1887

Abstract

A Gram-stain-positive, anaerobic, spore-forming, rod-shaped (0.4–0.6 µm×2.5–3.2 µm), flagellated bacterium, designated strain YB-6, was isolated from activated sludge of an anaerobic tank at Weizhou marine oil mining wastewater treatment plant in Beihai, Guangxi, PR China. The culture conditions were 25–45 °C (optimum, 37 °C), pH 4–12 (pH 7.0) and NaCl concentration of 0–7 % w/v (0%). Strain YB-6 grew slowly in petroleum wastewater and removed 68.2 % of the total organic carbon in petroleum wastewater within 10 days. Concentrations of naphthalene, anthracene and phenanthrene at an initial concentration of 50 mg l were reduced by 32.8, 40.4 and 14.6 %, respectively, after 7 days. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YB-6 belongs to cluster I and is most closely related to CK55 (98.5 % similarity). The genome size of strain YB-6 was 3.96 Mb, and the G+C content was 26.5 mol%. The average nucleotide identity value between strain YB-6 and CK55 was 81.9 %. The major fatty acids in strain YB-6 were C FAME, C FAME and summed feature 4 (unknown 14.762 and/or C FAME). The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified aminophospholipids, one unidentified glycolipid and one unidentified aminolipid. Diaminopimelic acid was not detected in the strain YB-6 cell walls. Whole-cell sugars mainly consisted of ribose and galactose. Based on the results of phenotypic and genotypic analyses, strain YB-6 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YB-6 (=GDMCC 1.2529=JCM 34754).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 51978189)
    • Principle Award Recipient: QinglinXie
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005330
2022-04-22
2024-04-24
Loading full text...

Full text loading...

