1887

Abstract

constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H and Ac_23_E3 were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H and Ac_23_E3 were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar -acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H and Ac_23_E3 were iso-C, summed feature 1 (C 3-OH/iso-C H), summed feature 3 (Cω7/Cω6) and anteiso-C. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H and Ac_23_E3 were 53.2 and 52.6 mol%, respectively. The closest described relative was A2-16, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4H and Ac_23_E3 displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus gen. nov. is proposed, with two novel species, the type species sp. nov. (type strain A22_HD_4H = DSM 26555 = LMG 27985) and a second species, sp. nov. (type strain Ac_23_E3 = DSM 26558 = LMG 27597).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.060236-0
2014-06-01
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/6/1866.html?itemId=/content/journal/ijsem/10.1099/ijs.0.060236-0&mimeType=html&fmt=ahah

References

  1. Angle J. S. , McGrath S. P. , Chaney R. L. . ( 1991; ). New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution. . Appl Environ Microbiol 57:, 3674–3676.[PubMed]
    [Google Scholar]
  2. 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]
  3. Balch W. E. , Fox G. E. , Magrum L. J. , Woese C. R. , Wolfe R. S. . ( 1979; ). Methanogens: reevaluation of a unique biological group. . Microbiol Rev 43:, 260–296.[PubMed]
    [Google Scholar]
  4. Barns S. M. 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]
  5. Barrow G. I. , Feltham R. K. A. . ( 1993; ). Cowan and Steel’s Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge & New York:: Cambridge University Press;.[CrossRef]
    [Google Scholar]
  6. Bast E. . ( 2011; ). Mikrobiologische Methoden. Eine Einführung in grundlegende Arbeitstechniken, , 3rd edn.. Heidelberg:: Spektrum (in German);.
    [Google Scholar]
  7. 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]
  8. Bryant D. A. , Costas A. M. , Maresca J. A. , Chew A. G. , Klatt C. G. , Bateson M. M. , Tallon L. J. , Hostetler J. , Nelson W. C. . & other authors ( 2007; ). Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium . . Science 317:, 523–526. [CrossRef] [PubMed]
    [Google Scholar]
  9. 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]
  10. Coates J. D. , Ellis D. J. , Gaw C. V. , Lovley D. R. . ( 1999; ). Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. . Int J Syst Bacteriol 49:, 1615–1622. [CrossRef] [PubMed]
    [Google Scholar]
  11. 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]
  12. Crowe M. A. , Power J. F. , Morgan X. C. , Dunfield P. F. , Lagutin K. , Rijpstra W. I. C. , Rijpstra I. C. , Sinninghe Damste J. S. , Houghton K. M. . & other authors ( 2014; ). Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils. . Int J Syst Evol Microbiol 64:, 220–227. [CrossRef] [PubMed]
    [Google Scholar]
  13. De Ley J. D. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142. [CrossRef] [PubMed]
    [Google Scholar]
  14. 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. . ( 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]
  15. 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]
  16. Foesel B. U. , Rohde M. , Overmann J. . ( 2013; ). Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savannah soil – the first described species of Acidobacteria subdivision 4. . Syst Appl Microbiol 36:, 82–89. [CrossRef] [PubMed]
    [Google Scholar]
  17. 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]
  18. Fukunaga Y. , Kurahashi M. , Yanagi K. , Yokota A. , Harayama S. . ( 2008; ). Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum ‘Acidobacteria’. . Int J Syst Evol Microbiol 58:, 2597–2601. [CrossRef] [PubMed]
    [Google Scholar]
  19. George I. F. , Hartmann M. , Liles M. R. , Agathos S. N. . ( 2011; ). Recovery of as-yet-uncultured soil acidobacteria on dilute solid media. . Appl Environ Microbiol 77:, 8184–8188. [CrossRef] [PubMed]
    [Google Scholar]
  20. Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . (editors) ( 1994; ). Methods for General and Molecular Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  21. Hobel C. F. V. , Marteinsson V. T. , Hreggvidsson G. Ó. , 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]
  22. Hugenholtz P. , Goebel B. M. , Pace N. R. . ( 1998; ). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. . J Bacteriol 180:, 4765–4774.[PubMed]
    [Google Scholar]
  23. Huss V. A. , 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]
  24. Izumi H. , Nunoura T. , Miyazaki M. , Mino S. , Toki T. , Takai K. , Sako Y. , Sawabe T. , Nakagawa S. . ( 2012; ). Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent chimney in the Southern Okinawa Trough. . Extremophiles 16:, 245–253. [CrossRef] [PubMed]
    [Google Scholar]
  25. Janssen P. H. . ( 2006; ). Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. . Appl Environ Microbiol 72:, 1719–1728. [CrossRef] [PubMed]
    [Google Scholar]
  26. Janssen P. H. , Yates P. S. , Grinton B. E. , Taylor P. M. , Sait M. . ( 2002; ). Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia . . Appl Environ Microbiol 68:, 2391–2396. [CrossRef] [PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. Kong H. H. , Oh J. , Deming C. , Conlan S. , Grice E. A. , Beatson M. A. , Nomicos E. , Polley E. C. , Komarow H. D. . & other authors ( 2012; ). Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. . Genome Res 22:, 850–859. [CrossRef] [PubMed]
