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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 1

sp. nov., isolated from the Bach Dang Estuary, Haiphong, Vietnam No Access

Abstract

A mesophilic, anaerobic, endospore-forming, fermentative bacterium designated strain 8C15b was isolated from bank sediment of the Bach Dang Estuary, Haiphong, Vietnam. The Bach Dang Estuary, where Haiphong harbour is located, is subject to strong anthropogenic influence, resulting in high concentrations of black carbon and heavy metals. Strain 8C15b grew optimally at 30 °C, pH 7.5 and with 2.5 % (w/v) NaCl. The main cellular fatty acids consisted of iso-C (51 %), iso-C ω7 (32 %) and iso-C (5 %). Genomic considerations of strain 8C15b and comparisons with the phylogenetically closest strains of the genus provide evidence that SC562 (=DSM 15285), DV1184 (=DSM 15518), B1 (=JCM 16806) and strain 8C15b could be differentiated at the species level. We propose the name sp. nov. for the type strain 8C15b (=JCM 35983=KCTC 25692). Finally, the nickel-tolerance properties of strain 8C15b are highlighted in this study.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): anti-phage defensome , Haiphong harbour , metal resistance and Peptostreptococcaceae
© 2024 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006237
2024-01-16
2025-07-15
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References

  1. Blakely JK, Neher DA, Spongberg AL. Soil invertebrate and microbial communities, and decomposition as indicators of polycyclic aromatic hydrocarbon contamination. Appl Soil Ecol 2002; 21:71–88 [View Article]
     [Google Scholar]
  2. Schloter M, Dilly O, Munch JC. Indicators for evaluating soil quality. Agric Ecosyst Environ 2003; 98:255–262 [View Article]
     [Google Scholar]
  3. Chen Y, Jiang Y, Huang H, Mou L, Ru J et al. Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments. Sci Total Environ 2018; 637–638:1400–1412 [View Article]
     [Google Scholar]
  4. Rochelle-Newall EJ, Chu VT, Pringault O, Amouroux D, Arfi R et al. Phytoplankton distribution and productivity in a highly turbid, tropical coastal system (Bach Dang Estuary, Vietnam). Mar Pollut Bull 2011; 62:2317–2329 [View Article] [PubMed]
     [Google Scholar]
  5. Chu TV, Torréton J-P, Mari X, Nguyen HMT, Pham KT et al. Nutrient ratios and the complex structure of phytoplankton communities in a highly turbid estuary of Southeast Asia. Environ Monit Assess 2014; 186:8555–8572 [View Article] [PubMed]
     [Google Scholar]
  6. Roberts LR, Panizzo VN, Taylor S, Watts M et al. In flux: annual transport and deposition of suspended heavy metals and trace elements in the urbanised, tropical Red River Delta, Vietnam. Water Res 2022; 224:119053 [View Article] [PubMed]
     [Google Scholar]
  7. Slobodkin AI, Tourova TP, Kostrikina NA, Chernyh NA, Bonch-Osmolovskaya EA et al. Tepidibacter thalassicus gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, fermentative bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:1131–1134 [View Article] [PubMed]
     [Google Scholar]
  8. Urios L, Cueff V, Pignet P, Barbier G. Tepidibacter formicigenes sp. nov., a novel spore-forming bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent. Int J Syst Evol Microbiol 2004; 54:439–443 [View Article] [PubMed]
     [Google Scholar]
  9. Tan HQ, Wu XY, Zhang XQ, Wu M, Zhu XF. Tepidibacter mesophilus sp. nov., a mesophilic fermentative anaerobe isolated from soil polluted by crude oil, and emended description of the genus Tepidibacter. Int J Syst Evol Microbiol 2012; 62:66–70 [View Article] [PubMed]
     [Google Scholar]
  10. Fouteau S, Bui Van V, Rouy Z, Beraud M, Cruaud C et al. Complete genome sequence of Tepidibacter sp. strain 8C15b, isolated from bank sediments of Haiphong Bay, Vietnam. Microbiol Resour Announc 2022; 11:e0013222 [View Article] [PubMed]
     [Google Scholar]
  11. Widdel F, Pfennig N. Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. I. Isolation of new sulfate-reducing bacteria enriched with acetate from saline environments. Description of Desulfobacter postgatei gen. nov., sp. nov. Arch Microbiol 1981; 129:395–400 [View Article] [PubMed]
     [Google Scholar]
  12. Hungate RE. A roll tube method for cultivation of strict anaerobes. Methods Microbiol 1969; 3:117–132 [View Article]
     [Google Scholar]
  13. Miller TL, Wolin MJ. A serum bottle modification of the hungate technique for cultivating obligate anaerobes. Appl Microbiol 1974; 27:985–987 [View Article] [PubMed]
     [Google Scholar]
  14. Cord-Ruwisch R. A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J Microbiol Methods 1985; 4:33–36 [View Article]
     [Google Scholar]
