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Genome-scale phylogenetic and DNA composition analyses of Antarctic Pseudoalteromonas bacteria reveal inconsistencies in current taxonomic affiliation

  • BIOLOGY OF THE ROSS SEA
  • Published:
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Abstract

Bacteria belonging to the Pseudoalteromonas genus have important ecological implications in marine environments, playing a role in the control of microbial community as producers of bioactive molecules endowed with antifouling activity and able to antagonize larvae, fungi and bacteria, including important human pathogens. For these reasons, representatives of this genus are very promising for biotechnological and biomedical applications. In this work, we used different genome-scale approaches to infer the taxonomy of 38 Pseudoalteromonas representatives (most of which isolated from Antarctica) and whose complete genome has been sequenced. We show that an accurate re-evaluation of the real taxonomic relationships of Pseudoalteromonas representatives is needed since many inconsistencies with the current taxonomic annotation were observed. Moreover, data obtained with different genome-scale methods are consistent, confirming the reliability of the genomic approaches. On the basis of these data, we propose a re-annotation for some Pseudoalteromonas species. This proposal should be validated in the future by comparing the phenotypes of these strains.

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Acknowledgments

This work is supported by 2013 MIUR/PNRA grants (Programma Nazionale di Ricerche in Antartide) 2013/B4.02 and 2013/AZ1.04. Elena Perrin is financed by a “Fondazione Adriano Buzzati-Traverso” fellowship.

We are very grateful to two anonymous reviewers for their helpful suggestions and comments in improving the manuscript.

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Authors and Affiliations

  1. Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, FI, Italy

    Emanuele Bosi, Marco Fondi, Isabel Maida, Elena Perrin & Renato Fani

  2. Institute of Protein Biochemistry, CNR, Napoli, Italy

    Donatella de Pascale

  3. Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario M. S. Angelo, Via Cintia, 80126, Napoli, Italy

    Maria Luisa Tutino & Ermenegilda Parrilli

  4. Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98124, Messina, Italy

    Angelina Lo Giudice

  5. Department of Biological and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontrès 31, 98166, Messina, Italy

    Angelina Lo Giudice

  6. Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW72AZ, UK

    Alain Filloux

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  1. Emanuele Bosi
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  2. Marco Fondi
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  9. Alain Filloux
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  10. Renato Fani
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Corresponding author

Correspondence to Renato Fani.

Additional information

Guest editors: Diego Fontaneto & Stefano Schiaparelli / Biology of the Ross Sea and Surrounding Areas in Antarctica

Electronic supplementary material

Below is the link to the electronic supplementary material.

10750_2015_2396_MOESM1_ESM.xls

Supplementary File 1 Matrix of ANI values. Each cell contains the ANI value between two Pseudoalteromonas strains. Supplementary material 1 (XLS 34 kb)

10750_2015_2396_MOESM2_ESM.xls

Supplementary File 2 Matrix of TET values. Each cell contains the TET value between two Pseudoalteromonas strains. Supplementary material 2 (XLS 35 kb)

10750_2015_2396_MOESM3_ESM.pdf

Supplementary File 3 Comparison of Phylogenetic tree based on MLSA (left) and dendrogram obtained with ANI (right). Clusters with same members share the same colour in the two dendrograms. Supplementary material 3 (PDF 454 kb)

10750_2015_2396_MOESM4_ESM.pdf

Supplementary File 4 Comparison of dendrogram obtained with ANI (left) and dendrogram obtained with TNF (right). Clusters with same members share the same colour in the two dendrograms. Supplementary material 4 (PDF 215 kb)

10750_2015_2396_MOESM5_ESM.pdf

Supplementary File 5 Comparison of Phylogenetic tree (left) and dendrogram obtained with TNF (right). Clusters with same members share the same colour in the two dendrograms. Supplementary material 5 (PDF 455 kb)

10750_2015_2396_MOESM6_ESM.pdf

Supplementary File 5 Comparison of Phylogenetic tree (left) and dendrogram obtained with TNF (right). Clusters with same members share the same colour in the two dendrograms.. Supplementary material 6 (PDF 2462 kb)

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Bosi, E., Fondi, M., Maida, I. et al. Genome-scale phylogenetic and DNA composition analyses of Antarctic Pseudoalteromonas bacteria reveal inconsistencies in current taxonomic affiliation. Hydrobiologia 761, 85–95 (2015). https://doi.org/10.1007/s10750-015-2396-9

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  • DOI: https://doi.org/10.1007/s10750-015-2396-9

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