1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 3

sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil No Access

Abstract

A strictly anaerobic bacterial strain, designated Jerry-YX, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YX was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YX was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C and C 7/C 6 (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus , being most closely related to (98.2 % similarity), (98.1 %) and (98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YX and GS-15 were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YX from its closest species, which suggested that strain Jerry-YX represents a novel species of the genus . The name for the proposed new species is sp. nov. The type strain is Jerry-YX (=MCCC 1K05659=JCM 39190).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): benzoate degradation , Geobacter benzoatilyticus , iron-reducing bacterium , novel species and polyphasic taxonomy
Funding
This study was supported by the:
  • Science and Technology Program of Guangzhou (Award 202002030123)
    • Principle Award Recipient: GuiqinYang
  • Natural Science Foundation of Guangdong Province (Award 2021A1515012570)
    • Principle Award Recipient: GuiqinYang
  • National Natural Science Foundation of China (Award 42077211)
    • Principle Award Recipient: LiZhuang
© 2022 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005281
2022-03-07
2024-04-23
Loading full text...

Full text loading...

References

  1. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ et al. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 1993; 159:336–344 [View Article]
     [Google Scholar]
  2. Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972–6016 [View Article] [PubMed]
     [Google Scholar]
  3. Lovley DR. Extracellular electron transfer: wires, capacitors, iron lungs, and more. Geobiology 2008; 6:225–231 [View Article] [PubMed]
     [Google Scholar]
  4. Coates JD, Bhupathiraju VK, Achenbach LA, Mclnerney MJ, Lovley DR. Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 2001; 51:581–588 [View Article] [PubMed]
     [Google Scholar]
  5. Zhang T, Tremblay P-L, Chaurasia AK, Smith JA, Bain TS et al. Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens. Front Microbiol 2014; 5:245 [View Article] [PubMed]
     [Google Scholar]
  6. Chaurasia AK, Tremblay P-L, Holmes DE, Zhang T. Genetic evidence that the degradation of para-cresol by Geobacter metallireducens is catalyzed by the periplasmic para-cresol methylhydroxylase. FEMS Microbiol Lett 2015; 362:fnv145 [View Article] [PubMed]
     [Google Scholar]
  7. Lovley DR, Phillips EJP. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 1988; 54:1472–1480 [View Article] [PubMed]
     [Google Scholar]
  8. Coppi MV, Leang C, Sandler SJ, Lovley DR. Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 2001; 67:3180–3187 [View Article] [PubMed]
     [Google Scholar]
  9. Zhou S, Yang G, Lu Q, Wu M. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil. Int J Syst Evol Microbiol 2014; 64:3786–3791 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. 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]
  12. Cai X, Huang L, Yang G, Yu Z, Wen J et al. Transcriptomic, proteomic, and bioelectrochemical characterization of an exoelectrogen Geobacter soli grown with different electron acceptors. Front Microbiol 2018; 9:1075 [View Article] [PubMed]
     [Google Scholar]
  13. Yang G, Chen S, Zhou S, Liu Y. Genome sequence of a dissimilatory Fe(III)-reducing bacterium Geobacter soli type strain GSS01(T). Stand Genomic Sci 2015; 10:118 [View Article] [PubMed]
     [Google Scholar]
  14. 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]
  15. 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]
  16. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  17. Farris JS. Estimating phylogenetic trees from distance matrices. The American Naturalist 1972; 106:645–668 [View Article]
     [Google Scholar]
  18. Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017; 33:2946–2947 [View Article] [PubMed]
     [Google Scholar]
  19. Yoon SH, Ha SM, Lim JM, Kwon SJ, 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]
  20. 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]
  21. Zhou S, Tang J, Yuan Y, Yang G, Xing B. TiO 2 nanoparticle-induced nanowire formation facilitates extracellular electron transferNanoparticle-Induced Nanowire Formation Facilitates Extracellular Electron Transfer. Environ Sci Technol Lett 2018; 5:564–570 [View Article]
     [Google Scholar]
  22. Liu X, Zhuo S, Jing X, Yuan Y, Rensing C et al. Flagella act as Geobacter biofilm scaffolds to stabilize biofilm and facilitate extracellular electron transfer. Biosens Bioelectron 2019; 146:111748 [View Article] [PubMed]
     [Google Scholar]
  23. Liu X, Zhuo S, Rensing C, Zhou S. Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species. ISME J 2018; 12:2142–2151 [View Article] [PubMed]
     [Google Scholar]
  24. Childers SE, Ciufo S, Lovley DR. Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 2002; 416:767–769 [View Article] [PubMed]
     [Google Scholar]
  25. Hopkins BT, McInerney MJ, Warikoo V. Evidence for anaerobic syntrophic benzoate degradation threshold and isolation of the syntrophic benzoate degrader. Appl Environ Microbiol 1995; 61:526–530 [View Article] [PubMed]
     [Google Scholar]
  26. Coates JD, Phillips EJP, Lonergan DJ, Jenter H, Lovley DR. Isolation of Geobacter species from diverse sedimentary environments. Appl Environ Microbiol 1996; 62:1531–1536 [View Article] [PubMed]
     [Google Scholar]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  28. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997; 47:1129–1133 [View Article]
     [Google Scholar]
  29. Sun D, Wang A, Cheng S, Yates M, Logan BE. Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems. Int J Syst Evol Microbiol 2014; 64:3485–3491 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005281
Loading
Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil
Int J Syst Evol Microbiol 72, 005281 (2022); https://doi.org/10.1099/ijsem.0.005281
/content/journal/ijsem/10.1099/ijsem.0.005281
/content/journal/ijsem/10.1099/ijsem.0.005281
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