Skip to main content

Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring

Current Microbiology volume 80, Article number: 31 (2023) Cite this article

Abstract

In this study, we present the characterization of the BNO1T bacterial strain isolated from the deep subsurface saline spring at the Baksan Neutrino Observatory INR RAS (Kabardino-Balkaria, Russia). The complete genome sequence of the strain BNO1T is 5,347,902 bp, with a GC content 41 and 49%. The cell wall peptidoglycan contains meso-diaminopimelic acid. The major isoprenoid quinone is MK-7 and the polar lipids are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The major fatty acids are anteiso-C15:0 (23.34%), iso-C15:0 (20.10%), C16:0 (11.96%), iso-C16:0 (10.88%), and anteiso-C17:0 (10.79%). The 16S rRNA gene sequence clearly demarcated the strain as belonging to Cytobacillus genera. Based on the phylogenetic analysis, ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization) assessments we propose to assign the strain BNO1T and other related strains to new species and to name it Cytobacillus pseudoceanisediminis sp. nov. (The values of ANI and dDDH between BNO1T and Cytobacillus oceanisediminis CGMCC 1.10115 T are 80.65% and 24.7%, respectively; values of ANI and dDDH between BNO1T and Cytobacillus firmus NCTC 10335 T are 89% and 38%, respectively). Genomic analysis of strain BNO1T revealed pathways for C1 compounds oxidation and two pathways for C1 compounds assimilation: serine and ribulose monophosphate pathways. In addition, strain BNO1T contains a plasmid (342,541 bp) coding multiple genes involved in heavy metal ion balance. Moreover, heavy metal toxicity testing confirmed the high potential of the strain BNO1T as a source of metal resistance genes and enzymes. The type strain is BNO1T (= BIM B-1921 T = VKM B-3664 T).

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

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. Shaw AJ, Podkaminer KK, Desai SG et al (2008) Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc Natl Acad Sci USA 105:13769–13774. https://doi.org/10.1073/pnas.0801266105

    Article  Google Scholar 

  2. Bustard MT, Grant Burgess J, Meeyoo V, Wright PC (2000) Novel opportunities for marine hyperthermophiles in emerging biotechnology and engineering industries. J Chem Technol Biotechnol 75:1095–1109. https://doi.org/10.1002/1097-4660(200012)75:12%3c1095::AID-JCTB327%3e3.0.CO;2-3

    Article  CAS  Google Scholar 

  3. Kim HJ, Lim JW, Jeong H et al (2016) Development of a highly specific and sensitive cadmium and lead microbial biosensor using synthetic CadC-T7 genetic circuitry. Biosens Bioelectron 79:701–708. https://doi.org/10.1016/j.bios.2015.12.101

    Article  CAS  Google Scholar 

  4. Seckbach J, Stan-Lotter H (2020) Extremophiles as astrobiological models. John Wiley & Sons Inc, Hoboken, NJ. https://doi.org/10.1002/9781119593096

    Book  Google Scholar 

  5. Gavriljuk JM, Gangapshev AM, Gezhaev AM et al (2013) Working characteristics of the New Low-Background Laboratory (DULB-4900). Nucl Instruments Methods Phys Res Sect A Accel Spectrometers, Detect Assoc Equip 729:576–580. https://doi.org/10.1016/j.nima.2013.07.090

    Article  CAS  Google Scholar 

  6. Kuzminov VV (2018) Research program of the baksan neutrino observatory of the institute for nuclear research of the russian academy of sciences: 50 Years in the Making. Phys Part Nucl 49:473–481. https://doi.org/10.1134/S1063779618040391

    Article  Google Scholar 

  7. Kuzminov VV (2012) The baksan neutrino observatory. Eur Phys J Plus 127:113. https://doi.org/10.1140/epjp/i2012-12113-0

    Article  Google Scholar 

  8. Zarubin M, Gangapshev A, Gavriljuk Y et al (2021) First transcriptome profiling of D. melanogaster after development in a deep underground low radiation background laboratory. PLoS ONE 16:e0255066. https://doi.org/10.1371/journal.pone.0255066

    Article  CAS  Google Scholar 

  9. Zarubin MP, Kuldoshina OA, Kravchenko EV (2021) Biological effects of low background radiation: prospects for future research in the low-background laboratory DULB-4900 of Baksan Neutrino Observatory INR RAS. Phys Part Nucl 52:19–30. https://doi.org/10.1134/S1063779621010056

    Article  CAS  Google Scholar 

  10. Logan NA, Berkeley RCW (1984) Identification of Bacillus strains using the API system. J Gen Microbiol 130:1871–1882. https://doi.org/10.1099/00221287-130-7-1871

    Article  CAS  Google Scholar 

  11. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. The Williams & Wilkins Co., Baltimore

