1887

Abstract

A Gram-stain-negative, rod-shaped, motile, catalase and cytochrome c oxidase-positive bacterial strain, designated S20-91, was isolated from alpine forest soil. Growth occurred within a temperature range of 0–25 °C. Yeast extract was required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain S20-91 was related to the genus Herminiimonas and had the highest 16S rRNA gene sequence similarity to Herminiimonas arsenicoxydans ULPAs1 (96.5 %). The strain contained ubiquinone 8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The major cellular fatty acids (>10 %) were C16 : 1ω7c (55.3 %) and C16 : 0 (25.6 %). The genomic DNA G+C content was 47.6 mol%. Combined data of genomic, phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-91 represents a novel genus and species, for which the name Solimicrobium silvestre gen. nov., sp. nov. is proposed. The type strain is S20-91 (=DSM 104733=LMG 30010).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002861
2018-06-25
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/8/2491.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002861&mimeType=html&fmt=ahah

References

  1. Fernandes C, Rainey FA, Nobre MF, Pinhal I, Folhas F et al. Herminiimonas fonticola gen. nov., sp. nov., a betaproteobacterium isolated from a source of bottled mineral water. Syst Appl Microbiol 2005; 28:596–603 [View Article][PubMed]
    [Google Scholar]
  2. Kämpfer P, Busse HJ, Falsen E. Herminiimonas aquatilis sp. nov., a new species from drinking water. Syst Appl Microbiol 2006; 29:287–291 [View Article][PubMed]
    [Google Scholar]
  3. Muller D, Simeonova DD, Riegel P, Mangenot S, Koechler S et al. Herminiimonas arsenicoxydans sp. nov., a metalloresistant bacterium. Int J Syst Evol Microbiol 2006; 56:1765–1769 [View Article][PubMed]
    [Google Scholar]
  4. Kämpfer P, Glaeser SP, Lodders N, Busse HJ, Falsen E. Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals. Int J Syst Evol Microbiol 2013; 63:412–417 [View Article][PubMed]
    [Google Scholar]
  5. Loveland-Curtze J, Miteva VI, Brenchley JE. Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. Int J Syst Evol Microbiol 2009; 59:1272–1277 [View Article][PubMed]
    [Google Scholar]
  6. Lang E, Swiderski J, Stackebrandt E, Schumann P, Spröer C et al. Herminiimonas saxobsidens sp. nov., isolated from a lichen-colonized rock. Int J Syst Evol Microbiol 2007; 57:2618–2622 [View Article][PubMed]
    [Google Scholar]
  7. 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 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Nielsen P, Fritze D, Priest FG. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 1995; 141:1745–1761 [View Article]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Degryse E, Glansdorff N, Piérard A. A comparative analysis of extreme thermophilic bacteria belonging to the genus Thermus. Arch Microbiol 1978; 117:189–196 [View Article][PubMed]
    [Google Scholar]
  16. Zhang DC, Schinner F, Margesin R. Pedobacter bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2592–2595 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. 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]
  20. Muller D, Médigue C, Koechler S, Barbe V, Barakat M et al. A tale of two oxidation states: bacterial colonization of arsenic-rich environments. PLoS Genet 2007; 3:e53 [View Article][PubMed]
    [Google Scholar]
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][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 [View Article][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 [View Article][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 [View Article][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
    [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 [View Article][PubMed]
    [Google Scholar]
  27. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article][PubMed]
    [Google Scholar]
  28. Xie C, Mao X, Huang J, Ding Y, Wu J et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res 2011; 39:W316–W322 [View Article][PubMed]
    [Google Scholar]
  29. 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 [View Article][PubMed]
    [Google Scholar]
  30. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010; 26:2460–2461 [View Article][PubMed]
    [Google Scholar]
  31. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  32. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article][PubMed]
    [Google Scholar]
  33. 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]
  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM 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]
  35. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article][PubMed]
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002861
Loading
/content/journal/ijsem/10.1099/ijsem.0.002861
Loading

Data & Media loading...

Supplements

Supplementary File 2

PDF
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