1887

Abstract

Three novel, facultatively anaerobic bacteria of the family (phylum ) were isolated from mesophilic laboratory-scale biogas reactors. The strains were Gram-negative rods. Optimal growth occurred between 35 and 45 °C and at pH 7.1–7.8. The main fermentation products were acetic and propionic acids. The predominant fatty acid in all strains was anteiso-C, and the only respiratory quinone detected was menaquinone MK-8. 16S rRNA gene sequence comparison indicated that strains M3/6 and ING2-E5B were most closely related to the type strain of , with sequence similarities of 97.3 and 94.5 %. Strain ING2-E5A showed the closest affiliation to the type strain of , with 97 % sequence identity. DNA–DNA hybridization of strain M3/6 and ING2-E5A with the most closely related type strains showed 43.3–45.6 and 23.8–25.7 % relatedness, respectively, which supports the conclusion that both isolates represent novel species. Phylogenetic analysis and comparison of cellular fatty acid patterns indicated that strain ING2-E5B cannot be classified as a member of any previously described genus. Therefore, because of the physiological, genotypic and chemotaxonomic differences, it is proposed to designate novel species within the genera and , sp. nov. (type strain M3/6 = DSM 28694 = CECT 8610 = LMG 28299) and sp. nov. (type strain ING2-E5A = DSM 28695 = CECT 8611), and a novel species of a new genus, gen. nov., sp. nov. (type strain of is ING2-E5B = DSM 28696 = CECT 8609 = LMG 28429). In addition, an emended description of the genus is provided.

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2016-03-01
2020-02-26
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References

