1887

Abstract

The proteolytic bacterium strain A7P-90m was isolated from Lake Untersee, Antarctica. The anoxic water was collected from a perennially sealed (~100 millennia) glacial ice lake. Gram-stain-negative cells were 0.18–0.3×8.0–25.0 µm in size, straight, slender rods with unusual gliding motility by external, not previously reported, organelles named here as antiae. At the end of stationary phase of growth, spheroplasts were terminally formed and the cells resembled dandelions. After death, cells were helical. The isolate was an athalassic, strictly anaerobic and catalase-negative proteolytic chemoorganotroph. It was moderately psychrophilic with a temperature range for growth of 3–26 °C and an optimum at 22–23 °C. The pH range for growth was 5.5–7.8 with an optimum at 6.9. Major cellular fatty acids were branched pentadecanoic and tridecanoic acids, and saturated tetradecanoic acids. The quinone system comprised menaquinone MK-7. The strain was sensitive to all checked antibiotics and ascorbic acid. The G+C content of the genomic DNA was 42.6 mol%. Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order and formed a novel family with the proposed name fam. nov. The description of the order was emended accordingly. The name gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain A7P-90m (=DSM 100563=JCM 30888). The complete draft genome sequence was deposited at the Joint Genomes Institute (JGI) under number IMG OID 2654588148 and in SRA listed as SRP088197.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002266
2017-10-01
2020-11-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/4132.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002266&mimeType=html&fmt=ahah