  12. Kudryashova EB, Karlyshev AV, Ariskina EV et al (2018) Cohnella kolymensis sp. nov., a novel Bacillus isolated from Siberian permafrost. Int J Syst Evol Microbiol 68:2912–2917. https://doi.org/10.1099/ijsem.0.002919

    Article  CAS  Google Scholar 

  13. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354. https://doi.org/10.1128/mr.45.2.316-354.1981

    Article  CAS  Google Scholar 

  14. Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586. https://doi.org/10.1128/jcm.16.3.584-586.1982

    Article  CAS  Google Scholar 

  15. Minnikin DE, O’Donnell AG, Goodfellow M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241. https://doi.org/10.1016/0167-7012(84)90018-6

    Article  CAS  Google Scholar 

  16. Koren S, Walenz BP, Berlin K et al (2017) Canu: scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation. Genome Res 27:722–736. https://doi.org/10.1101/gr.215087.116

    Article  CAS  Google Scholar 

  17. 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

    Article  CAS  Google Scholar 

  18. Parks DH, Rinke C, Chuvochina M et al (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533–1542. https://doi.org/10.1038/s41564-017-0012-7

    Article  CAS  Google Scholar 

  19. 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

    Article  CAS  Google Scholar 

  20. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691–699. https://doi.org/10.1093/oxfordjournals.molbev.a003851

    Article  CAS  Google Scholar 

  21. Huerta-Cepas J, Serra F, Bork P (2016) ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol Biol Evol 33:1635–1638. https://doi.org/10.1093/molbev/msw046

    Article  CAS  Google Scholar 

  22. Menardo F, Loiseau C, Brites D et al (2018) Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC Bioinformatics 19:164. https://doi.org/10.1186/s12859-018-2164-8

    Article  Google Scholar 

  23. Yoon SH, Ha min S, Lim J et al (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4

    Article  CAS  Google Scholar 

  24. 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. https://doi.org/10.1093/nar/gkab902

    Article  CAS  Google Scholar 

  25. Sievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75

    Article  Google Scholar 

  26. Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 9:678–687. https://doi.org/10.1093/oxfordjournals.molbev.a040752

    Article  CAS  Google Scholar 

  27. Overbeek R, Olson R, Pusch GD et al (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. https://doi.org/10.1093/nar/gkt1226

    Article  CAS  Google Scholar 

  28. Micha P, Corradini MG (2011) Microbial growth curves: what the models tell us and what they cannot. Crit Rev Food Sci Nutr 51:917–945. https://doi.org/10.1080/10408398.2011.570463

    Article  Google Scholar 

  29. Patel S, Gupta RS (2020) A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 70:406–438. https://doi.org/10.1099/ijsem.0.003775

    Article  CAS  Google Scholar 

  30. Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    Article  CAS  Google Scholar 

  31. Lee YJ, Lee SJ, Jeong H et al (2012) Draft genome sequence of Bacillus oceanisediminis 2691. J Bacteriol 194:6351–6352. https://doi.org/10.1128/JB.01643-12

    Article  CAS  Google Scholar 

  32. Zhang J, Wang J, Fang C et al (2010) Bacillus oceanisediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 60:2924–2929. https://doi.org/10.1099/ijs.0.019851-0

    Article  CAS  Google Scholar 

  33. Whitman WB, Woyke T, Klenk HP et al (2015) Genomic encyclopedia of bacterial and archaeal type strains, phase III: The genomes of soil and plant-associated and newly described type strains. Stand Genomic Sci 10:26. https://doi.org/10.1186/s40793-015-0017-x

    Article  CAS  Google Scholar 

  34. Ko KS, Oh WS, Lee MY et al (2006) Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Int J Syst Evol Microbiol 56:2541–2544. https://doi.org/10.1099/ijs.0.64213-0

    Article  CAS  Google Scholar 

  35. Tindall BJ, Rosselló-Móra R, Busse HJ et al (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266. https://doi.org/10.1099/ijs.0.016949-0

    Article  CAS  Google Scholar 

  36. Goris J, Konstantinidis KT, Klappenbach JA et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0

    Article  CAS  Google Scholar 

  37. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60

    Article  Google Scholar 

  38. Jung J, Jeong H, Kim HJ et al (2016) Complete genome sequence of Bacillus oceanisediminis 2691, a reservoir of heavy-metal resistance genes. Mar Genomics 30:73–76. https://doi.org/10.1016/j.margen.2016.07.002

    Article  Google Scholar 

  39. Kämpfer P (1994) Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 17:86–98. https://doi.org/10.1016/S0723-2020(11)80035-4

