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Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney
Standards in Genomic Sciences volume 6, pages21–30(2012)
Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum “Thermus-Deinococcus” to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1T is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain T1T (= DSM 14884 = JCM 11576) is the type strain of the species M. hydrothermalis, which is the type species of the monotypic genus Marinithermus [1,2]. The genus name is derived from the Latin word ‘marinus’ meaning ‘of the sea’ and the latinized Greek word ‘thermos’ meaning ‘hot’, yielding the Neo-Latin word ‘Marinithermus’ meaning ‘an organism living in hot marine places’ . The species epithet is derived from the Neo-Latin word ‘hydrothermalis’ (pertaining to a hydrothermal vent) . Strain T1T was isolated in November 2000 from the surface zone of a deep-sea hydrothermal vent chimney at Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1,385 m . M. hydrothermalis was the first isolate within the phylum “Thermus-Deinococcus” that grew optimally under a salinity equivalent to that of sea water .
The absolute requirement of NaCl for growth distinguishes M. hydrothermalis from members of the genera Thermus and Meiothermus [1,3]. No further isolates have been reported for M. hydrothermalis. Here we present a summary classification and a set of features for M. hydrothermalis T1T, together with the description of the complete genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA sequence of M. hydrothermalis T1T was compared using NCBI BLAST [4,5] under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  and the relative frequencies of taxa and keywords (reduced to their stem ) were determined, weighted by BLAST scores. The most frequently occurring genera were Thermus (91.0%), Oceanithermus (4.9%), Marinithermus (3.3%) and Thermothrix (0.8%) (118 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 100.0%, whereas the average coverage by HSPs was 98.0%. Among all other species, the one yielding the highest score was O. profundus (NR_027212), which corresponded to an identity of 91.9% and HSP coverage of 93.3%. (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 sequence was EU555123  (‘Microbial Sulfide Hydrothermal Vent Field Juan de Fuca Ridge Dudley hydrothermal vent clone 4132B16’), which showed an identity of 91.6% and HSP coverage of 92.1%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘spring’ (6.9%), ‘hot’ (5.3%), ‘microbi’ (3.7%), ‘nation, park, yellowston’ (3.2%) and ‘skin’ (3.0%) (132 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. These key words are in accordance with the biotope of the strain T1T in the original description , although ‘skin’ indicates the possible presence of relatives in a moderate environment.
Figure 1 shows the phylogenetic neighborhood of M. hydrothermalis T1T in a 16S rRNA based tree. The sequences of the three identical 16S rRNA gene copies in the genome differ by two nucleotides from the previously published 16S rRNA sequence (AB079382).
The cells of strain T1T are Gram-negative, non-motile, straight rods measuring 7.5–9.4 µm by 0.9–1.0 µm during the exponential growth phase  (Figure 2 and Table 1). In the stationary growth phase the cells tend to form filaments . Rotund bodies were not observed from the cells . Cells of strain T1T have an envelope which consists of a cytoplasmic membrane with a simple outline and a cell wall with an inner, electron-dense thin layer, which presumably represents the peptidoglycan . Colonies are whitish and have 2.5–3.0 mm of diameter . The organism is an obligate heterotroph and grows only under strictly aerobic culture conditions . Growth was not observed in anaerobic or autotrophic culture conditions . However, it should be noted that according to Mori and colleagues  this was tested only in the presence of sulfide. Steinsbu and colleagues  argue that it is therefore possible that M. hydrothermalis has the capability of anaerobic growth under unreduced conditions, as has been observed for Rhabdothermus arcticus, Vulcanithermus mediatlanticus, O. profundus and O. desulfurans [3,32–34]. Unlike members of the genus Thermus, reactions were negative for catalase- and cytochrome oxidase and hydrolysis of gelatin, starch or casein was negative . Growth occurs over the temperature range of 50.0–72.5°C (optimum 67.5°C), pH range 6.25–7.75 (optimum pH 7.0), and at NaCl concentrations in the range 0.5–4.5% (optimum 3%) . The generation time under the above listed optimal condition and in medium MJYPV is about 30 minutes . M. hydrothermalis T1T differs from the members of the genera Oceanithermus by having a higher optimal temperature for growth and a higher oxygen tolerance . Strain T1T is able to utilize complex organic substrates such as Casamino acids, tryptone and yeast extract as sole energy and carbon sources .
Strain T1T shares with its closest related genome-sequenced neighbors, O. profundus , Meiothermus silvanus  and Thermus thermophilus  (Figure 1), the presence of two linked 5S-23S rRNA gene clusters, with two 16S rRNA genes located separately in the genomes, but has one surplus, third 16S rRNA gene copy.
The major cellular fatty acids of strain T1T, when grown at 67.5°C, were iso-C15:0 (40.4%), iso-C17:0 (28.5%), C16:0 (12.9%), anteiso-C15:0 (6.0%), anteiso-C17:0 (5.4%), iso-C16:0 (2.8%) and iso 3-OH C11:0 (1.0%). Menaquinone-8 was the major respiratory quinone. The fatty acid and respiratory quinone composition were similar to those of members of the genus Thermus, as described previously [35,36]. However, the presence of iso 3-OH C11:0 in strain T1T distinguishes it from Thermus species .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position , and is part of the Genomic Encyclopedia of Bacteria and Archaea project . The genome project is deposited in the Genomes OnLine Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
M. hydrothermalis T1T, DSM 14884, was grown in DSMZ medium 973 (Marinithermus hydrothermalis medium)  at 70°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/DL for cell lysis as described in Wu et al. . DNA is available through the DNA Bank Network .
Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website . Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 70 contigs in one scaffold was converted into a phrap  assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (3,943.0 Mb) was assembled with Velvet  and the consensus sequences were shredded into 2.0 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 167.5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package  was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution , Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 97 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI . The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 1,666.5 × coverage of the genome. The final assembly contained 458,684 pyrosequence and 48,027,166 Illumina reads.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The genome consists of a 2,269,167 bp long chromosome with a 68.1% GC content (Figure 3 and Table 3). Of the 2,310 genes predicted, 2,251 were protein-coding genes, and 59 RNAs; 46 pseudogenes were also identified. The majority of the protein-coding genes (75.5%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Sako Y, Nakagawa S, Takai K, Horikoshi K. Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2003; 53:59–65. PubMed doi:10.1099/ijs.0.02364-0
Euzeby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590
Steinsbu BO, Tindall BJ, Torsvik VL, Thorseth IH, Daae FL, Pedersen RB. Rhabdothermus arcticus gen. nov., sp. nov., a novel member of the family Thermaceae isolated from a hydrothermal vent chimney from Soria Moria vent field at the Arctic Mid-Ocean Ridge. Int J Syst Evol Microbiol 2010. [Epub ahead of print, doi: 10.1099/ijs.0.027839-0].
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMed
Korf I, Yandell M, Bedell J. BLAST. Sebastopol, CA, O’Reilly, 2003.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05
Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.
Zhou H, Li J, Peng X, Meng J, Wang F, Ai Y. Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, Juan de Fuca Ridge. J Microbiol 2009; 47:235–247. PubMed doi:10.1007/s12275-008-0311-z
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. doi:10.1111/j.1095-8312.2007.00864.x
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-7_13
Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). 4.0 b10. Sunderland, Sinauer Associates, 2002.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, et al. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 2004; 22:547–553. PubMed doi:10.1038/nbt956
Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Oceanithermus profundus type strain (506T). Stand Genomic Sci 2011; 4:210–220. PubMed doi:10.4056/sigs.1734292
Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus silvanus type strain (VI-R2 T). Stand Genomic Sci 2010; 3:37–46. PubMed doi:10.4056/sigs.1042812
Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus ruber type strain (21T). Stand Genomic Sci 2010; 3:26–36. PubMed doi:10.4056/sigs.1032748
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; 26:541–547. PubMed doi:10.1038/nbt1360
Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
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; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 2 — The Bacteria: Phyla “Aquificae”, “Thermotogae”, “Thermodesulfobacteria”, “Deinococcus-Thermus”, “Chrysiogenetes”, “Chloroflexi”, “Thermomicrobia”, “Nitrospira”, “Deferribacteres”, “Cyanobacteria”, and “Chlorobi”. http://www.taxonomicoutline.org/index.php/toba/article/view/187/211.
Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 1989; 11:128–134. PubMed
Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 1989; 11:128–134. PubMed
List Editor. 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; 52:685–690. PubMed doi:10.1099/ijs.0.02358-0
Garrity GM, Holt JG. Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW, (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 395.
Rainey FA, da Costa MS. Order II. Thermales ord. nov. In: Garrity GM, Boone DR, Castenholz RW, (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403.
da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW, (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403–404.
BAuA. Classification of bacteria and archaea in risk groups. TRBA 466. Germany, Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, 2010. p 125.
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; 25:25–29. PubMed doi:10.1038/75556
Mori K, Kakegawa T, Higashi Y, Nakamura K, Maruyama A, Hanada S. Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount. Int J Syst Evol Microbiol 2004; 54:1561–1566. PubMed doi:10.1099/ijs.0.02962-0
Miroshnichenko ML, L’Haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA. Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:747–752. PubMed doi:10.1099/ijs.0.02367-0
Miroshnichenko ML, L’Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, et al. Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 2003; 53:1143–1148. PubMed doi:10.1099/ijs.0.02579-0
Hensel R, Demharter W, Kandler O, Kroppenstedt RM, Stackebrandt E. Chemotaxonomic and molecular-genetic studies of the genus Thermus: evidence for a phylogenetic relationship of Thermus aquaticus and Thermus ruber to the genus Deinococcus. Int J Syst Bacteriol 1986; 36:444–453. doi:10.1099/00207713-36-3-444
Prado A, da Costa MS, Madeira VMC. Effect of growth temperature on the lipid composition of two strains of Thermus sp. J Gen Microbiol 1988; 134:1653–1660.
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html.
Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029
DOE Joint Genome Institute. http://www.jgi.doe.gov.
Phrap and Phred for Windows. MacOS, Linux and Unix. http://www.phrap.com.
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107
Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26–29, 2006: 141–146.
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. 2008; Marco Island, FL.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457
Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing M. hydrothermalis cultures. This work was performed under the auspices of the US Department of Energy 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, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.
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Copeland, A., Gu, W., Yasawong, M. et al. Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney. Stand in Genomic Sci 6, 21–30 (2012). https://doi.org/10.4056/sigs.2435521
- strictly aerobic
- neutrophilic heterotroph
- hydrothermal vent