing that 16S rRNA gene sequence dissimilarities among Thermotogae genera (>11%) are much higher than in the vast majority of bacterial orders, but that physiology is homogeneous among the Thermotogae , with only a few or minor differences between genera (Additional file 4: Table S2).

Representatives of the four following groups: Defluviitoga / Petrotoga , Fervidobacterium / Thermotoga / Thermosipho , Marinitoga / Petrotoga , and Kosmotoga / Mesotoga (two genera characterized by their distinctly different temperature ranges for growth), shared all pairwise POCP values higher than 50%, which is the pairwise POCP value suggested as a threshold for genus delineation [37]. These clusters of genera are in agreement with the well-resolved clades identified in a previous comparative genomic analysis and supported by multiple conserved signature indels [10]. The compilation of physiological and genotypic features of the different genera (Additional file 4: Table S2), together with the POCP index (Fig. 4 and Additional file 3: Table S3) and 16S rRNA phylogenetic distance (Additional file 2: Figure S1) tend to indicate that the pairs of Defluviitoga-Petrotoga and Fervidobacterium-Thermosipho representatives are less genotypically distant and also have less differentiating characteristics than the other pairs of genera. The results of POCP values together with the physiology of these taxa call into question the classification of the Thermotogae at the genus phylogenetic level and suggest that either (i) there might be fewer genera of Thermotogae than currently described, and that Thermotogae could be reclassified at the genus level by taking into account genomic information, evolutionary history and discriminative physiological characteristics; or (ii) the POCP might not be a sufficiently resolved genomic index for the delineation of genera within a homogeneous phenotype. In the light of these observations, it could be interesting to perform deep phylogenetic analyses of the Thermotogae (with a maximum of genomes) to study the evolutionary history and parallel evolution of genotypes and phenotypes within this family.

Conclusions

Strain SLHLJ1T is the first strain of the genus Kosmotoga to be isolated from the deep-sea hydrothermal vent environment. Its physiology and genetic content were compared to those of other Thermotogae . This comprehensive analysis showed that genomic information is necessary to understand the evolutionary relationships of the different groups in this well-defined lineage characterized by homogeneous physiology.

Abbreviations

ANI: 

Average nucleotide identity

PGAP: 

Prokaryotic genome annotation pipeline

POCP: 

Percentage of conserved proteins

Declarations

Acknowledgements

We gratefully acknowledge Weiming Xiong for his help with the analysis of the genomic data. This work was financially supported by the National Program on Key Basic Research Project (973 Program) (No.2012CB417300), COMRA project (No.DY125-15-R-01), National Natural Science Foundation of China (No. 41672333), the EU FP7 program MaCuMBA (Grant agreement no 311975), the PICS-INEE Phypress, the PHC Cai Yuanpei Pandore (N° 30412WG), the PHC Cai Yuanpei Provirvent (No. 34634WE), the "Laboratoire d’Excellence” LabexMER (ANR-10-LABX-19) and the program “Investissements d’Avenir”. We are indebted to Helen McCombie [Bureau de Traduction de l’Université (BTU), Université de Bretagne Occidentale, Brest, e-mail: btu@univ-brest.fr] for improving the English.

Authors’ contributions

LJJ carried out the genome sequence analysis and drafted the manuscript. SLH and XHX performed the DNA extraction. KA, MJ and ZZS participated in the study design and finalized the manuscript. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

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)
Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA
(2)
State Key Laboratory Breeding Base of Marine Genetic Resources
(3)
Key Laboratory of Marine Genetic Resources of Fujian Province
(4)
Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM)
(5)
CNRS, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM)
(6)
Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Brest-Iroise, BP70

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