1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 5

sp. nov., a formate-oxidizing, organohalide-respiring bacterium isolated from grape pomace No Access

Abstract

A strictly anaerobic, organohalide-respiring bacterium, designated strain GP, was characterized using a polyphasic approach. GP is Gram-stain-negative, non-spore-forming and non-motile. Cells are irregular cocci ranging between 0.6 and 0.9 µm in diameter. GP couples growth with the reductive dechlorination of 1,2-dichloroethane, vinyl chloride and all polychlorinated ethenes, except tetrachloroethene, yielding ethene and inorganic chloride as dechlorination end products. H and formate serve as electron donors for organohalide respiration in the presence of acetate as carbon source. Major cellular fatty acids include C, Cω9, C, C and C. On the basis of 16S rRNA gene phylogeny, GP is most closely related to NSZ-14 and IP3-3 with 99.8 and 97.4 % sequence identities, respectively. Genome-wide pairwise comparisons based on average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization do not support the inclusion of GP in previously described species of the genus with validly published names. On the basis of phylogenetic, physiological and phenotypic traits, GP represents a novel species within the genus , for which the name sp. nov. is proposed. The type strain is GP (= JCM 39172 = CGMCC 1.17861).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Dehalococcoidia , Dehalogenimonas , organohalide respiration , reductive dechlorination and vinyl chloride
Funding
This study was supported by the:
  • Key Research Program of Frontier Sciences, Chinese Academy of Sciences (Award ZDBS-LY-DQC038)
    • Principle Award Recipient: YiYang
  • Liaoning Revitalization Talents Program (Award XLYC1807139)
    • Principle Award Recipient: YiYang
  • Natural Science Foundation of China (Award 41907287)
    • Principle Award Recipient: YiYang
  • Natural Science Foundation of China (Award 41907220)
    • Principle Award Recipient: YiYang
  • Natural Science Foundation of China (Award 41977295)
    • Principle Award Recipient: JunYan
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005881
2023-05-15
2024-05-14
Loading full text...

Full text loading...

