1887

Abstract

A free-living, nitrogen-fixing, mesophilic and facultative aerobe, designated strain USBA 369, was isolated from a terrestrial saline spring of the Colombian Andes. The non-sporulating rods (1.5×0.8 µm) with rounded ends stained Gram-negative and were motile by means of lophotrichous flagella. The strain grew optimally at 30 °C, at pH 6.9–7.5 and with 1.5 % (w/v) NaCl. The major fatty acids detected were Cω7 and C cyclo ω8, and the respiratory lipoquinone ubiquinone 10 (Q-10) was present. The genome consisted of 4.65 Mb with a DNA G+C content of 64.3 mol%. A total of 4371 genes were predicted and, of those, 4300 were protein coding genes and 71 were RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain USBA 369 formed a different lineage within the class , order , and DNA homology studies with the most closely related genera, and (95 % 16S rRNA gene sequence similarity), showed values of <15 %. The phylogenomic analysis provided evidence for clear phylogenetic divergence between strain USBA 369 and the closely related genera. On the basis of the phenotypic, chemotaxonomic and phylogenomic evidence, strain USBA 369 is considered to represent a novel genus and a novel species for which the name gen. nov., sp. nov. is proposed. The type strain is USBA 369 (=KCTC 22549=CMPUJ U369).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002185
2017-10-01
2021-07-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/3744.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002185&mimeType=html&fmt=ahah

