1887

Abstract

A novel Gram-stain-positive, rod-shaped, anaerobic, thermophilic bacterium, strain GGR1, was isolated from a thermophilic lab-scale biogas fermenter. The novel organism was effectively degrading crystalline cellulose. It seems to play a role in remineralization of plant biomass by hydrolysing its polysaccharides. 16S rRNA gene comparative sequence analysis demonstrated that the isolate formed a hitherto unknown subline within the family Ruminococcaceae . The closest phylogenetic relative of GGR1 among the taxa with validly published names was Clostridiumthermocellum , sharing 94.3 % 16S rRNA gene sequence similarity. Strain GGR1 was catalase-negative, indole-negative and produced acetate and ethanol as major end-products during fermentative cellulose utilization. The major cellular fatty acids (>1 %) were 16 : 0 iso fatty acid and 16 : 0 fatty acid. Cells were rod shaped and grew optimally at 60 °C and pH 7.0. The DNA G+C content was 34.9 mol%. A novel genus and species, Herbivoraxsaccincola gen. nov., sp. nov., is proposed on the basis of phylogenetic analysis and physiological properties of the novel isolate. Strain GGR1 (=DSM 101079=CECT 9155) represents the type strain for the novel genus and novel species Herbivoraxsaccincola gen. nov., sp. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001374
2016-11-01
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4458.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001374&mimeType=html&fmt=ahah

