Skip to main content
Download PDF

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

Standards in Genomic Sciences volume 12, Article number: 3 (2017) Cite this article

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.

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 [1–12]. 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
figure 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

Full size image

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
figure 2

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

Full size image
Table 1 Classification and general features of K. pacifica SLHLJ1T [12]
Full size table

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
Full size table

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
Full size table
Table 4 Number of genes associated with the general COG functional categories
Full size table
Fig. 3
figure 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

Full size image

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
Full size table

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
figure 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

Full size image

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

References

  1. Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M. Athalassotoga saccharophila gen. nov. sp. nov. isolated from an acidic terrestrial hot spring of Japan, and proposal of Mesoaciditogales ord. nov., Mesoaciditogaceae fam. nov. in the phylum Thermotogae. Int J Syst Evol Microbiol. 2016;66:1045–51. PubMed http://dx.doi.org/10.1099/ijsem.0.000833.

    Article  CAS  Google Scholar 

  2. Ben Hania W, Godbane R, Postec A, Hamdi M, Ollivier B, Fardeau ML. Defluviitoga tunisiensis gen. nov., sp. nov., a thermophilic bacterium isolated from a mesothermic and anaerobic whey digester. Int J Syst Evol Microbiol. 2012;62:1377–82. PubMed http://dx.doi.org/10.1099/ijs.0.033720-0.

    Article  CAS  PubMed  Google Scholar 

  3. Patel BKCMH, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, aldoactive, anaerobic bacterium. Arch Microbiol. 1985;141:63–9. http://dx.doi.org/10.1007/BF00446741.

    Article  CAS  Google Scholar 

  4. Davey MEWW, Key R, Nakamura K, Stahl D. Isolation of three species of Geotoga and Petrotoga: two new genera, representing a new lineage in the bacterial line of descent distantly related to the ‘Thermotogales’. Syst Appl Microbiol. 1993;16:191–200. http://dx.doi.org/10.1016/S0723-2020(11)80467-4.

    Article  Google Scholar 

  5. Dipippo JL, Nesbo CL, Dahle H, Doolittle WF, Birkland NK, Noll KM. Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J Syst Evol Microbiol. 2009;59:2991–3000. PubMed http://dx.doi.org/10.1099/ijs.0.008045-0.

    Article  CAS  PubMed  Google Scholar 

  6. Wery N, Lesongeur F, Pignet P, Derennes V, Cambon-Bonavita MA, Godfroy A, Barbier G. Marinitoga camini gen. nov., sp. nov., a rod-shaped bacterium belonging to the order Thermotogales, isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol. 2001;51:495–504. PubMed http://dx.doi.org/10.1099/00207713-51-2-495.

    Article  CAS  PubMed  Google Scholar 

  7. Reysenbach AL, Liu Y, Lindgren AR, Wagner ID, Sislak CD, Mets A, Schouten S. Mesoaciditoga lauensis gen. nov., sp. nov., a moderately thermoacidophilic member of the order Thermotogales from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol. 2013;63:4724–9. PubMed http://dx.doi.org/10.1099/ijs.0.050518-0.

    Article  CAS  PubMed  Google Scholar 

  8. Nesbo CL, Bradnan DM, Adebusuyi A, Dlutek M, Petrus AK, Foght J, Doolittle WF, Noll KM. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales. Extremophiles. 2012;16:387–93. PubMed http://dx.doi.org/10.1007/s00792-012-0437-0.

    Article  CAS  PubMed  Google Scholar 

  9. Jayasinghearachchi HS, Lal B. Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells. Int J Syst Evol Microbiol. 2011;61:554–60. PubMedhttp://dx.doi.org/10.1099/ijs.0.018036-0.

    Article  CAS  PubMed  Google Scholar 

  10. Bhandari V, Gupta RS. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie Van Leeuwenhoek. 2014;105:143–68. PubMed http://dx.doi.org/10.1007/s10482-013-0062-7.

    Article  PubMed  Google Scholar 

  11. Huber RWC, Langworthy TA, Fricke H, Stetter KO. Thermosipho africanus gen. nov., represents a new genus of thermophilic eubacteria within the ‘Thermotogales’. Syst Appl Microbiol. 1989;12:32–7. http://dx.doi.org/10.1016/S0723-2020(89)80037-2.

    Article  Google Scholar 

  12. Huber RLT, Ko¨nig H, Thomm M, Woese CR, Sleytr UB, Stetter KO. Thermotoga maritima sp. nov. represents a new genus of unique extremely thermophilic eubacteria growing up to 90. Arch Microbiol. 1986;144:324–33. http://dx.doi.org/10.1007/BF00409880.

