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Volume 71, Issue 8

sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave Open Access

Abstract

A novel facultatively anaerobic, non-motile, Gram-stain-negative, non-endospore-forming alphaproteobacterium, strain 1011MAR3C25, was isolated from a white biofilm colonizing the walls of the Andalusian show cave Gruta de las Maravillas (Huelva, Spain). Strain 1011MAR3C25 grew at 8–42 °C (optimum, 20–30 °C), at pH 5.0–9.0 (optimum, pH 5.0–6.0) and in the presence of 0–12 % (w/v) NaCl (optimum 3–5 %). Cells were catalase- and oxidase-positive. The strain grew heterotrophically with various carbon sources and chemoautotrophically with thiosulfate under aerobic conditions. Results of phylogenetic analysis showed that strain 1011MAR3C25 was related to DSM 18447 and LMG 30882 (97.90 % and 97.32 % 16S rRNA sequence identity values, respectively). The major respiratory quinone was ubiquinone Q-10 and the predominant fatty acid was Cω7. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified glycolipid and an unidentified polar lipid. The DNA G+C content was 60.3 mol%. Based on a polyphasic taxonomic study it is proposed that strain 1011MAR3C25 (=CECT 9092=LMG 29414) represents a novel species of the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Paracoccus , Proteobacteria , show cave and whole genome average nucleotide identity
Funding
This study was supported by the:
  • interreg (Award project 0483_PROBIOMA_5_E)
    • Principle Award Recipient: NotApplicable
© 2021 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.
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2021-08-13
2024-04-19
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References

