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Volume 58, Issue 10

sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids Free

Abstract

To obtain amino acid-utilizing sulfate reducers, enrichment culture was carried out with a medium containing Casamino acids and sulfate and inoculated with coastal marine sediment from the eutrophic Tokyo Bay, Japan. A sulfate reducer, designated strain C/L2, was isolated from the sulfide-producing enrichment culture after further enrichment with lactate and sulfate by means of the agar shake dilution method. Cells of strain C/L2 were vibrio-shaped, Gram-negative, motile rods (0.7–1.0 μm wide and 1.0–3.5 μm long) with single polar flagella. The optimum temperature for its growth was 37 °C, the optimum pH was around 7.5 and the optimum NaCl concentration was 20–25 g l. Hydrogen, formate, lactate, pyruvate, fumarate, malate, succinate, ethanol, propanol, glycerol, glycine, alanine, serine, aspartate, Casamino acids, peptone and yeast extract were used as electron donors. Sulfate, sulfite and thiosulfate each served as an electron acceptor, but elemental sulfur, nitrate, fumarate, acrylate and 2,4,6-tribromophenol did not. Disproportionation of thiosulfate was not observed. Desulfoviridin, -type cytochromes and catalase were present. The major respiratory quinone was MK-6(H). The G+C content of the genomic DNA was 46.2 mol%. Comparisons based on 16S rRNA gene sequences and on dissimilatory sulfite reductase gene sequences clearly showed that strain C/L2 belonged to the genus : its closest relatives were the uncharacterized sp. strain TBP-1 (16S rRNA gene sequence similarity of 99.4 %) and DSM 10141 (16S rRNA gene sequence similarity of 98.7 %). The level of DNA–DNA hybridization with DSM 10141 was 10.3 %. On the basis of the data from this study and the physiological and phylogenetic differences that exist between the isolate and , strain C/L2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is C/L2 (=NMRC 101113=JCM 14577=DSM 17456).

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Keyword(s): DSR, dissimilatory sulfite reductase and SRB, sulfate-reducing bacteria
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2008-10-01
2024-04-25
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References

