1887

Abstract

A novel obligately anaerobic bacterium, designated strain TC1, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based wastewater. Cells had a multicellular filamentous morphology, stained Gram-negative and were non-motile. The filaments were flexible, generally >100 μm long and 0.3–0.4 μm wide. Growth of the isolate was observed at 25–43 °C (optimum 37 °C) and pH 6.0–8.5 (optimum pH 7.0). Strain TC1 grew chemo-organotrophically on a range of carbohydrates under anaerobic conditions. Yeast extract was required for growth. The major fermentative end products of glucose, supplemented with yeast extract, were acetate, lactate, succinate, propionate, formate and hydrogen. Co-cultivation with the hydrogenotrophic methanogen DSM 864 enhanced growth of the isolate. The DNA G+C content was determined experimentally to be 42.1 mol%. The major cellular fatty acids were anteiso-C, iso-C and iso-C 3-OH. Based on 16S rRNA gene sequence analysis, strain TC1 belonged to the class in the phylum , in which P3M-1 was its closest phylogenetic relative (88.3 % nucleotide identity). Phylogenomic analyses using 38 and 83 single-copy marker genes also supported the novelty of strain TC1 at least at the genus level. Based on phylogenetic, genomic and phenotypic characteristics, we propose that strain TC1 represents a novel species of a new genus, for which we suggest the name gen. nov., sp. nov. The type strain of is strain TC1 ( = JCM 30897 = CGMCC 1.5202).

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2016-02-01
2021-08-03
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References

  1. Campbell A. G., Schwientek P., Vishnivetskaya T., Woyke T., Levy S., Beall C. J., Griffen A., Leys E., Podar M. 2014; Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Environ Microbiol 16:2635–2643 [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. IV, 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 pp 21–33Edited by Gerhardt P., Murray R. G. E., Costilow R. N., Nester E. W., Wood W. A., Krieg N. R., Phillips G. H. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  5. Felsenstein J. 1989; phylip - Phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  6. Grégoire P., Fardeau M.-L., Joseph M., Guasco S., Hamaide F., Biasutti S., Michotey V., Bonin P., Ollivier B. 2011; Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum Chloroflexi, isolated from a deep hot aquifer in the Aquitaine Basin. Syst Appl Microbiol 34:494–497 [View Article][PubMed]
    [Google Scholar]
  7. 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]
  8. 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 [CrossRef]
    [Google Scholar]
  9. Imachi H., Sekiguchi Y., Kamagata Y., Hanada S., Ohashi A., Harada H. 2002; Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. Int J Syst Evol Microbiol 52:1729–1735[PubMed]
    [Google Scholar]
  10. Imachi H., Sakai S., Lipp J. S., Miyazaki M., Saito Y., Yamanaka Y., Hinrichs K.-U., Inagaki F., Takai K. 2014; Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment. Int J Syst Evol Microbiol 64:812–818 [View Article][PubMed]
    [Google Scholar]
  11. Kamagata Y., Mikami E. 1991; Isolation and characterization of a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41:191–196 [View Article]
    [Google Scholar]
  12. Konstantinidis K. T., Tiedje J. M. 2005; Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. Matsuura N., Tourlousse D. M., Ohashi A., Hugenholtz P., Sekiguchi Y. 2015a; Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi). Genome Announc 3:e00975–e00915 [View Article][PubMed]
    [Google Scholar]
  15. Matsuura N., Tourlousse D. M., Sun L., Toyonaga M., Kuroda K., Ohashi A., Cruz R., Yamaguchi T., Sekiguchi Y. 2015b; Draft genome sequence of Anaerolineae strain TC1, a novel isolate from a methanogenic wastewater treatment system. Genome Announc 3:e01104–e01115 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Nunoura T., Hirai M., Miyazaki M., Kazama H., Makita H., Hirayama H., Furushima Y., Yamamoto H., Imachi H., Takai K. 2013; Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov. Microbes Environ 28:228–235 [View Article][PubMed]
    [Google Scholar]
  18. Pfennig N., Wagener S. 1986; An improved method of preparing wet mounts for photomicrographs of microorganisms. J Microbiol Methods 4:303–306 [View Article]
    [Google Scholar]
  19. Podosokorskaya O. A., Bonch-Osmolovskaya E. A., Novikov A. A., Kolganova T. V., Kublanov I. V. 2013; Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae . Int J Syst Evol Microbiol 63:86–92 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Roden E. E., Lovley D. R. 1993; Dissimilatory Fe(III) reduction by the marine microorganism Desulfuromonas acetoxidans . Appl Environ Microbiol 59:734–742[PubMed]
    [Google Scholar]
  22. Sekiguchi Y., Kamagata Y., Nakamura K., Ohashi A., Harada H. 1999; Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl Environ Microbiol 65:1280–1288[PubMed]
    [Google Scholar]
  23. 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]
  24. Sekiguchi Y., Takahashi H., Kamagata Y., Ohashi A., Harada H. 2001; In situ detection, isolation, and physiological properties of a thin filamentous microorganism abundant in methanogenic granular sludges: a novel isolate affiliated with a clone cluster, the green non-sulfur bacteria, subdivision I. Appl Environ Microbiol 67:5740–5749 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. 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]
  27. 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]
  28. 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., Hugenholtz P. 2014; An expanded genomic representation of the phylum Cyanobacteria. Genome Biol Evol 6:1031–1045 [View Article][PubMed]
    [Google Scholar]
  29. Speirs L. B. M, Tucci J., Seviour R. J. 2015; The activated sludge bulking filament Eikelboom morphotype 0803 embraces more than one member of the Chloroflexi . FEMS Microbiol Ecol 91:fiv100 [View Article][PubMed]
    [Google Scholar]
  30. 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 Bacteriol 44:846–849 [View Article]
    [Google Scholar]
  31. 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]
  32. Swofford D. L. 2003; PAUP *: phylogenetic analysis using parsimony, version 4.0b10.
    [Google Scholar]
  33. 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]
  34. Yamada T., Sekiguchi Y. 2009; Cultivation of uncultured Chloroflexi subphyla: significance and ecophysiology of formerly uncultured Chloroflexi ‘subphylum I’ with natural and biotechnological relevance. Microbes Environ 24:205–216 [View Article][PubMed]
    [Google Scholar]
  35. Yamada T., Sekiguchi Y., Imachi H., Kamagata Y., Ohashi A., Harada H. 2005; Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules. Appl Environ Microbiol 71:7493–7503 [View Article][PubMed]
    [Google Scholar]
  36. Yamada T., Sekiguchi Y., Hanada S., Imachi H., Ohashi A., Harada H., Kamagata Y. 2006; Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi . Int J Syst Evol Microbiol 56:1331–1340 [View Article][PubMed]
    [Google Scholar]
  37. Yamada T., Imachi H., Ohashi A., Harada H., Hanada S., Kamagata Y., Sekiguchi Y. 2007; Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol 57:2299–2306 [View Article][PubMed]
    [Google Scholar]
  38. 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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