Bacillus sediminis sp. nov., isolated from an electroactive biofilm

Abstract

A Gram-stain positive, facultative anaerobic, motile, spore-forming rod-shaped bacterium with peritrichous flagella, designated DX-5T, was isolated from an electroactive biofilm. Growth was observed to occur at 35–60 °C, at pH 7.0–10.0 and with 0.5–10 % (w/v) NaCl (optimum growth: 50 °C, pH 8.0 and 0.5–3 % NaCl). Cells were determined to be catalase- and oxidase-positive. The predominant respiratory quinone was identified as MK-7; the major polar lipids were determined to be diphosphatidylglycerol, phosphatidylglycerol, glycolipid, aminoglycolipid and an unidentified phospholipid; the DNA G+C content was determined to be 46.6 mol%; and the major fatty acids (>5 %) were identified as anteiso-C15:0 (33.6 %), iso-C15:0 (24.1 %) and anteiso-C17:0 (13.4 %). The phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain DX-5T should be assigned to the genus Bacillus, and was related most closely to the type strains of B. fortis DSM 16012T (96.3 %), B. composti KACC 16872T (96.3 %) and B. fordii DSM 16014T (95.8 %). Results of phenotypic, chemotaxonomic and genotypic analysis indicated that strain DX-5T represents a novel species, for which the name B. sediminis sp. nov. is proposed. The type strain is DX-5T (=CGMCC 1.12412T = KCTC 33102T).

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2

References

  1. Baker GC, Smith JJ, Cowan DA (2003) Review and reanalysis of domain-specific 16S primers. J Microbiol Methods 55:541–555

    PubMed  Article  CAS  Google Scholar 

  2. Breznak JA, Costilow RN (1994) Physicochemical factors in growth. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 137–154

    Google Scholar 

  3. Cohn F (1872) Genus Micrococcus. Beitr Biol Pflanz 1:127–224

    Google Scholar 

  4. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in Actinomycetes and Corynebacteria. J Gen Microbiol 100:221–230

    PubMed  Article  CAS  Google Scholar 

  5. Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Philips GB (eds) Mannual of methods for general bacteriology. American Society for Microbiology, Washington DC, pp 21–33

    Google Scholar 

  6. Dong X, Cai M (2001) Determination of biochemical properties. Manual for the systematic identification of General Bacteria. Science Press, Beijing, pp 364–398

    Google Scholar 

  7. Fahmy F, Flossdorf J, Claus D (1985) The DNA base composition of the type strains of the genus Bacillus. Syst Appl Microbiol 6:60–65

    Article  CAS  Google Scholar 

  8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  9. Han LC, Yang GQ, Zhou XM, Yang DH, Hu P, Lu Q, Zhou SG (2013) Bacillus thermocopriae sp. nov., isolated from a compost. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.046953-0

    Google Scholar 

  10. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeom YS, Lee JH, Yi H, Won S, Chun H (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    PubMed  Article  CAS  Google Scholar 

  11. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. J Mol Evol 16:111–120

    PubMed  Article  CAS  Google Scholar 

  12. Logan NA, De Vos P (2009) Genus Bacillus Cohn, 1872. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York

    Google Scholar 

  13. Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P, Fritze D, Heyndrickx M, Kämpfer P, Rabinovitch L et al (2009) Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59:2114–2121

    PubMed  Article  CAS  Google Scholar 

  14. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  15. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrate procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  16. Ohta H, Hattori T (1983) Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie van Leeuwenhoek 49:429–446

  17. Pettersson B, Lembke F, Hammer P, Stackebrandt E, Priest FG (1996) Bacillus sporothermodurans, a new species producing highly heat-resistant endospores. Int J Syst Bacteriol 46:759–764

    PubMed  Article  CAS  Google Scholar 

  18. Rheims H, Frühling A, Schumann P, Rohde M, Stackebrandt E (1999) Bacillus silvestris sp. nov., a new member of the genus Bacillus that contains lysine in its cell wall. Int J Syst Bacteriol 49:795–802

    PubMed  Article  Google Scholar 

  19. Scheldeman P, Rodríguez-Díaz M, Goris J, Pil A, De Clerck E, Herman L, De Vos P, Logan NA, Heyndrickx M (2004) Bacillus farraginis sp. nov., Bacillus fortis sp. nov. and Bacillus fordii sp. nov., isolated at dairy farms. Int J Syst Evol Microbiol 54:1355–1364

    PubMed  Article  CAS  Google Scholar 

  20. Sohn JH, Kwon KY, Kang J-H, Jung HB, Kim S-J (2004) Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54:1483–1487

    PubMed  Article  CAS  Google Scholar 

  21. Suzuki M, Nakagawa Y, Harayama S, Yamamoto S (2001) Phylogenetic analysis and taxonomic study of marine Cytophaga-like bacteria: proposal for Tenacibaculum gen. nov with Tenacibaculum maritimum comb. nov and Tenacibaculum ovolyticum comb. nov., and description of Tenacibaculum mesophilum sp. nov. and Tenacibaculum amylolyticum sp. nov. Int J Syst Evol Microbiol 51:1639–1652

    PubMed  Article  CAS  Google Scholar 

  22. Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  Google Scholar 

  23. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetic analysis (MEGA) software version 4.0. Mol Biol Evol 2:1596–1599

    Article  Google Scholar 

  24. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    PubMed  Article  CAS  Google Scholar 

  25. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    PubMed  Article  CAS  Google Scholar 

  26. Vaz-Moreira I, Figueira V, Lopes AR, Lobo-da-Cunha A, Sproer C, Schumann P, Nunes OC, Manaia CM (2012) Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant. Int J Syst Evol Microbiol 62:71–77

    PubMed  Article  CAS  Google Scholar 

  27. Yang GQ, Chen M, Yu Z, Lu Q, Zhou SG (2013) Bacillus composti sp. nov. and Bacillus thermophilus sp. nov., two thermophilic, Fe(III)-reducing bacteria isolated from compost. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.049106-0

    Google Scholar 

  28. Zhang J, Yang GQ, Zhou SG, Wang YQ, Yuan Y, Zhuang L (2012) Fontibacter ferrireducens sp. nov., an Fe(III)-reducing bacterium isolated from a microbial fuel cell. Int J Syst Evol Microbiol 63:925–929

    PubMed  Article  Google Scholar 

Download references

Acknowledgments

This work was supported by the Team Project of Guangdong Natural Science Foundation (S2011030002882 and S2012030006114), the Science and Technology Planning Project of Guangdong Province, China (2012B030800008 and 2012B010500035) and the Guangzhou Science and Technology Development Foundation, China (2011J2200039).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Guiqin Yang or Shungui Zhou.

Additional information

Zhen Yu and Yueqiang Wang contributed equally to this study.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 128 kb)

Supplementary material 2 (DOC 156 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Yu, Z., Wang, Y., Qin, D. et al. Bacillus sediminis sp. nov., isolated from an electroactive biofilm. Antonie van Leeuwenhoek 104, 1109–1116 (2013). https://doi.org/10.1007/s10482-013-0032-0

Download citation

Keywords

  • Bacillus sediminis sp. nov.
  • Electroactive biofilm
  • Polyphasic taxonomy