1887

Abstract

A strictly anaerobic, thermophilic, Gram-stain-negative bacterium, named as strain S15, was isolated from oily sludge of Shengli oilfield in PR China. Cells of strain S15 were straight or slightly curved rods with 0.4–0.8 µm width × 1.4–3 µm length and occurred mostly in pairs or short chains. Endospore-formation was not observed. The strain grew optimally at 55 °C (range from 30–65 °C), pH 6.5 (pH 6.0–8.5) and 0–30 g l NaCl (optimum with 10 g l NaCl). Yeast extract was an essential growth factor for strain S15. The major cellular fatty acid was iso-C (58.2 %), and the main polar lipids were amino phospholipid (APL), glycolipids (GLs) and phosphatidylethanolamine (PE). The G+C content of DNA of strain S15 was 52.2 mol%. Strain S15 shared 89.8 % 16S rRNA gene similarity with the most related organism DSM 22491 in the phylum . The paired genomic average amino acid identity (AAI) and percentage of conserved proteins (POCP) values showed relatedness of less than 58.0 and 39.7 % with type strains of the species in the phylum . On the basis of phenotypic, phylogenetic and phylogenomic evidences, strain S15 constitutes a novel species in a novel genus, for the name gen. nov., sp. nov. is proposed. The type strain is S15 (=CCAM 583=JCM 33159). fam. nov. is also proposed.

Funding
This study was supported by the:
  • Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CN) (Award 1610012017002_05103, Y2021PT02)
    • Principle Award Recipient: LeiCheng
  • Agricultural Science and Technology Innovation Project of the Chinese Academy of Agriculture Science (Award CAAS-ASTIP-2016-BIOMA)
    • Principle Award Recipient: LeiCheng
  • Sichuan Science and Technology Program (Award 2019YFH0037)
    • Principle Award Recipient: LeiCheng
  • National Natural Science Foundation of China (Award 92051108,31570009)
    • Principle Award Recipient: LeiCheng
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005031
2021-09-28
2021-10-24
Loading full text...

Full text loading...

