1887
  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 67, Issue 11
  5. Article

f Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample

HTML
70.20 Kb
PDF
314.80 Kb
  • Authors: Zi-Wen Yang1​,† ,  Nimaichand Salam1​,† ,  Zheng-Shuang Hua1​,† ,  Bing-Bing Liu1​ ,  Ming-Xian Han1​ ,  Bao-Zhu Fang1​ ,  Dong Wang1​ ,  Min Xiao1​ ,  Wael N. Hozzein2​,3​ , Wen-Jun Li1​,4​
    • VIEW AFFILIATIONS
    • 1​ 1​State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China 2​ 2​Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia 3​ 3​Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt 4​ 4​Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China
  • *Correspondence: Wael N. Hozzein [email protected], Wen-Jun Li [email protected]
  • First Published Online: 06 October 2017, International Journal of Systematic and Evolutionary Microbiology 67: 4862-4867, doi: 10.1099/ijsem.0.002397
  • Subject: New taxa - Proteobacteria
  • Received:
  • Accepted:
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample, Page 1 of 1

| /docserver/preview/fulltext/ijsem/67/11/4862_ijsem002397-1.gif

  • Strain SYSU D8009 was isolated from a desert sample collected from Saudi Arabia. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, non-motile, aerobic and non-spore-forming. It was able to grow at 4–45 °C and pH 4.0–8.0, and exhibited NaCl tolerance of up to 1.5 % (w/v). Strain SYSU D8009 shared the closest 16S rRNA gene sequence similarities with members of the family Acetobacteraceae , with a value of less than 96.0 %. In the phylogenetic dendrograms, the strain clustered with the genera Paracraurococcus , Craurococcus and Crenalkalicoccus within the family Acetobacteraceae but with a distinct lineage, thereby demonstrating that the strain should be classified within the family Acetobacteraceae . The respiratory ubiquinone was found to be Q-10. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminolipids. The predominant cellular fatty acids were summed feature 8 (C1 8 : 1ω7c and/or C1 8 : 1ω6c) and C16 : 0. The genomic DNA G+C content of strain SYSU D8009 was determined to be 71.6 mol%. Based on the results of the phylogenetic analyses and differences in the physiological and biochemical characteristics, strain SYSU D8009 merits representation of a novel species of a new genus within the family Acetobacteraceae , for which the name Siccirubricoccus deserti gen. nov., sp. nov. is proposed. The type strain of Siccirubricoccus deserti sp. nov. is SYSU D8009 (=CGMCC 1.15936=KCTC 62088).

  • †

    These authors contributed equally to this work.

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain SYSU D8009 is KY882041.

  • Five supplementary figures and one supplementary table are available with the online Supplementary Material.