References

  1. Euzéby J..( 2010;). List of new names and new combinations previously effectively, but not validly, published. . Int J Syst Evol Microbiol60:1009–1010. [CrossRef][PubMed]
    [Google Scholar]
  2. Felsenstein J..( 1985;). Confidence limits on phylogenies with a molecular clock. . Syst Zool34:152–161. [CrossRef]
    [Google Scholar]
  3. Freier D., Mothershed C. P., Wiegel J..( 1988;). Characterization of Clostridium thermocellum JW20. . Appl Environ Microbiol54:204–211.[PubMed]
    [Google Scholar]
  4. Johnson E. A., Madia A., Demain A. L..( 1981;). Chemically defined minimal medium for growth of the anaerobic cellulolytic thermophile Clostridium thermocellum. . Appl Environ Microbiol41:1060–1062.[PubMed]
    [Google Scholar]
  5. Johnson M. J., Thatcher E., Cox M. E..( 1995;). Techniques for controlling variability in gram staining of obligate anaerobes. . J Clin Microbiol33:755–758.[PubMed]
    [Google Scholar]
  6. Kato S., Haruta S., Cui Z. J., Ishii M., Yokota A., Igarashi Y..( 2004;). Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community. . Int J Syst Evol Microbiol54:2043–2047. [CrossRef][PubMed]
    [Google Scholar]
  7. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al.( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol62:716–721. [CrossRef][PubMed]
    [Google Scholar]
  8. Koeck D. E., Wibberg D., Maus I., Winkler A., Albersmeier A., Zverlov V. V., Liebl W., Pühler A., Schwarz W. H., Schlüter A..( 2014a;). Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant. . J Biotechnol188:136–137. [CrossRef][PubMed]
    [Google Scholar]
  9. Koeck D. E., Zverlov V. V., Liebl W., Schwarz W. H..( 2014b;). Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential. . Syst Appl Microbiol37:311–319. [CrossRef][PubMed]
    [Google Scholar]
  10. Koeck D. E., Zverlov V. V., Schwarz W. H., Wanner G., Liebl W., Ludwig W..( 2015a;). Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. . Int J Syst Evol Microbiol65:2365–2371. [CrossRef]
    [Google Scholar]
  11. Koeck D. E., Maus I., Wibberg D., Winkler A., Zverlov V. V., Liebl W., Pühler A., Schwarz W. H., Schlüter A..( 2015b;). Draft genome sequence of Herbinix hemicellulosilytica T3/55T, a new thermophilic cellulosedegrading bacterium isolated from a thermophilic biogas reactor. . J Biotechnol214:59–60. [CrossRef][PubMed]
    [Google Scholar]
  12. Ludwig W., Schleifer K.-H., Whitman W. B..( 2009;). Revised road map to the phylum Firmicutes. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol 3, pp. 1–13. Edited by De Vos P., Garrity G. M., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K. H., Whitman W. B.. New York:: Springer;.
    [Google Scholar]
  13. Madden R. H..( 1983;). Isolation and characterization of Clostridium stercorarium sp. nov., cellulolytic thermophile. . Int J Syst Bacteriol33:837–840. [CrossRef]
    [Google Scholar]
  14. Mc Bee R..( 1954;). The characteristics of Clostridium thermocellum. . J Bacteriol67:505–506.[PubMed]
    [Google Scholar]
  15. Miller G. L..( 1959;). Use of dinitrosalicylic acid reagent for determination of reducing sugar. . Anal Chem31:426–428. [CrossRef]
    [Google Scholar]
  16. Mohamed R., Chaudhry A. S..( 2008;). Methods to study degradation of ruminant feeds. . Nutr Res Rev21:68–81. [CrossRef][PubMed]
    [Google Scholar]
  17. Munoz 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 Microbiol34:169–170. [CrossRef][PubMed]
    [Google Scholar]
  18. Parte A. C..( 2014;). LPSN – list of prokaryotic names with standing in nomenclature. . Nucleic Acids Res42:D613–D616. [CrossRef][PubMed]
    [Google Scholar]
  19. Patel G. B., Khan A. W., Agnew B. J., Colvin J. R..( 1980;). Isolation and characterization of an Anaerobic, cellulolytic microorganism, Acetivibrio cellulolyticus gen. nov., sp. nov. . Int J Syst Bacteriol30:179–185. [CrossRef]
    [Google Scholar]
  20. Schwarz W. H..( 2001;). The cellulosome and cellulose degradation by anaerobic bacteria. . Appl Microbiol Biotechnol56:634–649. [CrossRef][PubMed]
    [Google Scholar]
  21. Shiratori H., Sasaya K., Ohiwa H., Ikeno H., Ayame S., Kataoka N., Miya A., Beppu T., Ueda K..( 2009;). Clostridium clariflavum sp. nov. and Clostridium caenicola sp. nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge. . Int J Syst Evol Microbiol59:1764–1770. [CrossRef][PubMed]
    [Google Scholar]
  22. Sievers F., Wilm A., Dineen D., Gibson T. J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M. et al.( 2011;). Fast, scalable generation of high-quality protein multiple sequence alignments using clustal Omega. . Mol Syst Biol7:539. [CrossRef][PubMed]
    [Google Scholar]
  23. Stamatakis A..( 2006;). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics22:2688–2690. [CrossRef][PubMed]
    [Google Scholar]
  24. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S..( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol30:2725–2729. [CrossRef][PubMed]
    [Google Scholar]
  25. Tap J., Mondot S., Levenez F., Pelletier E., Caron C., Furet J. P., Ugarte E., Muñoz-Tamayo R., Paslier D. L. E. et al.( 2009;). Towards the human intestinal microbiota phylogenetic core. . Environ Microbiol11:2574–2584. [CrossRef][PubMed]
    [Google Scholar]
  26. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P..( 2010;). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol60:249–266. [CrossRef][PubMed]
    [Google Scholar]
  27. Yang J. C., Chynoweth D. P., Williams D. S., Li A..( 1990;). Clostridium aldrichii sp. nov., a cellulolytic mesophile inhabiting a wood-fermenting anaerobic digester. . Int J Syst Bacteriol40:268–272. [CrossRef][PubMed]
    [Google Scholar]
  28. Yutin N., Galperin M. Y..( 2013;). A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia. . Environ Microbiol15:2631–2641. [CrossRef][PubMed]
    [Google Scholar]
  29. Zhilina T. N., Kevbrin V. V., Tourova T. P., Lysenko A. M., Kostrikina N. A., Zavarzin G. A..( 2005;). Clostridium alkalicellum sp. nov., an obligately alkaliphilic cellulolytic bacterium from a soda lake in the Baikal region. . Microbiology74:557–566. [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001374
Loading
/content/journal/ijsem/10.1099/ijsem.0.001374
Loading

Data & Media loading...

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