References

  1. Díaz-Cárdenas C, Baena S. Manantiales salinos: diversidad metabólica y filogenética de microorganismos de ambientes salinos. Rev Acad Colomb Cienc Ex Fis Nat 2015; 39:358–373 [View Article]
    [Google Scholar]
  2. Díaz-Cárdenas C, Patel BK, Baena S. Tistlia consotensis gen. nov., sp. nov., an aerobic, chemoheterotrophic, free-living, nitrogen-fixing alphaproteobacterium, isolated from a Colombian saline spring. Int J Syst Evol Microbiol 2010; 60:1437–1443 [View Article][PubMed]
    [Google Scholar]
  3. Imhoff-Stuckle D, Pfennig N. Isolation and characterization of a nicotinic acid-degrading sulfate-reducing bacterium, Desulfococcus niacini sp. nov. Arch Microbiol 1983; 136:194–198 [View Article]
    [Google Scholar]
  4. Patel BKC, Morgan HW, Daniel RM. Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch Microbiol 1985; 141:63–69 [View Article]
    [Google Scholar]
  5. Díaz-Cárdenas C, López G, Patel BK, Baena S. Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring. Int J Syst Evol Microbiol 2010; 60:850–853 [View Article][PubMed]
    [Google Scholar]
  6. Gómez-Gómez JA, Giraldo-Estrada C, Habeych D, Baena S. Evaluation of biological production of lactic acid in a synthetic medium and in Aloe vera (L.) Burm. f. processing by-products. Aloe vera, lactic acid, Thermoanaerobacter sp. USBA-018,313 thermophilic fermentation. Univ Sci 2015; 20:369–385 [Crossref]
    [Google Scholar]
  7. Baldani VLD, Döbereiner J. Host-plant specificity in the infection of cereals with Azospirillum spp. Soil Biol Biochem 1980; 12:433–439 [View Article]
    [Google Scholar]
  8. Bauer JS, Ghequire MGK, Nett M, Josten M, Sahl H-G et al. Biosynthetic origin of the antibiotic pseudopyronines A and B in Pseudomonas putida BW11M1. Am J Clin Pathol 1966; 45:493–496
    [Google Scholar]
  9. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  10. 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]
  11. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  12. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  13. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism I California: New York Academics Press; 1969 pp. 21–132 [Crossref]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  15. Nei M, Kumar S. Molecular Evolution and Phylogenetics Oxford University; 2000 pp. 352
    [Google Scholar]
  16. Bushnell B. 2016; BBTools software package. https://sourceforge.net/projects/bbmap/ [accessed 2016]
  17. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed]
    [Google Scholar]
  18. Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 2011; 108:1513–1518 [View Article][PubMed]
    [Google Scholar]
  19. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119–129 [View Article][PubMed]
    [Google Scholar]
  20. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 2017; 45:D507–D516 [View Article][PubMed]
    [Google Scholar]
  21. Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D et al. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 2015; 10:86–91 [View Article][PubMed]
    [Google Scholar]
  22. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E et al. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res 2012; 40:D115–D122 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Jurado V, Gonzalez JM, Laiz L, Saiz-Jimenez C. Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave. Int J Syst Evol Microbiol 2006; 56:2583–2585 [View Article][PubMed]
    [Google Scholar]
  25. Khalid R, Zhang YJ, Ali S, Sui XH, Zhang XX et al. Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan. Antonie van Leeuwenhoek 2015; 107:281–290 [View Article][PubMed]
    [Google Scholar]
  26. Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J et al. Comparative systems biology across an evolutionary gradient within the Shewanella genus. Proc Natl Acad Sci USA 2009; 106:15909–15914 [View Article][PubMed]
    [Google Scholar]
  27. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  30. Kim MS, Hoa KT, Baik KS, Park SC, Seong CN et al. Aurantimonas frigidaquae sp. nov., isolated from a water-cooling system. Int J Syst Evol Microbiol 2008; 58:1142–1146 [View Article][PubMed]
    [Google Scholar]
  31. Garrity G, Holt J, Boone D, Castenholz R. Class I. Alphaproteobacteria class. nov. In Brenner DK, Staley JT. (editors) Bergy's Manual of Systematic Bacteriology New York: Springer US; 2005 pp. 1–574
    [Google Scholar]
  32. Rathsack K, Reitner J, Stackebrandt E, Tindall BJ. Reclassification of Aurantimonas altamirensis (Jurado et al. 2006), Aurantimonas ureilytica (Weon et al. 2007) and Aurantimonas frigidaquae (Kim et al. 2008) as members of a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov., Aureimonas ureilytica comb. nov. and Aureimonas frigidaquae comb. nov., and emended descriptions of the genera Aurantimonas and Fulvimarina . Int J Syst Evol Microbiol 2011; 61:2722–2728 [View Article][PubMed]
    [Google Scholar]
  33. Liu BB, Wang HF, Li QL, Zhou XK, Zhang YG et al. Aurantimonas endophytica sp. nov., a novel endophytic bacterium isolated from roots of Anabasis elatior (C. A. Mey.) Schischk. Int J Syst Evol Microbiol 2016; 66:4112–4117 [View Article][PubMed]
    [Google Scholar]
  34. Cho Y, Lee I, Yang YY, Baek K, Yoon SJ et al. Aureimonas glaciistagni sp. nov., isolated from a melt pond on Arctic sea ice. Int J Syst Evol Microbiol 2015; 65:3564–3569 [View Article][PubMed]
    [Google Scholar]
  35. Cho JC, Giovannoni SJ. Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order ‘Rhizobiales’. Int J Syst Evol Microbiol 2003; 53:1853–1859 [View Article][PubMed]
    [Google Scholar]
  36. Rivas R, Sánchez-Márquez S, Mateos PF, Martínez-Molina E, Velázquez E. Martelella mediterranea gen. nov., sp. nov., a novel α-proteobacterium isolated from a subterranean saline lake. Int J Syst Evol Microbiol 2005; 55:955–959 [View Article][PubMed]
    [Google Scholar]
  37. Chung EJ, Hwang JM, Kim KH, Jeon CO, Chung YR. Martelella suaedae sp. nov. and Martelella limonii sp. nov., isolated from the root of halophytes. Int J Syst Evol Microbiol 2016; 66:3917–3922 [View Article][PubMed]
    [Google Scholar]
  38. Liang J, Liu J, Zhang XH. Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:1127–1132 [View Article][PubMed]
    [Google Scholar]
  39. Xu L, Zhang Y, Deng ZS, Zhao L, Wei XL et al. Rhizobium qilianshanense sp. nov., a novel species isolated from root nodule of Oxytropis ochrocephala Bunge in China. Antonie van Leeuwenhoek 2013; 103:559–565 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002185
Loading
/content/journal/ijsem/10.1099/ijsem.0.002185
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month 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