1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 7

gen. nov., sp. nov., a member of the family isolated from marine water of the Arabian Gulf Free

Abstract

Strain B66 was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15–45 °C (optimum, 30 °C), at pH 5–11 (optimum, pH 6.5–8) and with 0–6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66 was affiliated with the family , sharing the highest sequence similarities to the genera (93.7–95.4 %), (94.0–95.1 %), (93.3–93.7 %), (92.0–93.7 %), (93.2–93.3 %) and (92.9 %). In the phylogenetic trees, strain B66 demonstrated the novel organism formed a distinct lineage closely associated with and . Major fatty acids were C, summed feature 3 (C ω/C ω6/iso-C 2-OH and iso-C 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66 is considered to represent a novel species and genus for which the name gen. nov., sp. nov., is proposed. The type strain is B66 (=QCC B003/17=LMG 30288 =CCUG 70703).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): new taxa , Ningiella ruwaisensisgen. nov. sp. nov. and proteobacteria
Funding
This study was supported by the:
  • Qatar National Research Fund (Award NPRP 6-647-1-127)
    • Principle Award Recipient: Rashmi Fotedar
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004256
2020-07-02
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4130.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004256&mimeType=html&fmt=ahah

References

  1. Ivanova EP, Mikhailov VV, New Family A. Alteromonadaceae fam. nov., Including marine proteobacteria of the genera Alteromonas, Pseudoalteromonas, Idiomarina and Colwellia . Microbiology 2001; 70:10–17 [View Article]
     [Google Scholar]
  2. Yi H, Bae KS, Chun J. Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii . Int J Syst Evol Microbiol 2004; 54:571–576 [View Article][PubMed]
     [Google Scholar]
  3. Teramoto M, Nishijima M. Agaribacter marinus gen. nov., sp. nov., an agar-degrading bacterium from surface seawater. Int J Syst Evol Microbiol 2014; 64:2416–2423 [View Article][PubMed]
     [Google Scholar]
  4. Kurahashi M, Yokota A. Agarivorans albus gen. nov., sp. nov., a gamma-proteobacterium isolated from marine animals. Int J Syst Evol Microbiol 2004; 54:693–697 [View Article][PubMed]
     [Google Scholar]
  5. Jean WD, Huang S-P, Liu TY, Chen J-S, Shieh WY. Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation. Int J Syst Evol Microbiol 2009; 59:1880–1887 [View Article][PubMed]
     [Google Scholar]
  6. Jean WD, Hsu CY, Huang S-P, Chen J-S, Lin S et al. Reclassification of [Glaciecola] lipolytica and [Aestuariibacter] litoralis in Aliiglaciecola gen. nov., as Aliiglaciecola lipolytica comb. nov. and Aliiglaciecola litoralis comb. nov., respectively. Int J Syst Evol Microbiol 2013; 63:2859–2864 [View Article]
     [Google Scholar]
  7. Vogel BF, Venkateswaran K, Christensen H, Falsen E, Christiansen G et al. Polyphasic taxonomic approach in the description of Alishewanella fetalis gen. nov., sp. nov., isolated from a human foetus. Int J Syst Evol Microbiol 2000; 50 Pt 3:1133–1142 [View Article][PubMed]
     [Google Scholar]
  8. Lopez-Perez M, Rodriguez-Valera F. Rosenberg E, Edward F, DeLong StephenLory, Stackebrandt Erko, Thompson F. (editors) The family Alteromononadaceae The Prokaryotes Berlin Heidelberg: Springer; 2013 pp 69–92
     [Google Scholar]
  9. Jean WD, Chen J-S, Lin Y-T, Shieh WY. Bowmanella denitrificans gen. nov., sp. nov., a denitrifying bacterium isolated from seawater from An-Ping Harbour, Taiwan. Int J Syst Evol Microbiol 2006; 56:2463–2467 [View Article][PubMed]
     [Google Scholar]
  10. Yan S, Yu M, Wang Y, Shen C, Zhang X-H. Catenovulum agarivorans gen. nov., sp. nov., a peritrichously flagellated, chain-forming, agar-hydrolysing gammaproteobacterium from seawater. Int J Syst Evol Microbiol 2011; 61:2866–2873 [View Article][PubMed]
     [Google Scholar]
  11. Bowman JP, McCammon SA, Brown JL, McMeekin TA. Glaciecola punicea gen. nov., sp. nov. and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats. Int J Syst Bacteriol 1998; 48:1213–1222 [View Article]
     [Google Scholar]
  12. Urios L, Intertaglia L, Lesongeur F, Lebaron P. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea. Int J Syst Evol Microbiol 2008; 58:1233–1237 [View Article][PubMed]
     [Google Scholar]
  13. Liao H, Li Y, Guo X, Lin X, Lai Q et al. Mangrovitalea sediminis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from mangrove sediment. Int J Syst Evol Microbiol 2017; 67:5172–5178 [View Article][PubMed]
     [Google Scholar]
  14. Lim J-M, Jeon CO, Lee J-C, Song S-M, Kim K-Y et al. Marinimicrobium koreense gen. nov., sp. nov. and Marinimicrobium agarilyticum sp. nov., novel moderately halotolerant bacteria isolated from tidal flat sediment in Korea. Int J Syst Evol Microbiol 2006; 56:653–657 [View Article][PubMed]
     [Google Scholar]
  15. Gauthier MJ, Lafay B, Christen R, Fernandez L, Acquaviva M et al. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 1992; 42:568–576 [View Article][PubMed]
     [Google Scholar]
  16. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 1997; 47:369–376 [View Article][PubMed]
     [Google Scholar]
  17. Zhang D, Gui J, Zheng S, Zhu X, Wu S et al. Marisediminitalea mangrovi gen. nov., sp. nov., isolated from marine mangrove sediment, and reclassification of Aestuariibacter aggregatus as Marisediminitalea aggregata comb. nov. Int J Syst Evol Microbiol 2020; 70:457–464 [View Article][PubMed]
     [Google Scholar]
  18. Urios L, Agogué H, Intertaglia L, Lesongeur F, Lebaron P, Lebaron P. Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean sea. Int J Syst Evol Microbiol 2008; 58:2479–2483 [View Article][PubMed]
     [Google Scholar]
