1887

Abstract

A novel aerobic, chemo-organoheterotrophic bacterium, strain Ac_26_B10, was isolated from a semiarid savannah soil collected in northern Namibia (Mashare, Kavango region). Based on analysis of its nearly full-length 16S rRNA gene sequence, the isolate belongs to the genus (family , order , class ) and shares 98.3 and 96.9 % 16S rRNA gene sequence similarity with its closest relatives, DRP 35 and O3SUJ4. Cells were Gram-negative, coccoid to rod-shaped, non-motile and divided by binary fission. Strain Ac_26_B10 showed weak catalase activity and, in contrast to the other described species of the genus , was oxidase-positive. Compared with the already established species of the genus , the novel strain used a larger range of sugars and sugar alcohols for growth, lacked α-mannosidase activity and exhibited a higher temperature optimum of growth. DNA–DNA hybridization studies with its closest phylogenetic relative, DSM 28898, confirmed that strain Ac_26_B10 represents a distinct genomospecies. Its most abundant fatty acids were iso-C, summed feature 3 (Cω7 and/or Cω6) and C. Dominant polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The predominant menaquinone was MK-8; minor amounts of MK-7 and MK-8(H) were also recorded. The G+C content of the genomic DNA was 58.5 mol%. On the basis of our polyphasic analysis, Ac_26_B10 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Ac_26_B10 ( = DSM 26559 = LMG 27984).

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2015-10-01
2019-12-11
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References

  1. Baik K.S. , Choi J.S. , Kwon J. , Park S.C. , Hwang Y.M. , Kim M.S. , Kim E.M. , Seo D.C. , Cho J.S. , Seong C.N. . ( 2013;). Terriglobus aquaticus sp. nov., isolated from an artificial reservoir. Int J Syst Evol Microbiol 63: 4744–4749 [CrossRef] [PubMed].
    [Google Scholar]
  2. Barns S.M. , Takala S.L. , Kuske C.R. . ( 1999;). Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 65: 1731–1737 [PubMed].
    [Google Scholar]
  3. Barns S.M. , Cain E.C. , Sommerville L. , Kuske C.R. . ( 2007;). Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 73: 3113–3116 [CrossRef] [PubMed].
    [Google Scholar]
  4. Bligh E.G. , Dyer W.J. . ( 1959;). A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37: 911–917 [CrossRef] [PubMed].
    [Google Scholar]
  5. Cashion P. , Holder-Franklin M.A. , McCully J. , Franklin M. . ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81: 461–466 [CrossRef] [PubMed].
    [Google Scholar]
  6. Collins M.D. , Jones D. . ( 1981;). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45: 316–354 [PubMed].
    [Google Scholar]
  7. Cowan S.T. . ( 1974;). Cowan and Steel's Manual for the Identification of Medical Bacteria , 2nd edn. New York: Cambridge University Press;.
    [Google Scholar]
  8. Cruickshank R.H. , Wade G.C. . ( 1980;). Detection of pectic enzymes in pectin-acrylamide gels. Anal Biochem 107: 177–181 [CrossRef] [PubMed].
    [Google Scholar]
  9. Davis K.E. , Joseph S.J. , Janssen P.H. . ( 2005;). Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 71: 826–834 [CrossRef] [PubMed].
    [Google Scholar]
  10. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12: 133–142 [CrossRef] [PubMed].
    [Google Scholar]
  11. Dedysh S.N. , Kulichevskaya I.S. , Serkebaeva Y.M. , Mityaeva M.A. , Sorokin V.V. , Suzina N.E. , Rijpstra W.I.C. , Sinninghe Damsté J.S. . ( 2012;). Bryocella elongata gen. nov., sp. nov., a member of subdivision 1 of the Acidobacteria isolated from a methanotrophic enrichment culture, and emended description of Edaphobacter aggregans Koch et al. 2008. Int J Syst Evol Microbiol 62: 654–664 [CrossRef] [PubMed].
    [Google Scholar]
  12. Diaby N. , Dold B. , Pfeifer H.R. , Holliger C. , Johnson D.B. , Hallberg K.B. . ( 2007;). Microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste. Environ Microbiol 9: 298–307 [CrossRef] [PubMed].
    [Google Scholar]
  13. Eichorst S.A. , Breznak J.A. , Schmidt T.M. . ( 2007;). Isolation and characterization of soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria . Appl Environ Microbiol 73: 2708–2717 [CrossRef] [PubMed].
    [Google Scholar]
  14. Foesel B.U. , Rohde M. , Overmann J. . ( 2013;). Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil – the first described species of Acidobacteria subdivision 4. Syst Appl Microbiol 36: 82–89 [CrossRef] [PubMed].
    [Google Scholar]
  15. Foesel B.U. , Nägele V. , Naether A. , Wüst P.K. , Weinert J. , Bonkowski M. , Lohaus G. , Polle A. , Alt F. , other authors . ( 2014;). Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils. Environ Microbiol 16: 658–675 [CrossRef] [PubMed].