References

  1. Wand U, Schwarz G, Brüggemann E, Bräuer K. Evidence for physical and chemical stratification in lake untersee (central Dronning Maud Land, East Antarctica). Antarct Sci 1997;9:43–45 [CrossRef]
    [Google Scholar]
  2. Wand U, Samarkin VA, Nitzsche H-M, Hubberten H-W. Biogeochemistry of methane in the permanently ice-covered Lake Untersee, central Dronning Maud Land, East Antarctica. Limnol Oceanogr 2006;51:1180–1194 [CrossRef]
    [Google Scholar]
  3. Hoover RB. 2008; Schirmacher Oasis/Lake Untersee Antarctica Astrobiology Expeditions. Explorer's Club Expedition Report Flag #162https://explorers.org/flag_reports/Flag_162_Report_-_Richard_B._Hoover_9-29-08_.pdf
    [Google Scholar]
  4. Hoover RB, Pikuta EV, Townsend A, Anthony J, Guisler M et al. Microbial extremophiles from the 2008 Schirmacher Oasis expedition: preliminary results. In Hoover RB, Levin GV, AYu Rozanov, Davies PCW. (editors) Instruments, Methods, and Missions for Astrobiology XI Proceedings of SPIEvol. 7097 Bellingham, WA, USA: SPIE; 2008; pp.70970L–70970L-9[Crossref]
    [Google Scholar]
  5. Hoover RB, Pikuta EV. Psychrophilic and Psychrotolerant Microbial Extremophiles in Polar Environments. In Bej AK, Aislabie J, Atlas RM. (editors) Polar Microbiology: The Ecology, Biodiversity and Bioremediation Potential of Microorganisms in Extremely Cold Environments Boca Raton, London, New York: RM CRC Press, Taylor & Francis Group; 2009; pp.115–156[Crossref]
    [Google Scholar]
  6. Guisler MD, Pikuta EV, Townsend AM, Hoover RB. Psychrotolerant anaerobes from lake podprudnoye, Antarctica and penguin Spheniscus demersus colony, South Africa. In Hoover RB, Levin GV, AYu Rozanov, Davies PCW. (editors) Instruments, Methods, and Missions for Astrobiology XII. Proceedings of SPIEvol. 7441 Bellingham, WA, USA: SPIE; 2009; pp.74410L-1-7441012
    [Google Scholar]
  7. Townsend AM, Pikuta EV, Guisler MD, Stahl S, Hoover RB et al. Anaerobic psychrophiles from lake zub and lake untersee, Antarctica. In Hoover RB, Levin GV, AYu Rozanov, Davies PCW. (editors) Instruments, Methods, and Missions for Astrobiology XII. Proceedings of SPIEvol. 7441 Bellingham, WA, USA: SPIE; 2009; pp.74410K-1-12
    [Google Scholar]
  8. Andersen DT, Sumner DY, Hawes I, Webster-Brown J, Mckay CP. Discovery of large conical stromatolites in lake untersee, Antarctica. Geobiology 2011;9:280–293 [CrossRef][PubMed]
    [Google Scholar]
  9. Filippova SN, Surgucheva NA, Kulikov EE, Sorokin VV, Akimov VN et al. Detection of phage infection in the bacterial population of lake untersee (Antarctica). Microbiology 2013;82:383–386 [CrossRef]
    [Google Scholar]
  10. Pikuta EV, Hoover RB, Marsic D, Whitman WB, Lupa B et al. Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano. Int J Syst Evol Microbiol 2009;59:2302–2307 [CrossRef]
    [Google Scholar]
  11. Magot M, Fardeau ML, Arnauld O, Lanau C, Ollivier B et al. Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field. FEMS Microbiol Lett 1997;155:185–191 [CrossRef][PubMed]
    [Google Scholar]
  12. Pikuta EV, Hoover RB, Bej AK, Marsic D, Whitman WB et al. Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835. Int J Syst Evol Microbiol 2009;59:1798–1804 [CrossRef][PubMed]
    [Google Scholar]
  13. Krieg NR. Order I. Bacteroidales ord. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobac-teres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicro-bia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; pp.25
    [Google Scholar]
  14. Euzéby J. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012;62:1–4[Crossref]
    [Google Scholar]
  15. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016;39:281–296 [CrossRef]
    [Google Scholar]
  16. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016;7:1–37 [CrossRef][PubMed]
    [Google Scholar]
  17. Wj Wu, Zhao JX, Chen GJ, Zj D. Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales. Int J Syst Evol Microbiol 2016;66:4243–4249[Crossref]
    [Google Scholar]
  18. Wolin EA, Wolin MJ, Wolfe RS. Formation of methane by bacterial extracts. J Biol Chem 1963;238:2882–2886[PubMed]
    [Google Scholar]
  19. Kevbrin VV, Zavarzin GA. Effect of sulfur compounds on the growth of the halophilic homoacetic bacterium Acetohalobium arabaticum. Mikrobiologiia 1992;61:812–817
    [Google Scholar]
  20. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  21. Trueper HG, Schlegel HG. Sulphur metabolism in Thiorhodaceae I. Quantitative measurements on growing cells of Chromatium okenii. Antonie van Leeuwenhoek 1964;30:225–238 [CrossRef][PubMed]
    [Google Scholar]
  22. Lupa B, Hendrickson EL, Leigh JA, Whitman WB. Formate-dependent H2 production by the mesophilic methanogen Methanococcus maripaludis. Appl Environ Microbiol 2008;74:6584–6590 [CrossRef][PubMed]
    [Google Scholar]
  23. Pikuta EV, Menes RJ, Bruce AM, Lyu Z, Patel NB et al. Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere. Int J Syst Evol Microbiol 2016;66:1–8 [CrossRef][PubMed]
    [Google Scholar]
  24. Pikuta EV, Lyu Z, Williams MD, Patel NB, Liu Y et al. Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions for the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii. Int J Syst Evol Microbiol 2017;67:1442–1450[Crossref]
    [Google Scholar]
  25. Miller LT. A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 1982;16:584–586
    [Google Scholar]
  26. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988;38:358–361 [CrossRef]
    [Google Scholar]
  27. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42:989–1005 [CrossRef]
    [Google Scholar]
  28. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014;42:D633–D642 [CrossRef][PubMed]
    [Google Scholar]
  29. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009;26:1641–1650 [CrossRef][PubMed]
    [Google Scholar]
  30. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28:1647–1649 [CrossRef][PubMed]
    [Google Scholar]
  31. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005;187:6258–6264 [CrossRef]
    [Google Scholar]
  32. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 2014;42:D560–D567 [CrossRef]
    [Google Scholar]
  33. Sakamoto M, Lan PT, Benno Y. Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum. Int J Syst Evol Microbiol 2007;57:342–346 [CrossRef][PubMed]
    [Google Scholar]
  34. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014;12:635–645 [CrossRef][PubMed]
