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f Herbinix luporum sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor

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  • Authors: Daniela E. Koeck1​ ,  Sarah Hahnke2​ , Vladimir V. Zverlov1​,3​
    • VIEW AFFILIATIONS
    • 1​ 1​Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85354 Freising-Weihenstephan, Germany 2​ 2​Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), D-14469 Potsdam, Germany 3​ 3​Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia
  • Correspondence Daniela E. Koeck [email protected]
  • First Published Online: 01 October 2016, International Journal of Systematic and Evolutionary Microbiology 66: 4132-4137, doi: 10.1099/ijsem.0.001324
  • Subject: New taxa - Firmicutes and related organisms
  • Received:
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  • Phylogenetic studies were performed on a group of novel Gram-stain-positive, anaerobic, non-sporulating rod-shaped bacteria isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene sequence comparison indicated that the isolates SD1D, SD1G, SD1I and RK1P share 100 % sequence identity, and are most closely related to Herbinix hemicellulosilytica T3/55 with which they share a 16S rRNA gene sequence similarity of 96.4 %. As a representative of the whole group of isolates, strain SD1D was further characterized. Strain SD1D was catalase-negative, indole-negative, and produced acetate, ethanol, butyric acid and hydrogen as major end-products during fermentative cellobiose utilization. Cells are rod-shaped, growing optimally at 40–65 °C and pH 6.5–8.5. The major cellular fatty acids (>10 %) were C19 : 0 cyc 9,10 dimethyl acetal, C16 : 0 and C14 : 0. The DNA G+C content was 35.1 mol%. Due to the genetic and phenotypic differences to the most closely affiliated species, the isolates represent a novel species of the genus Herbinix within the family Lachnospiraceae , for which the name Herbinix luporum sp. nov. is proposed. The type strain is SD1D(=DSM 100831=CECT 8959).

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains SD1D, RK1P, SD1I and SD1G are LN626359, LN626356, LN626357 and LN626358, respectively.