    [Google Scholar]
  16. Gainvors A. , Frézier V. , Lemaresquier H. , Lequart C. , Aigle M. , Belarbi A. . ( 1994;). Detection of polygalacturonase, pectin-lyase and pectin-esterase activities in a Saccharomyces cerevisiae strain. Yeast 10: 1311–1319 [CrossRef] [PubMed].
    [Google Scholar]
  17. Hobel C.F. , Marteinsson V.T. , Hreggvidsson G.O. , Kristjánsson J.K. . ( 2005;). Investigation of the microbial ecology of intertidal hot springs by using diversity analysis of 16S rRNA and chitinase genes. Appl Environ Microbiol 71: 2771–2776 [CrossRef] [PubMed].
    [Google Scholar]
  18. Huber K.J. , Wüst P.K. , Rohde M. , Overmann J. , Foesel B.U. . ( 2014;). Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. Int J Syst Evol Microbiol 64: 1866–1875 [CrossRef] [PubMed].
    [Google Scholar]
  19. Hugenholtz P. , Pitulle C. , Hershberger K.L. , Pace N.R. . ( 1998;). Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180: 366–376 [PubMed].
    [Google Scholar]
  20. Huss V.A.R. , Festl H. , Schleifer K.H. . ( 1983;). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4: 184–192 [CrossRef] [PubMed].
    [Google Scholar]
  21. Jones R.T. , Robeson M.S. , Lauber C.L. , Hamady M. , Knight R. , Fierer N. . ( 2009;). A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J 3: 442–453 [CrossRef] [PubMed].
    [Google Scholar]
  22. Joseph S.J. , Hugenholtz P. , Sangwan P. , Osborne C.A. , Janssen P.H. . ( 2003;). Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69: 7210–7215 [CrossRef] [PubMed].
    [Google Scholar]
  23. Kim O.S. , Cho Y.J. , Lee K. , Yoon S.H. , Kim M. , Na H. , Park S.C. , Jeon Y.S. , Lee J.H. , other authors . ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721 [CrossRef] [PubMed].
    [Google Scholar]
  24. Kim M. , Oh H.S. , Park S.C. , Chun J. . ( 2014;). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64: 346–351 [CrossRef] [PubMed].
    [Google Scholar]
  25. Kishimoto N. , Kosako Y. , Tano T. . ( 1991;). Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22: 1–7 [CrossRef].
    [Google Scholar]
  26. Koch I.H. , Gich F. , Dunfield P.F. , Overmann J. . ( 2008;). Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 58: 1114–1122 [CrossRef] [PubMed].
    [Google Scholar]
  27. Kulichevskaya I.S. , Kostina L.A. , Valásková V. , Rijpstra W.I.C. , Sinninghe Damsté J.S. , de Boer W. , Dedysh S.N. . ( 2012;). Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood. Int J Syst Evol Microbiol 62: 1512–1520 [CrossRef] [PubMed].
    [Google Scholar]
  28. Lane D.J. . ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E. , Goodfellow M. . New York: Wiley;.
    [Google Scholar]
  29. Lee S.H. , Ka J.O. , Cho J.C. . ( 2008;). Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol Lett 285: 263–269 [CrossRef] [PubMed].
    [Google Scholar]
  30. Männistö M.K. , Rawat S. , Starovoytov V. , Häggblom M.M. . ( 2011;). Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int J Syst Evol Microbiol 61: 1823–1828 [CrossRef] [PubMed].
    [Google Scholar]
  31. Meisinger D.B. , Zimmermann J. , Ludwig W. , Schleifer K.H. , Wanner G. , Schmid M. , Bennett P.C. , Engel A.S. , Lee N.M. . ( 2007;). In situ detection of novel Acidobacteria in microbial mats from a chemolithoautotrophically based cave ecosystem (Lower Kane Cave, WY, USA). Environ Microbiol 9: 1523–1534 [CrossRef] [PubMed].
    [Google Scholar]
  32. Mesbah M. , Premachandran U. , Whitman W.B. . ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Evol Microbiol 39: 159–167.
    [Google Scholar]
  33. Muñoz R. , Yarza P. , Ludwig W. , Euzéby J. , Amann R. , Schleifer K.H. , Glöckner F.O. , Rosselló-Móra R. . ( 2011;). Release LTPs104 of the All-Species Living Tree. Syst Appl Microbiol 34: 169–170 [CrossRef] [PubMed].
    [Google Scholar]
  34. Narihiro T. , Terada T. , Kikuchi K. , Iguchi A. , Ikeda M. , Yamauchi T. , Shiraishi K. , Kamagata Y. , Nakamura K. , Sekiguchi Y. . ( 2009;). Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes Environ 24: 88–96 [CrossRef] [PubMed].
    [Google Scholar]
  35. Okamura K. , Kawai A. , Yamada T. , Hiraishi A. . ( 2011;). Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria . FEMS Microbiol Lett 317: 138–142 [CrossRef] [PubMed].
