1887

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Volume 69, Issue 2

Aestuariivirga litoralis gen. nov., sp. nov., a proteobacterium isolated from a water sample, and proposal of Aestuariivirgaceae fam. nov. Free

Abstract

A Gram-stain-negative, non-motile, short rod and aerobic bacterium, designated strain SYSU M10001, was isolated from a water sample collected from the coastal region of Pearl River Estuary, Guangdong Province, PR China. Strain SYSU M10001 showed optimal growth at 28 °C, pH 7.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and concatenation of 20 protein markers revealed a distinct lineage for strain SYSU M10001 in the order Rhizobiales . Strain SYSU M10001 showed highest 16S rRNA gene sequence similarities to Hyphomicrobium nitrativorans NL23 (91.1 %) and Hyphomicrobium hollandicum IFAM KB-677 (91.1 %). The respiratory ubiquinone was Q-8. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, two unidentified phospholipids and three unidentified lipids. The predominant cellular fatty acids identified were C19 : 0cyclo ω8c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The G+C content was determined to be 65.5 % (genome). On the basis of differences in the phenotypic, physiological and biochemical characteristics, and results of the phylogenetic analyses, strain SYSU M10001 is proposed to represent a novel species in a novel genus for which the name Aestuariivirga litoralis gen. nov., sp. nov. The type strain of the type species Aestuariivirga litoralis is SYSU M10001 (=NBRC 112960=KCTC 52945). Besides, the distinct phylogenetic lineage and the distinct chemotaxonomic profile among the families in the order Rhizobiales indicated that strain SYSU M10001 should represent a new family for which the name Aestuariivirgaceae fam. nov. is proposed.

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Keyword(s): Aestuariivirga litoralis gen. nov., sp. nov. , Aestuariivirgaceae fam. nov. and Pearl River estuary
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2019-01-04
2024-04-16
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References

