Mikrobiol. Z. 2016; 78(6):50-59.
doi: https://doi.org/10.15407/microbiolj78.06.050

Еcology, Systematics and Antibiotic Activity of Pseudomonas batumici and Alteromonas macleodii
in Connection with Analysis of their Genome Structure

Klochko V.V.

Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
154 Akad. Zabolotny Str., Kyiv, 03143, Ukraine

New data about ecology, systematics and synthesis of biologically active substances of the type strain Pseudomonas batumici UCM-321 producing the antibiotic batumin, highly effective against staphylococci, and of Alteromonas macleodii strains, as representatives of marine species widely inhabiting the world ocean, was obtained based on a complex analysis of their biological properties and genomic structure.
Analysis of taxonomic data indicated that P. batumici is a novel species. Illumina HiSeq sequencing of the chromosomal DNA enabled to obtain the complete genome sequence of P. batumici UCM B-321. Its DNA contained 127 contigs of the total length of 6608172 bp. Batumin biosynthesis operon was identified as 77 kbp operon containing in total 28 protein coding genes. This operon sequence was significantly less GC-rich and the program SeqWord Genomic Island Sniffer predicted a horizontal acquisition of this region. The closes relatives of UCM-321 were P. gingeri and P. protegens; both have no batumin operon in their genomes. HLPC-analysis of the culture broth has shown the presence of batumin in P. batumici broth and no any similar substances in P. gingeri culture medium.
The phenotypic, chemotaxonomic and genetic peculiarities of 5 deep-water strains of A. macleodii (isolated from a depth of 1000 – 3500 m) and 5 strains of the same species isolated from the surface layer have been studied. Electron microscopy has shown that the deep strains’ cells were, on average, two times longer (2.1 ± 0.2 × 0.7 ± 0.1 μm) than the surface strains (1.1 ± 0.1 × 0.6 ± 0.1 μm). Using fatty acid analysis the deep and surface isolates were clearly separated into two clusters. The distinctions between them were also found in different lectin binding capacity, which was probably determined by the structure of their extracellular polysaccharide matrix. Analysis of the PCR results with the primers to repeated nucleotide sequences revealed a higher level of genetic polymorphism in surface strains in comparison to the deep-water isolates. The described peculiarities probably reflect the specific conditions in which A. macleodii strains live on the surface or in the depth of the World Ocean.

Key words: Pseudomonas batumici, antibiotic batumin, Alteromonas macleodii, systematics, genomic structure.

Full text (PDF, in English)

  1. Bernd H, Rehm A. Pseudomonas: Model Organism, Pathogen, Cell Factory. Verlag GmbH: Wiley-VCH; 2008.
  2. Esipov SE, Kiprianova EA. Batumin, a novel antibiotic produced by Pseudomonas batumici. 5th Int. Conf. on Chemical Synthesis of Antibiotics and Related Microbial Products. Hungary: Debrecen; 1996. p. 14.
  3. Garcia-Martinez J, Acinas SG, Massana R, Rodriguez-Valera F. Prevalence and microdiversity of Alteromonas macleodii-like microorganisms in different oceanic regions. Environ. Microbiol. 2002; 4: 4250. https://doi.org/10.1046/j.1462-2920.2002.00255.x
  4. Ivars-Martinez E, D'Auria G, Rodrigues-Valera F, Sanches-Porro C, Ventosa, A, Joint I, et al. Biogeography of the ubiguitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol. Ecol. 2008; 17: 4092–4106. https://doi.org/10.1111/j.1365-294X.2008.03883.x
  5. Ivars-Martinez E, Martin-Cuadrado A, D'Auria G, Mira A, Ferriera S, Johnson J, et al. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. ISME J. 2008; 2: 1194–1212. https://doi.org/10.1038/ismej.2008.74
  6. Kim JY, Klochko VV, Zelena LB, Kiprianova EA, Avdeeva LV, Reva ON. Analysis of the complete genome sequence of batumin producing strain Pseudomonas batumici UCMB-321 revealed that the whole batumin synthesis encoding operon was acquired by horizontal gene transfer. III International Conference on Antimicrobial Research. Spain: Madrid; 2014. p. 150.
  7. Kim JY, Klochko VV, Zhuravel EV, Soldatkina MA, Reva ON. Similarity and difference in mechanisms of action of antistaphylococcal antibiotics mupirocin and batumin revealed by in-silico molecular docking . Drug discovery and Therapy World Congress. USA: Boston; 2015. p. 105.
  8. Kiprianova EA, Klochko VV. [Analysis of the relation between structure and the antibiotic activity of batumin]. Mikrobiol Z. 2009; 71(1): 28–33. Russian.
  9. Kiprianova EA, Klochko VV, Zelena LB, Churkina LN, Avdeeva LV. Pseudomonas batumici sp.nov., the antibiotic-producing bacteria isolated from soil of the Caucasus Black Sea coast. Mikrobiol Z. 2011; 73(5): 3–8.
  10. Klochko VV. Biosynthesis and properties of antibiotic batumin. Biotechnologia Acta. 2014; 7(6): 46–50. https://doi.org/10.15407/biotech7.06.046
  11. Klochko VV. [Comparative taxonomic analysis of Pseudomonas batumici and evolutionally related species]. Dopovidi NASU. 2015; 2: 152–157. Russian.
  12. Klochko VV, Kiprianova EA, Churkina LN, Avdeeva LV. [Antimicrobial spectrum of antibiotic batumin]. Mikrobiol Z. 2008; 70 (5): 41–46. Russian.
  13. Klochko VV, Zelena LB, Kim JY, Avdeeva LV, Reva ON. Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321. Int. J. of Antimicrobial Agents. 2016; 47: 56–61. https://doi.org/10.1016/j.ijantimicag.2015.10.006
  14. Klochko VV, Zelena LB, Voychuk SI, Ostapchuk AN. Peculiarities of Alteromonas macleodii strains reflects their deep/surface habitation rather than geographical distribution. J. Gen. Appl. Microbiol, 2012; 58: 129–135. https://doi.org/10.2323/jgam.58.129
  15. Lopez-Lopez AS, Stal BL, Onishchenko O, Rodriguez-Valera F. Genetic analysis of housekeeping genes reveals a deep-sea ecotype of Alteromonas macleodii in the Mediterranean Sea. Environ. Microbiol. 2005; 7: 649–659. https://doi.org/10.1111/j.1462-2920.2005.00733.x
  16. Smirnov VV, Churkina LN, Kiprianova EA. Antibiotic batumin for diagnostics of staphylococci and treatment of Staphylococcus aureus nasal carriage. 10th International symposium on staphylococci and staphilococcal infections. Japan: Tsukuba; 2002. p. 130.