Abstract
A novel mesophilic and neutrophilic sulfate-reducing bacterium, strain SF6T, was isolated from sediment of a brackish lake in Japan. Cells of strain SF6T were motile and rod-shaped with length of 1.2–2.5 μm and width of 0.6–0.9 μm. Growth was observed at 10–37 °C with an optimum growth temperature of 28 °C. The pH range for growth was 5.8–8.2 with an optimum pH of 7.0. The most predominant fatty acid was anteiso-C15:0. Under sulfate-reducing conditions, strain SF6T utilized lactate, ethanol and glucose as growth substrate. Chemolithoautotrophic growth on H2 was not observed, although H2 was used as electron donor. Fermentative growth occurred on pyruvate. As electron acceptor, sulfate, sulfite, thiosulfate and nitrate supported heterotrophic growth of the strain. The complete genome of strain SF6T is composed of a circular chromosome with length of 3.8 Mbp and G+C content of 54 mol%. Analyses of the 16S rRNA gene and whole genome sequence indicated that strain SF6T belongs to the genus Pseudodesulfovibrio but distinct form all existing species in the genus. On the basis of its genomic and phenotypic properties, strain SF6T (= DSM111931T = NBRC 114895T) is proposed as the type strain of a new species, with name of Pseudodesulfovibrio sediminis sp. nov.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bale SJ, Goodman K, Rochelle PA, Marchesi JR, Fry JC, Weightman AJ, Parkes RJ (1997) Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Evol Microbiol 47:515–521. https://doi.org/10.1099/00207713-47-2-515
Ben Ali Gam Z, Oueslati R, Abdelkafi S, Casalo L, Tholozan JL, Labat M (2009) Desulfovibrio tunisiensis sp. nov., a novel weakly halotolerant, sulfate-reducing bacterium isolated from exhaust water of a Tunisian oil refinery. Int J Syst Evol Microbiol 59:1059–1063. https://doi.org/10.1099/ijs.0.000943-0
Cao J, Gayet N, Zeng X, Shao Z, Jebbar M, Alain K (2016) Pseudodesulfovibrio indicus gen. nov., sp. nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio. Int J Syst Evol Microbiol 66:3904–3911. https://doi.org/10.1099/ijsem.0.001286
Caumette P, Cohen Y, Matheron R (1991) Isolation and characterization of Desulfovibrio halophilus sp. nov., a halophilic sulfate-reducing bacterium isolated from Solar Lake (Sinai). Syst Appl Microbiol 14:33–38. https://doi.org/10.1016/S0723-2020(11)80358-9
Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH (2020) GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 36:1925–1927. https://doi.org/10.1093/bioinformatics/btz848
Cord-Ruwisch R (1985) A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J Microbiol Methods 4:33–36. https://doi.org/10.1016/0167-7012(85)90005-3
Frolova A, Merkel AY, Kuchierskaya AA, Bonch-Osmolovskaya EA, Slobodkin AI (2021) Pseudodesulfovibrio alkaliphilus, sp. nov., an alkaliphilic sulfate-reducing bacterium isolated from a terrestrial mud volcano. Ant Van Leeuw 114:1387–1397. https://doi.org/10.1007/s10482-021-01608-5
Galushko A, Kuever M (2019) Pseudodesulfovibrio. In: Whitman WB et al (eds) Bergey’s manual of systematics of archaea and bacteria. Wiley, New York. https://doi.org/10.1002/9781118960608.gbm01574
Gilmour CC, Soren AB, Gionfriddo CM, Podar M, Wall JD, Brown SD et al (2021) Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment. Int J Syst Evol Microbiol 71:3. https://doi.org/10.1099/ijsem.0.004697
Khelaifia S, Fardeau ML, Pradel N, Aussignargues C, Garel M, Tamburini C et al (2011) Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea. Int J Syst Evol Microbiol 61:2706–2711. https://doi.org/10.1099/ijs.0.028670-0
Kim YJ, Yang JA, Lim JK, Park MJ, Yang SH, Lee HS et al (2020) Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov. J Microbiol 58:252–259. https://doi.org/10.1007/s12275-020-9376-0
