1887

Abstract

Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_−6_39, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_−6_39 are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3–8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16  : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6 with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39 represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_−6_39 (=DSM 100886=KCTC 52215).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001827
2017-06-05
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/5/1408.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001827&mimeType=html&fmt=ahah

References

  1. Janssen PH. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl Environ Microbiol 2006;72:1719–1728 [CrossRef][PubMed]
    [Google Scholar]
  2. Barns SM, Takala SL, Kuske CR. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl Environ Microbiol 1991;65:1731–1737
    [Google Scholar]
  3. Zhang Y, Cong J, Lu H, Li G, Qu Y et al. Community structure and elevational diversity patterns of soil Acidobacteria. J Environ Sci 2014;26:1717–1724 [CrossRef][PubMed]
    [Google Scholar]
  4. Navarrete AA, Kuramae EE, de Hollander M, Pijl AS, van Veen JA et al. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiol Ecol 2013;83:607–621 [CrossRef][PubMed]
    [Google Scholar]
  5. da Rocha UN, Plugge CM, George I, van Elsas JD, van Overbeek LS. The rhizosphere selects for particular groups of Acidobacteria and Verrucomicrobia. PLoS One 2013;8:e82443[CrossRef]
    [Google Scholar]
  6. Lee SH, Ka JO, Cho JC. Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil. FEMS Microbiol Lett 2008;285:263–269 [CrossRef][PubMed]
    [Google Scholar]
  7. O'Connor-Sánchez A, Rivera-Domínguez AJ, Santos-Briones CL, López-Aguiar LK, Peña-Ramírez YJ et al. Acidobacteria appear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid. Biol Res 2014;47:67 [CrossRef][PubMed]
    [Google Scholar]
  8. Quaiser A, López-García P, Zivanovic Y, Henn MR, Rodriguez-Valera F et al. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ Microbiol 2008;10:2704–2717 [CrossRef][PubMed]
    [Google Scholar]
  9. Liao L, Xu XW, Jiang XW, Wang CS, Zhang DS et al. Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific ocean. FEMS Microbiol Ecol 2011;78:565–585 [CrossRef][PubMed]
    [Google Scholar]
  10. Zimmermann J, Gonzalez JM, Saiz-Jimenez C, Ludwig W, Detection LW. Detection and phylogenetic relationships of highly diverse uncultured Acidobacterial communities in Altamira Cave using 23S rRNA sequence analyses. Geomicrobiol J 2005;22:379–388 [CrossRef]
    [Google Scholar]
  11. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998;180:366–376[PubMed]
    [Google Scholar]
  12. Kleinsteuber S, Müller FD, Chatzinotas A, Wendt-Potthoff K, Harms H. Diversity and in situ quantification of Acidobacteria subdivision 1 in an acidic mining lake. FEMS Microbiol Ecol 2008;63:107–117 [CrossRef][PubMed]
    [Google Scholar]
  13. Barns SM, Cain EC, Sommerville L, Kuske CR. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl Environ Microbiol 2007;73:3113–3116 [CrossRef][PubMed]
    [Google Scholar]
  14. Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 2016;7:744 [CrossRef][PubMed]
    [Google Scholar]
  15. Huber KJ, Geppert AM, Wanner G, Fösel BU, Wüst PK et al. The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. Int J Syst Evol Microbiol 2016;66:2971–2979[CrossRef]
    [Google Scholar]
  16. George IF, Hartmann M, Liles MR, Agathos SN. Recovery of as-yet-uncultured soil Acidobacteria on dilute solid media. Appl Environ Microbiol 2011;77:8184–8188 [CrossRef][PubMed]
    [Google Scholar]
  17. Fischer M, Bossdorf O, Gockel S, Hänsel F, Hemp A et al. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic Appl Ecol 2010;11:473–485 [CrossRef]
    [Google Scholar]
  18. Davis KE, Sangwan P, Janssen PH. Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony-forming soil bacteria. Environ Microbiol 2011;13:798–805 [CrossRef][PubMed]
    [Google Scholar]
  19. Davis KE, Joseph SJ, Janssen PH. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 2005;71:826–834 [CrossRef][PubMed]
    [Google Scholar]
  20. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 2002;68:2391–2396 [CrossRef][PubMed]
    [Google Scholar]
  21. Lunau M, Lemke A, Walther K, Martens-Habbena W, Simon M. An improved method for counting bacteria from sediments and turbid environments by epifluorescence microscopy. Environ Microbiol 2005;7:961–968 [CrossRef][PubMed]
    [Google Scholar]
  22. Angle JS, Mcgrath SP, Chaney RL. New culture medium containing ionic concentrations of nutrients similar to concentrations found in the soil solution. Appl Environ Microbiol 1991;57:3674–3676[PubMed]
    [Google Scholar]
  23. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979;43:260–296[PubMed]
