1887

Abstract

Strain AMP has been previously suggested as a strain of the species Jiang . 2009 (based on the high 16S rRNA gene identity, 98.3 %). However, genome-based phylogenetic analysis of strain AMP reveals that this bacterium is in fact a novel species of the genus . Genome relatedness indices between strain AMP and DSM 521 were below the minimum threshold values required to consider them members of the same species (digital DNA–DNA hybridization, 52.2 % (<70%); average nucleotide identity, 93.2 % (<95%)). Based on phylogenetic and phenotypic results we recommend that strain AMP (DSM 21394=JCM 35360) should be classified as representing new species, for which we propose the name sp. nov.

Funding
This study was supported by the:
  • Ministerie van Onderwijs, Cultuur en Wetenschap (Award 024.002.002)
    • Principle Award Recipient: AlfonsJ.M. Stams
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-05-26
2024-04-20
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References

  1. Fontaine FE, Peterson WH, McCoy E, Johnson MJ, Ritter GJ. A new type of glucose fermentation by Clostridium thermoaceticum. J Bacteriol 1942; 43:701–715 [View Article]
    [Google Scholar]
  2. Andreese JR, Schaupp A, Neurauter C, Brown A, Brown LG. Fermentation of glucose, fructose, and xylose by Clostridium thermoaceticum: effect of metals on growth yield, enzymes, and the synthesis of acetate from CO2. J Bacteriol 1973; 114:743–751 [View Article]
    [Google Scholar]
  3. Schaupp A, Ljungdahl LG. Purification and properties of acetate kinase from Clostridium thermoaceticum. Arch Microbiol 1974; 100:121–129 [View Article] [PubMed]
    [Google Scholar]
  4. Diekert GB, Thauer RK. Carbon monoxide oxidation by Clostridium thermoaceticum and Clostridium formicoaceticum. J Bacteriol 1978; 136:597–606 [View Article] [PubMed]
    [Google Scholar]
  5. Wang SN, Huang HY, Kahnt J, Thauer RK. A reversible electron-bifurcating ferredoxin- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Moorella thermoacetica. J Bacteriol 2013; 195:1267–1275 [View Article] [PubMed]
    [Google Scholar]
  6. Kerby R, Zeikus JG. Growth of Clostridium thermoaceticum on H2/CO2 or CO as energy source. Cur Microbiol 1983; 8:27–30 [View Article]
    [Google Scholar]
  7. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826 [View Article] [PubMed]
    [Google Scholar]
  8. Jiang B, Henstra A-M, Paulo PL, Balk M, van Doesburg W et al. Atypical one-carbon metabolism of an acetogenic and hydrogenogenic Moorella thermoacetica strain. Arch Microbiol 2009; 191:123–131 [View Article] [PubMed]
    [Google Scholar]
  9. Redl S, Poehlein A, Esser C, Bengelsdorf FR, Jensen et al. Genome-based comparison of all species of the genus Moorella, and status of the pecies Moorella thermoacetica and Moorella thermoautotrophica. Front Microbiol 2019; 10:3070 [View Article]
    [Google Scholar]
  10. Paulo PL, Jiang B, Rebac S, Hulshoff Pol L, Lettinga G. Thermophilic anaerobic digestion of methanol in UASB reactor. Water Sci Technol 2001; 44:129–136 [View Article]
    [Google Scholar]
  11. Paulo PL, Jiang B, Roest K, van Lier JB, Lettinga G. Start-up of a thermophilic methanol-fed UASB reactor: change in sludge characteristics. Water Sci Technol 2002; 45:145–150 [View Article]
    [Google Scholar]
  12. Stams AJM, Grolle KCF, Frijters CTM, Van Lier JB. Enrichment of thermophilic propionate-oxidizing bacteria in syntrophy with Methanobacterium thermoautotrophicum or Methanobacterium thermoformicicum. Appl Environ Microbiol 1992; 58:346–352 [View Article]
    [Google Scholar]
  13. Paulo PL, Jiang B, Cysneiros D, Stams AJM, Lettinga G. Effect of cobalt on the anaerobic thermophilic conversion of methanol. Biotechnol Bioeng 2004; 85:434–441 [View Article] [PubMed]
    [Google Scholar]
  14. Sayers EW, Cavanaugh M, Clark K, Pruitt KD, Schoch CL et al. GenBank. Nucleic Acids Res 2021; 49:D92–D96 [View Article]
    [Google Scholar]
  15. 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]
  16. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Goker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  17. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  18. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
    [Google Scholar]
  19. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
    [Google Scholar]
  20. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
    [Google Scholar]
  21. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
    [Google Scholar]
  22. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  23. Rodriguez-R LM, Jain C, Conrad RE, Aluru S, Konstantinidis KT. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species.”. Nat Commun 2021; 12: [View Article]