    Article  CAS  Google Scholar 

  13. Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA. 2009;106:5865–70. PubMed http://dx.doi.org/10.1073/pnas.0901260106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature. 1999;399:323–9. PubMed http://dx.doi.org/10.1038/20601.

    Article  CAS  PubMed  Google Scholar 

  15. Nunoura T, Hirai M, Imachi H, Miyazaki M, Makita H, Hirayama H, Furushima Y, Yamamoto H, Takai K. Kosmotoga arenicorallina sp. nov. a thermophilic and obligately anaerobic heterotroph isolated from a shallow hydrothermal system occurring within a coral reef, southern part of the Yaeyama Archipelago, Japan, reclassification of Thermococcoides shengliensis as Kosmotoga shengliensis comb. nov., and emended description of the genus Kosmotoga. Arch Microbiol. 2010;192:811–9. PubMed http://dx.doi.org/10.1007/s00203-010-0611-7.

    Article  CAS  PubMed  Google Scholar 

  16. L’Haridon S, Jiang LJ, Alain K, Chalopin M, Rouxel O, Beauverger M, Xu HX, Shao ZZ, Jebbar M. Kosmotoga pacifica sp. nov., a thermophilic chemoorganoheterotrophic bacterium isolated from an East Pacific hydrothermal sediment. Extremophiles. 2014;18:81–8. PubMed http://dx.doi.org/10.1007/s00792-013-0596-7.

    Article  PubMed  Google Scholar 

  17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990;87:4576–9. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Validation list no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2002; 52:3-4. PubMed http://dx.doi.org/10.1099/ijs.0.02358-0

  19. Reysenbach AL, Phylum II B. Thermotogae phyl. nov. In: Boone DR, Castenholz RW, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, second edition, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). New York: Springer; 2001. p. 369–87.

    Google Scholar 

  20. Reysenbach AL, Class I. Thermotogae class nov. In: Boone DR, Castenholz RW, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, second edition, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). New York: Springer; 2001. p. 369–70.

    Google Scholar 

  21. Reysenbach AL, Order I. Thermotogales ord. nov. In: Boone DR, Castenholz RW, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, second edition, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). New York: Springer; 2001. p. 369–70.

    Google Scholar 

  22. Reysenbach AL, Family I. Thermotogaceae fam. nov. In: Boone DR, Castenholz RW, Garrity GM, editors. Bergey’s Manual of Systematic Bacteriology, second edition, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria). New York: Springer; 2001. p. 370.

    Google Scholar 

  23. List Editor. Validation List no. 22. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1986; 36:573-576. http://dx.doi.org/10.1099/00207713-36-4-573

  24. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9. PubMed http://dx.doi.org/10.1038/75556.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7. PubMed http://dx.doi.org/10.1038/nbt1360.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Charbonnier F, Erauso G, Barbeyron T, Prieur D, Forterre P. Purification of plasmids from thermophilic and hyperthermophilic archaebacteria. In F. T. Robb, K. R. Sowers, S. DasSarma, A. R. Place, H. J. Schreier, and E. M. Fleischmann (ed.), Archaea: a laboratory manual, in press. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

  27. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–80. PubMed http://dx.doi.org/10.1038/nature03959.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Phred, Phrap and Consed software packages. http://www.genome.washington.edu

  29. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS. 2008;12:137–41. PubMed http://dx.doi.org/10.1089/omi.2008.0017.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, et al. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007;35:D237–40. PubMed http://dx.doi.org/10.1093/nar/gkl951.

    Article  CAS  PubMed  Google Scholar 

  31. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6. PubMed http://dx.doi.org/10.1093/nar/28.1.33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997; 28:405-420. PubMed http://dx.doi.org/10.1002/(SICI)1097-0134(199707)28:3 < 405::AID-PROT10 > 3.0.CO;2-L

  33. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305:567–80. PubMed http://dx.doi.org/10.1006/jmbi.2000.4315.

    Article  CAS  PubMed  Google Scholar 

  34. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004;340:783–95. PubMed http://dx.doi.org/10.1016/j.jmb.2004.05.028.

    Article  PubMed  Google Scholar 

  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A. 2009;106:19126–31. PubMedhttp://dx.doi.org/10.1073/pnas.0906412106.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015;43:6761–71. doi:10.1093/nar/gkv657. PubMedhttp://dx.doi.org/.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC, Zhou J, Oren A, Zhang YZ. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol. 2014;196:2210–5. PubMed http://dx.doi.org/10.1128/JB.01688-14.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Rev Microbiol. 2014;12:635–45. PubMed http://dx.doi.org/10.1038/nrmicro3330.

