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Volume 74, Issue 3

sp. nov. and sp. nov., two novel members isolated from deep-sea environments No Access

Abstract

Two Gram-stain-negative, rod-shaped and non-motile strains, designated as DY56-A-20 and G39, were isolated from deep-sea sediment of the Pacific Ocean and deep-sea seawater of the Indian Ocean, respectively. Strain DY56-A-20 was found to grow at 15–37 °C (optimum, 28 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.0) and in 0.5–6.0 % (w/v) NaCl (optimum, 1.0–2.0 %), while strain G39 was found to grow at 10–42 °C (optimum, 35–40 °C), at pH 5.5–10.0 (optimum, pH 6.5–7.0) and in 0–12.0 % (w/v) NaCl (optimum, 1.0–2.0 %). The 16S rRNA gene sequence identity analysis indicated that strain DY56-A-20 had the highest sequence identity with KEM-5 (97.6 %), while strain G39 displayed the highest sequence identity with H150 (98.8 %). The phylogenomic reconstruction indicated that both strains formed independent clades within the genus . The digital DNA–DNA hybridization and average nucleotide identity values between strains DY56-A-20/G39 and type strains were 17.8–23.8 % and 70.7–81.1 %, respectively, which are below species delineation thresholds. The genome DNA G+C contents were 65.0 and 63.5 mol% for strains DY56-A-20 and G39, respectively. The predominant cellular fatty acids (>10 %) of strain DY56-A-20 were C 6, summed feature 8 and summed feature 3, and the major cellular fatty acids of strain G39 were C 6 and summed feature 8. The major polar lipids in both strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and an unidentified polar lipid. The only respiratory quinone present in both strains was ubiquinone-10. Based on those genotypic and phenotypic results, the two strains represent two novel species belonging to the genus , for which the names sp. nov. and sp. nov. are proposed. The type strain of is DY56-A-20 (=MCCC M27941=KCTC 92309), and the type strain of is G39 (=MCCC M30353=KCTC 8208).

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Keyword(s): deep-sea environment , polyphasic taxonomy , Qipengyuania benthica and Qipengyuania profundimaris
Funding
This study was supported by the:
  • National Key Research and Development Program of China (Award 2023YFC2811500)
    • Principle Award Recipient: Xue-WeiXu
  • National Key Research and Development Program of China (Award 2022YFC2804005)
    • Principle Award Recipient: Ge-YiFu
  • National Natural Science Foundation of China (Award 32000001)
    • Principle Award Recipient: LinXu
  • National Key Research and Development Program of China (Award 2022YFC2803900)
    • Principle Award Recipient: LinXu
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: PengZhou
  • National Natural Science Foundation of China (Award 32170005)
    • Principle Award Recipient: Xue-WeiXu
© 2024 The Authors
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References

