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Abstract

A phylogenetically novel proteobacterium, strain Shr3, was isolated from sand gravels collected from the eastern margin of the Sahara Desert. The isolation strategy targeted bacteria filterable through 0.2-µm-pore-size filters. Strain Shr3 was determined to be a Gram-negative, aerobic, non-motile, filamentous bacterium. Oxidase and catalase reactions were positive. Strain Shr3 showed growth on R2A medium, but poor or no growth on nutrient agar, trypticase soy agar and standard method agar. The major isoprenoid quinone was menaquinone-7. The dominant cellular fatty acids detected were Cω5 and C, and the primary hydroxy acid present was C 3-OH. The DNA G+C content was 54.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Shr3 was affiliated with an uncultivated lineage of the phylum ; the nearest known type strain, with 83 % sequence similarity, was DSM 12838 in the class . The isolate and closely related environmental clones formed a novel class-level clade in the phylum with high bootstrap support (96–99 %). Based on these results, the novel class classis nov. in the phylum and the novel genus and species gen. nov., sp. nov. are proposed for strain Shr3, the first cultivated representative of the . The type strain of is Shr3 ( = JCM 16864 = NCIMB 14846). We also propose the subordinate taxa ord. nov. and fam. nov. in the class .

Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award 23570117)
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2014-10-01
2022-01-29
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [View Article] [PubMed]
    [Google Scholar]
  2. Amann R. I., Ludwig W., Schleifer K. H. ( 1995 ). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. . Microbiol Rev 59, 143169.[PubMed]
    [Google Scholar]
  3. Barrow G. I., Feltham R. K. A. (editors) ( 1993 ). Cowan and Steel’s Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge:: Cambridge University Press;. [View Article]
    [Google Scholar]
  4. Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (editors) ( 2005a ). Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2B. New York:: Springer;.
    [Google Scholar]
  5. Brenner D. J., Krieg N. R., Staley J. T., Garrity G. M. (editors) ( 2005b ). Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2C. New York:: Springer;.
    [Google Scholar]
  6. Collins M. D., Jones D. ( 1981 ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45, 316354.[PubMed]
    [Google Scholar]
  7. Elsaied H. E., Sato M., Naganuma T. ( 2001 ). Viable Cytophaga-like bacterium in the 0.2 µm-filtrate seawater. . Syst Appl Microbiol 24, 618622. [View Article] [PubMed]
    [Google Scholar]
  8. Emerson D., Rentz J. A., Lilburn T. G., Davis R. E., Aldrich H., Chan C., Moyer C. L. ( 2007 ). A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. . PLoS ONE 2, e667. [View Article] [PubMed]
    [Google Scholar]
  9. Hahn M. W. ( 2004 ). Broad diversity of viable bacteria in ‘sterile’ (0.2 µm) filtered water. . Res Microbiol 155, 688691. [View Article] [PubMed]
    [Google Scholar]
  10. Hahn M. W., Stadler P., Wu Q. L., Pöckl M. ( 2004 ). The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria. . J Microbiol Methods 57, 379390. [View Article] [PubMed]
    [Google Scholar]
  11. Hanaichi T., Sato T., Iwamoto T., Malavasi-Yamashiro J., Hoshino M., Mizuno N. ( 1986 ). A stable lead by modification of Sato’s method. . J Electron Microsc (Tokyo) 35, 304306.[PubMed]
    [Google Scholar]
  12. Ishii S., Yamamoto M., Kikuchi M., Oshima K., Hattori M., Otsuka S., Senoo K. ( 2009 ). Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. . Appl Environ Microbiol 75, 70707078. [View Article] [PubMed]
    [Google Scholar]
  13. Katayama-Fujimura Y., Komatsu Y., Kuraishi H., Kaneko T. ( 1984 ). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. . Agric Biol Chem 48, 31693172. [View Article]
