1887

Abstract

Three Gram-negative, non-spore-forming, encapsulated bacteria were isolated from a Namibian river-bank soil (strains 277 and 307) and a semiarid savannah soil (strain A2-1c). 16S rRNA gene sequence analyses placed them within subdivision 1 of the and revealed 100 % similarity between strains 277 and 307 and 98.2 % similarity between A2-1c and the former two strains. The closest relatives with validly published names were , and (94.7–95.9 % similarity to the type strains). Cells of all three strains were rod-shaped and motile and divided by binary fission. Ultrastructural analyses revealed a thick cell envelope, resulting mainly from a thick periplasmic space. Colonies of strains 277 and 307 were white to cream and light pink, respectively, while strain A2-1c displayed a bright pink colour. All three strains were aerobic, chemoheterotrophic mesophiles with a broad temperature range for growth and a moderately acidic pH optimum. Sugars and complex proteinaceous substrates were the preferred carbon and energy sources. A few polysaccharides were degraded. The major quinone in all three strains was MK-8; MK-7 occurred in strain A2-1c as a minor compound. Major fatty acids were iso-C and iso-Cω7. In addition, iso-C occurred in significant amounts. The DNA G+C contents of strains 277, 307 and A2-1c were 59.6, 59.9 and 58.5 mol%, respectively. Based on these characteristics, the three isolates are assigned to two novel species of the novel genus gen. nov., sp. nov. [type strain 277 ( = DSM 25168 = LMG 26948) and reference strain 307 ( = DSM 25169 = LMG 26947)] and sp. nov. [type strain A2-1c ( = DSM 25170 = LMG 26946)]. Together with several other recently described taxa, the novel isolates provide the basis for an emended description of the established family .

