1887

Abstract

An anaerobic bacterial strain, designated MA18, was isolated from a laboratory-scale biogas fermenter fed with maize silage. Cells stained Gram-negative and performed Gram-negative in the KOH test. The peptidoglycan type was found to be A1y-meso-Dpm direct. The major cellular fatty acids were C iso, C iso, anteiso and iso DMA as well as a C unidentified fatty acid. Oxidase and catalase activities were absent. Cells were slightly curved rods, motile, formed spores and measured approximately 0.35 µm in diameter and 3.0–5.0 µm in length. When cultivated on GS2 agar with cellobiose, round, arched, shiny and slightly yellow-pigmented colonies were formed. The isolate was mesophilic to moderately thermophilic with a growth optimum between 40 and 48 °C. Furthermore, neutral pH values were preferred and up to 1.2 % (w/v) NaCl supplemented to the GS2 medium was tolerated. Producing mainly acetate and ethanol, MA18 fermented arabinose, cellobiose, crystalline and amorphous cellulose, ribose, and xylan. The genome of MA18 consists of 4 817 678 bp with a G+C content of 33.16 mol%. In the annotated protein sequences, cellulosomal components were detected. Phylogenetically, MA18 is most closely related to DSM 19573 (76.88 % average nucleotide identity of the whole genome sequence; 97.23 % 16S rRNA gene sequence similarity) and can be clustered into one clade with other species of the genus , family , class . Based on morphological, physiological and genetic characteristics, this strain represents a novel species in the genus . Therefore, the name sp. nov. is proposed. The type strain is MA18 (=DSM 109966=JCM 39124).

Funding
This study was supported by the:
  • Bundesministerium für Ernährung und Landwirtschaft (Award 22021715)
    • Principle Award Recipient: WolfgangLiebl
  • Bundesministerium für Ernährung und Landwirtschaft (Award 22021715)
    • Principle Award Recipient: VladimirV. Zverlov
  • German Federal Ministry of Food and Agriculture (Award 22021715)
    • Principle Award Recipient: ReginaRettenmaier
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2021-02-08
2021-10-16
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References