  • Abbreviations:
    DMA Dimethyl acetal
    FAME fatty acid methyl ester

© 2016 IUMS | Published by the Microbiology Society

  • Biddle A., Stewart L., Blanchard J., Leschine S..( 2013;). Untangling the genetic basis of fibrolytic specialization by L achnospiraceae and R uminococcaceae in diverse gut communities. . Diversity 5: 627––640. [CrossRef]
    [Google Scholar]
  • Collins M. D., Lawson P. A., Willems A., Cordoba J. J., Fernandez-Garayzabal J., Garcia P., Cai J., Hippe H., Farrow J. A..( 1994;). The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. . Int J Syst Bacteriol 44: 812––826. [CrossRef] [PubMed]
    [Google Scholar]
  • DeLong E. F..( 2009;). The microbial ocean from genomes to biomes. . Nature 459: 200––206. [CrossRef] [PubMed]
    [Google Scholar]
  • Euzéby J..( 2010;). List of new names and new combinations previously effectively, but not validly, published. . Int J Syst Evol Microbiol 60: 1009––1010. [CrossRef] [PubMed]
    [Google Scholar]
  • Felsenstein J..( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39: 783––791. [CrossRef]
    [Google Scholar]
  • Gosalbes M. J., Durbán A., Pignatelli M., Abellan J. J., Jiménez-Hernández N., Pérez-Cobas A. E., Latorre A., Moya A..( 2011;). Metatranscriptomic approach to analyze the functional human gut microbiota. . PLoS One 6: e17447. [CrossRef] [PubMed]
    [Google Scholar]
  • Hardman J. K., Stadtman T. C..( 1960;). Metabolism of ω-amino acids. II. Fermentation of Δ-aminovaleric acid by Clostridium aminovalericum sp. nov. . J Bacteriol 79: 549––552.
     [Google Scholar]
  • Jeong H., Yi H., Sekiguchi Y., Muramatsu M., Kamagata Y., Chun J..( 2004;). Clostridium jejuense sp. nov., isolated from soil. . Int J Syst Evol Microbiol 54: 1465––1468. [CrossRef] [PubMed]
    [Google Scholar]
  • Jeong H., Lim Y. W., Yi H., Sekiguchi Y., Kamagata Y., Chun J..( 2007;). Anaerosporobacter mobilis gen. nov., sp. nov., isolated from forest soil. . Int J Syst Evol Microbiol 57: 1784––1787. [CrossRef] [PubMed]
    [Google Scholar]
  • Johnson E. A., Madia A., Demain A. L..( 1981;). Chemically defined minimal medium for growth of the anaerobic cellulolytic thermophile Clostridium thermocellum. . Appl Environ Microbiol 41: 1060––1062.[PubMed]
    [Google Scholar]
  • Johnson M. J., Thatcher E., Cox M. E..( 1995;). Techniques for controlling variability in Gram staining of obligate anaerobes. . J Clin Microbiol 33: 755––758.[PubMed]
    [Google Scholar]
  • 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 Microbiol 62: 716––721. [CrossRef] [PubMed]
    [Google Scholar]
  • Kittelmann S., Seedorf H., Walters W. A., Clemente J. C., Knight R., Gordon J. I., Janssen P. H..( 2013;). Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities. . PLoS One 8: e47879. [CrossRef] [PubMed]
    [Google Scholar]
  • 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 Biotechnol 188: 136––137. [CrossRef] [PubMed]
    [Google Scholar]
  • 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 Microbiol 37: 311––319. [CrossRef] [PubMed]
    [Google Scholar]
  • Koeck D. E., Ludwig W., Wanner G., Zverlov V. V., Liebl W., Schwarz W. H..( 2015;). Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. . Int J Syst Evol Microbiol 65:. [CrossRef] [PubMed]
    [Google Scholar]
  • Krause L., Diaz N. N., Edwards R. A., Gartemann K.-H., Krömeke H., Neuweger H., Pühler A., Runte K. J., Schlüter A. et al.( 2008;). Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. . J Biotechnol 136: 91––101. [CrossRef] [PubMed]
    [Google Scholar]
  • Kröber M., Bekel T., Diaz N. N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K. J., Viehöver P. et al.( 2009;). Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. . J Biotechnol 142: 38––49. [CrossRef] [PubMed]
    [Google Scholar]
  • 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., MGarrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A.. New York, NY:: Springer;.
     [Google Scholar]
  • Mechichi T., Labat M., Garcia J. L., Thomas P., Patel B. K..( 1999;). Characterization of a new xylanolytic bacterium, Clostridium xylanovorans sp. nov. . Syst Appl Microbiol 22: 366––371. [CrossRef] [PubMed]
    [Google Scholar]
  • Meehan C. J., Beiko R. G..( 2014;). A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria. . Genome Biol Evol 6: 703––713. [CrossRef] [PubMed]
    [Google Scholar]
  • Meyer F., Goesmann A., McHardy A. C., Bartels D., Bekel T., Clausen J., Kalinowski J., Linke B., Rupp O. et al.( 2003;). GenDB-an open source genome annotation system for prokaryote genomes. . Nucleic Acids Res 31: 2187––2195. [CrossRef] [PubMed]
    [Google Scholar]
  • Miller G. L..( 1959;). Use of dinitrosalicylic acid reagent for determination of reducing sugar. . Anal Chem 31: 426––428. [CrossRef]
    [Google Scholar]
  • 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 Microbiol 34: 169––170. [CrossRef] [PubMed]
    [Google Scholar]
  • Parte A. C..( 2014;). LPSN-list of prokaryotic names with standing in nomenclature. . Nucleic Acids Res 42: D613––D616. [CrossRef] [PubMed]
    [Google Scholar]
  • Podosokorskaya O. A., Bonch-Osmolovskaya E. A., Beskorovaynyy A. V., Toshchakov S. V., Kolganova T. V., Kublanov I. V..( 2014;). Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium. . Int J Syst Evol Microbiol 64: 2657––2661. [CrossRef] [PubMed]
    [Google Scholar]
  • Rainey F. A..( 2009;). Family V. Lachnospiraceae. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn.,vol 3 p. 921. Edited by De Vos G. M., Garrity D., Jones N. R., Krieg W., Ludwig F. A., Rainey K. H., Whitman W. B.. New York, NY:: Springer;.
     [Google Scholar]
  • Schlüter A., Bekel T., Diaz N. N., Dondrup M., Eichenlaub R., Gartemann K. H., Krahn I., Krause L., Krömeke H. et al.( 2008;). The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. . J Biotechnol 136: 77––90. [CrossRef] [PubMed]
    [Google Scholar]
  • 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 Biol 7:. [CrossRef] [PubMed]
    [Google Scholar]
  • Sleat R., Mah R. A..( 1985;). Clostridium populeti sp. nov., a cellulolytic species from a woody-biomass digestor. . Inter J Syst Bacteriol 35: 160––163. [CrossRef]
    [Google Scholar]
  • Stamatakis A..( 2006;). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. . Bioinformatics 22: 2688––2690. [CrossRef] [PubMed]
    [Google Scholar]
  • Stolze Y., Zakrzewski M., Maus I., Eikmeyer F., Jaenicke S., Rottmann N., Siebner C., Pühler A., Schlüter A..( 2015;). Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. . Biotechnol Biofuels 8: 14. [CrossRef] [PubMed]
    [Google Scholar]
  • Tamura K., Stecher G., Peterson D., Filipski A., Kumar S..( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30: 2725––2729. [CrossRef] [PubMed]
    [Google Scholar]
  • 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 Microbiol 60: 249––266. [CrossRef] [PubMed]
    [Google Scholar]
  • van Gylswyk N. O..( 1980;). Fusobacterium polysaccharolyticum sp.nov., a Gram-negative rod from the rumen that produces butyrate and ferments cellulose and starch. . J Gen Microbiol 116: 157––163. [CrossRef] [PubMed]
    [Google Scholar]
  • Van Gylswyk N. O., Van der Toorn J. J. T. K..( 1985;). Eubacterium uniforme sp. nov. and Eubacterium xylanophilum sp. nov., fiber-digesting bacteria from the rumina of sheep fed corn stover. . Inter J Syst Bacteriol 35: 323––326. [CrossRef]
    [Google Scholar]
  • Varel V. H., Tanner R. S., Woese C. R..( 1995;). Clostridium herbivorans sp. nov., a cellulolytic anaerobe from the pig intestine. . Int J Syst Bacteriol 45: 490––494. [CrossRef] [PubMed]
    [Google Scholar]
  • Warnick T. A., Methé B. A., Leschine S. B..( 2002;). Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. . Int J Syst Evol Microbiol 52: 1155––1160.[CrossRef]
    [Google Scholar]
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