  19. Shivaji S, Reddy GS. Phylogenetic analyses of the genus Glaciecola: emended description of the genus Glaciecola, transfer of Glaciecola mesophila, G. agarilytica, G. aquimarina, G. arctica, G. chathamensis, G. polaris and G. psychrophila to the genus Paraglaciecola gen. nov. as Paraglaciecola mesophila comb. nov., P. agarilytica comb. nov., P. aquimarina comb. nov., P. arctica comb. nov., P. chathamensis comb. nov., P. polaris comb. nov. and P. psychrophila comb. nov., and description of Paraglaciecola oceanifecundans sp. nov., isolated from the Southern Ocean. Int J Syst Evol Microbiol 2014; 64:3264–3275 [View Article][PubMed]
     [Google Scholar]
  20. Sheu D-S, Sheu S-Y, Lin K-R, Chen Y-LL, Chen W-M. Planctobacterium marinum gen. nov., sp. nov., a new member of the family Alteromonadaceae isolated from seawater. Int J Syst Evol Microbiol 2017; 67:974–980 [View Article][PubMed]
     [Google Scholar]
  21. Du J, Dong C, Lai Q, Liu Y, Xie Y et al. Pseudobowmanella zhangzhouensis gen. nov., sp. nov., isolated from the surface freshwater of the Jiulong River in China. Antonie van Leeuwenhoek 2015; 107:741–748 [View Article][PubMed]
     [Google Scholar]
  22. Ekborg NA, Gonzalez JM, Howard MB, Taylor LE, Hutcheson SW et al. Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides. Int J Syst Evol Microbiol 2005; 55:1545–1549 [View Article][PubMed]
     [Google Scholar]
  23. Jeon CO, Lim J-M, Park D-J, Kim C-J. Salinimonas chungwhensis gen. nov., sp. nov., a moderately halophilic bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 2005; 55:239–243 [View Article][PubMed]
     [Google Scholar]
  24. Verma A, Mual P, Mayilraj S, Krishnamurthi S. Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India. Int J Syst Evol Microbiol 2015; 65:3248–3255 [View Article][PubMed]
     [Google Scholar]
  25. Rios-Hernandez LA, Gieg LM, Suflita JM. Biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer. Appl Environ Microbiol 2003; 69:434–443 [View Article][PubMed]
     [Google Scholar]
  26. 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]
  27. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  30. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [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. 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]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  34. Schubert M, Lindgreen S, Orlando L. AdapterRemoval V2: rapid adapter trimming, identification, and read merging. BMC Res Notes 2016; 9:88 [View Article][PubMed]
     [Google Scholar]
  35. Hyatt D, Chen G-L, 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]
  36. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  37. 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]
  38. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  39. 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]
  40. 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]
  41. Rodriguez RLM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peerj Prepr 2016:e1900v1
     [Google Scholar]
  42. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. Morishima. KKEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:45 gkw1092 D361 [View Article][PubMed]
     [Google Scholar]
  43. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative Systematics methods for general and molecular. Microbiology 2007330–393
     [Google Scholar]
  44. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note #101. 2001
     [Google Scholar]
  45. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  46. Collins MD. Gottschalk G. editor Analysis of Isoprenoid Quinones Methods in Microbiology 18 1985 pp p 329-–3366
     [Google Scholar]
  47. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  48. 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 [View Article][PubMed]
     [Google Scholar]
  49. Barbeyron T, Zonta E, Le Panse S, Duchaud E, Michel G. Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas. Int J Syst Evol Microbiol 2019; 69:2514–2521 [View Article]
     [Google Scholar]
  50. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Mag 2014; 9:111–118 [View Article]
     [Google Scholar]
  51. NicholsonAC GCA, Whitney MA, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020
     [Google Scholar]
  52. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
     [Google Scholar]
  53. Whitman WB. The need for change: embracing the genome. Method Microbiol 2014; 41:1–12
     [Google Scholar]
  54. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217–222 [View Article][PubMed]
     [Google Scholar]
  55. Lee I, Ouk Kim Y, Park S-C, 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]
  56. 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]
  57. 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; 14:60 [View Article][PubMed]
     [Google Scholar]
  58. Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME et al. Genotype to phenotype: identification of diagnostic Vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 2014; 64:357–365 [View Article][PubMed]
     [Google Scholar]
  59. Barona-Gómez F, Cruz-Morales P, Noda-García L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics?. Antonie van Leeuwenhoek 2012; 101:35–43 [View Article][PubMed]
     [Google Scholar]
  60. Lawson PA, Sankaranarayanan K, Patel NB, Busse HJ. In-silico chemotaxonomy: A tool for 21st century microbial systematics Bergey’s International Society for Microbial Systematics; 2016p 27
  61. Patel NB, Sankaranarayanan K, Busse HJ, Lawson PA. Investigating genomic tools for polar lipid prediction Bergey’s International Society for Microbial Systematics; 2016p 41
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004256
Loading
Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf
Int J Syst Evol Microbiol 70, 4130 (2020); https://doi.org/10.1099/ijsem.0.004256
/content/journal/ijsem/10.1099/ijsem.0.004256
/content/journal/ijsem/10.1099/ijsem.0.004256
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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