1887

Abstract

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012, was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012 shared the highest 16S rRNA gene sequence relatedness (96.9–95.5 %) with members of the genus . The isolate and all known species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012 and other type strains of the genus were below the proposed thresholds for species discrimination. The genome of strain B2012 was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012 displayed moderately halophilic and alkaliphilic properties, growing optimally at 2–3 % (w/v) NaCl concentration and at pH 8–9. The major cellular fatty acids (>10 %) were anteiso-C, C dimethyl aldehyde (DMA) and C. Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the type species is B2012 (=MCCC 1K04418=KCTC 72962).

Funding
This study was supported by the:
  • Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry (Award 17-259-74)
    • Principle Award Recipient: ShushiHuang
  • The Fundamental Research Funds for Guangxi Academy of Sciences (Award 2018YBJ303)
    • Principle Award Recipient: ShushiHuang
  • The Fundamental Research Funds for Guangxi Academy of Sciences (Award 2019YBJ101)
    • Principle Award Recipient: ShushiHuang
  • the Guangxi Natural Science Foundation for Youth Scholar (Award 2018GXNSFBA050021)
    • Principle Award Recipient: ShushiHuang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005137
2021-12-07
2022-01-29
Loading full text...

Full text loading...

References

  1. Giri C, Ochieng E, Tieszen LL, Zhu Z, Singh A et al. Status and distribution of mangrove forests of the world using Earth observation satellite data. Global Ecology and Biogeography 2011; 20:154–159 [View Article]
    [Google Scholar]
  2. Andreote FD, Jiménez DJ, Chaves D, Dias ACF, Luvizotto DM et al. The microbiome of Brazilian mangrove sediments as revealed by metagenomics. PLoS One 2012; 7:e38600. [View Article] [PubMed]
    [Google Scholar]
  3. Ancheeva E, Daletos G, Proksch P. Lead compounds from mangrove-associated microorganisms. Mar Drugs 2018; 16:E319. [View Article] [PubMed]
    [Google Scholar]
  4. Zhao H, Yan B, Mo S, Nie S, Li Q et al. Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis. J Microbiol 2019; 57:575–586 [View Article] [PubMed]
    [Google Scholar]
  5. Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K et al. Ocean plankton. structure and function of the global ocean microbiome. Science 2015; 348:1261359. [View Article] [PubMed]
    [Google Scholar]
  6. Buijs Y, Bech PK, Vazquez-Albacete D, Bentzon-Tilia M, Sonnenschein EC et al. Marine Proteobacteria as a source of natural products: advances in molecular tools and strategies. Nat Prod Rep 2019; 36:1333–1350 [View Article] [PubMed]
    [Google Scholar]
  7. Béjà O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM et al. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 2002; 415:630–633 [View Article] [PubMed]
    [Google Scholar]
  8. Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J 2020; 14:2060–2077 [View Article] [PubMed]
    [Google Scholar]
  9. Li F, Huang Y, Hu W, Li Z, Wang Q et al. Roseomonas coralli sp. nov., a heavy metal resistant bacterium isolated from coral. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  10. Hou L, Zhang Y, Sun J, Xie X. Acuticoccus yangtzensis gen. nov., sp. nov., a novel member in the family Rhodobacteraceae, isolated from the surface water of the Yangtze Estuary. Curr Microbiol 2015; 70:176–182 [View Article] [PubMed]
    [Google Scholar]
  11. Yin Q, Liang J, Zhang L, Ma K, Hu Z-L et al. Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis. Int J Syst Evol Microbiol 2018; 68:3316–3321 [View Article] [PubMed]
    [Google Scholar]
  12. Lai Q, Liu X, Sun F, Shao Z. Acuticoccus sediminis sp. nov., isolated from deep-sea sediment of the Indian Ocean and proposal of Acuticoccaceae fam. nov. Int J Syst Evol Microbiol 2019; 69:1173–1178 [View Article] [PubMed]
    [Google Scholar]
  13. Lane DJ. Nucleic acid techniques in bacterial systematics. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–174
    [Google Scholar]
  14. 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]
  15. 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]
    [Google Scholar]
  16. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 2012; 1:18 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. In Kollmar M. eds Gene Prediction: Methods and Protocols New York, NY: Springer New York; 2019 pp 227–245
    [Google Scholar]
  19. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article]
    [Google Scholar]
  20. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
    [Google Scholar]
  21. Rodriguez-R LM, Konstantinidis K. Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Magazine 2014; 9:111–118
    [Google Scholar]
  22. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182. [View Article] [PubMed]
    [Google Scholar]
  24. Chaudhari NM, Gupta VK, Dutta C. BPGA–an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373. [View Article] [PubMed]
    [Google Scholar]
  25. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  26. Holguin G, Vazquez P, Bashan Y. The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biology and Fertility of Soils 2001; 33:265–278 [View Article]
    [Google Scholar]
  27. Radman M, Prakash L. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis: Springfield, IL; Harvard Univ., Cambridge, MA: Charles C Thomas Publisher; 1974
    [Google Scholar]
  28. Slade D, Radman M. Oxidative stress resistance in Deinococcus radiodurans. Microbiol Mol Biol Rev 2011; 75:133–191 [View Article] [PubMed]
    [Google Scholar]
  29. Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K. Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci USA 2014; 111:9259–9264 [View Article] [PubMed]
    [Google Scholar]
  30. Wieme AD, Spitaels F, Aerts M, De Bruyne K, Van Landschoot A et al. Identification of beer-spoilage bacteria using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Int J Food Microbiol 2014; 185:41–50 [View Article] [PubMed]
    [Google Scholar]
  31. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters GC-FAME MIDI Technical Note; 2006
    [Google Scholar]
  32. 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]
  33. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  34. Westerlund B, Slotte JP. How the molecular features of glycosphingolipids affect domain formation in fluid membranes. Biochim Biophys Acta 2009; 1788:194–201 [View Article] [PubMed]
    [Google Scholar]
  35. Simons K, Ikonen E. Functional rafts in cell membranes. Nature 1997; 387:569–572 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005137
Loading
/content/journal/ijsem/10.1099/ijsem.0.005137
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