1887

Abstract

A heterotrophic and acidophilic bacterial strain, G45-3, was isolated from acidic mine drainage sampled in Fujian Province, PR China. Cells of strain G45-3 were Gram-stain-negative, non-spore-forming, non-motile and rod-shaped. Catalase and oxidase activities were positive. Strain G45-3 grew aerobically at 20–45 °C (optimum, 37 °C) and at pH 2.5–5.0 (optimum, pH 4.0). Photosynthetic pigments were not produced. Analysis of 16S rRNA gene sequences showed that strain G45-3 was phylogenetically related to different members of the family , and the sequence identities to JCM 10600, G2-11 and ATCC 35887 were 95.9 , 95.3 and 95.3 %, respectively. Strain G45-3 contained ubiquinone-10 as its respiratory quinone. The major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminophospholipid and an unidentified aminolipid. The predominant fatty acids were cyclo-Cω8, Cω7, C and C. The genome of G45-3 consists of one chromosome (3 907 406 bp) and three plasmids (68 344, 45 771 and 16 090 bp), with an average G+C content of 65.9 mol%. Based on the results of phenotypic and genomic analyses, it is concluded that strain G45-3 represents a novel species of a new genus, for which the name gen. nov., sp. nov. is proposed. is nominated as type species and its type strain is G45-3 (=CGMCC 1.16069=KCTC 62275).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003618
2019-10-01
2024-10-11
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3248.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003618&mimeType=html&fmt=ahah