References

  1. Jumas-Bilak E, Roudière L, Marchandin H. Description of “Synergistetes” phyl. nov. and emended description of the phylum “Deferribacteres” and of the family Syntrophomonadaceae, phylum Firmicutes . Int J Syst Evol Microbiol 2009; 59:1028–1035 [View Article] [PubMed]
    [Google Scholar]
  2. Díaz C, Baena S, Fardeau M-L, Patel BKC. Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor. Int J Syst Evol Microbiol 2007; 57:1914–1918 [View Article] [PubMed]
    [Google Scholar]
  3. Honda T, Fujita T, Tonouchi A. Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field. Int J Syst Evol Microbiol 2013; 63:3679–3686 [View Article] [PubMed]
    [Google Scholar]
  4. Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P et al. Aminobacterium colombiense gen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge. Anaerobe 1998; 4:241–250 [View Article] [PubMed]
    [Google Scholar]
  5. Baena S, Fardeau ML, Labat M, Ollivier B, Garcia JL et al. Aminobacterium mobile sp. nov., a new anaerobic amino-acid-degrading bacterium. Int J Syst Evol Microbiol 2000; 50:259–264 [View Article] [PubMed]
    [Google Scholar]
  6. Hamdi M, Ben Hania W, Postec A, Bouallagui H, Hamdi M et al. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes. Int J Syst Evol Microbiol 2015; 65:609–614 [View Article] [PubMed]
    [Google Scholar]
  7. Baena S, Fardeau ML, Ollivier B, Labat M, Thomas P et al. Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int J Syst Bacteriol 1999; 49:975–982 [View Article] [PubMed]
    [Google Scholar]
  8. Menes RJ, Muxí L. Anaerobaculum mobile sp. nov., a novel anaerobic, moderately thermophilic, peptide-fermenting bacterium that uses crotonate as an electron acceptor, and emended description of the genus Anaerobaculum . Int J Syst Evol Microbiol 2002; 52:157–164 [View Article] [PubMed]
    [Google Scholar]
  9. Rees GN, Patel BKC, Grassia GS, Sheehy AJ. Anaerobaculum thermoterrenum gen. nov., sp. nov., a novel, thermophilic bacterium which ferments citrate. Int J Syst Evol Microbiol 1997; 47:150–154
    [Google Scholar]
  10. Soutschek E, Winter J, Schindler F, Kandler O. Acetomicrobium flavidum, gen. nov., sp. nov., a thermophilic, anaerobic bacterium from sewage sludge, forming acetate, CO2 and H2 from Glucose. Syst Appl Microbiol 1984; 5:377–390 [View Article]
    [Google Scholar]
  11. Hania WB, Bouanane-Darenfed A, Cayol JL, Ollivier B, Fardeau ML. Reclassification of Anaerobaculum mobile, Anaerobaculum thermoterrenum, Anaerobaculum hydrogeniformans as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively, and emendation of the genus Acetomicrobium . Int J Syst Evol Microbiol 2016; 66:1506 [View Article] [PubMed]
    [Google Scholar]
  12. Ganesan A, Chaussonnerie S, Tarrade A, Dauga C, Bouchez T et al. Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum ‘Synergistetes’, isolated from an anaerobic sludge digester. Int J Syst Evol Microbiol 2008; 58:2003–2012 [View Article] [PubMed]
    [Google Scholar]
  13. Looft T, Levine UY, Stanton TB. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus . Int J Syst Evol Microbiol 2013; 63:1960–1966 [View Article] [PubMed]
    [Google Scholar]
  14. Surkov AV, Dubinina GA, Lysenko AM, Glöckner FO, Kuever J. Dethiosulfovibrio russensis sp. nov., Dethosulfovibrio marinus sp. nov. and Dethosulfovibrio acidaminovorans sp. nov., novel anaerobic, thiosulfate- and sulfur-reducing bacteria isolated from “Thiodendron” sulfur mats in different saline environments. Int J Syst Evol Microbiol 2001; 51:327–337 [View Article] [PubMed]
    [Google Scholar]
  15. Magot M, Ravot G, Campaignolle X, Ollivier B, Patel BK et al. Dethiosulfovibrio peptidovorans gen. nov., sp. nov., a new anaerobic, slightly halophilic, thiosulfate-reducing bacterium from corroding offshore oil wells. Int J Syst Bacteriol 1997; 47:818–824 [View Article] [PubMed]
    [Google Scholar]
  16. Díaz-Cárdenas C, López G, Patel BKC, Baena S. Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring. Int J Syst Evol Microbiol 2010; 60:850–853 [View Article] [PubMed]
    [Google Scholar]
  17. Vartoukian SR, Downes J, Palmer RM, Wade WG. Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2013; 63:458–463 [View Article] [PubMed]
    [Google Scholar]
  18. Jumas-Bilak E, Carlier J-P, Jean-Pierre H, Citron D, Bernard K et al. Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum ‘Synergistetes’ isolated from man. Int J Syst Evol Microbiol 2007; 57:2743–2748 [View Article] [PubMed]
    [Google Scholar]
  19. Qiu YL, Hanada S, Kamagata Y, Guo RB, Sekiguchi Y. Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate- and amino-acid-degrading bacterium in the phylum Synergistetes . Int J Syst Evol Microbiol 2014; 64:2137–2145 [View Article] [PubMed]
    [Google Scholar]
