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Desulfofustis limnaeus sp. nov., a freshwater sulfate-reducing bacterium isolated from marsh soil

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Abstract

A novel sulfate-reducing bacterium, strain PPLLT, was isolated from marsh soil. Cells of strain PPLLT were rod-shaped with length of 1.5 μm and width of 0.7 μm. Growth was observed at 22–37 °C (optimum 35 °C) and pH 6.8–8.4 (optimum 7.3). Lactate, succinate, fumarate, formate and malate were utilized as electron donors for sulfate reduction. Fermentative growth was not observed on tested organic acids. Besides sulfate, sulfite, thiosulfate and elemental sulfur were utilized as electron acceptors. Hydrogen is used only in the presence acetate or yeast extract. The major fatty acid was C16:0. The complete genome of strain PPLLT was composed of a circular chromosome with length of 4.2 Mbp and G + C content of 57.7 mol%. Sequence analysis of the 16S rRNA gene showed that strain PPLLT was affiliated with the genus Desulfofustis in the family Desulfocapsaceae. On the basis of differences in the phylogenetic and phenotypic properties between the strain and the type strain of the genus Desulfofustis, strain PPLLT (DSM 110475T = JCM 39161T) is proposed as the type strain of a new species, with name of Desulfofustis limnaeus sp. nov.

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Data availability

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene and genome sequence of strain PPLLT are LC702440 and AP025516. The genome sequence of the strain PPLL was published in public database.

References

  • Cantalapiedra CP, Hernández-Plaza A, Letunic I et al (2021) eggNOG-mapper v2: functional annotation, orthologyassignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38(12):5825–5829

    Article  CAS  Google Scholar 

  • Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH (2020) GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz848

    Article  Google Scholar 

  • Friedrich M, Springer N, Ludwig W, Schink B (1996) Phylogenetic positions of Desulfofustis glycolicus gen. nov., sp. nov., and Syntrophobotulus glycolicus gen. nov., sp. nov., two new strict anaerobes growing with glycolic acid. Int J Syst Bacteriol 46:1065–1069. https://doi.org/10.1099/00207713-46-4-1065/CITE/REFWORKS

    Article  CAS  PubMed  Google Scholar 

  • Galushko A, Kuever J (2019) Desulfofustis. In: DeVos P, Dedysh S, Hedlund B, Kämpfer P, Rainey F, Trujillo ME, Bowman J, Brown DR, Glöckner FO, Oren A, Paster BJ, Wade W, Ward N, Busse HJ, Reysenbach AL, Whitman WB (eds) Bergey’s manual of systematic bacteriology. Wiley, Hoboken

    Google Scholar 

  • Higashioka Y, Kojima H, Fukui M (2009) Isolation and characterization of novel sulfate-reducing bacterium capable of anaerobic degradation of p-xylene. Microbes Environ 27(3):273–277

    Article  Google Scholar 

  • Kim D, Park S, Chun J (2021) Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 59:476–480

    Article  Google Scholar 

  • Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP et al (2007) Clustal w and Clustal x version 2.0. Bioinformatics 23:2947–2948. https://doi.org/10.1093/bioinformatics/btm404

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50:D801–D807

    Article  CAS  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    Article  CAS  Google Scholar 

  • Parks DH, Chuvochina M, Waite DW et al (2018) A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996. https://doi.org/10.1038/nbt.4229

    Article  CAS  PubMed  Google Scholar 

  • Qin Q-L, Xie B-B, Zhang X-Y et al (2014) A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196:2210–2215

    Article  Google Scholar 

  • Rabus R, Nordhaus R, Ludwig W, Widdel F (1993) Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59:1444–1451

    Article  CAS  Google Scholar 

  • Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118

    Google Scholar 

  • Rodriguez-R LM, Konstantinidis KT (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints, UK

    Google Scholar 

  • Stackebrandt E (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 6:152–155

    Google Scholar 

  • Tanizawa Y, Fujisawa T, Nakamura Y (2018) DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 34:1037–1039

    Article  CAS  Google Scholar 

  • Waite DW, Chuvochina M, Pelikan C 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(11):5972–6016

    Article  CAS  Google Scholar 

  • Watanabe M, Kojima H, Fukui M (2017) Desulfocucumis palustris gen. nov., sp. nov., a mesophilic sulfate reducer belonging to Desulfotomaculum subcluster Ig. Int J Syst Evol Microbiol 67:2679–2682. https://doi.org/10.1099/ijsem.0.002005

    Article  CAS  PubMed  Google Scholar 

  • Widdel F, Bak F (1992) Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes, vol 4, 2nd edn. Springer-verlag, New York, pp 3352–3378

    Chapter  Google Scholar 

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Acknowledgements

We thank A. Shinohara for technical assistance. Genome analysis was partially performed on the NIG supercomputer at ROIS National Institute of Genetics

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The authors declare that no funds, grants, or other support were received during the preparation of this manuscript.

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Authors and Affiliations

  1. Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita, 010-0195, Japan

    Miho Watanabe, Hisaya Kojima & Naoyuki Miyata

  2. Graduate School of Environmental Science, Hokkaido University, Kita-10, Nishi-5, Kita-ku, Sapporo, 060-0810, Japan

    Ayaka Takahashi

  3. The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan

    Ayaka Takahashi, Hisaya Kojima & Manabu Fukui

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  1. Miho Watanabe
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  2. Ayaka Takahashi
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  4. Naoyuki Miyata
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Correspondence to Miho Watanabe.

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Communicated by Erko Stackebrandt.

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Watanabe, M., Takahashi, A., Kojima, H. et al. Desulfofustis limnaeus sp. nov., a freshwater sulfate-reducing bacterium isolated from marsh soil. Arch Microbiol 204, 647 (2022). https://doi.org/10.1007/s00203-022-03261-6

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