1887

Abstract

A Gram-stain-negative, facultatively anaerobic, rod-shaped (1.8–4.4×0.5–0.7 µm) and motile marine bacterium, designated as MEBiC13590, was isolated from tidal flat sediment sampled at Incheon City, on the west coast of the Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC13590 showed high similarity to CC-AMH-0 (98.2 %), followed by StC1 (97.5 %); however, it clustered with . The phylogenomic tree inferred by the up-to-date bacterial core gene set suggested that strain MEBiC13590 shared a phyletic line with . Average nucleotide identity and digital DNA–DNA hybridization values (75.0 and 19.3 %, respectively) between strain MEBiC13590 and CC-AMH-0 were below the respective species delineation cutoffs. Growth was observed at 22–50 °C (optimum, 45 °C), at pH 5–9 (optimum, pH 7) and with 1–6 % (optimum, 3 %) NaCl. The predominant cellular fatty acids were C (7.6 %), C (12.2 %), 11-methyl C ω7 (5.7 %), C cyclo ω6 and summed feature 8 (comprising C ω7 and/or C ω6; 38 %). The DNA G+C content was 63.5 mol%. The major respiratory quinone was Q-10. Several phenotypic characteristics such as growth temperature, oxygen requirement, enzyme activities of urease, gelatinase, lipase (C), α-chymotrypsin, acid phosphatase, β-galactosidase, β-glucosidase etc. differentiate strain MEBiC13590 from CC-AMH-0. Based on this polyphasic taxonomic data, strain MEBiC13590 should be classified as representing a novel species in the genus for which the name sp. nov. is proposed . The type strain is MEBiC13590 (=KCCM 43313=JCM 33661).

Funding
This study was supported by the:
  • Ministry of Ocean and Fisheries (KR) (Award 20170431)
    • Principle Award Recipient: KaeKyoung Kwon
  • Korea Institute of Ocean Science and Technology (KR) (Award PE99822)
    • Principle Award Recipient: KaeKyoung Kwon
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004574
2020-12-02
2021-08-02
Loading full text...

Full text loading...

References

  1. Hameed A, Shahina M, Lai W-A, Lin S-Y, Young L-S et al. Oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family Phyllobacteriaceae isolated from surface seashore water, and emended descriptions of Mesorhizobium loti and Phyllobacterium myrsinacearum . Antonie van Leeuwenhoek 2015; 107:759–771 [View Article][PubMed]
    [Google Scholar]
  2. Jiang X, Jiao N. Vertical distribution of bacterial communities in the Indian Ocean as revealed by analyses of 16S rRNA and nasA genes. Indian J Microbiol 2016; 56:309–317 [View Article][PubMed]
    [Google Scholar]
  3. Cho HY, Lee J-H, Hyun J-H. Bacterial community structure and diversity using 16S rDNA analysis in the intertidal sediment of Ganghwa island. Kor J Microbiol 2004; 40:189–198
    [Google Scholar]
  4. Dabadé DS, Wolkers-Rooijackers JCM, Azokpota P, Hounhouigan DJ, Zwietering MH et al. Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment. Int J Food Microbiol 2016; 218:96–104 [View Article][PubMed]
    [Google Scholar]
  5. Har JY, Helbig T, Lim JH, Fernando SC, Reitzel AM et al. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression. Front Microbiol 2015; 6:818 [View Article][PubMed]
    [Google Scholar]
  6. Fidalgo C, Henriques I, Rocha J, Tacão M, Alves A. Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination. Environ Sci Pollut Res Int 2016; 23:10200–10214 [View Article][PubMed]
    [Google Scholar]
  7. Grueneberg J, Engelen AH, Costa R, Wichard T. Macroalgal morphogenesis induced by waterborne compounds and bacteria in coastal seawater. PLoS One 2016; 11:E0146307 [View Article][PubMed]
    [Google Scholar]
  8. Yoshida-Takashima Y, Nunoura T, Kazama H, Noguchi T, Inoue K et al. Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments. Appl Environ Microbiol 2012; 78:1311–1320 [View Article][PubMed]
    [Google Scholar]
  9. D’Auria G, Barón-Rodríguez MM, Durbán-Vicente A, Moya A, Rojo C et al. Unravelling the bacterial diversity found in the semi-arid Tablas de Daimiel National Park wetland (central Spain). Aquat Microb Ecol 2010; 59:33–44 [View Article]
    [Google Scholar]
  10. Green DH, Llewellyn LE, Negri AP, Blackburn SI, Bolch CJS. Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum . FEMS Microbiol Ecol 2004; 47:345–357 [View Article][PubMed]
    [Google Scholar]
  11. Hollants J, Leroux O, Leliaert F, Decleyre H, De Clerck O et al. Who is in there? exploration of endophytic bacteria within the siphonous green seaweed Bryopsis (Bryopsidales, Chlorophyta). PLoS One 2011; 6:E26458 [View Article][PubMed]
    [Google Scholar]
  12. Jeong SE, Kim KH, Lhee D, Yoon HS, Quan ZX et al. Oceaniradius stylonematis gen. nov., sp. nov., isolated from a red alga, Stylonema cornu-cervi. Int J Syst Evol Microbiol 2019; 69:1967–1973 [View Article][PubMed]
    [Google Scholar]
  13. Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B et al. The gut of geographically disparate Ciona intestinalis harbors a core microbiota. PLoS One 2014; 9:E93386 [View Article][PubMed]
    [Google Scholar]
  14. Zheng Q, Wang Y, Lu J, Lin W, Chen F et al. Metagenomic and Metaproteomic Insights into Photoautotrophic and Heterotrophic Interactions in a Synechococcus Culture. mBio 2020; 11:e03261–19 [View Article][PubMed]
    [Google Scholar]
  15. Giovannoni SJ. The polymerase chain reaction. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 177–203
    [Google Scholar]
  16. Lee J-W, Kwon KK, Azizi A, Oh H-M, Kim W et al. Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea. Mar Petrol Geol 2013; 47:136–146 [View Article]
    [Google Scholar]
  17. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  18. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [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. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian protein Metabolism 3 New York: Academic Press; 1969 pp 21–132
    [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  23. 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]
  24. 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]
  25. 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 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. Kwon KK, Lee H-S, Yang SH, Kim S-J. Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'. Int J Syst Evol Microbiol 2005; 55:2033–2037 [View Article][PubMed]
    [Google Scholar]
  28. Yang S-H, Kwon KK, Lee H-S, Kim S-J. Shewanella spongiae sp. nov., isolated from a marine sponge. Int J Syst Evol Microbiol 2006; 56:2879–2882 [View Article][PubMed]
    [Google Scholar]
  29. Zobell CE. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
    [Google Scholar]
  30. 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 pp 607–654
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  32. Yang S-H, Seo H-S, Oh H-M, Kim S-J, Lee J-H et al. Brumimicrobium mesophilum sp. nov., isolated from a tidal flat sediment, and emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale. Int J Syst Evol Microbiol 2013; 63:1105–1110 [View Article][PubMed]
    [Google Scholar]
  33. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Goodfellow M, Minikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004574
Loading
/content/journal/ijsem/10.1099/ijsem.0.004574
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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