  15. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296 [View Article] [PubMed]
     [Google Scholar]
  16. Hall TA. Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  17. 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]
  18. 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]
  19. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 2004; 101:11030–11035 [View Article] [PubMed]
     [Google Scholar]
  20. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
     [Google Scholar]
  21. Hon J, Martínek T, Zendulka J, Lexa M. pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics 2017; 33:3373–3379 [View Article] [PubMed]
     [Google Scholar]
  22. Bedrat A, Lacroix L, Mergny J-L. Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res 2016; 44:1746–1759 [View Article] [PubMed]
     [Google Scholar]
  23. Hon J, Martínek T, Rajdl K, Lexa M. Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences. Bioinformatics 2013; 29:1900–1901 [View Article] [PubMed]
     [Google Scholar]
  24. Schroth GP, Chou PJ, Ho PS. Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J Biol Chem 1992; 267:11846–11855 [View Article] [PubMed]
     [Google Scholar]
  25. Achaz G, Boyer F, Rocha EPC, Viari A, Coissac E. Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics 2007; 23:119–121 [View Article] [PubMed]
     [Google Scholar]
  26. Karlin S, Ost F. Maximal segmental match length among random sequences from a finite alphabet. Cam LML, Olshen RA. Proceedings of the Berkeley Conference in Honor of Jerzy Neyman and Jack Kiefer Wadsworth, Belmont, CA: 1985225–243
     [Google Scholar]
  27. Tesson F, Hervé A, Mordret E, Touchon M, d’Humières C et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun 2022; 13:2561 [View Article] [PubMed]
     [Google Scholar]
  28. Lee CG, Yuki M, Iida T, Nakaho K, Ohkuma M. Draft genome sequence of Tepidibacter mesophilus strain JCM 16806T isolated from soil polluted by crude oil in China. Genome Announc 2017; 5:e01308–17 [View Article]
     [Google Scholar]
  29. Martínez-Carranza E, Barajas H, Alcaraz LD, Servín-González L, Ponce-Soto GY et al. Variability of bacterial essential genes among closely related bacteria: the case of Escherichia coli. Front Microbiol 2018; 9:2330 [View Article] [PubMed]
     [Google Scholar]
  30. Oliveira PH, Touchon M, Cury J, Rocha EPC. The chromosomal organization of horizontal gene transfer in bacteria. Nat Commun 2017; 8:841 [View Article]
     [Google Scholar]
  31. Kang W, Zheng J, Bao J, Wang Z, Zheng Y et al. Characterization of the copper resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain isolated from copper mine sludge. Environ Sci Pollut Res 2020; 27:7922–7933 [View Article]
     [Google Scholar]
  32. Hwang C, Copeland A, Lucas S, Lapidus A, Barry K et al. Complete genome sequence of Alkaliphilus metalliredigens strain QYMF, an alkaliphilic and metal-reducing bacterium isolated from borax-contaminated leachate ponds. Genome Announc 2016; 4:e01226-16 [View Article] [PubMed]
     [Google Scholar]
  33. Xing XJ, Tian YS, Peng RH, Xu J, Zhao W et al. Functional characterization of 5-enopyruvylshikimate-3-phosphate synthase from Alkaliphilus metalliredigens in transgenic arabidopsis. J Microbiol Biotechnol 2014; 24:1421–1426 [View Article] [PubMed]
     [Google Scholar]
  34. Monachese M, Burton JP, Reid G. Bioremediation and tolerance of humans to heavy metals through microbial processes: a potential role for probiotics?. Appl Environ Microbiol 2012; 78:6397–6404 [View Article] [PubMed]
     [Google Scholar]
  35. Beveridge TJ, Fyfe WS. Metal fixation by bacterial cell walls. Can J Earth Sci 1985; 22:1893–1898 [View Article]
     [Google Scholar]
  36. Hans Wedepohl K. The composition of the continental crust. Geochimica et Cosmochimica Acta 1995; 59:1217–1232 [View Article]
     [Google Scholar]
  37. Alam SI, Dube S, Agarwal MK, Singh L. Purification and characterization of an extracellular protease produced by psychrotolerant Clostridium sp. LP3 from lake sediment of Leh, India. Can J Microbiol 2006; 52:1238–1246 [View Article] [PubMed]
     [Google Scholar]
  38. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  39. Miele V, Penel S, Duret L. Ultra-fast sequence clustering from similarity networks with SiLiX. BMC Bioinformatics 2011; 12:116 [View Article] [PubMed]
     [Google Scholar]
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Tepidibacter aestuarii sp. nov., isolated from the Bach Dang Estuary, Haiphong, Vietnam
Int J Syst Evol Microbiol 74, 006237 (2024); https://doi.org/10.1099/ijsem.0.006237
/content/journal/ijsem/10.1099/ijsem.0.006237
/content/journal/ijsem/10.1099/ijsem.0.006237
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