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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 4

sp. nov. and sp. nov., anaerobic bacteria isolated from deep-marine sediment No Access

Abstract

Two obligately anaerobic, Gram-stain-negative, non-spore-forming, rod-shaped, motile and mesophilic bacteria, designated as strains AN17-1 and AN17-2, were isolated from deep-marine sediments collected from the western Pacific Ocean. The phylogenetic analysis based on the 16S rRNA gene with the most closely related species showed 98.5 and 98.8% similarities of strains AN17-1 and AN17-2 with Ra1766G1, respectively. The genome sizes and G+C contents of strains AN17-1 and AN17-2 were 6.0 Mb and 30.3 mol% and 5.4 Mb and 30.9 mol%, respectively. The genome-to-genome distance and the average nucleotide identity values between strains AN17-1 and AN17-2 and Ra1766G1 were lower than the thresholds for species delimitation. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate and nitrite were not used as terminal electron acceptors by strains AN17-1 and AN17-2. The most abundant fatty acids of strains AN17-1 and AN17-2 were iso-C and C, respectively. The commonly detected polar lipids of both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid, two unidentified phospholipids and one unidentified polar lipid. The results suggest that strains AN17-1 and AN17-2 represent novel species of the genus . Therefore, the new names, sp. nov. and sp. nov., are proposed for strains AN17-1 (=NBRC 115486=DSM 116091) and AN17-2 (=NBRC 115487=DSM 116092) as the type strains, respectively.

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Keyword(s): anaerobic bacteria , marine sediment and Vallitalea
© 2025 The Authors
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2025-04-04
2026-01-21

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References

  1. LPSN-List of Prokaryotic names with Standing in Nomenclature Genus Vallitalea. n.d https://lpsn.dsmz.de/genus/vallitalea accessed 22 August 2024
  2. Lakhal R, Pradel N, Postec A, Hamdi M, Ollivier B et al. Vallitalea guaymasensis gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2013; 63:3019–3023 [View Article] [PubMed]
     [Google Scholar]
  3. Schouw A, Leiknes Eide T, Stokke R, Pedersen RB, Steen IH et al. Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica. Int J Syst Evol Microbiol 2016; 66:1724–1734 [View Article] [PubMed]
     [Google Scholar]
  4. Schouw A, Vulcano F, Roalkvam I, Hocking WP, Reeves E et al. Genome analysis of Vallitalea guaymasensis strain L81 isolated from a deep-sea hydrothermal vent system. Microorganisms 2018; 6:63 [View Article] [PubMed]
     [Google Scholar]
  5. Ben Aissa F, Postec A, Erauso G, Payri C, Pelletier B et al. Vallitalea pronyensis sp. nov., isolated from a marine alkaline hydrothermal chimney. Int J Syst Evol Microbiol 2014; 64:1160–1165 [View Article] [PubMed]
     [Google Scholar]
  6. Sun Y-T, Zhou N, Wang B-J, Liu X-D, Jiang C-Y et al. Vallitalea okinawensis sp. nov., isolated from Okinawa Trough sediment and emended description of the genus Vallitalea. Int J Syst Evol Microbiol 2019; 69:404–410 [View Article] [PubMed]
     [Google Scholar]
  7. Hirano S, Terahara T, Mori K, Hamada M, Matsumoto R et al. Vallitalea longa sp. nov., an anaerobic bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2023; 73:005882 [View Article] [PubMed]
     [Google Scholar]
  8. Kvenvolden KA. A review of the geochemistry of methane in natural gas hydrate. Org Geochem 1995; 23:997–1008 [View Article]
     [Google Scholar]
  9. Boswell R, Collett TS. Current perspectives on gas hydrate resources. Energy Environ Sci 2011; 4:1206–1215 [View Article]
     [Google Scholar]
  10. Shipley TH, Houston MH, Buffer RT, Shwab J, McMillan KJ. Seismic evidence for widespread possible gas hydrate horizons on continental slopes and rises. AAPG Bulletin 1979; 63:2204–2213 [View Article]
     [Google Scholar]
  11. Hayashi M, Saeki T, Inamori T, Noguchi S. The distribution of BSRs related to methane hydrates, offshore Japan. J Petroleum Tech 2010; 75:42–53 [View Article]
     [Google Scholar]
  12. Hachikubo A, Moriya Y, Yahagi D, Sakagami H, Kida M et al. Characteristics of gas hydrate crystals and sediment gases retrieved off Hidaka (Hokkaido). Proc Annual Conf Jpn Inst Energy 202228–29 [View Article]
     [Google Scholar]
  13. NITE Biological Resource Center, National Institute of Technology and Evaluation n.d https://www.nite.go.jp/nbrc/catalogue/NBRCMediumDetailServlet?NO=911 accessed 20 May 2021
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
     [Google Scholar]
  15. Phromraksa P, Nagano H, Boonmars T, Kamboonruang C. Identification of proteolytic bacteria from Thai traditional fermented foods and their allergenic reducing potentials. J Food Sci 2008; 73:M189–M195 [View Article] [PubMed]
     [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  17. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  18. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ et al. Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res 2003; 31:3497–3500 [View Article] [PubMed]
     [Google Scholar]
  19. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  20. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  21. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  22. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  23. Tanizawa Y, Fujisawa T, Kaminuma E, Nakamura Y, Arita M. DFAST and DAGA: web-based integrated genome annotation tools and resources. Biosci Microbiota Food Health 2016; 35:173–184 [View Article] [PubMed]
     [Google Scholar]
  24. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinform 2018; 34:1037–1039 [View Article] [PubMed]
     [Google Scholar]
  25. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article] [PubMed]
     [Google Scholar]
  26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:1–15 [View Article] [PubMed]
     [Google Scholar]
  27. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article] [PubMed]
     [Google Scholar]
  28. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinform 2022; 38:5315–5316 [View Article] [PubMed]
     [Google Scholar]
  29. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article]
     [Google Scholar]
  30. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 2010; 11:1–11 [View Article] [PubMed]
     [Google Scholar]
  31. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
     [Google Scholar]
  32. Wang HC, Minh BQ, Susko E, Roger AJ. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst Biol 2018; 67:216–235 [View Article] [PubMed]
     [Google Scholar]
  33. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article] [PubMed]
     [Google Scholar]
  34. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  35. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
     [Google Scholar]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  37. Hamouda T, Shih AY, Baker JR. A rapid staining technique for the detection of the initiation of germination of bacterial spores. Lett Appl Microbiol 2002; 34:86–90 [View Article] [PubMed]
     [Google Scholar]
  38. Sasser M. Technical note 101: identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE: MIDI Inc; 1990
  39. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  40. Dittmer JC, Lester RL. A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 1964; 5:126–127 [View Article] [PubMed]
     [Google Scholar]
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Vallitalea sediminicola sp. nov. and Vallitalea maricola sp. nov., anaerobic bacteria isolated from deep-marine sediment
Int J Syst Evol Microbiol 75, 006721 (2025); https://doi.org/10.1099/ijsem.0.006721
/content/journal/ijsem/10.1099/ijsem.0.006721
/content/journal/ijsem/10.1099/ijsem.0.006721
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