    [Google Scholar]
  32. Kulichevskaya I. S. , Suzina N. E. , Liesack W. , Dedysh S. N. . ( 2010; ). Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria . . Int J Syst Evol Microbiol 60:, 301–306. [CrossRef] [PubMed]
    [Google Scholar]
  33. Kulichevskaya I. S. , Kostina L. A. , Valásková V. , Rijpstra W. I. C. , Sinninghe Damsté J. , 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]
  34. 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]
  35. LaPara T. M. , Nakatsu C. H. , Pantea L. M. , Alleman J. E. . ( 2000; ). Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. . Appl Environ Microbiol 66:, 3951–3959. [CrossRef] [PubMed]
    [Google Scholar]
  36. Lauber C. L. , Hamady M. , Knight R. , Fierer N. . ( 2009; ). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. . Appl Environ Microbiol 75:, 5111–5120. [CrossRef] [PubMed]
    [Google Scholar]
  37. Liesack W. , Bak F. , Kreft J. U. , Stackebrandt E. . ( 1994; ). Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. . Arch Microbiol 162:, 85–90. [CrossRef] [PubMed]
    [Google Scholar]
  38. Lin X. , Kennedy D. , Fredrickson J. , Bjornstad B. , Konopka A. . ( 2012; ). Vertical stratification of subsurface microbial community composition across geological formations at the Hanford Site. . Environ Microbiol 14:, 414–425. [CrossRef] [PubMed]
    [Google Scholar]
  39. Losey N. A. , Stevenson B. S. , Busse H.-J. , Sinninghe Damsté J. S. , Rijpstra W. I. C. , Rudd S. , Lawson P. A. . ( 2013; ). Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of Acidobacteria subdivision 23, isolated from a hot spring. . Int J Syst Evol Microbiol 63:, 4149–4157. [CrossRef] [PubMed]
    [Google Scholar]
  40. Ludwig W. , Strunk O. , Westram R. , Richter L. , Meier H. , Yadhukumar , Buchner A. , Lai T. , Steppi S. . & other authors ( 2004; ). arb: a software environment for sequence data. . Nucleic Acids Res 32:, 1363–1371. [CrossRef] [PubMed]
    [Google Scholar]
  41. 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]
  42. Männistö M. K. , Rawat S. , Starovoytov V. , Häggblom M. M. . ( 2012; ). Granulicella arctica sp. nov., Granulicella mallensis sp. nov., Granulicella tundricola sp. nov. and Granulicella sapmiensis sp. nov., novel acidobacteria from tundra soil. . Int J Syst Evol Microbiol 62:, 2097–2106. [CrossRef] [PubMed]
    [Google Scholar]
  43. 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 Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  44. Moissl C. , Osman S. , La Duc M. T. , Dekas A. , Brodie E. , DeSantis T. , Venkateswaran K. . ( 2007; ). Molecular bacterial community analysis of clean rooms where spacecraft are assembled. . FEMS Microbiol Ecol 61:, 509–521. [CrossRef] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
  47. 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]
  48. Pointing S. B. , Chan Y. , Lacap D. C. , Lau M. C. Y. , Jurgens J. A. , Farrell R. L. . ( 2009; ). Highly specialized microbial diversity in hyper-arid polar desert. . Proc Natl Acad Sci U S A 106:, 19964–19969. [CrossRef] [PubMed]
    [Google Scholar]
  49. Pruesse E. , Quast C. , Knittel K. , Fuchs B. M. , Ludwig W. , Peplies J. , Glöckner F. O. . ( 2007; ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35:, 7188–7196. [CrossRef] [PubMed]
    [Google Scholar]
  50. Rosselló-Mora R. , Amann R. . ( 2001; ). The species concept for prokaryotes. . FEMS Microbiol Rev 25:, 39–67. [CrossRef] [PubMed]
    [Google Scholar]
  51. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, Technical Note no. 101. Newark, DE:: MIDI Inc;.
    [Google Scholar]
  52. Schabereiter-Gurtner C. , Saiz-Jimenez C. , Piñar G. , Lubitz W. , Rölleke S. . ( 2004; ). Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma). . FEMS Microbiol Ecol 47:, 235–247. [CrossRef] [PubMed]
    [Google Scholar]
  53. Stackebrandt E. , Ebers J. . ( 2006; ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33:, 152–155.
    [Google Scholar]
  54. 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]
  55. Stott M. B. , Crowe M. A. , Mountain B. W. , Smirnova A. V. , Hou S. , Alam M. , Dunfield P. F. . ( 2008; ). Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. . Environ Microbiol 10:, 2030–2041. [CrossRef] [PubMed]
    [Google Scholar]
  56. 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]
  57. Tindall B. J. . ( 1990; ). Lipid composition of Halobacterium lacusprofundi . . FEMS Microbiol Lett 66:, 199–202. [CrossRef]
    [Google Scholar]
  58. 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;.
    [Google Scholar]
  59. Tschech A. , Pfennig N. . ( 1984; ). Growth yield increase linked to caffeate reduction Acetobacterium woodii . . Arch Microbiol 137:, 163–167. [CrossRef]
    [Google Scholar]
  60. 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]
  61. 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]
  62. Wood T. M. , Bhat K. M. . ( 1988; ). Methods for measuring cellulase activities. . Methods Enzymol 160:, 87–112. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.060236-0
Loading
/content/journal/ijsem/10.1099/ijs.0.060236-0
Loading

Data & Media loading...

Supplements

Supplementary Material 

PDF

Most Cited This Month

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