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Volume 66, Issue 7

gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum , and proposal of fam. nov. Free

Abstract

A novel, strictly anaerobic, short rod-shaped bacterium, designated strain TBC1, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based organic wastewater. Cells of this strain were 2–4 µm long and 0.4–0.6 µm wide. They were non-motile and Gram-stain-negative. The optimum growth temperature was 30–37 °C, with a range of 20–40 °C. The optimum pH for growth was around pH 7.0, while growth occurred in a range of pH 6.5–9.0. Strain TBC1grew chemo-organotrophically on a narrow range of carbohydrates under anaerobic conditions. Yeast extract was required for its growth. The major fermentative end products from glucose, supplemented with yeast extract, were acetate, malate, propionate, formate and hydrogen. Doubling time under optimal growth conditions was estimated to be 1 day. The DNA G+C content of strain TBC1 was 49.2 mol% as determined by HPLC. Major cellular fatty acids were C, C, C 9 and C 9. Based on its 16S rRNA gene sequence, strain TBC1 was shown to represent a distinct lineage at the family level in the phylum . Among previously described species of this phylum, BDR-9 () displayed the highest sequence similarity (85.9 %) with strain TBC1. Phylogenomic analyses using 38–83 single copy marker genes also supported the novelty of strain TBC1 at the family level. Based on its characteristics, strain TBC1 (=JCM 30898=DSM 100618) is considered to be the type strain of a novel species of a new genus, gen. nov., sp. nov. A new family, fam. nov., is also proposed encompassing the strain and related environmental 16S rRNA gene clone sequences.

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  • Accepted:
  • Published Online:
Keyword(s): anaerobe , Bacteroidetes , new family , phylogenomics and Wastewater treatment
© 2016 IUMS
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2016-07-01
2024-04-26
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References

