1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 3

sp. nov. and sp. nov., two acidophilic bacteria isolated from acid mine drainage Open Access

Abstract

Two acidophilic strains, designated as ALEF1 and S30H14, were isolated from acid mine drainage sediment. Cells of both strains were Gram-stain-positive, aerobic, endospore-forming rods. Strains ALEF1 and S30H14 were acidophilic and mesophilic, the former grew at 20–40 °C (optimum, 30 °C) and pH 2.5–4.5 (optimum, pH 3.5), while the latter grew at 20–45 °C (optimum, 30 °C) and pH 2.0–5.5 (optimum, pH 4.5). The 16S rRNA gene-based sequence analysis revealed that strains ALEF1 and S30H14 belonged to the genus , and were phylogenetically close to TC-34 with 97.1 and 97.4% similarity, respectively. The similarity between the two novel strains was 98.6 %. The average nucleotide identity value between the genome sequences of ALEF1 and S30H14 was 79.5 %, and that between each of the two isolates and TC-34 were 72.0 and 74.3 %. In addition, the digital DNA–DNA hybridization value between ALEF1 and S30H14 was 24.9 %, between strain ALEF1 and TC-34 was 21.7 %, and between S30H14 and TC-34 was 26.3 %, far below the interspecies threshold. Both strains could utilize diverse carbon sources for heterotrophic growth; strain ALEF1 could utilize ferrous iron as the energy source for autotrophic growth. Menaquinone 7 was the only quinone detected in either strain. Both strains contained anteiso-C and anteiso-C, while -alicyclic fatty acids were not detected. Based on their phylogenetic positions, as well as phenotypic and genomic data, it is considered that strains ALEF1 and S30H14 represent two novel species within the genus , for which the names sp. nov. (type strain ALEF1=CGMCC 1.17055=KCTC 43124) and sp. nov. (S30H14=CGMCC 1.17050=KCTC 43125) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): acid mine drainage , acidophile , Alicyclobacillus curvatus and Alicyclobacillus mengziensis
Funding
This study was supported by the:
  • CAS-NSTDA Joint Research Program (Award NO. 153211KYSB20200039)
    • Principle Award Recipient: Cheng-YingJiang
  • National Nature Science Foundation of China (Award 31670124)
    • Principle Award Recipient: Cheng-YingJiang
  • Innovation Academy for Green Manufacture, Chinese Academy of Sciences (Award IAGM2020C24)
    • Principle Award Recipient: Cheng-YingJiang
  • CAS Engineering Laboratory for Advanced Microbial Technology of Agriculture, Chinese Academy of Sciences (Award KFJ-PTXM-016)
    • Principle Award Recipient: Cheng-YingJiang
  • Major Research Plan of National Natural Science Foundation of China (Award 91851206)
    • Principle Award Recipient: Cheng-YingJiang
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005285
2022-03-21
2024-12-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/3/ijsem005285.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005285&mimeType=html&fmt=ahah