    [Google Scholar]
  24. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
    [Google Scholar]
  25. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  26. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:1–19 [View Article] [PubMed]
    [Google Scholar]
  27. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  28. Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–W235 [View Article]
    [Google Scholar]
  29. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  30. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article]
    [Google Scholar]
  31. Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 1995; 12:546–557 [View Article] [PubMed]
    [Google Scholar]
  32. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences; 1986; 1757–86
  33. Hoang DT, Chernomor O, von A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article]
    [Google Scholar]
  34. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  35. Mukherjee S, Stamatis D, Li CT, Ovchinnikova G, Bertsch J et al. Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9. Nucleic Acids Res 2023; 51:D957–D963 [View Article]
    [Google Scholar]
  36. Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J et al. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res 2023; 51:D723–D732 [View Article] [PubMed]
    [Google Scholar]
  37. Megrian D, Taib N, Witwinowski J, Beloin C, Gribaldo S. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide. Mol Microbiol 2020; 113:659–671 [View Article] [PubMed]
    [Google Scholar]
  38. Alves JI, van Gelder AH, Alves MM, Sousa DZ, Plugge CM. Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge. Int J Syst Evol Microbiol 2013; 63:4072–4076 [View Article] [PubMed]
    [Google Scholar]
  39. Daniel SL, Hsu T, Dean SI, Drake HL. Characterization of the H2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui. J Bacteriol 1990; 172:4464–4471 [View Article] [PubMed]
    [Google Scholar]
  40. Daniel SL, Keith ES, Yang HC, Lin YS, Drake HL. Utilization of methoxylated aromatic compounds by the acetogen Clostridium thermoaceticum: Expression and specificity of the CO-dependent O-demethylating activity. Biochem Biophys Res Commun 1991; 180:416–422 [View Article] [PubMed]
    [Google Scholar]
  41. Daniel SL, Wu ZG, Drake HL. Growth of thermophilic acetogenic bacteria on methoxylated aromatic acids. Fems Microbiol Lett 1988; 52:25–28 [View Article]
    [Google Scholar]
  42. Gossner A, Daniel SL, Drake HL. Acetogenesis coupled to the oxidation of aromatic aldehyde groups. Arch Microbiol 1994; 161:126–131 [View Article]
    [Google Scholar]
  43. Lux MF, Keith E, Hsu TD, Drake HL. Biotransformations of aromatic aldehydes by acetogenic bacteria. FEMS Microbiol Lett 1990; 55:73–77 [View Article] [PubMed]
    [Google Scholar]
  44. Naidu D, Ragsdale SW. Characterization of a three-component vanillate O-demethylase from Moorella thermoacetica. J Bacteriol 2001; 183:3276–3281 [View Article]
    [Google Scholar]
  45. Gottwald M, AndreesenJR JR, JLeGall J, Ljungdahl LG. Presence of cytochrome and menaquinone in Clostridium formicoaceticum and Clostridium thermoaceticum. J Bacteriol 1975; 122:325–328 [View Article]
    [Google Scholar]
  46. Rosenbaum FP, Müller V. Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria. Extremophiles 2021; 25:413–424 [View Article] [PubMed]
    [Google Scholar]
  47. Das A, Silaghi-Dumitrescu R, Ljungdahl LG, Kurtz DM. Cytochrome bd oxidase, oxidative stress, and dioxygen tolerance of the strictly anaerobic bacterium Moorella thermoacetica. J Bacteriol 2005; 187:2020–2029 [View Article] [PubMed]
    [Google Scholar]
  48. Seifritz C, Daniel SL, Gössner A, Drake HL. Nitrate as a preferred electron sink for the acetogen Clostridium thermoaceticum. J Bacteriol 1993; 175:8008–8013 [View Article] [PubMed]
    [Google Scholar]
  49. Balk M, Weijma J, Friedrich MW, Stams AJ. Methanol utilization by a novel thermophilic homoacetogenic bacterium, Moorella mulderi sp. nov., isolated from a bioreactor. Arch Microbiol 2003; 179:315–320 [View Article]
    [Google Scholar]
  50. Slobodkin A, Reysenbach AL, Mayer F, Wiegel J. Isolation and characterization of the homoacetogenic thermophilic bacterium Moorella glycerini sp. nov. Int J Syst Bacteriol 1997; 47:969–974 [View Article] [PubMed]
    [Google Scholar]
  51. Nepomnyashchaya YN, Slobodkina GB, Baslerov RV, Chernyh NA, Bonch-Osmolovskaya EA et al. Moorella humiferrea sp. nov., a thermophilic, anaerobic bacterium capable of growth via electron shuttling between humic acid and Fe(III). Int J Syst Evol Microbiol 2012; 62:613–617 [View Article] [PubMed]
    [Google Scholar]
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