1887

Abstract

A non-motile, coccobacilli-shaped and yellow-coloured bacterium, designated strain SYSU D60003, was isolated from a desert soil sample. Cells were Gram-stain-positive, catalase-negative and oxidase-positive. The whole cell hydrolysates contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C16 : 0. The respiratory menaquinones were MK-9(H8), MK-9(H4) and MK-9(H6). The DNA G+C content was determined to be 70.2 % (genome). The polar lipids detected were diphosphatidylglycerol, an unidentified glycolipid and seven unidentified polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SYSU D60003 belonged to the order Acidimicrobiales (class Acidimicrobiia ), but formed a clade closely linked to members of the genus Ilumatobacter . Data from a polyphasic taxonomy study suggested that the isolate represents a novel species of a novel genus in the order Acidimicrobiales , for which the name Desertimonas flava gen. nov., sp. nov. is proposed. The type strain of the proposed new taxon is SYSU D60003 (=KCTC 39917=NBRC 112924). Additionally, the new taxon along with the genus Ilumatobater (family unassigned) were distinctly separated from the related families Acidimicrobiaceae , Iamiaceae and ‘Microtrichaceae’ in the phylogenetic trees, besides presenting a unique 16S rRNA gene signature nucleotides. Therefore, we propose a new family Ilumatobacteraceae fam. nov. within the order Acidimicrobiales to accommodate members of these two genera.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003038
2018-10-04
2020-01-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/11/3593.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003038&mimeType=html&fmt=ahah

References

  1. 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 [CrossRef][PubMed]
    [Google Scholar]
  2. 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;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  3. 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]
  4. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  5. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  6. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  7. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
    [Google Scholar]
  8. Harrison P. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000;10:3–42
    [Google Scholar]
  9. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  10. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982;44:992–993[PubMed]
    [Google Scholar]
  11. 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 [CrossRef][PubMed]
    [Google Scholar]
  12. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956;178:703–704 [CrossRef][PubMed]
    [Google Scholar]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef][PubMed]
    [Google Scholar]
  15. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society of Microbiology; 2007; pp.330–393
    [Google Scholar]
  16. Uchida K, Kudo T, Suzuki KI, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999;45:49–56 [CrossRef][PubMed]
    [Google Scholar]
  17. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231[PubMed]
    [Google Scholar]
  18. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef][PubMed]
    [Google Scholar]
  19. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983;54:31–36[PubMed]
    [Google Scholar]
  20. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48:459–470 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. Sasser M. 2001; Identification of bacteria by gas chromatography of cellular fatty acids [database on the Internet]. Available fromwww.microbialid.com/PDF/TechNote_101.pdf
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  24. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012;28:1033–1034 [CrossRef][PubMed]
    [Google Scholar]
  25. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  26. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000;17:540–552 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 [CrossRef][PubMed]
    [Google Scholar]
  28. Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat Commun 2018;9:2832 [CrossRef][PubMed]
    [Google Scholar]
  29. Matsumoto A, Kasai H, Matsuo Y, Omura S, Shizuri Y et al. Ilumatobacter fluminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary. J Gen Appl Microbiol 2009;55:201–205 [CrossRef][PubMed]
    [Google Scholar]
  30. Matsumoto A, Kasai H, Matsuo Y, Shizuri Y, Ichikawa N et al. Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 2013;63:3404–3408 [CrossRef][PubMed]
    [Google Scholar]
  31. Stackebrandt E. The Family Acidimicrobiaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Actinobacteria Berlin, Heidelberg: Springer; 2014; pp.5–12
    [Google Scholar]
  32. Yokota A. The Family Iamiaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Actinobacteria Berlin, Heidelberg: Springer; 2014; pp.391–395
    [Google Scholar]
  33. Clark DA, Norris PR. Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology 1996;142:785–790 [CrossRef]
    [Google Scholar]
  34. Itoh T, Yamanoi K, Kudo T, Ohkuma M, Takashina T. Aciditerrimonas ferrireducens gen. nov., sp. nov., an iron-reducing thermoacidophilic actinobacterium isolated from a solfataric field. Int J Syst Evol Microbiol 2011;61:1281–1285 [CrossRef][PubMed]
    [Google Scholar]
  35. Jones RM, Johnson DB. Acidithrix ferrooxidans gen. nov., sp. nov.; a filamentous and obligately heterotrophic, acidophilic member of the Actinobacteria that catalyzes dissimilatory oxido-reduction of iron. Res Microbiol 2015;166:111–120 [CrossRef][PubMed]
    [Google Scholar]
  36. Johnson DB, Bacelar-Nicolau P, Okibe N, Thomas A, Hallberg KB. Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria. Int J Syst Evol Microbiol 2009;59:1082–1089 [CrossRef][PubMed]
    [Google Scholar]
  37. Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota A. Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov. Int J Syst Evol Microbiol 2009;59:869–873 [CrossRef][PubMed]
    [Google Scholar]
  38. Jin L, Huy H, Kim KK, Lee HG, Kim HS et al. Aquihabitans daechungensis gen. nov., sp. nov., an actinobacterium isolated from reservoir water. Int J Syst Evol Microbiol 2013;63:2970–2974 [CrossRef][PubMed]
    [Google Scholar]
  39. Blackall LL, Stratton H, Bradford D, Dot TD, Sjörup C et al. "Candidatus Microthrix parvicella", a filamentous bacterium from activated sludge sewage treatment plants. Int J Syst Bacteriol 1996;46:344–346 [CrossRef][PubMed]
    [Google Scholar]
  40. Levantesi C, Rossetti S, Thelen K, Kragelund C, Krooneman J et al. Phylogeny, physiology and distribution of 'Candidatus Microthrix calida', a new Microthrix species isolated from industrial activated sludge wastewater treatment plants. Environ Microbiol 2006;8:1552–1563 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003038
Loading
/content/journal/ijsem/10.1099/ijsem.0.003038
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