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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 8

Description of novel members of the family : gen. nov., sp. nov., and sp. nov., isolated from freshwater sediment Free

Abstract

Two Gram-stain-negative bacterial strains, DS48-3 and CH68-4, were isolated from freshwater sediment taken from the Daechung Reservoir, Republic of Korea. Cells of strains DS48-3 and CH68-4 were aerobic, non-motile, non-spore-forming and rod-shaped. Strain DS48-3 was isolated from a sediment surface sample at a depth of 48 m from the Daechung Reservoir and was most closely related to the genus according to 16S rRNA gene sequence analysis (94.5–95.9 % similarity). Strain CH68-4 was isolated from the very bottom of a 67-cm-long sediment core collected from Daechung Reservoir at a water depth of 17 m and was most closely related to the genus (16S rRNA gene sequence similarity of 93.7–95.0 %). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the two strains formed a separate lineage within the order showing similarity values below 95.9 % with their closest phylogenetic neighbours, and sharing 97.3 % similarity with each other. The combined genotypic and phenotypic data showed that strains DS48-3 and CH68-4 could be distinguished from all genera within the family and represented two distinct species of a novel genus, gen. nov., sp. nov. (type strain DS48-3=KCTC 52068=CCTCC AB 2018061) and sp. nov. (type strain CH68-4=KCTC 62205=CCTCC AB 2018062).

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Keyword(s): Aquisediminimona , Aquisediminimonas profunda , Aquisediminimonas sediminicola , CH68-4T , DS48-3T and sediment
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2019-08-01
2024-04-27
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References