    [Google Scholar]
  36. Pankratov T.A. , Dedysh S.N. . ( 2010;). Granulicella paludicola gen. nov., sp. nov., Granulicella pectinivorans sp. nov., Granulicella aggregans sp. nov. and Granulicella rosea sp. nov., acidophilic, polymer-degrading acidobacteria from Sphagnum peat bogs. Int J Syst Evol Microbiol 60: 2951–2959 [CrossRef] [PubMed].
    [Google Scholar]
  37. Pankratov T.A. , Kirsanova L.A. , Kaparullina E.N. , Kevbrin V.V. , Dedysh S.N. . ( 2012;). Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991. Int J Syst Evol Microbiol 62: 430–437 [CrossRef] [PubMed].
    [Google Scholar]
  38. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI, Inc;.
    [Google Scholar]
  39. Scheirlinck T. , De Meutter J. , Arnaut G. , Joos H. , Claeyssens M. , Michiels F. . ( 1990;). Cloning and expression of cellulase and xylanase genes in Lactobacillus plantarum . Appl Microbiol Biotechnol 33: 534–541 [CrossRef].
    [Google Scholar]
  40. Sinninghe Damsté J.S. , Rijpstra W.I.C. , Hopmans E.C. , Weijers J.W.H. , Foesel B.U. , Overmann J. , Dedysh S.N. . ( 2011;). 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid), a common membrane-spanning lipid of Acidobacteria subdivisions 1 and 3. Appl Environ Microbiol 77: 4147–4154 [CrossRef] [PubMed].
    [Google Scholar]
  41. Soden D.M. , O'Callaghan J. , Dobson A.D. . ( 2002;). Molecular cloning of a laccase isozyme gene from Pleurotus sajor-caju and expression in the heterologous Pichia pastoris host. Microbiology 148: 4003–4014 [PubMed].[CrossRef]
    [Google Scholar]
  42. Stackebrandt E. , Goebel B.M. . ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846–849 [CrossRef].
    [Google Scholar]
  43. Sundman V. , Nase L. . ( 1971;). A simple plate test for direct visualization for biological lignin degradation. Paper Timber 53: 67–71.
    [Google Scholar]
  44. Tamaoka J. , Komagata K. . ( 1984;). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25: 125–128 [CrossRef].
    [Google Scholar]
  45. Tan G.L. , Shu W.S. , Hallberg K.B. , Li F. , Lan C.Y. , Huang L.N. . ( 2007;). Cultivation-dependent and cultivation-independent characterization of the microbial community in acid mine drainage associated with acidic Pb/Zn mine tailings at Lechang, Guangdong, China. FEMS Microbiol Ecol 59: 118–126 [CrossRef] [PubMed].
    [Google Scholar]
  46. Teather R.M. , Wood P.J. . ( 1982;). Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43: 777–780 [PubMed].
    [Google Scholar]
  47. Tekere M. , Mswaka A.Y. , Zvauya R. , Read J.S. . ( 2001;). Growth, dye degradation and ligninolytic activity studies on Zimbabwean white rot fungi. Enzyme Microb Technol 28: 420–426 [CrossRef] [PubMed].
    [Google Scholar]
  48. Thiagarajan V. , Revathia R. , Aparanjinib K. , Sivamanic P. , Girilala M. , Priyad C. , Kalaichelvana P. . ( 2011;). Extracellular chitinase production by Streptomyces sp. PTK19 in submerged fermentation and its lytic activity on Fusarium oxysporum PTK2 cell wall. Int J Curr Sci 1: 30–44.
    [Google Scholar]
  49. Tindall B.J. . ( 1990;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66: 199–202 [CrossRef].
    [Google Scholar]
  50. Tindall B.J. , Sikorski J. , Smibert R.M. , Krieg N.R. . ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology , 3rd edn.., pp. 330–393. Edited by Reddy C. A. , Beveridge T. J. , Breznak J. A. , Marzluf G. , Schmidt T. M. , Snyder L. R. . Washington, DC: American Society for Microbiology; [CrossRef].
    [Google Scholar]
  51. Wayne L.G. , Brenner D.J. , Colwell R.R. , Grimont P.A.D. , Kandler O. , Krichevsky M.I. , Moore L.H. , Moore W.E.C. , Murray R.G.E. , other authors . ( 1987;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463–464 [CrossRef].
    [Google Scholar]
  52. Whang K.S. , Lee J.C. , Lee H.R. , Han S.I. , Chung S.H. . ( 2014;). Terriglobus tenax sp. nov., an exopolysaccharide-producing acidobacterium isolated from rhizosphere soil of a medicinal plant. Int J Syst Evol Microbiol 64: 431–437 [CrossRef] [PubMed].
    [Google Scholar]
  53. Wood T. , Bhat K. . ( 1988;). Methods for measuring cellulase activities. Methods Enzymol 160: 87–112 [CrossRef].
    [Google Scholar]
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