References

  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 [View Article]
    [Google Scholar]
  2. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  3. Komagata K, Iino T, Yamada Y. The Family Acetobacteraceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes: Alphaproteobacteria and Betaproteobacteria Berlin, Heidelberg: Springer Berlin Heidelberg; 2014 pp. 3–78
    [Google Scholar]
  4. Sengun IY, Karabiyikli S. Importance of acetic acid bacteria in food industry. Food Control 2011; 22:647–656 [View Article]
    [Google Scholar]
  5. Yamada Y, Yukphan P. Genera and species in acetic acid bacteria. Int J Food Microbiol 2008; 125:15–24 [View Article][PubMed]
    [Google Scholar]
  6. Saichana N, Matsushita K, Adachi O, Frébort I, Frebortova J. Acetic acid bacteria: A group of bacteria with versatile biotechnological applications. Biotechnol Adv 2015; 33:1260–1271 [View Article][PubMed]
    [Google Scholar]
  7. Harrison AP. Acidiphilium cryptum gen. nov., sp. nov., heterotrophic bacterium from acidic mineral environments. Int J Syst Bacteriol 1981; 31:327–332 [View Article]
    [Google Scholar]
  8. Kishimoto N, Kosako Y, Wakao N, Tano T, Hiraishi A. Transfer of Acidiphilium facilis and Acidiphilium aminolytica to the Genus Acidocella gen. nov., and emendation of the Genus Acidiphilium . Syst Appl Microbiol 1995; 18:85–91 [View Article]
    [Google Scholar]
  9. Johnson DB, Okibe N, Roberto FF. Novel thermo-acidophilic bacteria isolated from geothermal sites in Yellowstone National Park: physiological and phylogenetic characteristics. Arch Microbiol 2003; 180:60–68 [View Article][PubMed]
    [Google Scholar]
  10. Johnson DB, Stallwood B, Kimura S, Hallberg KB. Isolation and characterization of Acidicaldus organivorus, gen. nov., sp. nov.: a novel sulfur-oxidizing, ferric iron-reducing thermo-acidophilic heterotrophic Proteobacterium . Arch Microbiol 2006; 185:212–221 [View Article][PubMed]
    [Google Scholar]
  11. Hiraishi A, Matsuzawa Y, Kanbe T, Wakao N. Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments. Int J Syst Evol Microbiol 2000; 50 Pt 4:1539–1546 [View Article][PubMed]
    [Google Scholar]
  12. Belova SE, Pankratov TA, Detkova EN, Kaparullina EN, Dedysh SN. Acidisoma tundrae gen. nov., sp. nov. and Acidisoma sibiricum sp. nov., two acidophilic, psychrotolerant members of the Alphaproteobacteria from acidic northern wetlands. Int J Syst Evol Microbiol 2009; 59:2283–2290 [View Article][PubMed]
    [Google Scholar]
  13. Brock TD, Brock KM, Belly RT, Weiss RL. Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Archiv für Mikrobiologie 1972; 84:54–68 [View Article]
    [Google Scholar]
  14. Zhang D, Yang H, Zhang W, Huang Z, Liu SJ. Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant. Int J Syst Evol Microbiol 2003; 53:1111–1114 [View Article][PubMed]
    [Google Scholar]
  15. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  16. Li R, Yu C, Li Y, Lam TW, Yiu SM et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009; 25:1966–1967 [View Article][PubMed]
    [Google Scholar]
  17. Li R, Li Y, Fang X, Yang H, Wang J et al. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009; 19:1124–1132 [View Article][PubMed]
    [Google Scholar]
  18. Breznak JA, Costilow RN. Physicochemical factors in growth. Methods for General and Molecular Microbiolsogy, 3rd ed. American Society of Microbiology; 2007 pp. 309–329
    [Google Scholar]
  19. Dong X, Cai M. Determinative Manual for Routine Bacteriology Beijing Scientific Press; 2001
    [Google Scholar]
  20. Lanyi B. 1 Classical and rapid identification methods for medically important bacteria. Methods in microbiology 1988; 19:1–67
    [Google Scholar]
  21. Okamura K, Hisada T, Kanbe T, Hiraishi A. Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil. J Gen Appl Microbiol 2009; 55:43–50 [View Article][PubMed]
    [Google Scholar]
  22. Imhoff JF, Truper HG, Pfennig N. Rearrangement of the species and genera of the phototrophic "purple nonsulfur bacteria". Int J Syst Bacteriol 1984; 34:340–343 [View Article]
    [Google Scholar]
  23. Clayton RK. Toward the isolation of a photochemical reaction center in rhodopseudomonas spheroides. Biochim Biophys Acta 1963; 75:312–323 [View Article][PubMed]
    [Google Scholar]
  24. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids; 1990
  25. Jiang CY, Liu Y, Liu YY, You XY, Guo X et al. Alicyclobacillus ferrooxydans sp. nov., a ferrous-oxidizing bacterium from solfataric soil. Int J Syst Evol Microbiol 2008; 58:2898–2903 [View Article][PubMed]
    [Google Scholar]
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  27. 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: [View Article][PubMed]
    [Google Scholar]
  28. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  29. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  32. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.5 c. Distributed by the author, Department of Genetics, University of Washington, Seattle, 1993. Prog Nucleic Acid Res Mol Biol 1993; 33:19–56
    [Google Scholar]
  33. 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]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  35. Qi J, Wang B, Hao BI. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 2004; 58:1–11 [View Article][PubMed]
    [Google Scholar]
  36. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genom Proteom Bioinf 2015; 13:321–331 [View Article][PubMed]
    [Google Scholar]
  37. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  38. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  39. 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]
  40. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998; 26:544–548 [View Article][PubMed]
    [Google Scholar]
  41. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641 [View Article][PubMed]
    [Google Scholar]
  42. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article][PubMed]
    [Google Scholar]
  43. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962; 5:109–118 [View Article][PubMed]
    [Google Scholar]
  44. 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 [View Article][PubMed]
    [Google Scholar]
  45. Greenberg DE, Porcella SF, Stock F, Wong A, Conville PS et al. Granulibacter bethesdensis gen. nov., sp. nov., a distinctive pathogenic acetic acid bacterium in the family Acetobacteraceae . Int J Syst Evol Microbiol 2006; 56:2609–2616 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.003618
Loading
/content/journal/ijsem/10.1099/ijsem.0.003618
Loading

Data & Media loading...

Supplements

Supplementary File 1

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