  1. Zverlov VV, Hiegl W, Köck DE, Kellermann J, Köllmeier T et al. Hydrolytic bacteria in mesophilic and thermophilic degradation of plant biomass. Eng Life Sci 2010; 10:528–536 [View Article]
    [Google Scholar]
  2. Antoni D, Zverlov VV, Schwarz WH. Biofuels from microbes. Appl Microbiol Biotechnol 2007; 77:23–35 [View Article]
    [Google Scholar]
  3. Koeck DE, Pechtl A, Zverlov VV, Schwarz WH. Genomics of cellulolytic bacteria. Curr Opin Biotechnol 2014; 29:171–183 [View Article][PubMed]
    [Google Scholar]
  4. Yutin N, Galperin MY. A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia . Environ Microbiol 2013; 15:2631–2641 [View Article][PubMed]
    [Google Scholar]
  5. Zhang X, Tu B, Dai L-R, Lawson PA, Zheng Z-Z et al. Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov. Int J Syst Evol Microbiol 2018; 68:3197–3211 [View Article][PubMed]
    [Google Scholar]
  6. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 68, part 10 of the IJSEM. Int J Syst Evol Microbiol 2019; 69:10–12 [View Article][PubMed]
    [Google Scholar]
  7. Tindall BJ. The names Hungateiclostridium Zhang et al. 2018, Hungateiclostridium thermocellum (Viljoen et al. 1926) Zhang et al. 2018, Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 contravene Rule 51b of the international code of nomenclature of prokaryotes and require replacement names in the genus Acetivibrio Patel et al. 1980. Int J Syst Evol Microbiol 2019; 69:3927–3932 [View Article][PubMed]
    [Google Scholar]
  8. Hungate RE. Studies on cellulose fermentation: I. the culture and physiology of an anaerobic Cellulose-digesting bacterium. J Bacteriol 1944; 48:499–513 [View Article][PubMed]
    [Google Scholar]
  9. Dassa B, Borovok I, Lombard V, Henrissat B, Lamed R et al. Pan-Cellulosomics of Mesophilic Clostridia: variations on a theme. Microorganisms 2017; 5:E74 [View Article][PubMed]
    [Google Scholar]
  10. Tindall BJ. Replacement of the illegitimate genus name Hungateiclostridium Zhang et al. 2018 in Hungateiclostridium mesophilum Rettenmaier et al. 2019 by Acetivibrio Patel et al. 1980, creating Acetivibrio mesophilus (Rettenmaier et al. 2019). Int J Syst Evol Microbiol 2019; 69:3967–3968 [View Article][PubMed]
    [Google Scholar]
  11. Rettenmaier R, Gerbaulet M, Liebl W, Zverlov VV. Hungateiclostridium mesophilum sp. nov., a mesophilic, cellulolytic and spore-forming bacterium isolated from a biogas fermenter fed with maize silage. Int J Syst Evol Microbiol 2019; 69:3567–3573 [View Article][PubMed]
    [Google Scholar]
  12. Rettenmaier R, Duerr C, Neuhaus K, Liebl W, Zverlov VV. Comparison of sampling techniques and different media for the enrichment and isolation of cellulolytic organisms from biogas fermenters. Syst Appl Microbiol 2019; 42:481–487 [View Article][PubMed]
    [Google Scholar]
  13. Johnson EA, Madia A, Demain AL. Chemically defined minimal medium for growth of the Anaerobic Cellulolytic thermophile Clostridium thermocellum . Appl Environ Microbiol 1981; 41:1060–1062 [View Article][PubMed]
    [Google Scholar]
  14. Koeck DE, Ludwig W, Wanner G, Zverlov VV, Liebl W et al. Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. Int J Syst Evol Microbiol 2015; 65:2365–2371 [View Article][PubMed]
    [Google Scholar]
  15. Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening-Röser A et al. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol 1998; 64:3042–3051 [View Article][PubMed]
    [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  17. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. mega X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  18. Felsenstein J. Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 1981; 35:1229–1242 [View Article][PubMed]
    [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  20. Camin JH, Sokal RR. A method for deducing branching sequences in phylogeny. Evolution 1965; 19:311–326 [View Article]
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  22. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  23. Nishiyama T, Ueki A, Kaku N, Ueki K. Clostridium sufflavum sp. nov., isolated from a methanogenic reactor treating cattle waste. Int J Syst Evol Microbiol 2009; 59:981–986 [View Article][PubMed]
    [Google Scholar]
  24. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F-J et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154 [View Article][PubMed]
    [Google Scholar]
  25. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  26. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. Refseq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article][PubMed]
    [Google Scholar]
  27. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  28. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
    [Google Scholar]
  29. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article][PubMed]
    [Google Scholar]
  30. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H et al. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999; 27:29–34 [View Article][PubMed]
    [Google Scholar]
  31. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 2020; 36:2251–2252 [View Article][PubMed]
    [Google Scholar]
  32. Klingl A, Moissl-Eichinger C, Wanner G, Zweck J, Huber H et al. Analysis of the surface proteins of Acidithiobacillus ferrooxidans strain SP5/1 and the new, pyrite-oxidizing Acidithiobacillus isolate HV2/2, and their possible involvement in pyrite oxidation. Arch Microbiol 2011; 193:867–882 [View Article][PubMed]
    [Google Scholar]
  33. Schuster JA, Klingl A, Vogel RF, Ehrmann MA. Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov. Syst Appl Microbiol 2019; 42:126023 [View Article][PubMed]
    [Google Scholar]
  34. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72:248–254 [View Article][PubMed]
    [Google Scholar]
  35. Baudrexl M, Schwarz WH, Zverlov VV, Liebl W. Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium . Sci Rep 2019; 9:15924 [View Article][PubMed]
    [Google Scholar]
  36. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
    [Google Scholar]
  37. Monserrate E, Leschine SB, Canale-Parola E. Clostridium hungatei sp. nov., a mesophilic, N2-fixing cellulolytic bacterium isolated from soil. Int J Syst Evol Microbiol 2001; 51:123–132 [View Article][PubMed]
    [Google Scholar]
  38. Sukhumavasi J, Ohmiya K, Shimizu S, Ueno K. Clostridium josui sp. nov., a cellulolytic, moderate thermophilic species from thai compost. Int J Syst Bacteriol 1988; 38:179–182 [View Article]
    [Google Scholar]
  39. Madden RH, Bryder MJ, Poole NJ. Isolation and characterization of an anaerobic, cellulolytic bacterium, Clostridium papyrosolvens sp. nov. Int J Syst Bacteriol 1982; 32:87–91 [View Article]
    [Google Scholar]
  40. Petitdemange E, Caillet F, Giallo J, Gaudin C. Clostridium cellulolyticum sp. nov., a cellulolytic, mesophilic: species from decayed grass. Int J Syst Bacteriol 1984; 34:155–159 [View Article]
    [Google Scholar]
  41. Hethener P, Brauman A, Garcia J-L. Clostridium termitidis sp. nov., a cellulolytic bacterium from the gut of the Wood-feeding termite, Nasutitermes lujae. Syst Appl Microbiol 1992; 15:52–58 [View Article]
    [Google Scholar]
  42. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
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