    Article  CAS  Google Scholar 

  39. Podosokorskaya OA, Merkel AY, Kolganova TV, Chernyh NA, Miroshnichenko ML, Bonch-Osmolovskaya EA, Kublanov IV. Fervidobacterium riparium sp. nov., a thermophilic anaerobic cellulolytic bacterium isolated from a hot spring. Int J Syst Evol Microbiol. 2011;61:2697–701. PubMed http://dx.doi.org/10.1099/ijs.0.026070-0.

    Article  CAS  PubMed  Google Scholar 

  40. Postec A, Ciobanu M, Birrien JL, Bienvenu N, Prieur D, Romancer ML. Marinitoga litoralis sp. nov., a thermophilic, heterotrophic bacterium isolated from a coastal thermal spring on Ile Saint-Paul, Southern Indian Ocean. Int J Syst Evol Microbiol. 2010;60:1778–82. PubMed http://dx.doi.org/10.1099/ijs.0.017574-0.

    Article  CAS  PubMed  Google Scholar 

  41. Miranda-Tello E, Fardeau ML, Joulian C, Magot M, Thomas P, Tholozan JL, Ollivier B. Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo. Int J Syst Evol Microbiol. 2007;57:40–4. PubMed http://dx.doi.org/10.1099/ijs.0.64516-0.

    Article  CAS  PubMed  Google Scholar 

  42. Podosokorskaya OA, Bonch-Osmolovskaya EA, Godfroy A, Gavrilov SN, Beskorovaynaya DA, Sokolova TG, Kolganova TV, Toshchakov SV, Kublanov IV. Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep-sea sample. Int J Syst Evol Microbiol. 2014;64:3307–13. PubMed http://dx.doi.org/10.1099/ijs.0.063156-0.

    Article  CAS  PubMed  Google Scholar 

  43. Mori K, Yamazoe A, Hosoyama A, Ohji S, Fujita N, Ishibashi J, Kimura H, Suzuki K. Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs. Int J Syst Evol Microbiol. 2014;64:2128–36. PubMed http://dx.doi.org/10.1099/ijs.0.060137-0.

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, 361005, China

    Lijing Jiang, Hongxiu Xu & Zongze Shao

  2. State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China

    Lijing Jiang, Hongxiu Xu & Zongze Shao

  3. Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China

    Lijing Jiang, Hongxiu Xu & Zongze Shao

  4. Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d’Urville, 29 280, Plouzané, France

    Stéphane L’Haridon, Mohamed Jebbar & Karine Alain

  5. CNRS, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d’Urville, 29 280, Plouzané, France

    Stéphane L’Haridon, Mohamed Jebbar & Karine Alain

  6. Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Brest-Iroise, BP70, 29 280, Plouzané, France

    Stéphane L’Haridon, Mohamed Jebbar & Karine Alain

Authors
  1. Lijing Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stéphane L’Haridon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mohamed Jebbar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hongxiu Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karine Alain
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zongze Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Karine Alain or Zongze Shao.

Additional files

Additional file 1: Table S1.

List of the core genes chosen for the whole genome phylogenetic analysis. This list is composed of 499 orthologous genes from 20 genomes within the phylum Thermotogae. (XLS 210 kb)

Additional file 2: Figure S1.

Phylogenetic tree based on 16S rRNA gene sequences showing the position of K. pacifica strain SLHLJ1T within the phylum Thermotogae. The alignment was performed with 16S rDNA sequences of related species and environmental sequences. The topology shown was obtained with the neighbor-joining algorithm. Bootstrap values (from 1000 replicates) are indicated at the branch nodes. The scale bar represents 2% sequence divergence. (PDF 462 kb)

Additional file 3: Table S3.

Comparison of POCP value and 16S rRNA gene identity for pairs of genomes from different genera of Thermotogae. (DOCX 21 kb)

Additional file 4: Table S2.

Differential characteristics of eight genera of Thermotogae, with genome sequences. Data were taken from Defluviitoga [2], Fervidobacterium [3, 39], Kosmotoga [5, 15, 16], Marinitoga [6, 40], Mesotoga [8], Petrotoga [4, 41], Thermosipho [10, 42], and Thermotoga [12, 43]. ND, No data available; +, positive; -, negative; ±, positive for some species, but not all. (DOCX 18 kb)

Rights and permissions

Open Access This 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.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jiang, L., L’Haridon, S., Jebbar, M. et al. Complete genome sequence and whole-genome phylogeny of Kosmotoga pacifica type strain SLHLJ1T from an East Pacific hydrothermal sediment. Stand in Genomic Sci 12, 3 (2017). https://doi.org/10.1186/s40793-016-0214-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s40793-016-0214-2

Keywords

  • Marine
  • Hydrothermal vent
  • Thermotogales
  • Chemoorganoheterotroph
  • Thermophile

Environmental Microbiome

ISSN: 2524-6372