    Article  Google Scholar 

  40. Albert RA, Archambault J, Rosselló-Mora R et al (2005) Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Int J Syst Evol Microbiol 55:2125–2130. https://doi.org/10.1099/ijs.0.02337-0

    Article  CAS  Google Scholar 

  41. Priest FG, Goodfellow M, Todd C (1988) A numerical classification of the genus Bacillus. J Gen Microbiol 134:1847–1882. https://doi.org/10.1099/00221287-134-7-1847

    Article  CAS  Google Scholar 

  42. Lim JM, Jeon CO, Kim CJ (2006) Bacillus taeanensis sp. nov., a halophilic Gram-positive bacterium from a solar saltern in Korea. Int J Syst Evol Microbiol 56:2903–2908. https://doi.org/10.1099/ijs.0.64036-0

    Article  CAS  Google Scholar 

  43. Tatusova T, Dicuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569

    Article  CAS  Google Scholar 

  44. Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2622. https://doi.org/10.1111/j.1462-2920.2011.02464.x

    Article  CAS  Google Scholar 

  45. Wu TY, Chen CT, Liu JTJ et al (2016) Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1. Appl Microbiol Biotechnol 100:4969–4983. https://doi.org/10.1007/s00253-016-7320-3

    Article  CAS  Google Scholar 

  46. Arfman N, Van Beeumen J, De Vries GE et al (1991) Purification and characterization of an activator protein for methanol dehydrogenase from thermotolerant Bacillus spp. J Biol Chem 266:3955–3960. https://doi.org/10.1016/s0021-9258(19)67886-5

    Article  CAS  Google Scholar 

  47. Verma S, Kuila A (2019) Bioremediation of heavy metals by microbial process. Environ Technol Innov. https://doi.org/10.1016/j.eti.2019.100369

    Article  Google Scholar 

  48. Utami U, Harianie L, Dunyana NR, Romaidi R (2020) Lead-resistant bacteria isolated from oil wastewater sample for bioremediation of lead. Water Sci Technol 81:2244–2249. https://doi.org/10.2166/wst.2020.281

    Article  CAS  Google Scholar 

  49. Abdollahi S, Golchin A, Shahryari F (2020) Lead and cadmium-resistant bacterial species isolated from heavy metal-contaminated soils show plant growth-promoting traits. Int Microbiol 23:625–640. https://doi.org/10.1007/s10123-020-00133-1

    Article  CAS  Google Scholar 

  50. Sun F, Shao Z (2007) Biosorption and bioaccumulation of lead by Penicillium sp. Psf-2 isolated from the deep sea sediment of the Pacific Ocean. Extremophiles 11:853–858. https://doi.org/10.1007/s00792-007-0097-7

    Article  Google Scholar 

  51. Chen J, Li J, Zhang H et al (2019) Bacterial heavy-metal and antibiotic resistance genes in a copper tailing dam area in northern China. Front Microbiol 10:1916. https://doi.org/10.3389/fmicb.2019.01916

    Article  Google Scholar 

  52. Bogatikov OA, Bortnikov NS, Dokuchaev AY et al (2014) Primary aspects of technogenic deposits at the modern stage: the example of the Tyrnyauz deposit. Dokl Earth Sci 456:585–589. https://doi.org/10.1134/S1028334X14050237

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dzhelepov Laboratory of Nuclear Problems, Joint Institute for Nuclear Research, Dubna, Russia

    Kirill Tarasov, Alena Yakhnenko, Mikhail Zarubin & Elena Kravchenko

  2. Baksan Neutrino Observatory, Institute for Nuclear Research RAS, Moscow, Russia

    Albert Gangapshev

  3. Lomonosov Moscow State University, Moscow, Russia

    Natalia V. Potekhina

  4. All-Russian Collection of Microorganisms (VKM), G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Scientific Center for Biological Research RAS, Pushchino, Russia

    Alexander N. Avtukh

Authors
  1. Kirill Tarasov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alena Yakhnenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mikhail Zarubin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Albert Gangapshev
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Natalia V. Potekhina
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Alexander N. Avtukh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Elena Kravchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

EK coordinated the overall study, performed the experiments, and prepared and analyzed the data; AY, MZ, and AG collected the samples; KT performed the experiments and bioinformatic analysis; AY performed the experiments; NP and AA performed the chemotaxonomic characterization; EK, KT, AY, and MZ wrote the first draft; EK and KT edited the final version. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Elena Kravchenko.

Ethics declarations

Conflict of interest

The authors declare that they do not have any conflict of interest to report.

Additional information

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.

Supplementary file1 (DOCX 1055 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Tarasov, K., Yakhnenko, A., Zarubin, M. et al. Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring. Curr Microbiol 80, 31 (2023). https://doi.org/10.1007/s00284-022-03141-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-022-03141-8