1887

Abstract

An aerobic, Gram-stain-negative ovoid, designated as strain A21, was isolated using the dilution-to-extinction method from a soil sample taken from Rambla Salada, an athalassohaline habitat located in Murcia (south-eastern Spain). Strain A21 is non-motile, has a respiratory metabolism and grows at NaCl concentrations within the range 0.5–15 % (w/v) [optimum, 5 % (w/v)], at 5–35 °C (optimum, 28 °C) and at pH 6–8 (optimum, pH 7.0). This strain is positive for catalase activity, oxidase activity and nitrate reduction. The 16S rRNA gene sequence indicates that it belongs to the genus in the class . The most closely related species are to which the strain A21 shows 16S rRNA gene sequence similarity values of 98.06 and 97.7 %, respectively. The average nucleotide identity in and digital DNA–DNA hybridization values between strain A21 and LMG 24575 are 76.8 and 21 %, respectively. The DNA G+C content based on the genome is 61.28 mol%. The major fatty acids (>5 % of the total fatty acids) of strain A21 are C ω7/C ω6 and C. The only detected isoprenoid quinone in strain A21 is ubiquinone 10 (Q-10). The polar lipid profile contains phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and three unidentified polar lipids. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, the strain represents a novel species of the genus , for which the name sp. nov. is proposed. Strain A21 (=CECT 9817=LMG 31311) is the type strain.

Funding
This study was supported by the:
  • Dirección General de Investigación Científica y Técnica (Award CGL2011-25748)
    • Principle Award Recipient: Fernando Martínez-Checa
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004154
2020-04-08
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/5/3194.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004154&mimeType=html&fmt=ahah