  1. Cashion P., Holder-Franklin M. A., McCully J., Franklin M.. 1977; A rapid method for the base ratio determination of bacterial DNA. Anal Biochem81:461–466 [CrossRef][PubMed]
    [Google Scholar]
  2. Chen S., Dong X.. 2005; Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. Int J Syst Evol Microbiol55:2257–2261 [CrossRef][PubMed]
    [Google Scholar]
  3. Claus D.. 1992; A standardized Gram staining procedure. World J Microbiol Biotechnol8:451–452 [CrossRef][PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A.. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  5. Grabowski A., Tindall B. J., Bardin V., Blanchet D., Jeanthon C.. 2005; Petrimonas sulfuriphila gen. nov., sp. nov., a mesophilic fermentative bacterium isolated from a biodegraded oil reservoir. Int J Syst Evol Microbiol55:1113–1121 [CrossRef][PubMed]
    [Google Scholar]
  6. Hahnke S., Striesow J., Elvert M., Mollar X. P., Klocke M.. 2014; Clostridium bornimense sp. nov., isolated from a mesophilic, two-phase, laboratory-scale biogas reactor. Int J Syst Evol Microbiol64:2792–2797 [CrossRef][PubMed]
    [Google Scholar]
  7. Hahnke S., Maus I., Wibberg D., Tomazetto G., Pühler A., Klocke M., Schlüter A.. 2015; Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor. J Biotechnol193:34–36 [CrossRef][PubMed]
    [Google Scholar]
  8. Hanreich A., Schimpf U., Zakrzewski M., Schlüter A., Benndorf D., Heyer R., Rapp E., Pühler A., Reichl U., Klocke M.. 2013; Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol36:330–338 [CrossRef][PubMed]
    [Google Scholar]
  9. Hasegawa M., Kishino H., Yano T.. 1985; Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol22:160–174 [CrossRef][PubMed]
    [Google Scholar]
  10. Huss V. A., Festl H., Schleifer K. H.. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  11. Kampmann K., Ratering S., Kramer I., Schmidt M., Zerr W., Schnell S.. 2012; Unexpected stability of Bacteroidetes and Firmicutes communities in laboratory biogas reactors fed with different defined substrates. Appl Environ Microbiol78:2106–2119 [CrossRef][PubMed]
    [Google Scholar]
  12. Kampmann K., Ratering S., Geißler-Plaum R., Schmidt M., Zerr W., Schnell S.. 2014; Changes of the microbial population structure in an overloaded fed-batch biogas reactor digesting maize silage. Bioresour Technol174:108–117 [CrossRef][PubMed]
    [Google Scholar]
  13. Klang J., Theuerl S., Szewzyk U., Huth M., Tölle R., Klocke M.. 2015; Dynamic variation of the microbial community structure during the long-time mono-fermentation of maize and sugar beet silage. Microb Biotechnol8:764–775 [CrossRef][PubMed]
    [Google Scholar]
  14. Kodama Y., Shimoyama T., Watanabe K.. 2012; Dysgonomonas oryzarvi sp. nov., isolated from a microbial fuel cell. Int J Syst Evol Microbiol62:3055–3059 [CrossRef][PubMed]
    [Google Scholar]
  15. Koeck D. E., Zverlov V. V., Liebl W., Schwarz W. H.. 2014; 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]
  16. Krause L., Diaz N. N., Edwards R. A., Gartemann K. H., Krömeke H., Neuweger H., Pühler A., Runte K. J., Schlüter A., other authors. 2008; Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J Biotechnol136:91–101 [CrossRef][PubMed]
    [Google Scholar]
  17. Krieg N. R., Ludwig W., Euzéby J., Whitman W. B.. 2010; Phylum XIV. Bacteroidetes phyl. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn.Vol. 4 p25Edited by Krieg N. R., Staley J. T., Brown D. R., Hedlund B. P., Paster B. J., Ward N., Ludwig W., Whitman W. B.. New York: Springer; [CrossRef]
    [Google Scholar]
  18. Kröber M., Bekel T., Diaz N. N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K. J., Viehöver P., other authors. 2009; Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol142:38–49 [CrossRef][PubMed]
    [Google Scholar]
  19. Kuykendall L. D., Roy M. A., O'Neill J. J., Devine T. E.. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol38:358–361 [CrossRef]
    [Google Scholar]
  20. Lee Y.-J., Romanek C. S., Wiegel J.. 2007; Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment. Int J Syst Evol Microbiol57:311–315 [CrossRef][PubMed]
    [Google Scholar]
  21. Li T., Mazéas L., Sghir A., Leblon G., Bouchez T.. 2009; Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions. Environ Microbiol11:889–904 [CrossRef][PubMed]
    [Google Scholar]
  22. Liu F. H., Wang S. B., Zhang J. S., Zhang J., Yan X., Zhou H. K., Zhao G. P., Zhou Z. H.. 2009; The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J Appl Microbiol106:952–966 [CrossRef][PubMed]
    [Google Scholar]
  23. 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 Res32:1363–1371 [CrossRef][PubMed]
    [Google Scholar]
  24. Mesbah M., Premachandran U., Whitman W. B.. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol39:159–167 [CrossRef]
    [Google Scholar]
  25. Miller G. I.. 1959; Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem31:426–428 [CrossRef]
    [Google Scholar]
  26. Miller L. T.. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol16:584–586[PubMed]
    [Google Scholar]
  27. Mumme J., Linke B., Tölle R.. 2010; Novel upflow anaerobic solid-state (UASS) reactor. Bioresour Technol101:592–599 [CrossRef][PubMed]
    [Google Scholar]
  28. Pramono A. K., Sakamoto M., Iino T., Hongoh Y., Ohkuma M.. 2015; Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus. Int J Syst Evol Microbiol65:681–685 [CrossRef][PubMed]
    [Google Scholar]
  29. Rademacher A., Zakrzewski M., Schlüter A., Schönberg M., Szczepanowski R., Goesmann A., Pühler A., Klocke M.. 2012; Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol Ecol79:785–799 [CrossRef][PubMed]
    [Google Scholar]
  30. Sakamoto M., Suzuki M., Umeda M., Ishikawa I., Benno Y.. 2002; Reclassification of Bacteroides forsythus (Tanner et al. 1986) as Tannerella forsythensis corrig., gen. nov., comb. nov. Int J Syst Evol Microbiol52:841–849[PubMed]
    [Google Scholar]
  31. Sánchez-Andrea I., Sanz J. L., Stams A. J.. 2014; Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond. Int J Syst Evol Microbiol64:3936–3942 [CrossRef][PubMed]
    [Google Scholar]
  32. Schlüter A., Bekel T., Diaz N. N., Dondrup M., Eichenlaub R., Gartemann K. H., Krahn I., Krause L., Krömeke H., other authors. 2008; The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol136:77–90 [CrossRef][PubMed]
    [Google Scholar]
  33. Smibert R. M., Krieg N. R.. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp607–654Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R.. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  34. St-Pierre B., Wright A. D.. 2014; Comparative metagenomic analysis of bacterial populations in three full-scale mesophilic anaerobic manure digesters. Appl Microbiol Biotechnol98:2709–2717 [CrossRef][PubMed]
    [Google Scholar]
  35. Tamaoka J., Komagata K.. 1984; Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett25:125–128 [CrossRef]
    [Google Scholar]
  36. Theuerl S., Kohrs F., Benndorf D., Maus I., Wibberg D., Schlüter A., Kausmann R., Heiermann M., Rapp E., other authors. 2015; Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome. Appl Microbiol Biotechnol99:7791–7803 [CrossRef][PubMed]
    [Google Scholar]
  37. 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]
  38. Ueki A., Akasaka H., Suzuki D., Ueki K.. 2006; Paludibacter propionicigenes gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, propionate-producing bacterium isolated from plant residue in irrigated rice-field soil in Japan. Int J Syst Evol Microbiol56:39–44 [CrossRef][PubMed]
    [Google Scholar]
  39. Wagener K., Drillich M., Baumgardt S., Kämpfer P., Busse H.-J., Ehling-Schulz M.. 2014; Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988. Int J Syst Evol Microbiol64:642–649 [CrossRef][PubMed]
    [Google Scholar]
  40. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., other authors. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37:463–464 [CrossRef]
    [Google Scholar]
  41. Wood T. M.. 1988; Preparation of crystalline, amorphous, and dyed cellulase substrates. Methods Enzymol160:19–25 [CrossRef]
    [Google Scholar]
  42. Yang Y. J., Zhang N., Ji S. Q., Lan X., Zhang K. D., Shen Y. L., Li F. L., Ni J. F.. 2014; Dysgonomonas macrotermitis sp. nov., isolated from the hindgut of a fungus-growing termite. Int J Syst Evol Microbiol64:2956–2961 [CrossRef][PubMed]
    [Google Scholar]
  43. Yarza P., Richter M., Peplies J., Euzéby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R.. 2008; The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol31:241–250 [CrossRef][PubMed]
    [Google Scholar]
  44. Zakrzewski M., Goesmann A., Jaenicke S., Jünemann S., Eikmeyer F., Szczepanowski R., Al-Soud W. A., Sørensen S., Pühler A., Schlüter A.. 2012; Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol158:248–258 [CrossRef][PubMed]
    [Google Scholar]
  45. Ziganshin A. M., Liebetrau J., Pröter J., Kleinsteuber S.. 2013; Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biotechnol97:5161–5174 [CrossRef][PubMed]
    [Google Scholar]
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