References

  1. Wisotzkey JD, Jurtshuk P, Fox GE, Deinhard G, Poralla K. Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov. Int J Syst Bacteriol 1992; 42:263–269 [View Article] [PubMed]
     [Google Scholar]
  2. Goto K, Mochida K, Asahara M, Suzuki M, Kasai H et al. Alicyclobacillus pomorum sp. nov., a novel thermo-acidophilic, endospore-forming bacterium that does not possess omega-alicyclic fatty acids, and emended description of the genus Alicyclobacillus. Int J Syst Evol Microbiol 2003; 53:1537–1544 [View Article] [PubMed]
     [Google Scholar]
  3. Karavaiko GI, Bogdanova TI, Tourova TP, Kondrat’eva TF, Tsaplina IA et al. Reclassification of “Sulfobacillus thermosulfidooxidans subsp. thermotolerans” strain K1 as Alicyclobacillus tolerans sp. nov. and Sulfobacillus disulfidooxidans Dufresne et al. 1996 as Alicyclobacillus disulfidooxidans comb. nov., and emended description of the genus Alicyclobacillus. Int J Syst Evol Microbiol 2005; 55:941–947 [View Article]
     [Google Scholar]
  4. Guo X, You X-Y, Liu L-J, Zhang J-Y, Liu S-J et al. Alicyclobacillus aeris sp. nov., a novel ferrous- and sulfur-oxidizing bacterium isolated from a copper mine. Int J Syst Evol Microbiol 2009; 59:2415–2420 [View Article] [PubMed]
     [Google Scholar]
  5. Jiang C-Y, Liu Y, Liu Y-Y, You X-Y, Guo X et al. Alicyclobacillus ferrooxydans sp. nov., a ferrous-oxidizing bacterium from solfataric soil. Int J Syst Evol Microbiol 2008; 58:2898–2903 [View Article] [PubMed]
     [Google Scholar]
  6. Kim MG, Lee JC, Park DJ, Li WJ, Kim CJ. Alicyclobacillus tengchongensis sp. nov., a thermo-acidophilic bacterium isolated from hot spring soil. J Microbiol 2014; 52:884–889 [View Article] [PubMed]
     [Google Scholar]
  7. Goto K, Matsubara H, Mochida K, Matsumura T, Hara Y et al. Alicyclobacillus herbarius sp. nov., a novel bacterium containing omega-cycloheptane fatty acids, isolated from herbal tea. Int J Syst Evol Microbiol 2002; 52:109–113 [View Article] [PubMed]
     [Google Scholar]
  8. Matsubara H, Goto K, Matsumura T, Mochida K, Iwaki M et al. Alicyclobacillus acidiphilus sp. nov., a novel thermo-acidophilic, omega-alicyclic fatty acid-containing bacterium isolated from acidic beverages. Int J Syst Evol Microbiol 2002; 52:1681–1685 [View Article] [PubMed]
     [Google Scholar]
  9. Nakano C, Takahashi N, Tanaka N, Okada S. Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product. Int J Syst Evol Microbiol 2015; 65:716–722 [View Article] [PubMed]
     [Google Scholar]
  10. Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592 [View Article] [PubMed]
     [Google Scholar]
  11. Darland G, Brock TD. Bacillus acidocaldarius sp.nov., an acidophilic thermophilic spore-forming bacterium. J Gen Microbiol 1971; 67:9–15 [View Article]
     [Google Scholar]
  12. Liu Z, Liang Z, Zhou Z, Li L, Meng D et al. Mobile genetic elements mediate the mixotrophic evolution of novel Alicyclobacillus species for acid mine drainage adaptation. Environ Microbiol 2021; 23:3896–3912 [View Article] [PubMed]
     [Google Scholar]
  13. Johnson DB, Hallberg KB. Techniques for detecting and identifying acidophilic mineral-oxidizing microorganisms. In Rawlings DE, Johnson DB. eds Biomining Berlin, Heidelberg: Springer Berlin Heidelberg; 2007 pp 237–261
     [Google Scholar]
  14. Farrand SG, Linton JD, Stephenson RJ, McCarthy WV. The use of response surface analysis to study the growth of Bacillus acidocaldarius throughout the growth range of temperature and pH. Arch Microbiol 1983; 135:272–275 [View Article]
     [Google Scholar]
  15. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article] [PubMed]
     [Google Scholar]
  16. Haseltine C, Montalvo-Rodriguez R, Carl A, Bini E, Blum P. Extragenic pleiotropic mutations that repress glycosyl hydrolase expression in the hyperthermophilic archaeon Sulfolobus solfataricus. Genetics 1999; 152:1353–1361 [View Article] [PubMed]
     [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  23. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  24. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  25. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article] [PubMed]
     [Google Scholar]
  29. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  30. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
     [Google Scholar]
  31. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  32. Garber AI, Nealson KH, Okamoto A, McAllister SM, Chan CS et al. FeGenie: A comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies. Front Microbiol 2020; 11:37 [View Article] [PubMed]
     [Google Scholar]
  33. Hucker GJ. A new modification and application of the Gram stain. J Bacteriol 1921; 6:395–397 [View Article] [PubMed]
     [Google Scholar]
  34. Albuquerque L, Rainey FA, Chung AP, Sunna A, Nobre MF et al. Alicyclobacillus hesperidum sp. nov. and a related genomic species from solfataric soils of São Miguel in the Azores. Int J Syst Evol Microbiol 2000; 50:451–457 [View Article] [PubMed]
     [Google Scholar]
  35. Tamura H, Goto K, Yotsuyanagi T, Nagayama M. Spectrophotometric determination of iron(II) with 1,10-phenanthroline in the presence of large amounts of iron(III). Talanta 1974; 21:314–318 [View Article] [PubMed]
     [Google Scholar]
  36. Tabatabai MA. A rapid method for determination of sulfate in water samples. Environmental Letters 2009; 7:237–243 [View Article]
     [Google Scholar]
  37. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article] [PubMed]
     [Google Scholar]
  38. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30:178–182 [View Article] [PubMed]
     [Google Scholar]
  39. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical note 101. Newark, DE: MIDI inc; 1990
     [Google Scholar]
  40. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  41. Muhadesi J-B, Huang Y, Wang B-J, Jiang C-Y, Liu S-J. Acidibrevibacterium fodinaquatile gen. nov., sp. nov., isolated from acidic mine drainage. Int J Syst Evol Microbiol 2019; 69:3248–3255 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005285
Loading
Alicyclobacillus curvatus sp. nov. and Alicyclobacillus mengziensis sp. nov., two acidophilic bacteria isolated from acid mine drainage
Int J Syst Evol Microbiol 72, 005285 (2022); https://doi.org/10.1099/ijsem.0.005285
/content/journal/ijsem/10.1099/ijsem.0.005285
/content/journal/ijsem/10.1099/ijsem.0.005285
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error