  1. Baena, S., Fardesu, M.-L., Labat, M., Ollivier, B., Garcia, J.-L. & Patel, B. K. C.(1998).Desulfovibrio aminophilus sp. nov., a novel amino acid degrading and sulfate reducing bacterium from an anaerobic dairy wastewater lagoon. Syst Appl Microbiol 21, 498–504.[CrossRef] [Google Scholar]
  2. Boyle, A. W., Phelps, C. D. & Young, L. Y.(1999). Isolation from estuarine sediments of a Desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2,4,6-tribromophenol. Appl Environ Microbiol 65, 1133–1140. [Google Scholar]
  3. Burdige, D.(1989). The effects of sediment slurrying on microbial processes, and the role of amino acids as substrates for sulfate reduction in anoxic marine sediments. Biogeochemistry 8, 1–23.[CrossRef] [Google Scholar]
  4. Burdige, D.(1991). Microbial processes affecting alanine and glutamic acid in anoxic marine sediments. FEMS Microbiol Ecol 85, 211–232.[CrossRef] [Google Scholar]
  5. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M.(1977). A rapid method for base ratio determination of bacterial DNA. Anal Biochem 81, 461–466.[CrossRef] [Google Scholar]
  6. Christensen, D.(1984). Determination of substrates oxidized by sulfate reduction in intact cores of marine sediments. Limnol Oceanogr 29, 189–192.[CrossRef] [Google Scholar]
  7. De Ley, J., Cattoir, H. & Reynaerts, A.(1970). The quantitative measurement of DNA hybridization from renaturation of bacterial DNA. Eur J Biochem 12, 133–142.[CrossRef] [Google Scholar]
  8. Dhillon, A., Teske, A., Dillon, J., Stahl, D. A. & Sogin, M. L.(2003). Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl Environ Microbiol 69, 2765–2772.[CrossRef] [Google Scholar]
  9. Doetsch, R. N.(1981). Determinative methods of light microscopy. In Manual of Methods for General Bacteriology, pp. 21–33. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington DC: American Society of Microbiology.
  10. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  11. Finster, K., Thomsen, T. R. & Ramsing, N. B.(2001).Desulfomusa hansenii gen. nov., sp. nov., a novel marine propionate-degrading, sulfate-reducing bacterium isolated from Zostera marina root. Int J Syst Evol Microbiol 51, 2055–2061.[CrossRef] [Google Scholar]
  12. Fukui, M., Suh, J., Yonezawa, Y. & Urushigawa, Y.(1997). Major substrates for microbial sulfate reduction in the sediments of Ise Bay, Japan. Ecol Res 12, 201–209.[CrossRef] [Google Scholar]
  13. Gregersen, T.(1978). Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5, 123–127.[CrossRef] [Google Scholar]
  14. Hansen, L. S. & Blackburn, T. H.(1995). Amino acid degradation by sulfate-reducing bacteria: evaluation of four methods. Limnol Oceanogr 40, 502–510.[CrossRef] [Google Scholar]
  15. Hansen, L. S., Holmer, M. & Blackburn, T. H.(1993). Mineralization of organic nitrogen and carbon (fish food) added to anoxic sediment microcosms: role of sulphate reduction. Mar Ecol Prog Ser 102, 199–204.[CrossRef] [Google Scholar]
  16. Haouari, O., Fardeau, M.-L., Casalot, L., Tholozan, J.-L., Hamdi, M. & Olliver, B.(2006). Isolation of sulfate-reducing bacteria from Tunisian marine sediments and description of Desulfovibrio bizertensis sp. nov. Int J Syst Evol Microbiol 56, 2909–2913.[CrossRef] [Google Scholar]
  17. Huß, V. A. R., Festl, H. & Schleifer, K. H.(1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef] [Google Scholar]
  18. Jørgensen, B. B.(1982). Mineralization of organic matter in the sea bed – the role of sulphate reduction. Nature 296, 643–645.[CrossRef] [Google Scholar]
  19. Katayama-Fujimura, Y., Komatsu, Y., Kuraishi, H. & Kaneko, T.(1984). Estimation of DNA base composition by high performance liquid chromatography of its nuclease P1 hydrolysate. Agric Biol Chem 48, 3169–3172.[CrossRef] [Google Scholar]
  20. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M.(2001).mega2: molecular evolutionary genetics analysis software. Bioinformatics 17, 1244–1245.[CrossRef] [Google Scholar]
  21. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S. & other authors(2004).arb: a software environment for sequence data. Nucleic Acids Res 32, 1363–1371.[CrossRef] [Google Scholar]
  22. Parkes, R. J., Gibson, G. R., Mueller-Harvey, I., Buckingham, W. J. & Herbert, R. J.(1989). Determination of the substrates for sulphate-reducing bacteria within marine and estuarine sediments with different rates of sulphate reduction. J Gen Microbiol 135, 175–187. [Google Scholar]
