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.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000902
2016-03-01
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/3/1466.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000902&mimeType=html&fmt=ahah

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 Biochem 81: 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 Microbiol 55: 2257–2261 [CrossRef] [PubMed].
    [Google Scholar]
  3. Claus D.. ( 1992;). A standardized Gram staining procedure. World J Microbiol Biotechnol 8: 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 Biochem 12: 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 Microbiol 55: 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 Microbiol 64: 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 Biotechnol 193: 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 Microbiol 36: 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 Evol 22: 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 Microbiol 4: 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 Microbiol 78: 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 Technol 174: 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 Biotechnol 8: 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 Microbiol 62: 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 Microbiol 37: 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 Biotechnol 136: 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, p. 25. Edited 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 Biotechnol 142: 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 Bacteriol 38: 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 Microbiol 57: 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 Microbiol 11: 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 Microbiol 106: 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 Res 32: 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 Bacteriol 39: 159–167 [CrossRef].
    [Google Scholar]
  25. Miller G. I.. ( 1959;). Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31: 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 Microbiol 16: 584–586 [PubMed].
    [Google Scholar]
  27. Mumme J., Linke B., Tölle R.. ( 2010;). Novel upflow anaerobic solid-state (UASS) reactor. Bioresour Technol 101: 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 Microbiol 65: 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 Ecol 79: 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 Microbiol 52: 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 Microbiol 64: 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 Biotechnol 136: 77–90 [CrossRef] [PubMed].
    [Google Scholar]
  33. Smibert R. M., Krieg N. R.. ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited 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 Biotechnol 98: 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 Lett 25: 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 Biotechnol 99: 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 Microbiol 60: 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 Microbiol 56: 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 Microbiol 64: 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 Bacteriol 37: 463–464 [CrossRef].
    [Google Scholar]
  41. Wood T. M.. ( 1988;). Preparation of crystalline, amorphous, and dyed cellulase substrates. Methods Enzymol 160: 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 Microbiol 64: 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 Microbiol 31: 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 Biotechnol 158: 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 Biotechnol 97: 5161–5174 [CrossRef] [PubMed].
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000902
Loading
/content/journal/ijsem/10.1099/ijsem.0.000902
Loading

Data & Media loading...

Supplements

Supplementary Data



PDF

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