    [Google Scholar]
  24. Tschech A, Pfennig N. Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 1984;137:163–167 [CrossRef]
    [Google Scholar]
  25. Foesel BU, Rohde M, Overmann J. Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil - the first described species of Acidobacteria subdivision 4. Syst Appl Microbiol 2013;36:82–89 [CrossRef][PubMed]
    [Google Scholar]
  26. Pascual J, Wüst PK, Geppert A, Foesel BU, Huber KJ et al. Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015;38:534–544 [CrossRef][PubMed]
    [Google Scholar]
  27. Gerhardt P. Methods for General and Molecular Bacteriology Washington, DC: American society for microbiology; 1994
    [Google Scholar]
  28. Bast E. Mikrobiologische Methoden, 3rd ed. Germany: Springer spektrum; 2014
    [Google Scholar]
  29. Wanner G, Vogl K, Overmann J. Ultrastructural characterization of the prokaryotic symbiosis in "Chlorochromatium aggregatum". J Bacteriol 2008;190:3721–3730 [CrossRef][PubMed]
    [Google Scholar]
  30. Foesel BU, Mayer S, Luckner M, Wanner G, Rohde M et al. Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae. Int J Syst Evol Microbiol 2016;66:219–229 [CrossRef][PubMed]
    [Google Scholar]
  31. Wüst PK, Foesel BU, Geppert A, Huber KJ, Luckner M et al. Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae. Int J Syst Evol Microbiol 2016;66:3355–3366 [CrossRef][PubMed]
    [Google Scholar]
  32. Cowan ST, Barrow GI, Steel KJ, Cowan F. Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge, United Kingdom: Cambridge University Press; 1993
    [Google Scholar]
  33. Huber KJ, Wüst PK, Rohde M, Overmann J, Foesel BU. 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 2014;64:1866–1875 [CrossRef][PubMed]
    [Google Scholar]
  34. Pankratov TA, Dedysh SN. 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 2010;60:2951–2959 [CrossRef][PubMed]
    [Google Scholar]
  35. Männistö MK, Rawat S, Starovoytov V, Häggblom MM. Terriglobus saanensis sp. nov., an acidobacterium isolated from tundra soil. Int J Syst Evol Microbiol 2011;61:1823–1828 [CrossRef][PubMed]
    [Google Scholar]
  36. Kulichevskaya IS, Suzina NE, Liesack W, Dedysh SN. Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 2010;60:301–306 [CrossRef][PubMed]
    [Google Scholar]
  37. Kulichevskaya IS, Suzina NE, Rijpstra WI, Sinninghe Damsté JS, Dedysh SN. Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria. Int J Syst Evol Microbiol 2014;64:2857–2864 [CrossRef][PubMed]
    [Google Scholar]
  38. Huang S, Vieira S, Bunk B, Riedel T, Spröer C et al. First complete genome sequence of a subdivision 6 Acidobacterium strain. Genome Announc 2016;4:e00469-16
    [Google Scholar]
  39. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981;45:316–354[PubMed]
    [Google Scholar]
  40. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202[CrossRef]
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. 2001
    [Google Scholar]
  42. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37:911–917 [CrossRef][PubMed]
    [Google Scholar]
  43. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007; pp.330–393
    [Google Scholar]
  44. Kishimoto N, Kosako Y, Tano T. Acidobacterium capsulatum gen. nov., sp. nov.: an acidophilic chemoorganotrophic bacterium containing menaquinone from acidic mineral environment. Curr Microbiol 1991;22:1–7 [CrossRef]
    [Google Scholar]
  45. Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 1999;46:327–338 [CrossRef][PubMed]
    [Google Scholar]
  46. Lane D. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: John Wiley and Sons; 1991; pp.115–175
    [Google Scholar]
  47. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  48. Fukunaga Y, Kurahashi M, Yanagi K, Yokota A, Harayama S. 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 2008;58:2597–2601 [CrossRef][PubMed]
    [Google Scholar]
  49. Coates JD, Ellis DJ, Gaw CV, Lovley DR. Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer. Int J Syst Bacteriol 1999;49:1615–1622 [CrossRef][PubMed]
    [Google Scholar]
  50. Liesack W, Bak F, Kreft JU, Stackebrandt E. Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Arch Microbiol 1994;162:85–90 [CrossRef][PubMed]
    [Google Scholar]
  51. Izumi H, Nunoura T, Miyazaki M, Mino S, Toki T et al. 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 2012;16:245–253 [CrossRef][PubMed]
    [Google Scholar]
  52. Losey NA, Stevenson BS, Busse HJ, Sinninghe Damsté JS, Rijpstra WI et al. Thermoanaerobaculum aquaticum gen. nov., sp. nov., the first cultivated member of acidobacteria subdivision 23, isolated from a hot spring. Int J Syst Evol Microbiol 2013;63:4149–4157 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001827
Loading
/content/journal/ijsem/10.1099/ijsem.0.001827
Loading

Data & Media loading...

Supplements



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