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Abstract

An acid/alcohol-producing, Gram-stain-positive, obligately anaerobic, rod-shaped, non-motile, non-spore forming acetogen, designated as strain P21, was isolated from old hay after enrichment with CO as the substrate. Spores not observed even after prolonged incubation (30 days). Phylogenetic analysis of the 16S rRNA gene sequence of strain P21 showed it was closely related to DSM 15243 (97.9%), DSM 757 (97.7 %) and DSM 12750 (97.7 %). The genome is 5.6 Mb and the G+C content is 29.4 mol%. Average nucleotide identity between strain P21, , and was 87.1, 86.4, 86.4 %, respectively. Strain P21 grew on CO:CO, H:CO, -arabinose, ribose, xylose, fructose, galactose, glucose, lactose, mannose, cellobiose, sucrose, cellulose, starch, pyruvate, choline, glutamate, histidine, serine, threonine and casamino acids. End products of metabolism were acetate, butyrate, caproate, ethanol and hexanol. Dominant cellular fatty acids (>10 %) were C (41.5 %), C ω7/C ω6 (10.0 %), and a summed feature containing cyclo C/C (17.3 %). Based on the phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain P21 represents a new species in the genus , for which the name sp. nov. is proposed. The type strain is P21 (=DSM 111390=NCIMB 15261).

Keyword(s): acetogens , Clostridium and CO-oxidizing
Funding
This study was supported by the:
  • Cooperative State Research, Education, and Extension Service (Award 01-34447-10302)
    • Principle Award Recipient: RalphS. Tanner
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2022-03-30
2024-10-13
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References