  23. Postgate, J.(1959). A diagnostic reaction of Desulfovibrio desulfuricans. Nature 183, 481–482. [Google Scholar]
  24. Purdy, K. J., Nedwell, D. B., Embley, T. M. & Takii, S.(1997). Use of 16S rRNA-targeted oligonucleotide probes to investigate the occurrence and selection of sulfate-reducing bacteria in response to nutrient addition to sediment slurry microcosms from a Japanese estuary. FEMS Microbiol Ecol 24, 221–234.[CrossRef] [Google Scholar]
  25. Rees, G. N., Harfoot, C. G. & Sheehy, A. J.(1998). Amino acid degradation by the mesophilic sulfate-reducing bacterium Desulfobacterium vacuolatum. Arch Microbiol 169, 76–80. [Google Scholar]
  26. Saitou, N. & Nei, M.(1987). The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  27. Sass, A., Rutters, H., Cypionka, H. & Sass, H.(2002).Desulfobulbus mediterraneus sp. nov., a sulfate-reducing bacterium growing on mono- and disaccharides. Arch Microbiol 177, 468–474.[CrossRef] [Google Scholar]
  28. Shintani, T., Liu, W.-T., Hanada, S., Kamagata, Y., Miyaoka, S., Suzuki, T. & Nakamura, K.(2000).Micropruina glycogenisa gen. nov., sp. nov., a new Gram-positive glycogen-accumulating bacterium isolated from activated sludge. Int J Syst Evol Microbiol 50, 201–207.[CrossRef] [Google Scholar]
  29. Sørensen, J., Christensen, D. & Jørgensen, B. B.(1981). Volatile fatty acids and hydrogen as substrates for sulfate-reducing bacteria in anaerobic marine sediment. Appl Environ Microbiol 42, 5–11. [Google Scholar]
  30. Stams, A. J. M. & Hansen, T. A.(1986). Metabolism of l-alanine in Desulfotomaculum ruminis and two marine Desulfovibrio strains. Arch Microbiol 145, 277–279.[CrossRef] [Google Scholar]
  31. Stams, A. J. M., Hansen, T. A. & Skyring, G. W.(1985). Utilization of amino acids as energy substrates by two marine Desulfovibrio strains. FEMS Microbiol Ecol 31, 11–15.[CrossRef] [Google Scholar]
  32. Takii, S.(2003). Amino acids as main substrates for sulfate-reducing bacteria in surface sediment of a eutrophic bay. J Gen Appl Microbiol 49, 329–336.[CrossRef] [Google Scholar]
  33. Takii, S., Tanaka, H., Kohata, K., Nakamura, Y., Ogura, H. & Takeshita, S.(2002). Seasonal changes in sulfate reduction in sediments in the inner part of Tokyo Bay. Microbes Environ 17, 10–17.[CrossRef] [Google Scholar]
  34. Takii, S., Hanada, S., Tamaki, H., Ueno, Y., Sekiguchi, Y., Ibe, A. & Matsuura, K.(2007).Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids. Int J Syst Evol Microbiol 57, 2320–2326.[CrossRef] [Google Scholar]
  35. Thompson, J. D., Higgins, D. G. & Gibson, T. J.(1994).clustalw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef] [Google Scholar]
  36. van der Maarel, M., van Bergeijk, S., van Werkhoven, A. F., Laverman, A. M., Meijer, W. G., Stam, W. T. & Hansen, T. A.(1996). Cleavage of dimethylsulfoniopropionate and reduction of acrylate by Desulfovibrio acrylicus sp. nov. Arch Microbiol 166, 109–115.[CrossRef] [Google Scholar]
  37. Wagner, M., Roger, A. J., Flax, J. L., Brusseau, G. A. & Stahl, D. R.(1998). Phylogeny of dissimilatory sulfate reductases supports an early origin of sulfate respiration. J Bacteriol 180, 2975–2982. [Google Scholar]
  38. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463–464.[CrossRef] [Google Scholar]
  39. Widdel, F. & Bak, F.(1992). Gram-negative mesotrophic sulfate-reducing bacteria. In The Prokaryotes, 2nd edn, vol. 4, pp. 3352–3378. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer. New York: Springer.
  40. Winfrey, M. R. & Ward, D. M.(1983). Substrates for sulfate reduction and methane production in intertidal sediments. Appl Environ Microbiol 45, 193–199. [Google Scholar]
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Desulfovibrio marinisediminis sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids
Int J Syst Evol Microbiol 58, 2433 (2008); https://doi.org/10.1099/ijs.0.65750-0
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Phase-contrast photomicrograph of cells of strain C/L2 ( sp. nov.). [PDF](723 KB)

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Phylogenetic tree based on gene sequences. [PDF](28 KB)

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