1887

Abstract

To date, there is sparse information for the genus with CC-AMO-30D as the only described member. We report here a new species isolated from mangrove soil collected at Malaysia Tanjung Piai National Park and perform polyphasic characterization to determine its taxonomic position. Strain CL23 is a Gram-negative, yellow-pigmented, strictly aerobic, catalase-positive and oxidase-positive bacterium. The optimal growth conditions were determined to be at pH 7.0, 30–37 °C and in 1–2 % (w/v) NaCl. The major respiratory quinone was menaquinone-6 (MK-6) and the highly abundant polar lipids were four unidentified lipids, a phosphatidylethanolamine and two unidentified aminolipids. The 16S rRNA gene similarity between strain CL23 and CC-AMO-30D is 96.67 %. Strain CL23 and CC-AMO-30D clustered together and were distinguished from taxa of closely related genera in 16S rRNA gene phylogenetic analysis. Genome sequencing revealed that strain CL23 has a genome size of 4.4 Mbp and a G+C content of 40.72 mol%. Overall genome related indexes including digital DNA–DNA hybridization value and average nucleotide identity are 17.70 % and approximately 70%, below the cutoffs of 70 and 95%, respectively, indicated that strain CL23 is a distinct species from CC-AMO-30D. Collectively, based on the phenotypic, chemotaxonomic, phylogenetic and genomic evidences presented here, strain CL23 is proposed to represent a new species with the name sp. nov. (KCTC 72252=LMG 31418). An emended description of the genus is also proposed.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003970
2020-01-24
2020-02-28
Loading full text...

Full text loading...

References

  1. Parte AC. LPSN - list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018;68:1825–1829 [CrossRef]
    [Google Scholar]
  2. Hameed A, Shahina M, Lin S-Y, Lai W-A, Liu Y-C et al. Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter. Int J Syst Evol Microbiol 2014;64:533–539 [CrossRef]
    [Google Scholar]
  3. Thevarajoo S, Selvaratnam C, Goh KM, Hong KW, Chan XY et al. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2016;66:3662–3668 [CrossRef]
    [Google Scholar]
  4. Li Y, Bai S, Yang C, Lai Q, Zhang H et al. Mangrovimonas yunxiaonensis gen. nov., sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2013;63:2043–2048 [CrossRef]
    [Google Scholar]
  5. Wang B, Sun F, Du Y, Liu X, Li G et al. Meridianimaribacter flavus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment of the South China Sea. Int J Syst Evol Microbiol 2010;60:121–127 [CrossRef]
    [Google Scholar]
  6. Alongi DM.Mangrove forests Blue Carbon: Coastal Sequestration for Climate Change Mitigation Cham: Springer; 2018; pp23–36
    [Google Scholar]
  7. Lin X, Hetharua B, Lin L, Xu H, Zheng T et al. Mangrove sediment microbiome: adaptive microbial assemblages and their routed biogeochemical processes in Yunxiao mangrove national nature reserve, China. Microb Ecol 2019;78:57–69 [CrossRef]
    [Google Scholar]
  8. Castro RA, Dourado MN, Almeida JRde, Lacava PT, Nave A et al. Mangrove endophyte promotes reforestation tree (Acacia polyphylla) growth. Braz J Microbiol 2018;49:59–66 [CrossRef]
    [Google Scholar]
  9. Kathiresan K.Salt-tolerant microbes in mangroves: ecological role and bioprospecting potential In Dagar JC, Yadav RK, Sharma PC. (editors) Research Developments in Saline Agriculture Singapore: Springer Singapore; 2019; pp237–255
    [Google Scholar]
  10. Lam MQ, Oates NC, Thevarajoo S, Tokiman L, Goh KM et al. Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter. Genomics In press 2019; [CrossRef]
    [Google Scholar]
  11. Thatoi H, Behera BC, Mishra RR, Dutta SK. Biodiversity and biotechnological potential of microorganisms from mangrove ecosystems: a review. Ann Microbiol 2013;63:1–19 [CrossRef]
    [Google Scholar]
  12. Bernardet J-F, Nakagawa Y, Holmes B.Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef]
    [Google Scholar]
  13. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010;60:249–266 [CrossRef]
    [Google Scholar]
  14. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef]
    [Google Scholar]
  15. Claus D. A standardized gram staining procedure. World J Microbiol Biotechnol 1992;8:451–452 [CrossRef]
    [Google Scholar]
  16. Smibert RM, Krieg NR.Phenotypic characterization In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp607–654
    [Google Scholar]
  17. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936;31:575–580 [CrossRef]
    [Google Scholar]
  18. Facklam RR, Moody MD. Presumptive identification of group D streptococci: the bile-esculin test. Appl Microbiol 1970;20:245–250 [CrossRef]
    [Google Scholar]
  19. Lam MQ, Nik Mut NN, Thevarajoo S, Chen SJ, Selvaratnam C et al. Characterization of detergent compatible protease from halophilic Virgibacillus sp. CD6. 3 Biotech 2018;8:104 [CrossRef]
    [Google Scholar]
  20. Jorgensen JH, Turnidge JD.Susceptibility test methods: dilution and disk diffusion methods In James HJ, Michael AP, Karen CC, Guido F, Marie LL. (editors) Manual of Clinical Microbiology, 11th edn. Washington, DC: American Society of Microbiology; 2015; pp1253–1273
    [Google Scholar]
  21. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990;20:16
    [Google Scholar]
  22. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  23. Tindall BJ, Sikorski J, Smibert RA, Krieg NR.Phenotypic characterization and the principles of comparative systematics In Reddy CA, Beveridge TJ, Breznak JA, Maxluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: American Society of Microbiology; 2007; pp330–393
    [Google Scholar]
  24. Lane DJ.16S/23S rRNA sequencing In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, United Kingdom: Wiley; 1991; pp125–175
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef]
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef]
    [Google Scholar]
  27. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef]
    [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  29. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef]
    [Google Scholar]
  30. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016;44:6614–6624 [CrossRef]
    [Google Scholar]
  31. Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 2014;31:1077–1088 [CrossRef]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110:1281–1286 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. 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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003970
Loading
/content/journal/ijsem/10.1099/ijsem.0.003970
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