    [Google Scholar]
  14. Kearns D. B., Venot A., Bonner P. J., Stevens B., Boons G.-J., Shimkets L. J. ( 2001 ). Identification of a developmental chemoattractant in Myxococcus xanthus through metabolic engineering. . Proc Natl Acad Sci U S A 98, 1399013994. [View Article] [PubMed]
    [Google Scholar]
  15. Mara D. D., Williams D. J. A. ( 1970 ). The evaluation of media used to enumerate sulphate reducing bacteria. . J Appl Bacteriol 33, 543552. [View Article] [PubMed]
    [Google Scholar]
  16. Miyoshi T., Iwatsuki T., Naganuma T. ( 2005 ). Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters. . Appl Environ Microbiol 71, 10841088. [View Article] [PubMed]
    [Google Scholar]
  17. Naganuma T., Miyoshi T., Kimura H. ( 2007 ). Phylotype diversity of deep-sea hydrothermal vent prokaryotes trapped by 0.2- and 0.1-µm-pore-size filters. . Extremophiles 11, 637646. [View Article] [PubMed]
    [Google Scholar]
  18. Nakai R., Abe T., Takeyama H., Naganuma T. ( 2011 ). Metagenomic analysis of 0.2-µm-passable microorganisms in deep-sea hydrothermal fluid. . Mar Biotechnol (NY) 13, 900908. [View Article] [PubMed]
    [Google Scholar]
  19. Nakai R., Shibuya E., Justel A., Rico E., Quesada A., Kobayashi F., Iwasaka Y., Shi G.-Y., Amano Y. & other authors ( 2013 ). Phylogeographic analysis of filterable bacteria with special reference to Rhizobiales strains that occur at cryospheric habitats. . Antarct Sci 25, 219228. [View Article]
    [Google Scholar]
  20. Nishijima M., Araki-Sakai M., Sano H. ( 1997 ). Identification of isoprenoid quinones by frit-FAB liquid chromatography-mass spectrometry for the chemotaxonomy of microorganisms. . J Microbiol Methods 28, 113122. [View Article]
    [Google Scholar]
  21. Nishijima M., Takadera T., Imamura N., Kasai H., An K. D., Adachi K., Nagao T., Sano H., Yamasato K. ( 2009 ). Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod–coccus cell cycle in association with the growth phase. . Int J Syst Evol Microbiol 59, 16961707. [View Article] [PubMed]
    [Google Scholar]
  22. Palleroni N. J., Doudoroff M. ( 1972 ). Some properties and taxonomic sub-divisions of the genus Pseudomonas . . Annu Rev Phytopathol 10, 73100. [View Article]
    [Google Scholar]
  23. Rappé M. S., Giovannoni S. J. ( 2003 ). The uncultured microbial majority. . Annu Rev Microbiol 57, 369394. [View Article] [PubMed]
    [Google Scholar]
  24. Reasoner D. J., Geldreich E. E. ( 1985 ). A new medium for the enumeration and subculture of bacteria from potable water. . Appl Environ Microbiol 49, 17.[PubMed]
    [Google Scholar]
  25. Rodrigues J. L. M., Duffy M. A., Tessier A. J., Ebert D., Mouton L., Schmidt T. M. ( 2008 ). Phylogenetic characterization and prevalence of “Spirobacillus cienkowskii,” a red-pigmented, spiral-shaped bacterial pathogen of freshwater Daphnia species. . Appl Environ Microbiol 74, 15751582. [View Article] [PubMed]
    [Google Scholar]
  26. Shimkets L. J., Dworkin M., Reichenbach H. ( 2006 ). The myxobacteria. . In The Prokaryotes, , 3rd edn., vol. 7, pp. 31115. Edited by Dworkin M., Falkow S., Rosenberg E., Schleifer K.-H., Stackebrandt E. . New York:: Springer;. [View Article]
    [Google Scholar]
  27. Tazato N., Nishijima M., Handa Y., Kigawa R., Sano C., Sugiyama J. ( 2012 ). Gluconacetobacter tumulicola sp. nov. and Gluconacetobacter asukensis sp. nov., isolated from the stone chamber interior of the Kitora Tumulus. . Int J Syst Evol Microbiol 62, 20322038. [View Article] [PubMed]
    [Google Scholar]
  28. Veron M. ( 1975 ). Nutrition et taxonomie des entérobactéries. I. Méthodes d’études des auxanogrammes. . Ann Microbiol 126A, 267274 (in French).
    [Google Scholar]
  29. Williams K. P., Kelly D. P. ( 2013 ). Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria . . Int J Syst Evol Microbiol 63, 29012906. [View Article] [PubMed]
    [Google Scholar]
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