References

  1. Moe WM, Yan J, Nobre MF, da Costa MS, Rainey FA. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 2009; 59:2692–2697 [View Article] [PubMed]
     [Google Scholar]
  2. Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA et al. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 2013; 63:625–635 [View Article] [PubMed]
     [Google Scholar]
  3. Wu QZ, Watts JEM, Sowers KR, May HD. Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. Appl Environ Microbiol 2002; 68:807–812 [View Article] [PubMed]
     [Google Scholar]
  4. Bowman KS, Nobre MF, da Costa MS, Rainey FA, Moe WM. Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater. Int J Syst Evol Microbiol 2013; 63:1492–1498 [View Article] [PubMed]
     [Google Scholar]
  5. Key TA, Bowman KS, Lee I, Chun J, Albuquerque L et al. Dehalogenimonas formicexedens sp. nov., a chlorinated alkane-respiring bacterium isolated from contaminated groundwater. Int J Syst Evol Microbiol 2017; 67:1366–1373 [View Article] [PubMed]
     [Google Scholar]
  6. Yang Y, Higgins SA, Yan J, Şimşir B, Chourey K et al. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. ISME J 2017; 11:2767–2780 [View Article] [PubMed]
     [Google Scholar]
  7. Lv Y, Li X, Wang J, Jin H, Cui Y et al. Isolation and basic characterization of a novel organohaliderespiring bacterium within the genus Dehalogenimonas. Acta Microbiol Sin 2021; 61:1016–1029
     [Google Scholar]
  8. Yan J, Wang J, Villalobos Solis MI, Jin H, Chourey K et al. Respiratory vinyl chloride reductive dechlorination to ethene in TceA-expressing Dehalococcoides mccartyi.. Environ Sci Technol 2021; 55:4831–4841 [View Article] [PubMed]
     [Google Scholar]
  9. Cupples AM, Spormann AM, McCarty PL. Growth of a Dehalococcoides-like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR. Appl Environ Microbiol 2003; 69:953–959 [View Article] [PubMed]
     [Google Scholar]
  10. He JZ, Ritalahti KM, Yang KL, Koenigsberg SS, Löffler FE. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 2003; 424:62–65 [View Article] [PubMed]
     [Google Scholar]
  11. Sung Y, Ritalahti KM, Apkarian RP, Löffler FE. Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Appl Environ Microbiol 2006; 72:1980–1987 [View Article] [PubMed]
     [Google Scholar]
  12. Chen G, Kara Murdoch F, Xie Y, Murdoch RW, Cui Y et al. Dehalogenation of chlorinated ethenes to ethene by a novel isolate, “Candidatus Dehalogenimonas etheniformans”.. Appl Environ Microbiol 2022; 88:e0044322 [View Article] [PubMed]
     [Google Scholar]
  13. Löffler FE, Sanford RA, Ritalahti KM. Enrichment, cultivation, and detection of reductively dechlorinating bacteria. Methods Enzymol 2005; 397:77–111 [View Article] [PubMed]
     [Google Scholar]
  14. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker 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] [PubMed]
     [Google Scholar]
  15. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28:1647–1649 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  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. 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]
  19. Yang Y, Yan J, Li X, Lv Y, Cui Y et al. Genome sequence of “Candidatus Dehalogenimonas etheniformans” strain GP, a vinyl chloride-respiring anaerobe. Microbiol Resour Announc 2020; 9:e01212-20 [View Article] [PubMed]
     [Google Scholar]
  20. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H et al. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains. Stand Genomic Sci 2012; 6:251–264 [View Article] [PubMed]
     [Google Scholar]
  21. Key TA, Richmond DP, Bowman KS, Cho Y-J, Chun J et al. Genome sequence of the organohalide-respiring Dehalogenimonas alkenigignens type strain (IP3-3T). Stand Genomic Sci 2016; 11:44 [View Article] [PubMed]
     [Google Scholar]
  22. Molenda O, Quaile AT, Edwards EA. Dehalogenimonas sp. strain WBC-2 genome and identification of its trans-dichloroethene reductive dehalogenase, TdrA. Appl Environ Microbiol 2016; 82:40–50 [View Article] [PubMed]
     [Google Scholar]
  23. Trueba-Santiso A, Wasmund K, Soder-Walz JM, Marco-Urrea E, Adrian L. Genome sequence, proteome profile, and identification of a multiprotein reductive dehalogenase complex in Dehalogenimonas alkenigignens strain BRE15M. J Proteome Res 2021; 20:613–623 [View Article] [PubMed]
     [Google Scholar]
  24. Hölscher T, Krajmalnik-Brown R, Ritalahti KM, Von Wintzingerode F, Görisch H et al. Multiple nonidentical reductive-dehalogenase-homologous genes are common in Dehalococcoides. Appl Environ Microbiol 2004; 70:5290–5297 [View Article] [PubMed]
     [Google Scholar]
  25. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 2005; 307:105–108 [View Article] [PubMed]
     [Google Scholar]
  26. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM et al. Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol 2004; 70:6347–6351 [View Article] [PubMed]
     [Google Scholar]
  27. Adrian L, Rahnenführer J, Gobom J, Hölscher T. Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol 2007; 73:7717–7724 [View Article] [PubMed]
     [Google Scholar]
  28. Cheng D, He J. Isolation and characterization of “Dehalococcoides” sp. strain MB, which dechlorinates tetrachloroethene to trans-1,2-dichloroethene. Appl Environ Microbiol 2009; 75:5910–5918 [View Article] [PubMed]
     [Google Scholar]
  29. Pöritz M, Schiffmann CL, Hause G, Heinemann U, Seifert J et al. Dehalococcoides mccartyi strain DCMB5 respires a broad spectrum of chlorinated aromatic compounds. Appl Environ Microbiol 2015; 81:587–596 [View Article] [PubMed]
     [Google Scholar]
  30. Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 2021; 49:D344–D354 [View Article] [PubMed]
     [Google Scholar]
  31. Müller JA, Rosner BM, Von Abendroth G, Meshulam-Simon G, McCarty PL et al. Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain vs and its environmental distribution. Appl Environ Microbiol 2004; 70:4880–4888 [View Article] [PubMed]
     [Google Scholar]
  32. Padilla-Crespo E, Yan J, Swift C, Wagner DD, Chourey K et al. Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring Chloroflexi. Appl Environ Microbiol 2014; 80:808–818 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  35. 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]
  36. Sexton DL, Chen G, Kara Murdoch F, Hashimi A, Löffler FE et al. Ultrastructure of organohalide-respiring Dehalococcoidia revealed by cryo-electron tomography. Appl Environ Microbiol 2022; 88:e0190621 [View Article] [PubMed]
     [Google Scholar]
  37. Li X, Yang Y, Wang J, Jin H, Zhang Y et al. Organohalide respiration with diclofenac by Dehalogenimonas.. Environ Sci Technol 2022; 56:11266–11276 [View Article] [PubMed]
     [Google Scholar]
  38. Jiang L, Yang Y, Jin H, Wang H, Swift CM et al. Geobacter sp. strain IAE dihaloeliminates 1,1,2-trichloroethane and 1,2-dichloroethane. Environ Sci Technol 2022; 56:3430–3440 [View Article] [PubMed]
     [Google Scholar]
  39. Chen J, Bowman KS, Rainey FA, Moe WM. Reassessment of PCR primers targeting 16S rRNA genes of the organohalide-respiring genus Dehalogenimonas. Biodegradation 2014; 25:747–756 [View Article] [PubMed]
     [Google Scholar]
  40. Maymó-Gatell X, Anguish T, Zinder SH. Reductive dechlorination of chlorinated ethenes and 1,2-dichloroethane by “ Dehalococcoides ethenogenes ” 195. Appl Environ Microbiol 1999; 65:3108–3113 [View Article]
     [Google Scholar]
  41. Fennell DE, Nijenhuis I, Wilson SF, Zinder SH, Häggblom MM. Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ Sci Technol 2004; 38:2075–2081 [View Article] [PubMed]
     [Google Scholar]
  42. Adrian L, Hansen SK, Fung JM, Görisch H, Zinder SH. Growth of Dehalococcoides strains with chlorophenols as electron acceptors. Environ Sci Technol 2007; 41:2318–2323 [View Article] [PubMed]
     [Google Scholar]
  43. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of fatty acids in bacteria. In Rainey F, Oren A. eds Methods in Microbiology (Taxonomy of Prokaryotes) London: Elsevier Ltd; 2011 pp 183–196
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005881
Loading
Dehalogenimonas etheniformans sp. nov., a formate-oxidizing, organohalide-respiring bacterium isolated from grape pomace
Int J Syst Evol Microbiol 73, 005881 (2023); https://doi.org/10.1099/ijsem.0.005881
/content/journal/ijsem/10.1099/ijsem.0.005881
/content/journal/ijsem/10.1099/ijsem.0.005881
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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