  1. Feng X-M, Mo Y-X, Han L, Nogi Y, Zhu Y-H et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015; 65:3658–3665 [View Article] [PubMed]
     [Google Scholar]
  2. Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470–4495 [View Article] [PubMed]
     [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  4. Liu Y, Pei T, Deng MR, Zhu H. Qipengyuania soli sp. nov., isolated from mangrove soil. Curr Microbiol 2021; 78:2806–2814 [View Article] [PubMed]
     [Google Scholar]
  5. Denner EBM, Vybiral D, Koblízek M, Kämpfer P, Busse H-J et al. Erythrobacter citreus sp. nov., a yellow-pigmented bacterium that lacks bacteriochlorophyll a, isolated from the western Mediterranean Sea. Int J Syst Evol Microbiol 2002; 52:1655–1661 [View Article] [PubMed]
     [Google Scholar]
  6. Yoon JH, Kim H, Kim IG, Kang KH, Park YH. Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int J Syst Evol Microbiol 2003; 53:1169–1174 [View Article] [PubMed]
     [Google Scholar]
  7. Yoon JH, Kang KH, Oh TK, Park YH. Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2004; 54:1981–1985 [View Article] [PubMed]
     [Google Scholar]
  8. Wu H-X, Lai PY, Lee OO, Zhou X-J, Miao L et al. Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea. Int J Syst Evol Microbiol 2012; 62:1348–1353 [View Article] [PubMed]
     [Google Scholar]
  9. Kristyanto S, Lee SD, Kim J. Porphyrobacter algicida sp. nov., an algalytic bacterium isolated from seawater. Int J Syst Evol Microbiol 2017; 67:4526–4533 [View Article] [PubMed]
     [Google Scholar]
  10. Park S, Won SM, Yoon JH. Erythrobacter marisflavi sp. nov., isolated from isolated from estuary water. Int J Syst Evol Microbiol 2019; 69:2696–2702 [View Article] [PubMed]
     [Google Scholar]
  11. Yoon JH, Oh TK, Park YH. Erythrobacter seohaensis sp. nov. and Erythrobacter gaetbuli sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:71–75 [View Article] [PubMed]
     [Google Scholar]
  12. Xu M, Xin Y, Yu Y, Zhang J, Zhou Y et al. Erythrobacter nanhaisediminis sp. nov., isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2010; 60:2215–2220 [View Article] [PubMed]
     [Google Scholar]
  13. Yang Y, Zhang G, Sun Z, Cheung MK, Huang C. Altererythrobacter oceanensis sp. nov., isolated from the Western Pacific. Antonie van Leeuwenhoek 2014; 106:1191–1198 [View Article] [PubMed]
     [Google Scholar]
  14. Liu Y, Pei T, Du J, Yao Q, Deng M-R et al. Comparative genomics reveals genetic diversity and metabolic potentials of the genus Qipengyuania and suggests fifteen novel species. Microbiol Spectr 2022; 10:e0126421 [View Article] [PubMed]
     [Google Scholar]
  15. Tareen S, Risdian C, Müsken M, Wink J. Qipengyuania pacifica sp. nov., a novel carotenoid-producing marine bacterium of the family Erythrobacteraceae, isolated from sponge (Demospongiae), and antimicrobial potential of its crude extract. Diversity 2022; 14:295 [View Article]
     [Google Scholar]
  16. Ivanova EP, Bowman JP, Lysenko AM, Zhukova NV, Gorshkova NM et al. Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates. Syst Appl Microbiol 2005; 28:123–130 [View Article] [PubMed]
     [Google Scholar]
  17. Ludwig W. Nucleic acid techniques in bacterial systematics and identification. Int J Food Microbiol 2007; 120:225–236 [View Article] [PubMed]
     [Google Scholar]
  18. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
     [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  21. Saitou NM, 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  24. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  30. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  31. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  32. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725–731 [View Article] [PubMed]
     [Google Scholar]
  35. Xu L, Wu Y-H, Jian S-L, Wang C-S, Wu M et al. Pseudohongiellanitratireducens sp. nov., isolated from seawater, and emended description of the genus Pseudohongiella. Int J Syst Evol Microbiol 2016; 66:5155–5160 [View Article] [PubMed]
     [Google Scholar]
  36. ZoBell CE. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
     [Google Scholar]
  37. You H, Xu L, Kong Y-H, Sun C, Zhou P et al. Sphingomicrobium nitratireducens sp. nov., isolated from a tidal flat in Guangxi. Arch Microbiol 2022; 204:671 [View Article] [PubMed]
     [Google Scholar]
  38. Xu L, Huo Y-Y, Li Z-Y, Wang C-S, Oren A et al. Chryseobacterium profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment. Antonie van Leeuwenhoek 2015; 107:979–989 [View Article] [PubMed]
     [Google Scholar]
  39. Leifson E. Determination of carbohydrate metabolism of marine bacteria. J Bacteriol 1963; 85:1183–1184 [View Article] [PubMed]
     [Google Scholar]
  40. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial Systematics. In Current Methods for Classification and Identification of Microorganisms 1988 pp 161–207
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  42. Bligh ELG, Dyer WJA. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article]
     [Google Scholar]
  43. Tindall B, Sikorski J, Smibert R, Krieg N. Phenotypic characterization and the principles of comparative systematics. Methods Gen Mol Microbiol 2007330–393 [View Article]
     [Google Scholar]
  44. Liu Y, Pei T, Du J, Huang H, Deng M-R et al. Comparative genomic analysis of the genus Novosphingobium and the description of two novel species Novosphingobium aerophilum sp. nov. and Novosphingobium jiangmenense sp. nov. Syst Appl Microbiol 2021; 44:126202 [View Article] [PubMed]
     [Google Scholar]
  45. Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A. Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales. Microb Genom 2018; 4:e000172 [View Article] [PubMed]
     [Google Scholar]
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Qipengyuania benthica sp. nov. and Qipengyuania profundimaris sp. nov., two novel Erythrobacteraceae members isolated from deep-sea environments
Int J Syst Evol Microbiol 74, 006313 (2024); https://doi.org/10.1099/ijsem.0.006313
/content/journal/ijsem/10.1099/ijsem.0.006313
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