  1. Sly LI, Cahill MM. Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov. Int J Syst Bacteriol 1997; 47:566–568 [View Article][PubMed]
     [Google Scholar]
  2. Chen C, Zheng Q, Wang YN, Yan XJ, Hao LK et al. Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. Int J Syst Evol Microbiol 2010; 60:2857–2861 [View Article][PubMed]
     [Google Scholar]
  3. Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ et al. Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov. Int J Syst Evol Microbiol 2013; 63:735–743 [View Article][PubMed]
     [Google Scholar]
  4. Felföldi T, Vengring A, Márialigeti K, András J, Schumann P et al. Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge. Int J Syst Evol Microbiol 2014; 64:738–744 [View Article][PubMed]
     [Google Scholar]
  5. Wang BZ, Guo P, Zheng JW, Hang BJ, Li L et al. Sphingobium wenxiniae sp. nov., a synthetic pyrethroid (SP)-degrading bacterium isolated from activated sludge in an SP-manufacturing wastewater treatment facility. Int J Syst Evol Microbiol 2011; 61:1776–1780 [View Article][PubMed]
     [Google Scholar]
  6. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article][PubMed]
     [Google Scholar]
  7. Baek SH, Lim JH, Jin L, Lee HG, Lee ST. Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. Int J Syst Evol Microbiol 2011; 61:2464–2468 [View Article][PubMed]
     [Google Scholar]
  8. Lee LH, Azman AS, Zainal N, Eng SK, Fang CM et al. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. Int J Syst Evol Microbiol 2014; 64:1194–1201 [View Article][PubMed]
     [Google Scholar]
  9. Francis IM, Jochimsen KN, de Vos P, van Bruggen AH. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:1340–1350 [View Article][PubMed]
     [Google Scholar]
  10. Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA et al. Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana . Int J Syst Evol Microbiol 2014; 64:594–598 [View Article][PubMed]
     [Google Scholar]
  11. Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi Y et al. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 2012; 62:2224–2228
     [Google Scholar]
  12. Huang HY, Li J, Zhao GZ, Zhu WY, Yang LL et al. Sphingomonas endophytica sp. nov., isolated from Artemisia annua L. Int J Syst Evol Microbiol 2012; 62:1576–1580 [View Article][PubMed]
     [Google Scholar]
  13. Kim M, Kang O, Zhang Y, Ren L, Chang X et al. Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii . Int J Syst Evol Microbiol 2016; 66:91–100 [View Article][PubMed]
     [Google Scholar]
  14. Young CC, Ho MJ, Arun AB, Chen WM, Lai WA et al. Sphingobium olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2007; 57:2613–2617 [View Article][PubMed]
     [Google Scholar]
  15. Chaudhary DK, Kim J. Sphingomonas naphthae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:4621–4627 [View Article][PubMed]
     [Google Scholar]
  16. Fukuda W, Chino Y, Araki S, Kondo Y, Imanaka H et al. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock. Int J Syst Evol Microbiol 2014; 64:2034–2040 [View Article][PubMed]
     [Google Scholar]
  17. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  18. Jin L, Lee CS, Ahn CY, Lee HG, Lee S et al. Abundant iron and sulfur oxidizers in the stratified sediment of a eutrophic freshwater reservoir with annual cyanobacterial blooms. Sci Rep 2017; 7:43814 [View Article][PubMed]
     [Google Scholar]
  19. Jin L, Lee HG, La HJ, Ko SR, Ahn CY et al. Ferruginibacter profundus sp. nov., a novel member of the family Chitinophagaceae, isolated from freshwater sediment of a reservoir. Antonie van Leeuwenhoek 2014; 106:319–323 [View Article][PubMed]
     [Google Scholar]
  20. Jin L, Ko SR, Ahn CY, Lee HG, Oh HM. Rhizobacter profundi sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2016; 66:1926–1931 [View Article][PubMed]
     [Google Scholar]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  22. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of Members of the Family Pasteurellaceae Based on Polyamine Patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
     [Google Scholar]
  23. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
     [Google Scholar]
  24. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  25. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  26. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
     [Google Scholar]
  27. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley & Sons; 1991
     [Google Scholar]
  28. Yoon SH, Ha SM, 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]
  29. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  30. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  33. 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]
  34. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  36. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  37. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  38. Chaudhary DK, Dahal RH, Kim J. Sphingopyxis solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:1820–1826 [View Article][PubMed]
     [Google Scholar]
  39. Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C. Sphingopyxis italica sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2013; 63:2565–2569 [View Article][PubMed]
     [Google Scholar]
  40. Jogler M, Chen H, Simon J, Rohde M, Busse HJ et al. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int J Syst Evol Microbiol 2013; 63:1342–1349 [View Article][PubMed]
     [Google Scholar]
  41. Chaudhary DK, Kim J. Sphingopyxis nepalensis sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:364–370 [View Article][PubMed]
     [Google Scholar]
  42. Verma H, Rani P, Kumar Singh A, Kumar R, Dwivedi V et al. Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3720–3726 [View Article][PubMed]
     [Google Scholar]
  43. Oelschlägel M, Rückert C, Kalinowski J, Schmidt G, Schlömann M et al. Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid. Int J Syst Evol Microbiol 2015; 65:3008–3015 [View Article][PubMed]
     [Google Scholar]
  44. Sharma P, Verma M, Bala K, Nigam A, Lal R. Sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. Int J Syst Evol Microbiol 2010; 60:780–784 [View Article][PubMed]
     [Google Scholar]
  45. Vancanneyt M, Schut F, Snauwaert C, Goris J, Swings J et al. Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int J Syst Evol Microbiol 2001; 51:73–79 [View Article][PubMed]
     [Google Scholar]
  46. Takeuchi M, Kawai F, Shimada Y, Yokota A. Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol 1993; 16:227–238 [View Article]
     [Google Scholar]
  47. Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VV. Sphingorhabdus pacificus sp. nov., isolated from sandy sediments of the Sea of Japan seashore. Arch Microbiol 2015; 197:147–153 [View Article][PubMed]
     [Google Scholar]
  48. Baik KS, Choe HN, Park SC, Hwang YM, Kim EM et al. Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis . Int J Syst Evol Microbiol 2013; 63:1297–1303 [View Article][PubMed]
     [Google Scholar]
  49. Kim BS, Lim YW, Chun J. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 2008; 58:2415–2419
     [Google Scholar]
  50. Yasir M, Aslam Z, Song GC, Jeon CO, Chung YR et al. Sphingopyxis marina sp. nov. and isolated from vermicompost, and emended description of the genus Sphingosinicella . Int J Syst Evol Microbiol 2010; 60:580–584
     [Google Scholar]
  51. Yoon JH, Kang SJ, Lee JS, Nam SW, Kim W et al. Sphingosinicella soli sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol 2008; 58:173–177 [View Article][PubMed]
     [Google Scholar]
  52. Maruyama T, Park HD, Ozawa K, Tanaka Y, Sumino T et al. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:85–89 [View Article][PubMed]
     [Google Scholar]
  53. Park S, Park JM, Sun Joo E, Won SM, Kyum Kim M et al. Sphingomicrobium aestuariivivum sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015; 65:2678–2683 [View Article][PubMed]
     [Google Scholar]
  54. Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC et al. Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium . Int J Syst Evol Microbiol 2013; 63:3415–3422 [View Article][PubMed]
     [Google Scholar]
  55. Kämpfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J et al. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 2012; 62:1326–1330 [View Article][PubMed]
     [Google Scholar]
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Description of novel members of the family Sphingomonadaceae: Aquisediminimonas profunda gen. nov., sp. nov., and Aquisediminimonas sediminicola sp. nov., isolated from freshwater sediment
Int J Syst Evol Microbiol 69, 2179 (2019); https://doi.org/10.1099/ijsem.0.003347
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