    [Google Scholar]
  35. Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 2014;38:996–1047 [CrossRef][PubMed]
    [Google Scholar]
  36. Slw O, Lee A, O’Rourke JL, Dewhirst FE, Paster BJ et al. Genus I. Helicobacter. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology, The Proteobacteria, Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, 2nd ed.vol. 2 New York: Springer; 2005; pp.1169–1189
    [Google Scholar]
  37. Garrity GM, Bell JA, Lilburn T. Family II. Helicobacteraceae fam. nov. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey’s Manual of Systematic Bacteriology, The Proteobacteria, Part C The Alpha-, Beta-, Delta-, and Epsilonproteobacteria, 2nd ed.vol. 2 London: Dordrecht Heidelberg; 2005; pp.1168
    [Google Scholar]
  38. Zhilina TN, Zavarzin GA, Rainey F, Kevbrin VV, Kostrikina NA et al. Spirochaeta alkalica sp. nov., Spirochaeta africana sp. nov., and Spirochaeta asiatica sp. nov., alkaliphilic anaerobes from the continental soda lakes in Central Asia and the East African Rift. Int J Syst Bacteriol 1996;46:305–312 [CrossRef][PubMed]
    [Google Scholar]
  39. Hoover RB, Pikuta EV, Bej AK, Marsic D, Whitman WB et al. Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochaete isolated from soda Mono Lake in California. Int J Syst Evol Microbiol 2003;53:815–821 [CrossRef][PubMed]
    [Google Scholar]
  40. McBride MJ. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu Rev Microbiol 2001;55:49–75 [CrossRef][PubMed]
    [Google Scholar]
  41. Titz B, Rajagopala SV, Ester C, Häuser R, Uetz P. Novel conserved assembly factor of the bacterial flagellum. J Bacteriol 2006;188:7700–7706 [CrossRef][PubMed]
    [Google Scholar]
  42. Olson JW, Maier RJ. Molecular hydrogen as an energy source for Helicobacter pylori. Science 2002;298:1788–1790 [CrossRef][PubMed]
    [Google Scholar]
  43. Kuhns LG, Benoit SL, Bayyareddy K, Johnson D, Orlando R et al. Carbon fixation driven by molecular hydrogen results in chemolithoautotrophically enhanced growth of Helicobacter pylori. J Bacteriol 2016;198:1423–1428 [CrossRef][PubMed]
    [Google Scholar]
  44. Wang G, Romero-Gallo J, Benoit SL, Piazuelo MB, Dominguez RL et al. Hydrogen metabolism in Helicobacter pylori plays a role in gastric carcinogenesis through facilitating CagA translocation. MBio 2016;7:e01022-16 [CrossRef][PubMed]
    [Google Scholar]
  45. Flint J, Racaniello VR, Rall GF, Skalka AM. Structure, genome organization, and infectious cycles. In: Principles of Virology, 4th ed.vol. 1 Washington, DC: ASM Press; 2015; pp.502–534[Crossref]
    [Google Scholar]
  46. Miyazaki M, Sakai S, Yamanaka Y, Saito Y, Takai K et al. Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta. Int J Syst Evol Microbiol 2014;64:2798–2804 [CrossRef][PubMed]
    [Google Scholar]
  47. Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y et al. Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. Int J Syst Evol Microbiol 2014;64:4147–4154 [CrossRef][PubMed]
    [Google Scholar]
  48. Arroua B, Ranchou-Peyruse A, Ranchou-Peyruse M, Magot M, Urios L et al. Pleomorphochaeta caudata gen. nov., sp. nov., an anaerobic bacterium isolated from an offshore oil well, reclassification of Sphaerochaeta multiformis MO-SPC2T as Pleomorphochaeta multiformis MO-SPC2T comb. nov. as the type strain of this novel genus and emended description of the genus Sphaerochaeta. Int J Syst Evol Microbiol 2017;67:417–424 [CrossRef][PubMed]
    [Google Scholar]
  49. Pribram E. Klassification der Schizomyceten, Deuticke F Leipzig: 1933; pp.1–143
    [Google Scholar]
  50. The editorial board Famili I. Bacteroidaceae Pribram 1933, 10AL. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicu-tes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicrobia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; p.25
    [Google Scholar]
  51. Hardham JM, King KW, Dreier K, Wong J, Strietzel C et al. Transfer of Bacteroides splanchnicus to Odoribacter gen. nov. as Odoribacter splanchnicus comb. nov., and description of Odoribacter denticanis sp. nov., isolated from the crevicular spaces of canine periodontitis patients. Int J Syst Evol Microbiol 2008;58:103–109 [CrossRef][PubMed]
    [Google Scholar]
  52. Nagai F, Morotomi M, Watanabe Y, Sakon H, Tanaka R. Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces. Int J Syst Evol Microbiol 2010;60:1296–1302 [CrossRef][PubMed]
    [Google Scholar]
  53. Sakamoto M, Takagaki A, Matsumoto K, Kato Y, Goto K et al. Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces. Int J Syst Evol Microbiol 2009;59:1748–1753 [CrossRef][PubMed]
    [Google Scholar]
  54. Lino T, Mori K, Itoh T, Kudo T, Suzuki K et al. Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov. Int J Syst Evol Microbiol 2014;64:3660–3667 [CrossRef][PubMed]
    [Google Scholar]
  55. Ludwig W, Euzeby J, Whitman WB. Family II. Marinilabiliaceae fam. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicrobia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; pp.49–54
    [Google Scholar]
  56. The editorial board Famili III. Rikenellaceae fam. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes(Mollicutes), Acidobacte-ria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicrobia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; pp.54–61
    [Google Scholar]
  57. Krieg NR. Family Porphyromonadaceae fam. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobac-teres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicro-bia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; pp.61–85
    [Google Scholar]
  58. Krieg NR. Family V. Prevotellaceae fam. nov. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacte-res, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentispherae, Verrucomicro-bia, Chlamydiae, and Planctomycetes, 2nd ed.vol. 4 New York: Springer; 2011; pp.85–105
    [Google Scholar]
  59. Huang XF, Liu YJ, Dong JD, Qu LY, Zhang YY et al. Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov. Int J Syst Evol Microbiol 2014;64:875–881 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002266
Loading
/content/journal/ijsem/10.1099/ijsem.0.002266
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Supplementary File 2

Supplementary File 3

MOVIE

Supplementary File 4

Supplementary File 5

Supplementary File 6

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error