  1. Drake HL. Acetogenesis Boston, MA: Chapman & Hall; 1994 [View Article]
    [Google Scholar]
  2. Fischer F, Lieske R, Winzer K. Biologische gasreaktionen. II. über die bildung von essigsäure bei der biologischen umsetzung von kohlenoxyd und kohlensäure mit wasserstoff zu methan. Biochem 1932; 245:2–12
    [Google Scholar]
  3. Drake HL, Gössner AS, Daniel SL. Old acetogens, new light. Ann N Y Acad Sci 2008; 1125:100–128 [View Article] [PubMed]
    [Google Scholar]
  4. Braun M, Mayer F, Gottschalk G. Clostridium aceticum (Wieringa), a microorganism producing acetic acid from molecular hydrogen and carbon dioxide. Arch Microbiol 1981; 128:288–293 [View Article] [PubMed]
    [Google Scholar]
  5. Tanner RS, Miller LM, Yang D. Clostridium ljungdahlii sp. nov., an acetogenic species in clostridial rRNA homology group I. Int J Syst Bacteriol 1993; 43:232–236 [View Article] [PubMed]
    [Google Scholar]
  6. Liou J-C, Balkwill DL, Drake GR, Tanner RS. Clostridium carboxidivorans sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei sp. nov. Int J Syst Evol Microbiol 2005; 55:2085–2091 [View Article]
    [Google Scholar]
  7. Hungate RE. A roll-tube method for cultivation of strict anaerobes. Methods Microbiol 1969; 3B:117–132
    [Google Scholar]
  8. Tanner RS et al. Cultivation of bacteria and fungi. In Hurst CJ, Crawford RL, Garland JL, Lipson DA, Mills AL. eds Manual of Environmental Microbiology, 3rd edn. Washington, DC: ASM Press; 2007 pp 69–78
    [Google Scholar]
  9. Saxena J, Tanner RS. Effect of trace metals on ethanol production from synthesis gas by the ethanologenic acetogen, Clostridium ragsdalei. J Ind Microbiol Biotechnol 2011; 38:513–521 [View Article] [PubMed]
    [Google Scholar]
  10. Oldham AL, Drilling HS, Stamps BW, Stevenson BS, Duncan KE. Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities. AMB Express 2012; 2:60–71 [View Article] [PubMed]
    [Google Scholar]
  11. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  12. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  13. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2016; 44:D67–72 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Stecher G, Tamura K, Kumar S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol Biol Evol 2020; 37:1237–1239 [View Article] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Doyle DA, Duncan KE, Tanner RS. Genome Sequence of Clostridium sp. Strain P21, a CO-Fermenting Acetogen Isolated from Old Hay. Microbiol Resour Announc 2021; 10:e00864-20 [View Article] [PubMed]
    [Google Scholar]
  22. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  24. Koransky JR, Allen SD, Dowell VR Jr. Use of ethanol for selective isolation of sporeforming microorganisms. Appl Environ Microbiol 1978; 35:762–765 [View Article] [PubMed]
    [Google Scholar]
  25. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. Methods for General and Molecular Microbiology, 3rd edn. Washington, DC, USA: ASM Press; 2007
    [Google Scholar]
  26. Girgis HS, Liu Y, Ryu WS, Tavazoie S, Guttman DS. A comprehensive genetic characterization of bacterial motility. PLoS Genet 2007; 3:e154 [View Article] [PubMed]
    [Google Scholar]
  27. Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI et al. Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ Microbiol 2012; 14:2870–2890 [View Article]
    [Google Scholar]
  28. Rainey F, Hollen B, Small A. Genus I. Clostridium. In Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W. eds Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp 738–828
    [Google Scholar]
  29. Diallo M, Kengen S, López-Contreras A. Sporulation in solventogenic and acetogenic clostridia. Appl Microbiol Biot 2021; 105:3533–3557 [View Article]
    [Google Scholar]
  30. Liu K, Atiyeh HK, Tanner RS, Wilkins MR, Huhnke RL. Fermentative production of ethanol from syngas using novel moderately alkaliphilic strains of Alkalibaculum bacchi. Bioresour Technol 2012; 104:336–341 [View Article] [PubMed]
    [Google Scholar]
  31. Phillips JR, Atiyeh HK, Tanner RS, Torres JR, Saxena J et al. Butanol and hexanol production in Clostridium carboxidivorans syngas fermentation: Medium development and culture techniques. Bioresour Technol 2015; 190:114–121 [View Article] [PubMed]
    [Google Scholar]
  32. Truffaut N, Hubert J, Reysset G. Construction of shuttle vectors useful for transforming Clostridium acetobutylicum. FEMS Microbiol Lett 1989; 58:15–19 [View Article]
    [Google Scholar]
  33. Patel NB, Tito RY, Obregón-Tito AJ, O’Neal L, Trujillo-Villaroel O et al. Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru. Anaerobe 2015; 32:43–48 [View Article]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  36. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
    [Google Scholar]
  37. Whitman WB. Chapter 1 the need for change embracing the genome. Method Microbiol 2014; 41:1–12
    [Google Scholar]
  38. Amaral GRS, Dias GM, Wellington-Oguri M, Chimetto L, Campeão ME et al. Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 2014; 64:357–365 [View Article] [PubMed]
    [Google Scholar]
  39. Barona-Gómez F, Cruz-Morales P, Noda-García L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics?. Antonie van Leeuwenhoek 2012; 101:35–43 [View Article] [PubMed]
    [Google Scholar]
  40. Fotedar R, Caldwell ME, Sankaranarayanan K, Al-Zeyara A, Al-Malki A et al. Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf. Int J Syst Evol Microbiol 2020; 70:4130–4138 [View Article]
    [Google Scholar]
  41. Lawson PA, Patel NB. The strength of chemotaxonomy. In Bridge P, Smith D, Stackebrandt E. eds Trends in the Systematics of Bacteria and Fungi CABI Publishing UK; 2021 pp 141–167
    [Google Scholar]
  42. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article] [PubMed]
    [Google Scholar]
  43. Sohlenkamp C, Geiger O. Bacterial membrane lipids: diversity in structures and pathways. FEMS Microbiol Rev 2016; 40:133–159 [View Article] [PubMed]
    [Google Scholar]
  44. Goldfine H, Johnston N. Membrane lipids of clostridia. In Durre P. eds Handbook on Clostridia Boca Raton, FL: Taylor and Francis; 2005 pp 297–310
    [Google Scholar]
  45. Schumann P. Peptidoglycan structure. In Rainey F, Oren A. eds Taxonomy of Prokaryotes Academic Press; 2011 pp 101–129
    [Google Scholar]
  46. Schuchmann K, Müller V. Energetics and application of heterotrophy in acetogenic bacteria. Appl Environ Microbiol 2016; 82:4056–4069 [View Article] [PubMed]
    [Google Scholar]
  47. Westphal L, Wiechmann A, Baker J, Minton NP, Müller V. The Rnf complex is an energy-coupled transhydrogenase essential to reversibly link cellular NADH and ferredoxin pools in the acetogen Acetobacterium woodii. J Bacteriol 2018; 200:e00357-18 [View Article] [PubMed]
    [Google Scholar]
  48. UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article]
    [Google Scholar]
  49. Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
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