  1. Kuykendall LD. Order VI. Rhizobiales ord. nov. In Brebber DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 2, part C New York, NY: Springer; 2006 p. 324
     [Google Scholar]
  2. Fukuda W, Yamada K, Miyoshi Y, Okuno H, Atomi H et al. Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake. Int J Syst Evol Microbiol 2012; 62:1945–1950 [View Article][PubMed]
     [Google Scholar]
  3. Patt TE, Cole GC, Hanson RS. Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Bacteriol 1976; 26:226–229 [View Article]
     [Google Scholar]
  4. Deng SK, Chen GQ, Chen Q, Cai S, Yao L et al. Rhodoligotrophos jinshengii sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2014; 64:3325–3330 [View Article][PubMed]
     [Google Scholar]
  5. Kämpfer P, Arun AB, Busse HJ, Zhang ZL, Young CC et al. Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov. Int J Syst Evol Microbiol 2015; 65:1646–1652 [View Article][PubMed]
     [Google Scholar]
  6. Denner EB, Smith GW, Busse HJ, Schumann P, Narzt T et al. Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol 2003; 53:1115–1122 [View Article][PubMed]
     [Google Scholar]
  7. Thompson JP, Skerman VBD. Azobacteraceae: The Taxonomy and Ecology of the Aerobic Nitrogen-Fixing Bacteria London: Academic Press; 1980 pp. 405
     [Google Scholar]
  8. Jordan DC. Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int J Syst Evol Microbiol 1982; 32:136–139
     [Google Scholar]
  9. Frank B. Über die Pilzsymbiose der Leguminosen. Berichte der Deutschen Botanischen Gesellschaft 1889; 7:332–346
     [Google Scholar]
  10. Mergaert J, Cnockaert MC, Swings J. Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend. Int J Syst Evol Microbiol 2002; 52:1821–1823 [View Article][PubMed]
     [Google Scholar]
  11. Meyer KF, Shaw EB. A comparison of the morphologic, cultural and biochemical characteristics of B. Abortus and B. Melitensis: studies on the genus Brucella nov. gen. J Infect Dis 1920; 27:173–184 [View Article]
     [Google Scholar]
  12. Auling G, Busse H-J, Egli T, El-Banna T, Stackebrandt E. Description of the Gram-negative, obligately aerobic, nitrilotriacetate (nta)-utilizing bacteria as Chelatobacter heintzii, gen. nov., sp. nov., and Chelatococcus asaccharovorans, gen. nov., sp. nov. Syst Appl Microbiol 1993; 16:104–112 [View Article]
     [Google Scholar]
  13. Hwang CY, Cho BC. Cohaesibacter gelatinilyticus gen. nov., sp. nov., a marine bacterium that forms a distinct branch in the order Rhizobiales, and proposal of Cohaesibacteraceae fam. nov. Int J Syst Evol Microbiol 2008; 58:267–277 [View Article][PubMed]
     [Google Scholar]
  14. Hou L, Zhang Y, Sun J, Xie X. Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary. Curr Microbiol 2015; 70:176–182 [View Article][PubMed]
     [Google Scholar]
  15. Hiraishi A, Urata K, Satoh T. A new genus of marine budding phototrophic bacteria, Rhodobium gen. nov., which includes Rhodobium orientis sp. nov. and Rhodobium marinum comb. nov. Int J Syst Bacteriol 1995; 45:226–234 [View Article][PubMed]
     [Google Scholar]
  16. Martineau C, Villeneuve C, Mauffrey F, Villemur R. Hyphomicrobium nitrativorans sp. nov., isolated from the biofilm of a methanol-fed denitrification system treating seawater at the Montreal Biodome. Int J Syst Evol Microbiol 2013; 63:3777–3781 [View Article][PubMed]
     [Google Scholar]
  17. Huang Z, Guo F, Lai Q, Shao Z. Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria. Int J Syst Evol Microbiol 2017; 67:2527–2531 [View Article][PubMed]
     [Google Scholar]
  18. Li JL, Salam N, Wang PD, Chen LX, Jiao JY et al. Discordance between resident and active bacterioplankton in free-living and particle-associated communities in estuary ecosystem. Microb Ecol 2018; 76:637–647 [View Article][PubMed]
     [Google Scholar]
  19. Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM et al. Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102:297–305 [View Article][PubMed]
     [Google Scholar]
  20. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960
     [Google Scholar]
  21. Nie GX, Ming H, Li S, Zhou EM, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article][PubMed]
     [Google Scholar]
  22. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed]
     [Google Scholar]
  23. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
     [Google Scholar]
  24. McFaddin JF. Biochemical Tests for Identification of Medical Bacteria USA: Williams & Wilkins Co; 1976
     [Google Scholar]
  25. Smibert R, 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]
  26. Cui HL, Lin ZY, Dong Y, Zhou PJ, Liu SJ. Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2007; 57:2204–2206 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
     [Google Scholar]
  29. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
     [Google Scholar]
  30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  31. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
     [Google Scholar]
  32. 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; 67:1613–1618 [View Article][PubMed]
     [Google Scholar]
  33. 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]
  34. 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]
  35. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  36. 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]
  37. 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]
  38. 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]
  39. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1984
     [Google Scholar]
  40. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  41. Harrison P, Strulo B. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000; 10:3–42 [View Article]
     [Google Scholar]
  42. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  43. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article][PubMed]
     [Google Scholar]
  44. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  45. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
     [Google Scholar]
  46. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  47. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article][PubMed]
     [Google Scholar]
  48. Gliesche C, Fesefeldt A, Hirsch P. Hyphomicrobium. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. (editors) Bergey's Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
  49. Jin L, Kim KK, Baek SH, Lee ST. Kaistia geumhonensis sp. nov. and Kaistia dalseonensis sp. nov., two members of the class Alphaproteobacteria. Int J Syst Evol Microbiol 2011; 61:2577–2581 [View Article][PubMed]
     [Google Scholar]
  50. Im WT, Yokota A, Kim MK, Lee ST. Kaistia adipata gen. nov., sp. nov., a novel α-proteobacterium. J Gen Appl Microbiol 2004; 50:249–254[PubMed]
     [Google Scholar]
  51. Nakagawa Y, Sakane T, Yokota A. Devosia. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. (editors) Bergey's Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
  52. Zeevi Ben Yosef D, Ben-Dov E, Kushmaro A. Amorphus coralli gen. nov., sp. nov., a marine bacterium isolated from coral mucus, belonging to the order Rhizobiales. Int J Syst Evol Microbiol 2008; 58:2704–2709 [View Article][PubMed]
     [Google Scholar]
  53. Wang YX, Liu JH, Chen YG, Zhang XX, Wang ZG et al. Amorphus orientalis sp. nov., an exopolysaccharide-producing bacterium isolated from salt mine sediment. Int J Syst Evol Microbiol 2010; 60:1750–1754 [View Article][PubMed]
     [Google Scholar]
  54. Hwang JM, Chung EJ, Park JA, Jeong JH, Jeon CO et al. Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima. Int J Syst Evol Microbiol 2013; 63:3868–3872 [View Article][PubMed]
     [Google Scholar]
  55. Dedysh SN, Dunfield PF. Methyloferula. In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J et al. (editors) Bergey's Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
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Aestuariivirga litoralis gen. nov., sp. nov., a proteobacterium isolated from a water sample, and proposal of Aestuariivirgaceae fam. nov.
Int J Syst Evol Microbiol 69, 299 (2019); https://doi.org/10.1099/ijsem.0.003087
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