1887

Abstract

A Gram-stain-negative, rod-shaped, motile, catalase-positive and cytochrome oxidase-positive bacterial strain, designated AM20-91, was isolated from alpine forest soil. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain AM20-91 was related to the genus and had highest 16S rRNA gene sequence similarities to the type strains of THG-PC7 (97.8 %), UM1 (97.7 %) and XM415 (97.0 %). The strain contained ubiquinone 8 as the predominant respiratory quinone; its polar lipid profile contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids. The major cellular fatty acids (>10 %) were iso-C, iso-C 3-OH and iso-C. The DNA G+C content was 63.35 % (draft genome sequence). The combined results of phylogenetic, phenotypic, DNA–DNA relatedness and chemotaxonomic analyses demonstrated that strain AM20-91 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is AM20-91 (=DSM 104734=LMG 30011). In this study, it is also proposed that be reclassified as member of the genus

Keyword(s): alpine , forest , Luteimonas and Lysobacter
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002710
2018-05-01
2020-01-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/5/1571.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002710&mimeType=html&fmt=ahah

References

  1. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978;28:367–393 [CrossRef]
    [Google Scholar]
  2. França L, Sannino C, Turchetti B, Buzzini P, Margesin R. Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils. Extremophiles 2016;20:855–873 [CrossRef][PubMed]
    [Google Scholar]
  3. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49:1–7[PubMed]
    [Google Scholar]
  4. Wang Y, Dai J, Zhang L, Luo X, Li Y et al. Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009;59:786–789 [CrossRef][PubMed]
    [Google Scholar]
  5. Singh H, du J, Won KH, Yang JE, Akter S et al. Lysobacter novalis sp. nov., isolated from fallow farmland soil. Int J Syst Evol Microbiol 2015;65:3131–3136 [CrossRef][PubMed]
    [Google Scholar]
  6. Rani P, Mukherjee U, Verma H, Kamra K, Lal R. Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016;66:1851–1856 [CrossRef][PubMed]
    [Google Scholar]
  7. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995;141:1745–1761 [CrossRef]
    [Google Scholar]
  8. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 1996;46:1088–1092 [CrossRef][PubMed]
    [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 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 [CrossRef][PubMed]
    [Google Scholar]
  13. Margesin R, Gander S, Zacke G, Gounot AM, Schinner F. Hydrocarbon degradation and enzyme activities of cold-adapted bacteria and yeasts. Extremophiles 2003;7:451–458 [CrossRef][PubMed]
    [Google Scholar]
  14. Zhang DC, Schinner F, Margesin R. Pedobacter bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010;60:2592–2595 [CrossRef][PubMed]
    [Google Scholar]
  15. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of fatty acids in bacteria. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes)vol. 38 London: Elsevier Ltd; 2011; pp.183–196
    [Google Scholar]
  16. da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes)vol. 38 London: Elsevier Ltd; 2011; pp.197–206
    [Google Scholar]
  17. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes)vol. 38 London: Elsevier Ltd; 2011; pp.165–181
    [Google Scholar]
  18. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  19. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983;4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  20. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef][PubMed]
    [Google Scholar]
  22. 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 [CrossRef][PubMed]
    [Google Scholar]
  23. Egas C, Barroso C, Froufe HJ, Pacheco J, Albuquerque L et al. Complete genome sequence of the radiation-resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014;9:1062–1075 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Lagesen K, Hallin PF, Rødland E, Staerfeldt HH, Rognes T et al. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res 2007;35:3100–3108[Crossref]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  27. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013;4:2304 [CrossRef][PubMed]
    [Google Scholar]
  28. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26:2460–2461 [CrossRef][PubMed]
    [Google Scholar]
  29. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  30. Price MN, Dehal PS, Arkin AP. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One 2010;5:e9490 [CrossRef][PubMed]
    [Google Scholar]
  31. Field D, Garrity G, Gray T, Morrison N, Selengut J et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008;26:541–547 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002710
Loading
/content/journal/ijsem/10.1099/ijsem.0.002710
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited articles

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