References

  1. Liu L, Jiao J-Y, Fang B-Z, Lv A-P, Ming Y-Z et al. Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production. Syst Appl Microbiol 2020; 43:126104 [View Article] [PubMed]
    [Google Scholar]
  2. Lanjekar VB, Marathe NP, Shouche YS, Ranade DR. Clostridium punense sp. nov., an obligate anaerobe isolated from healthy human faeces. Int J Syst Evol Microbiol 2015; 65:4749–4756 [View Article] [PubMed]
    [Google Scholar]
  3. Minton NP, Clarke DJ. Introduction to the Physiology and Biochemistry of the Genus Clostridium Boston, MA: Springer; 1989 pp 27–62 [View Article]
    [Google Scholar]
  4. Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016; 66:1009–1016 [View Article] [PubMed]
    [Google Scholar]
  5. Alam SI, Dixit A, Reddy GSN, Dube S, Palit M et al. Clostridium schirmacherense sp. nov., an obligately anaerobic, proteolytic, psychrophilic bacterium isolated from lake sediment of Schirmacher Oasis, Antarctica. Int J Syst Evol Microbiol 2006; 56:715–720 [View Article] [PubMed]
    [Google Scholar]
  6. Inglett KS, Bae HS, Aldrich HC, Hatfield K, Ogram AV. Clostridium chromiireducens sp. nov., isolated from Cr(VI)-contaminated soil. Int J Syst Evol Microbiol 2011; 61:2626–2631 [View Article]
    [Google Scholar]
  7. Kuhner CH, Matthies C, Acker G, Schmittroth M, Gössner AS et al. Clostridium akagii sp. nov. and Clostridium acidisoli sp. nov.: acid-tolerant, N2-fixing clostridia isolated from acidic forest soil and litter. Int J Syst Evol Microbiol 2000; 50:873–881 [View Article]
    [Google Scholar]
  8. del Mar Gamboa M, Rodríguez E, Vargas P. Diversity of mesophilic clostridia in Costa Rican soils. Anaerobe 2005; 11:322–326 [View Article]
    [Google Scholar]
  9. Domingo M-C, Huletsky A, Boissinot M, Hélie M-C, Bernal A et al. Clostridium lavalense sp. nov., a glycopeptide-resistant species isolated from human faeces. Int J Syst Evol Microbiol 2009; 59:498–503 [View Article]
    [Google Scholar]
  10. Romano V, Pasquale V, Krovacek K, Mauri F, Demarta A et al. Toxigenic Clostridium difficile PCR ribotypes from wastewater treatment plants in southern switzerland. Appl Environ Microbiol 2012; 78:6643–6646 [View Article]
    [Google Scholar]
  11. Lawson PA. The taxonomy of the genus Clostridium: current status and future perspectives. Microbiology China 2016; 43: [View Article]
    [Google Scholar]
  12. Tushar L, Sasi Jyothsna TS, Sasikala C, Ramana CV. Draft genome sequence of antimicrobial-producing Clostridium sp. JC272, isolated from marine sediment. Genome Announc 2015; 3:27–26 [View Article]
    [Google Scholar]
  13. Monir MU, Aziz AA, Khatun F, Yousuf A. Bioethanol production through syngas fermentation in a tar free bioreactor using Clostridium butyricum. Renewable Energy 2020; 157:1116–1123 [View Article]
    [Google Scholar]
  14. Jiang Y, Guo D, Lu J, Dürre P, Dong W et al. Consolidated bioprocessing of butanol production from xylan by a thermophilic and butanologenic Thermoanaerobacterium sp. M5. Biotechnol Biofuels 2018; 11:89 [View Article] [PubMed]
    [Google Scholar]
  15. Nguyen TH, Watari T, Hatamoto M, Sutani D, Setiadi T et al. Evaluation of a combined anaerobic baffled reactor–downflow hanging sponge biosystem for treatment of synthetic dyeing wastewater. Environ Technol Innov 2020; 19:100913 [View Article]
    [Google Scholar]
  16. Li J, Sun S, Yan P, Fang L, Yu Y et al. Microbial communities in the functional areas of a biofilm reactor with anaerobic-aerobic process for oily wastewater treatment. Bioresour Technol 2017; 238:7–15 [View Article] [PubMed]
    [Google Scholar]
  17. Chen C, Ming J, Yoza BA, Liang J, Li QX et al. Characterization of aerobic granular sludge used for the treatment of petroleum wastewater. Bioresour Technol 2019; 271:353–359 [View Article] [PubMed]
    [Google Scholar]
  18. Sayed K, Baloo L, Kutty SRBM, Makba F. Potential biodegradation of Tapis Light Crude Petroleum Oil, using palm oil mill effluent final discharge as biostimulant for isolated halotolerant Bacillus strains. Mar Pollut Bull 2021; 172:112863 [View Article] [PubMed]
    [Google Scholar]
  19. Ma M, Gao W, Li Q, Han B, Zhu A et al. Biodiversity and oil degradation capacity of oil-degrading bacteria isolated from deep-sea hydrothermal sediments of the South Mid-Atlantic Ridge. Mar Pollut Bull 2021; 171:112770 [View Article] [PubMed]
    [Google Scholar]
  20. Pasumarthi R, Chandrasekaran S, Mutnuri S. Biodegradation of crude oil by Pseudomonas aeruginosa and Escherichia fergusonii isolated from the Goan coast. Mar Pollut Bull 2013; 76:276–282 [View Article] [PubMed]
    [Google Scholar]
  21. Dong Y, Liu Y, Chen N, Zhong Y, Liu L et al. Clostridium beihaiense sp. nov., an anaerobic bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:2789–2793 [View Article] [PubMed]
    [Google Scholar]
  22. Huang Y, Wei Z, Cong L, Qiu Z, Chen R et al. Clostridium prolinivorans sp. nov., a thermophilic bacterium isolated from an anaerobic reactor degrading propionate. Int J Syst Evol Microbiol 2020; 70:5190–5196 [View Article] [PubMed]
    [Google Scholar]
  23. Beveridge TJ. Use of the Gram stain in microbiology. Biotech Histochem 2001; 76:111–118 [View Article] [PubMed]
    [Google Scholar]
  24. Pandolfi D, Pons M-N. Gram-staining characterisation of activated sludge filamentous bacteria by automated colour analysis. Biotechnol Lett 2004; 26:1841–1846 [View Article] [PubMed]
    [Google Scholar]
  25. Jiang Y, Qi H, Zhang XM. Co-biodegradation of anthracene and naphthalene by the bacterium Acinetobacter johnsonii. J Environ Sci Health A Tox Hazard Subst Environ Eng 2018; 53:448–456 [View Article] [PubMed]
    [Google Scholar]
  26. Xu X, Liu W, Wang W, Tian S, Jiang P et al. Potential biodegradation of phenanthrene by isolated halotolerant bacterial strains from petroleum oil polluted soil in Yellow River Delta. Sci Total Environ 2019; 664:1030–1038 [View Article] [PubMed]
    [Google Scholar]
  27. Huang Y, Sun Y, Ma S, Chen L, Zhang H et al. Isolation and characterization of Keratinibaculum paraultunense gen. nov., sp. nov., a novel thermophilic, anaerobic bacterium with keratinolytic activity. FEMS Microbiol Lett 2013; 345:56–63 [View Article]
    [Google Scholar]
  28. 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]
  29. 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]
  30. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  31. Bhattacharya D. Analysis of the distribution of bootstrap tree lengths using the maximum parsimony method. Mol Phylogenet Evol 1996; 6:339–350 [View Article]
    [Google Scholar]
  32. Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993; 42:182–192 [View Article]
    [Google Scholar]
  33. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
    [Google Scholar]
  34. Oren A, Duker S, Ritter S. The polar lipid composition of walsby’s square bacterium. FEMS Microbiol Lett 1996; 138:135–140 [View Article]
    [Google Scholar]
  35. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
    [Google Scholar]
  36. Harper JJ, Davis GHG. Notes: two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol 1979; 29:56–58 [View Article]
    [Google Scholar]
  37. 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]
    [Google Scholar]
  38. Kim M, Oh HS, Park SC, 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]
    [Google Scholar]
  39. Ratnikova NM, Slobodkin AI, Merkel AY, Kopitsyn DS, Kevbrin VV et al. Sulfurimonas crateris sp. nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. Int J Syst Evol Microbiol 2020; 70:487–492 [View Article]
    [Google Scholar]
  40. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  41. 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] [PubMed]
    [Google Scholar]
  42. Lee I, Ouk Kim Y, Park SC, 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]
  43. Matthies C, Kuhner CH, Acker G, Drake HL. Clostridium uliginosum sp. nov., a novel acid-tolerant, anaerobic bacterium with connecting filaments. Int J Syst Evol Microbiol 2001; 51:1119–1125 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005330
Loading
/content/journal/ijsem/10.1099/ijsem.0.005330
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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