  20. Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T et al. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum ‘Synergistetes’ isolated from the human oral cavity. Int J Syst Evol Microbiol 2009; 59:972–980 [View Article] [PubMed]
    [Google Scholar]
  21. Allison MJ, Mayberry WR, McSweeney CS, Stahl DA. Synergistes jonesii, gen. nov., sp.nov.: A Rumen Bacterium That Degrades Toxic Pyridinediols. Syst Appl Microbiol 1992; 15:522–529 [View Article]
    [Google Scholar]
  22. Zavarzina DG, Zhilina TN, Tourova TP, Kuznetsov BB, Kostrikina NA et al. Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio . Int J Syst Evol Microbiol 2000; 50:1287–1295 [View Article] [PubMed]
    [Google Scholar]
  23. Dahle H, Birkeland N-K. Thermovirga lienii gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, amino-acid-degrading bacterium isolated from a North Sea oil well. Int J Syst Evol Microbiol 2006; 56:1539–1545 [View Article] [PubMed]
    [Google Scholar]
  24. Jumas-Bilak E, Marchandin H. The phylum Synergistetes . Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F. eds In The Prokaryotes: Other Major Lineages of Bacteria and the Archaea Berlin, Heidelberg: Springer Berlin Heidelberg; 2014 pp 931–954
    [Google Scholar]
  25. Godon J-J, Morinière J, Moletta M, Gaillac M, Bru V et al. Rarity associated with specific ecological niches in the bacterial world: the ‘Synergistes’ example. Environ Microbiol 2005; 7:213–224 [View Article] [PubMed]
    [Google Scholar]
  26. Bhandari V, Gupta RS. Molecular signatures for the phylum Synergistetes and some of its subclades. Antonie Van Leeuwenhoek 2012; 102:517–540 [View Article] [PubMed]
    [Google Scholar]
  27. Vartoukian SR, Palmer RM, Wade WG. Cultivation of a Synergistetes strain representing a previously uncultivated lineage. Environ Microbiol 2010; 12:916–928 [View Article] [PubMed]
    [Google Scholar]
  28. Rivière D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S et al. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 2009; 3:700–714 [View Article] [PubMed]
    [Google Scholar]
  29. Ito T, Yoshiguchi K, Ariesyady HD, Okabe S. Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME J 2011; 5:1844–1856 [View Article] [PubMed]
    [Google Scholar]
  30. Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL et al. A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J 2008; 2:1146–1156 [View Article] [PubMed]
    [Google Scholar]
  31. Cheng L, He Q, Ding C, Dai LR, Li Q et al. Novel bacterial groups dominate in a thermophilic methanogenic hexadecane-degrading consortium. FEMS Microbiol Ecol 2013; 85:568–577 [View Article] [PubMed]
    [Google Scholar]
  32. Parks D, Chuvochina M, Chaumeil P-A, Rinke C, Mussig A et al. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol 2020; 38:1079–1086 [View Article] [PubMed]
    [Google Scholar]
  33. Hungate RE. Chapter IV A Roll tube method for cultivation of strict anaerobes. Norris J, Ribbons D. eds In Methods in Microbiology Academic Press; 1969 pp 117–132
    [Google Scholar]
  34. Kuykendall L, Roy M, O’Neill J, Devine T. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  35. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  36. Tindall B, Sikorski J, Smibert R, Krieg N. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. edn American Society of Microbiology; 2007
    [Google Scholar]
  37. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  38. Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics; Stackebrandt 1991115–175
    [Google Scholar]
  39. 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]
  40. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945
    [Google Scholar]
  41. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  42. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  43. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  44. Eddy SR. Accelerated profile HMM Searches. PLoS Comput Biol 2011; 7:e1002195 [View Article] [PubMed]
    [Google Scholar]
  45. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article] [PubMed]
    [Google Scholar]
  46. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:2304 [View Article] [PubMed]
    [Google Scholar]
  47. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  48. 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]
  49. Maune MW, Tanner RS. Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum . Int J Syst Evol Microbiol 2012; 62:832–838 [View Article] [PubMed]
    [Google Scholar]
  50. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  51. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
    [Google Scholar]
  52. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High-throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun225342
    [Google Scholar]
  53. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005031
Loading
/content/journal/ijsem/10.1099/ijsem.0.005031
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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