© 2017 IUMS | Published by the Microbiology Society

  • 1. Gillis M, de Ley J. Intra- and intergeneric similarities of the ribosomal ribonucleic acid cistrons of Acetobacter and Gluconobacter. Int J Syst Bacteriol 1980; 30: 7– 27 [CrossRef]
    [Google Scholar]
  • 2. Margesin R, Zhang DC. Humitalea rosea gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium of the family Acetobacteraceae isolated from soil. Int J Syst Evol Microbiol 2013; 63: 1411– 1416 [CrossRef] [PubMed]
    [Google Scholar]
  • 3. Saitoh S, Suzuki T, Nishimura Y. Proposal of Craurococcus roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil. Int J Syst Bacteriol 1998; 48: 1043– 1047 [CrossRef] [PubMed]
    [Google Scholar]
  • 4. Ramírez-Bahena MH, Tejedor C, Martín I, Velázquez E, Peix A. Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil. Int J Syst Evol Microbiol 2013; 63: 1760– 1765 [CrossRef] [PubMed]
    [Google Scholar]
  • 5. Eder W, Peplies J, Wanner G, Frühling A, Verbarg S. Hydrobacter penzbergensis gen. nov., sp. nov., isolated from purified water. Int J Syst Evol Microbiol 2015; 65: 920– 926 [CrossRef] [PubMed]
    [Google Scholar]
  • 6. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994; 44: 427– 434 [CrossRef] [PubMed]
    [Google Scholar]
  • 7. Boldareva EN, Turova TP, Kolganova TV, Moskalenko AA, Makhneva ZK et al. Roseococcus suduntuyensis sp. nov., a new aerobic bacteriochlorophyll a-containing bacterium isolated from a low-mineralized soda lake of Eastern Siberia. Microbiology 2009; 78: 92– 101 [CrossRef] [PubMed]
    [Google Scholar]
  • 8. Alarico S, Rainey FA, Empadinhas N, Schumann P, Nobre MF et al. Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the α-1 subclass of the Proteobacteria. Syst Appl Microbiol 2002; 25: 198– 206 [CrossRef] [PubMed]
    [Google Scholar]
  • 9. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria. Int J Syst Evol Microbiol 2008; 58: 773– 778 [CrossRef] [PubMed]
    [Google Scholar]
  • 10. Dong L, Ming H, Yin YR, Duan YY, Zhou EM et al. Roseomonas alkaliterrae sp. nov., isolated from an alkali geothermal soil sample in Tengchong, Yunnan, South-West China. Antonie van Leeuwenhoek 2014; 105: 899– 905 [CrossRef] [PubMed]
    [Google Scholar]
  • 11. Ming H, Duan YY, Yin YR, Meng XL, Li S et al. Crenalkalicoccus roseus gen. nov., sp. nov., a thermophilic bacterium isolated from alkaline hot springs. Int J Syst Evol Microbiol 2016; 66: 2319– 2326 [CrossRef] [PubMed]
    [Google Scholar]
  • 12. Han XY, Pham AS, Tarrand JJ, Rolston KV, Helsel LO et al. Bacteriologic characterization of 36 strains of Roseomonas species and proposal of Roseomonas mucosa sp. nov. and Roseomonas gilardii subsp. rosea subsp. nov. Am J Clin Pathol 2003; 120: 256– 264 [CrossRef] [PubMed]
    [Google Scholar]
  • 13. Cavalcante VA, Dobereiner J. A new acid-tolerant nitrogen-fixing bacterium associated with sugarcane. Plant Soil 1988; 108: 23– 31 [CrossRef]
    [Google Scholar]
  • 14. Kim WH, Kim DH, Kang K, Ahn TY. Dankookia rubra gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream. J Microbiol 2016; 54: 420– 425 [CrossRef] [PubMed]
    [Google Scholar]
  • 15. Takemura H, Kondo K, Horinouchi S, Beppu T. Induction by ethanol of alcohol dehydrogenase activity in Acetobacter pasteurianus. J Bacteriol 1993; 175: 6857– 6866 [CrossRef] [PubMed]
    [Google Scholar]
  • 16. Reddy GS, Nagy M, Garcia-Pichel F. Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. Int J Syst Evol Microbiol 2006; 56: 51– 58 [CrossRef] [PubMed]
    [Google Scholar]
  • 17. 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]
  • 18. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44: 992– 993 [PubMed]
    [Google Scholar]
  • 19. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960; [Crossref]
    [Google Scholar]
  • 20. 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]
  • 21. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178: 703– 704 [CrossRef] [PubMed]
    [Google Scholar]
  • 22. 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]
  • 23. McFaddin JF. Biochemical Tests for Identification of Medical Bacteria USA: Williams & Wilkins Co; 1976
    [Google Scholar]
  • 24. Smibert R, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  • 25. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994; 44: 427– 434 [CrossRef] [PubMed]
    [Google Scholar]
  • 26. 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]
  • 27. 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] [Crossref]
    [Google Scholar]
  • 28. 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]
  • 29. 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]
  • 30. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20: 16
    [Google Scholar]
  • 31. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39: 159– 167 [CrossRef]
    [Google Scholar]
  • 32. Liu YH, Guo JW, Salam N, Li L, Zhang YG et al. Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny, distribution and screening for industrially important traits. 3 Biotech 2016; 6: 209 [CrossRef] [PubMed]
    [Google Scholar]
  • 33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403– 410 [CrossRef] [PubMed]
    [Google Scholar]
  • 34. 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– 1618 [CrossRef] [PubMed]
    [Google Scholar]
  • 35. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876– 4882 [CrossRef] [PubMed]
    [Google Scholar]
  • 36. 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]
  • 37. 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]
  • 38. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  • 39. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  • 40. 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]
  • 41. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1984
    [Google Scholar]
  • 42. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  • 43. Rihs JD, Brenner DJ, Weaver RE, Steigerwalt AG, Hollis DG et al. Roseomonas, a new genus associated with bacteremia and other human infections. J Clin Microbiol 1993; 31: 3275– 3283 [PubMed]
    [Google Scholar]
http://sgm.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002397
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002397
2017-10-06
2019-03-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/11/4862.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002397&mimeType=html&fmt=ahah

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error