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2016-01-01
2024-03-29
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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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  4. Beveridge T. J., Lawrence J. R., Murray R. G. E. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd edn. pp 19–33Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder R. L. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  5. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 75:4801–4805 [View Article][PubMed]
    [Google Scholar]
  6. Buck J. D. 1982; Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
    [Google Scholar]
  7. 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 [View Article][PubMed]
    [Google Scholar]
  8. Cataldo D. A., Haroon M., Schrader L. E., Young V. L. 1975; Rapid colorimetric determination of nitrate in plant tissue by nitration of salicylic acid. Commun Soil Sci Plant Anal 6:71–80 [View Article]
    [Google Scholar]
  9. Cavalier-Smith T. 2002; The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:7–76 [View Article][PubMed]
    [Google Scholar]
  10. 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]
  11. Cowan S. T. 1974 Cowan and Steel's Manual for the Identification of Medical Bacteria, 2nd edn. New York: Cambridge University Press;
    [Google Scholar]
  12. Cruickshank R. H., Wade G. C. 1980; Detection of pectic enzymes in pectin-acrylamide gels. Anal Biochem 107:177–181 [View Article][PubMed]
    [Google Scholar]
  13. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][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. 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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. Gadkari D. 1984; Influence of herbicides Goltix and Sencor on nitrification. Zentralbl Mikrobiol 139:623–631
    [Google Scholar]
  18. 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 [View Article][PubMed]
    [Google Scholar]
  19. Harrigan W. F., McCance M. E. 1966 Laboratory Methods in Microbiology London: Academic Press;
    [Google Scholar]
  20. 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 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. Kishimoto N., Kosako Y., Tano T. 1991a; Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 22:1–7 [View Article]
    [Google Scholar]
  23. Kishimoto N., Kosako Y., Tano T. 1991b; Acidobacterium capsulatum gen. nov., sp. nov. In Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB, List no. 38. Int J Syst Bacteriol 41:456–457 [CrossRef]
    [Google Scholar]
  24. 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 [View Article][PubMed]
    [Google Scholar]
  25. 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 [View Article][PubMed]
    [Google Scholar]
  26. Lane D. J. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp 115–175Edited by Stackebrandt E., Goodfellow M. New York: Wiley;
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. 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 [View Article][PubMed]
    [Google Scholar]
  30. Meier-Kolthoff J. P., Göker M., Spröer C., Klenk H.-P. 2013; When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 195:413–418 [View Article][PubMed]
    [Google Scholar]
  31. 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 [View Article]
    [Google Scholar]
  32. Montero-Calasanz M. C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Tindall B. J., Klenk H.-P., Camacho M. 2013; Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 63:4386–4395 [View Article][PubMed]
    [Google Scholar]
  33. Montero-Calasanz M. C., Göker M., Rohde M., Spröer C., Schumann P., Busse H.-J., Schmid M., Klenk H.-P., Tindall B. J., Camacho M. 2014; Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium,, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 37:342–350 [View Article][PubMed]
    [Google Scholar]
  34. 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 [View Article][PubMed]
    [Google Scholar]
  35. 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 [View Article][PubMed]
    [Google Scholar]
  36. 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 [View Article][PubMed]
    [Google Scholar]
  37. Pascual J., Wüst P. K., Geppert A., Foesel B. U., Huber K. J., Overmann J. 2015; Terriglobus albidus sp. nov., a novel acidobacterial species of the family Acidobacteriaceae isolated from Namibian semiarid savannah soil. Int J Syst Evol Microbiol
    [Google Scholar]
  38. Rawat S. R., Männistö M. K., Bromberg Y., Häggblom M. M. 2012; Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils. FEMS Microbiol Ecol 82:341–355 [View Article][PubMed]
    [Google Scholar]
  39. Rosselló-Móra R., Amann R. 2015; Past and future species definitions for Bacteria and Archaea . Syst Appl Microbiol 38:209–216 [View Article][PubMed]
    [Google Scholar]
  40. Sasser M. 1990 Identification of bacteria by gas chromatography of cellular fatty acids Technical Note no 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  41. 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 [View Article]
    [Google Scholar]
  42. 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 [View Article][PubMed]
    [Google Scholar]
  43. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp 607–657Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  44. Soden D. M., O'Callaghan J., Dobson A. D. W. 2002; Molecular cloning of a laccase isozyme gene from Pleurotus sajor-caju and expression in the heterologous Pichia pastoris host. Microbiology 148:4003–4014 [View Article][PubMed]
    [Google Scholar]
  45. Sundman V., Nase L. 1971; A simple plate test for direct visualization for biological lignin degradation. Paper Timber 53:67–71
    [Google Scholar]
  46. Tabatabai M. A. 1992; Methods of measurements of sulfur in soils, plants, materials and water. In Sulfur Cycling on the Continents: Wetlands, Terrestrial Ecosystems and Associated Water Bodies (Scope 48) pp 307–344Edited by Howarth R. W., Stewart J. W. B., Ivanov M. V. Chichester: Wiley;
    [Google Scholar]
  47. Tamaoka J., Komagata K. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128 [View Article]
    [Google Scholar]
  48. Tamura H., Goto K., Yotsuyanagi T., Nagayama M. 1974; Spectrophotometric determination of iron(II) with 1,10-phenanthroline in the presence of large amounts of iron(III). Talanta 21:314–318 [View Article][PubMed]
    [Google Scholar]
  49. 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]
  50. 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 [View Article][PubMed]
    [Google Scholar]
  51. Thiagarajan V., Revathi R., Aparanjini K., Sivamani P., Girilal M., Priya C. S., Kalaichelvan P. T. 2011; Extra cellular 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]
  52. Thrash J. C., Coates J. D. 2011a; Phylum XVII. Acidobacteria phyl. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol. 4 pp 725–727Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. New York: Springer;
    [Google Scholar]
  53. Thrash J. C., Coates J. D. 2011b; Family I. Acidobacteriaceae fam. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol. 4 p 728Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N. L., Ludwig W., Whitman W. B. New York: Springer;
    [Google Scholar]
  54. Thrash J. C., Coates J. D. 2012; Acidobacteriaceae fam. nov. In List of new names and new combinations previously effectively, but not validly, published, Validation List no. 143. Int J Syst Evol Microbiol 62:1–4 [View Article]
    [Google Scholar]
  55. Tindall B. J. 1990; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  56. Wanner G., Vogl K., Overmann J. 2008; Ultrastructural characterization of the prokaryotic symbiosis in Chlorochromatium aggregatum . J Bacteriol 190:3721–3730 [View Article][PubMed]
    [Google Scholar]
  57. Ward N. L., Challacombe J. F., Janssen P. H., Henrissat B., Coutinho P. M., Wu M., Xie G., Haft D. H., Sait M., other authors. 2009; Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl Environ Microbiol 75:2046–2056 [View Article][PubMed]
    [Google Scholar]
  58. 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 [View Article]
    [Google Scholar]
  59. 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 [View Article][PubMed]
    [Google Scholar]
  60. Yamada K., Okuno Y., Meng X.-Y., Tamaki H., Kamagata Y., Hanada S. 2014; Granulicella cerasi sp. nov., an acidophilic bacterium isolated from cherry bark. Int J Syst Evol Microbiol 64:2781–2785 [View Article][PubMed]
    [Google Scholar]
  61. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K.-H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
    [Google Scholar]
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