References

  1. Labrenz M, Collins MD, Lawson PA, Tindall BJ, Schumann P et al. Roseovarius tolerans gen. nov., sp. nov., a budding bacterium with variable bacteriochlorophyll a production from hypersaline Ekho Lake. Int J Syst Bacteriol 1999; 49 Pt 1:137–147 [View Article][PubMed][PubMed]
    [Google Scholar]
  2. Yoon J-H, Kang S-J, Oh T-K. Roseovarius aestuarii sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2008; 58:1198–1202 [View Article][PubMed][PubMed]
    [Google Scholar]
  3. Jung Y-T, Park S, Yoon J-H. Roseovarius litoreus sp. nov., isolated from seawater of southern coast of Korean Peninsula. Antonie van Leeuwenhoek 2012; 102:141–148 [View Article][PubMed][PubMed]
    [Google Scholar]
  4. Oh Y-S, Lim H-J, Cha I-T, Im W-T, Yoo J-S et al. Roseovarius halotolerans sp. nov., isolated from deep seawater. Int J Syst Evol Microbiol 2009; 59:2718–2723 [View Article][PubMed][PubMed]
    [Google Scholar]
  5. Li G, Lai Q, Dong C, Ma R, Du Y et al. Roseovarius atlanticus sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2016; 66:639–644 [View Article][PubMed][PubMed]
    [Google Scholar]
  6. Rajasabapathy R, Mohandass C, Dastager SG, Liu Q, Khieu T-N et al. Roseovarius azorensis sp. nov., isolated from seawater at Espalamaca, Azores. Antonie van Leeuwenhoek 2014; 105:571–578 [View Article][PubMed][PubMed]
    [Google Scholar]
  7. Castro DJ, Cerezo I, Sampedro I, Martínez-Checa F. Roseovarius ramblicola sp. nov., a moderately halophilic bacterium isolated from saline soil in Spain. Int J Syst Evol Microbiol 2018; 68:1851–1856 [View Article][PubMed][PubMed]
    [Google Scholar]
  8. Wang B, Tan T, Shao Z, Tianfeng T, Zongze S. Roseovarius pacificus sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2009; 59:1116–1121 [View Article][PubMed][PubMed]
    [Google Scholar]
  9. Oueriaghli N, Castro DJ, Llamas I, Béjar V, Martínez-Checa F. Study of bacterial community composition and correlation of environmental variables in Rambla Salada, a hypersaline environment in south-eastern Spain. Front Microbiol 2018; 9:1377 [View Article][PubMed][PubMed]
    [Google Scholar]
  10. Sait M, Davis KER, Janssen PH. Effect of pH on isolation and distribution of members of subdivision 1 of the phylum Acidobacteria occurring in soil. Appl Environ Microbiol 2006; 72:1852–1857 [View Article][PubMed][PubMed]
    [Google Scholar]
  11. Rodríguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microb Ecol 1981; 7:235–243 [View Article][PubMed][PubMed]
    [Google Scholar]
  12. Bruns A, Hoffelner H, Overmann J. A novel approach for high throughput cultivation assays and the isolation of planktonic bacteria. FEMS Microbiol Ecol 2003; 45:161–171 [View Article][PubMed][PubMed]
    [Google Scholar]
  13. Button DK, Schut F, Quang P, Martin R, Robertson BR. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 1993; 59:881–891 [View Article][PubMed][PubMed]
    [Google Scholar]
  14. Connon SA, Giovannoni SJ. High-Throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 2002; 68:3878–3885 [View Article][PubMed][PubMed]
    [Google Scholar]
  15. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article][PubMed][PubMed]
    [Google Scholar]
  16. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article][PubMed][PubMed]
    [Google Scholar]
  17. Martínez-Checa F, Quesada E, Martínez-Cánovas MJ, Llamas I, Béjar V. Palleronia marisminoris gen. nov., sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium belonging to the 'Alphaproteobacteria', isolated from a saline soil. Int J Syst Evol Microbiol 2005; 55:2525–2530 [View Article][PubMed][PubMed]
    [Google Scholar]
  18. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped blast and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article][PubMed][PubMed]
    [Google Scholar]
  19. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 2014; 42:D643–D648 [View Article][PubMed][PubMed]
    [Google Scholar]
  20. 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][PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed][PubMed]
    [Google Scholar]
  22. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Metabolism Protein New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  23. Biebl H, Allgaier M, Lünsdorf H, Pukall R, Tindall BJ et al. Roseovarius mucosus sp. nov., a member of the Roseobacter clade with trace amounts of bacteriochlorophyll a . Int J Syst Evol Microbiol 2005; 55:2377–2383 [View Article][PubMed][PubMed]
    [Google Scholar]
  24. 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][PubMed]
    [Google Scholar]
  25. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A et al. Assembling genomes and mini-metagenomes from highly chimeric reads. In Deng M, Jiang R, Sun F, Zhang X. (editors) Research in Computational Molecular Biology 201 Berlin, Heidelberg: Springer Berlin Heidelberg; pp 158–170
    [Google Scholar]
  26. 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][PubMed]
    [Google Scholar]
  27. 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][PubMed]
    [Google Scholar]
  28. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed][PubMed]
    [Google Scholar]
  29. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [View Article][PubMed][PubMed]
    [Google Scholar]
  30. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed][PubMed]
    [Google Scholar]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed][PubMed]
    [Google Scholar]
  32. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article][PubMed][PubMed]
    [Google Scholar]
  33. Xie Q-yi, Lin H-peng, Li L, Brown R, Goodfellow M et al. Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2012; 102:1–7 [View Article][PubMed][PubMed]
    [Google Scholar]
  34. Komagata K. Bacteria (1) – the aerobic bacteria. In Hasegawa T. editor Classification and I 259 dentification of Microorganisms 2 Tokyo: Gakkai Shuppan; 1985 pp 99–161
    [Google Scholar]
  35. Mata JA, Martínez-Cánovas J, Quesada E, Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002; 25:360–375 [View Article][PubMed][PubMed]
    [Google Scholar]
  36. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed][PubMed]
    [Google Scholar]
  37. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article][PubMed][PubMed]
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: DE: MIDI I; 1990
    [Google Scholar]
  39. MIDI Sherlock Microbial Identification System Operating Manual, version 6.1 Newark, DE: MIDI Inc; 2008
    [Google Scholar]
  40. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed][PubMed]
    [Google Scholar]
  41. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC USA: L. R. Snyder ASM Press; 2007 pp 330–393
    [Google Scholar]
  42. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990a; 13:128–130 [View Article]
    [Google Scholar]
  43. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990b; 66:199–202 [View Article]
    [Google Scholar]
  44. Kim Y-O, Kong HJ, Park S, Kang S-J, Kim W-J et al. Roseovarius halocynthiae sp. nov., isolated from the sea squirt Halocynthia roretzi . Int J Syst Evol Microbiol 2012; 62:931–936 [View Article][PubMed][PubMed]
    [Google Scholar]
  45. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ et al. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera . Int J Syst Evol Microbiol 2006; 56:1293–1304 [View Article][PubMed][PubMed]
    [Google Scholar]
  46. Hiraishi A, Nagashima KV, Matsuura K, Shimada K, Takaichi S et al. Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria: its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov. Int J Syst Bacteriol 1998; 48 Pt 4:1389–1398 [View Article][PubMed][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004154
Loading
/content/journal/ijsem/10.1099/ijsem.0.004154
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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