  1. Davis DH, Doudoroff M, Stanier RY, Mandel M. Proposal to reject the genus Hydrogenomonas: taxonomic implications. Int J Syst Bacteriol 1969; 19:375–390 [View Article]
     [Google Scholar]
  2. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MA. The Family Rhodobacteraceae. Rosenberg E, DeLong E, Stackebrandt E, Lory S, Thompson F. eds In The Prokaryotes Berlin, Heidelberg: Springer; 2014 pp 439–512 https://doi.org/10.1007/978-3-642-30197-1_377
     [Google Scholar]
  3. Roh SW, Nam YD, Chang HW, Kim KH, Kim M-S et al. Paracoccus aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2009; 59:790–794 [View Article] [PubMed]
     [Google Scholar]
  4. Dastager SG, Deepa CK, Li W-J, Tang S-K, Pandey A. Paracoccus niistensis sp. nov., isolated from forest soil, India. Antonie van Leeuwenhoek 2011; 99:501–506 [View Article]
     [Google Scholar]
  5. Siller H, Rainey FA, Stackebrandt E, Winter J. Isolation and characterization of a new gram-negative, acetone-degrading, nitrate-reducing bacterium from soil, Paracoccus solventivorans sp. nov. Int J Syst Bacteriol 1996; 46:1125–1130 [View Article] [PubMed]
     [Google Scholar]
  6. Wang Y, Tang SK, Lou K, Mao PH, Jin X et al. Paracoccus saliphilus sp. nov., a halophilic bacterium isolated from a saline soil. Int J Syst Evol Microbiol 2009; 59:1924–1928 [View Article] [PubMed]
     [Google Scholar]
  7. van Spanning RJM, Stouthamer AH, Baker SC, van Verseveld HW. Genus Paracoccus davis 1969, 384AL emend. Ludwig, Mittenhuber and Friedrich 1993, 366. Breener D, Krieg N, Staley J, Garrity G. eds In Bergey´s Manual of Systematic Bacteriology New York: Springer; 2005 pp 197–204
     [Google Scholar]
  8. Dominguez-Moñino I, Jurado V, Hermosin B, Saiz-Jimenez C. Paracoccus cavernae sp. nov., isolated from a show cave. Int J Syst Evol Microbiol 2016; 66:1–6 [View Article]
     [Google Scholar]
  9. Riquelme C, Hathaway JJM, Dapkevicius M, Miller AZ, Kooser A et al. Actinobacterial diversity in volcanic caves and associated geomicrobiological interactions. Front Microbiol 2015; 6:1342 [View Article] [PubMed]
     [Google Scholar]
  10. Lavoie KH, Winter AS, Read KJH, Hughes EM, Spilde MN et al. Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA. PLoS ONE 2017; 12:e0169339 [View Article] [PubMed]
     [Google Scholar]
  11. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
     [Google Scholar]
  12. Jurado V, Miller AZ, Alias-Villegas C, Laiz L, Saiz-Jimenez C. Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument. Syst Appl Microbiol 2012; 35:306–309 [View Article] [PubMed]
     [Google Scholar]
  13. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  14. Campbell JH, O’Donoghue P, Campbell AG, Schwientek P, Sczyrba A et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci USA 2013; 110:5540–5545 [View Article] [PubMed]
     [Google Scholar]
  15. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  18. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000 pp 1–333
     [Google Scholar]
  19. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  20. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  21. Richter M, Rosselló-Móra R Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  22. Lee I, Kim YO, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2015; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  23. Urdiain M, López-López A, Gonzalo C, Busse HJ, Langer S et al. Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense. Syst Appl Microbiol 2008; 31:339–351 [View Article] [PubMed]
     [Google Scholar]
  24. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  25. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  26. Muñoz-Mérida A, Viguera E, Claros MG, Trelles O, Pérez-Pulido AJ. Sma3s: a three-step modular annotator for large sequence datasets. DNA Res 2014; 21:341–353 [View Article] [PubMed]
     [Google Scholar]
  27. Consortium U. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article] [PubMed]
     [Google Scholar]
  28. Tambalo DD, Del Bel KL, Bustard DE, Greenwood PR, Steedman AE et al. Regulation of flagellar, motility and chemotaxis genes in Rhizobium leguminosarum by the VisN/R-Rem cascade. Microbiology 2010; 156:1673–1685 [View Article] [PubMed]
     [Google Scholar]
  29. Hucker GJ. A new modification and application of the gram stain. J Bacteriol 1921; 6:395–397 [View Article] [PubMed]
     [Google Scholar]
  30. Halebian S, Harris B, Finegold SM, Rolfe RD. Rapid method that aids in distiguishing Gram-positive from Gram-negative anaerobic bacteria. J Clin Microbiol 1981; 13:444–448 [View Article] [PubMed]
     [Google Scholar]
  31. Khan ST, Takaichi S, Harayama S. Paracoccus marinus sp. nov., an adonixanthin diglucoside-producing bacterium isolated from coastal seawater in Tokyo Bay. Int J Syst Evol Microbiol 2008; 58:383–386 [View Article] [PubMed]
     [Google Scholar]
  32. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article] [PubMed]
     [Google Scholar]
  33. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1965 pp 21–45
     [Google Scholar]
  34. Lányi B. Classical and rapid identification methods for medically important bacteria. Colwell R, Grigorova R. eds In Methods in Microbiology Vol 19 London: Current Methods for Classification and Identification of Microorganisms, Academic Press; 1987 pp 1–67
     [Google Scholar]
  35. Wood AP, Kelly DP. Physiological characteristics of a new thermophilic obligately chemolithotrophic Thiobacillus species Thiobacillus tepidarius. Int J Syst Bacteriol 1985; 35:434–437 [View Article]
     [Google Scholar]
  36. Boden R, Hutt LP, Rae AW. Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the “Proteobacteria”, and four new families within the orders Nitrosomonadales and Rhodocyclales. Int J Syst Evol Microbiol 2017; 67:1191–1205 [View Article] [PubMed]
     [Google Scholar]
  37. Kelly DP, Wood AP. Autotrophic growth of Thiobacillus A2 on methanol. FEMS Microbiol Lett 1982; 15:229–233
     [Google Scholar]
  38. Jurado V, Kroppenstedt RM, Saiz-Jimenez C, Klenk HP, Mouniée D et al. Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm. Int J Syst Evol Microbiol 2009; 59:3105–3110 [View Article] [PubMed]
     [Google Scholar]
  39. Liu Y, Q-y X, Hong K, Li L, Zhao YM et al. Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract. Anton Leeuw 2013; 105:1133–1139
     [Google Scholar]
  40. Kim BY, Weon HY, Yoo SH, Kwon SW, Cho YH et al. Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 2006; 56:2387–2390 [View Article] [PubMed]
     [Google Scholar]
  41. Zhang YX, Li X, F-L L, S-C M, Zheng GD et al. Paracoccus alkanivorans sp. nov., isolated from a deep well with oil reservoir water. Int J Syst Evol Microbiol 2020; 70:2312–2317 [View Article] [PubMed]
     [Google Scholar]
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Paracoccus onubensis sp. nov., a novel alphaproteobacterium isolated from the wall of a show cave
Int J Syst Evol Microbiol 71, 004942 (2021); https://doi.org/10.1099/ijsem.0.004942
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