Krekeler D, Sigalevich P, Teske A, Cypionka H, Cohen Y (1997) A sulfate-reducing bacterium from the oxic layer of a microbial mat from Solar Lake (Sinai), Desulfovibrio oxyclinae sp. nov. Arch Microbiol 167:369–375. https://doi.org/10.1007/s002030050457
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60–14. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Göker M, Klenk H-P (2014) Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356. https://doi.org/10.1099/ijs.0.056994-0
Motamedi M, Pedersen K (1998) Desulfovibrio aespoeensis sp. nov., a mesophilic sulfate-reducing bacterium from deep groundwater at äspö hard rock laboratory, Sweden. Int J Syst Bacteriol 48:311–315. https://doi.org/10.1099/00207713-48-1-311
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. https://doi.org/10.1038/nbt.4229
Ranchou-Peyruse M, Goni-Urriza M, Guignard M, Goas M, Ranchou-Peyruse A, Guyoneaud R (2018) Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment. Int J Syst Evol Microbiol 68:1461–1466. https://doi.org/10.1099/ijsem.0.002173
Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ et al (2020) The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 11:1–12. https://doi.org/10.1038/s41467-020-18906-7
Sun B, Cole JR, Sanford RA, Tiedje JM (2000) Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol. Appl Environ Microbiol 66:2408–2413. https://doi.org/10.1128/AEM.66.6.2408-2413.2000
Suzuki D, Ueki A, Amaishi A, Ueki K (2009) Desulfovibrio portus sp. nov., a novel sulfate-reducing bacterium in the class Deltaproteobacteria isolated from an estuarine sediment. J Gen Appl Microbiol 55:125–133. https://doi.org/10.2323/jgam.55.125
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
Tanizawa Y, Fujisawa T, Nakamura Y (2018) DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039. https://doi.org/10.1093/bioinformatics/btx713
Tarasov AL, Osipov GA, Borzenkov IA (2015) Desulfovibrios from marine biofoulings at the South Vietnam coastal area and description of Desulfovibrio hontreensis sp. nov. Microbiology 84:654–664. https://doi.org/10.1134/S0026261715050161
Thioye A, Gam ZBA, Mbengue M, Cayol JL, Joseph-Bartoli M, Toure-Kane C et al (2017) Desulfovibrio senegalensis sp. nov., a mesophilic sulfate reducer isolated from marine sediment. Int J Syst Evol Microbiol 67:3162–3166. https://doi.org/10.1099/ijs.0.028670-0
Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M et al (2020) 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 70:5972–6016. https://doi.org/10.1099/ijsem.0.004213
Warthmann R, Vasconcelos C, Sass H, McKenzie JA (2005) Desulfovibrio brasiliensis sp. nov., a moderate halophilic sulfate-reducing bacterium from Lagoa Vermelha (Brazil) mediating dolomite formation. Extremophiles 9:255–261. https://doi.org/10.1007/s00792-005-0441-8
Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer K (eds) The prokaryotes. Springer, New York, pp 3352–3378
Zheng R, Wu S, Sun C (2021) Pseudodesulfovibrio cashew sp. nov., a novel deep-sea sulfate-reducing bacterium, linking heavy metal resistance and sulfur cycle. Microorganisms 9:429. https://doi.org/10.3390/microorganisms9020429
Acknowledgements
We thank A. Shinohara for technical assistance.
Funding
No external funding was used.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interests
The authors declare that no funds, grants, or other support were received during the preparation of this manuscript. The authors have no relevant financial or non-financial interests to disclose.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Takahashi, A., Kojima, H., Watanabe, M. et al. Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake. Arch Microbiol 204, 307 (2022). https://doi.org/10.1007/s00203-022-02870-5
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-02870-5