  1. Albuquerque L., Rainey F. A., Nobre M. F., da Costa M. S. 2011; Schleiferia thermophila gen. nov., sp. nov., a slightly thermophilic bacterium of the phylum ‘Bacteroidetes' and the proposal of Schleiferiaceae fam. nov. Int J Syst Evol Microbiol 61:2450–2455 [View Article][PubMed]
     [Google Scholar]
  2. Caporaso J. G., Bittinger K., Bushman F. D., DeSantis T. Z., Andersen G. L., Knight R. 2010; PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267 [View Article][PubMed]
     [Google Scholar]
  3. Darling A. E., Jospin G., Lowe E., Matsen F. A., Bik H. M., Eisen J. A. 2014; PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243 [View Article][PubMed]
     [Google Scholar]
  4. Doetsch R. N. 1981; Determinative methods of light microscopy. In Manual of Methods for General Bacteriology Edited by Gerhardt P. Washington DC: American Society for Microbiology;
     [Google Scholar]
  5. Dojka M. A., Hugenholtz P., Haack S. K., Pace N. R. 1998; Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64:3869–3877[PubMed]
     [Google Scholar]
  6. Du Z.-J., Wang Y., Dunlap C., Rooney A. P., Chen G.-J. 2014; Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Bacteriol 64:1690–1696 [CrossRef]
     [Google Scholar]
  7. Faith J. J., Guruge J. L., Charbonneau M., Subramanian S., Seedorf H., Goodman A. L., Clemente J. C., Knight R., Heath A. C. et al. 2013; The long-term stability of the human gut microbiota. Science 341: [View Article][PubMed]
     [Google Scholar]
  8. Felsenstein J. 1989; PHYLIP - Phylogeny inference package (version 3.2). Cladistics 5:164–166
     [Google Scholar]
  9. Hanada S., Takaichi S., Matsuura K., Nakamura K. 2002; Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52:187–193 [View Article][PubMed]
     [Google Scholar]
  10. Hiraishi A. 1992; Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett Appl Microbiol 15:210–213 [View Article][PubMed]
     [Google Scholar]
  11. Holmes D. E., Nevin K. P., Woodard T. L., Peacock A. D., Lovley D. R. 2007; Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell. Int J Syst Evol Microbiol 57:701–707 [View Article][PubMed]
     [Google Scholar]
  12. Huang X.-F., Liu Y. J., Dong J.-D., Qu L.-Y., Zhang Y.-Y., Wang F.-Z., Tian X.-P., Zhang S. 2014; Mangrovibacterium diazotrophicum gen. nov., sp. nov., a nitrogen-fixing bacterium isolated from a mangrove sediment, and proposal of Prolixibacteraceae fam. nov. Int J Syst Bacteriol 64:875–881 [CrossRef]
     [Google Scholar]
  13. Kamagata Y., Mikami E. 1991; Isolation and characterization of a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41:191–196 [CrossRef]
     [Google Scholar]
  14. Konstantinidis K. T., Tiedje J. M. 2005; Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264 [View Article][PubMed]
     [Google Scholar]
  15. Krieg N. R., Parte A., Ludwig W., Whitman W. B., Hedlund B. P., Paster B. J., Staley J. T., Ward N., Brown D. 2011 Bergey's Manual of Systematic Bacteriology, 2 edn. vol. 4 Edited by Whitman W. B. Springer: New York, NY;
     [Google Scholar]
  16. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. 2004; ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
     [Google Scholar]
  17. Markowitz V. M., Chen I. M., Chu K., Szeto E., Palaniappan K., Pillay M., Ratner A., Huang J., Pagani I. et al. 2014; IMG/M 4 version of the integrated metagenome comparative analysis system. Nucleic Acids Res 42:D568–573 [View Article][PubMed]
     [Google Scholar]
  18. Matsuura N., Tourlousse D. M., Sun L., Toyonaga M., Kuroda K., Ohashi A., Cruz R., Yamaguchi T., Sekiguchi Y. 2015; Draft Genome Sequence of Anaerolineae Strain TC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc 3:e01104e01115 [View Article][PubMed]
     [Google Scholar]
  19. McBride M. J., Zhu Y. 2013; Gliding motility and Por secretion system genes are widespread among members of the phylum bacteroidetes. J Bacteriol 195:270–278 [View Article][PubMed]
     [Google Scholar]
  20. McDonald D., Price M. N., Goodrich J., Nawrocki E. P., DeSantis T. Z., Probst A., Andersen G. L., Knight R., Hugenholtz P. 2012; An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618 [View Article][PubMed]
     [Google Scholar]
  21. Narihiro T., Terada T., Kikuchi K., Iguchi A., Ikeda M., Yamauchi T., Shiraishi K., Kamagata Y., Nakamura K. et al. 2009; Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes Environ 24:88–96 [View Article][PubMed]
     [Google Scholar]
  22. Pfennig N., Wagener S. 1986; An improved method of preparing wet mounts for photomicrographs of microorganisms. J Microbiol Methods 4:303–306 [CrossRef]
     [Google Scholar]
  23. Price M. N., Dehal P. S., Arkin A. P. 2010; FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490 [View Article][PubMed]
     [Google Scholar]
  24. Rivière D., Desvignes V., Pelletier E., Chaussonnerie S., Guermazi S., Weissenbach J., Li T., Camacho P., Sghir A. 2009; Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 3:700–714 [View Article][PubMed]
     [Google Scholar]
  25. Sato K., Naito M., Yukitake H., Hirakawa H., Shoji M., McBride M. J., Rhodes R. G., Nakayama K. 2010; A protein secretion system linked to bacteroidete gliding motility and pathogenesis. Proc Natl Acad Sci U S A 107:276–281 [View Article][PubMed]
     [Google Scholar]
  26. Sekiguchi Y., Kamagata Y., Syutsubo K., Ohashi A., Harada H., Nakamura K. 1998; Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144:2655–2665 [View Article][PubMed]
     [Google Scholar]
  27. Sekiguchi Y., Kamagata Y., Nakamura K., Ohashi A., Harada H. 2000; Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int J Syst Evol Microbiol 50:771–779 [View Article][PubMed]
     [Google Scholar]
  28. Sekiguchi Y., Yamada T., Hanada S., Ohashi A., Harada H., Kamagata Y. 2003; Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 53:1843–1851 [View Article][PubMed]
     [Google Scholar]
  29. Sekiguchi Y., Ohashi A., Parks D. H., Yamauchi T., Tyson G. W., Hugenholtz P. 2015; First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ 3:e740 [View Article][PubMed]
     [Google Scholar]
  30. Shintani T., Liu W. T., Hanada S., Kamagata Y., Miyaoka S., Suzuki T., Nakamura K. 2000; Micropruina glycogenica gen. nov., sp. nov., a new Gram-positive glycogen-accumulating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 50:201–207 [View Article][PubMed]
     [Google Scholar]
  31. Slakeski N., Seers C. A., Ng K., Moore C., Cleal S. M., Veith P. D., Lo A. W., Reynolds E. C. 2011; C-terminal domain residues important for secretion and attachment of RgpB in Porphyromonas gingivalis . J Bacteriol 193:132–142 [View Article][PubMed]
     [Google Scholar]
  32. Soo R. M., Skennerton C. T., Sekiguchi Y., Imelfort M., Paech S. J., Dennis P. G., Steen J. A., Parks D. H., Tyson G. W. et al. 2014; An expanded genomic representation of the phylum cyanobacteria. Genome Biol Evol 6:1031–1045 [View Article][PubMed]
     [Google Scholar]
  33. 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 Evol Microbiol 44:846–849 [CrossRef]
     [Google Scholar]
  34. Stamatakis A. 2006; RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 [View Article][PubMed]
     [Google Scholar]
  35. Sun L., Toyonaga M., Matsuura N., Tourlousse D. M., Meng X.-Y., Tamaki H., Hanada S., Ohashi A., Cruz R. et al. 2015; Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi . Int J Syst Evol Microbiol 66:988–996 [CrossRef]
     [Google Scholar]
  36. Swofford D. L. 2003 PAUP*: Phylogenetic Analysis Using Parsimony, 4.0b10
  37. Talavera G., Castresana J. 2007; Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577 [View Article][PubMed]
     [Google Scholar]
  38. Tourlousse D. M., Matsuura N., Sun L., Toyonaga M., Kuroda K., Ohashi A., Cruz R., Yamaguchi T., Sekiguchi Y. 2015; Draft Genome Sequence of Bacteroidales Strain TBC1, a Novel Isolate from a Methanogenic Wastewater Treatment System. Genome Announc 3:e0116815 [View Article][PubMed]
     [Google Scholar]
  39. Xiao L., Feng Q., Liang S., Sonne S. B., Xia Z., Qiu X., Li X., Long H., Zhang J. et al. 2015; A catalog of the mouse gut metagenome. Nat Biotechnol 33:1103–1108 [View Article][PubMed]
     [Google Scholar]
  40. Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K. H., Glöckner F. O., Rosselló-Móra R. 2010; Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299 [View Article][PubMed]
     [Google Scholar]
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Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.
Int J Syst Evol Microbiol 66, 2635 (2016); https://doi.org/10.1099/ijsem.0.001103
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