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Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica

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Abstract

A pink pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain 36B243T), was isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) in the Chilean Antarctica. Strain 36B243T has a 5.26 Mb chromosome with a DNA G + C content of 35.4 mol%. The draft genome includes the prediction and annotation of 4585 coding genes, and 46 tRNA, 1 tmRNA, and 2735 hypothetical proteins. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain 36B243T into the genus Pedobacter with high sequence similarity to the type strains of Pedobacter sandarakinus (97.5%) and Pedobacter petrophilus (97.1%). Sequence similarities to type strains of all other current Pedobacter species were below 97.1%. Predominant fatty acids are summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0 followed by iso-C17:0 3-OH and C16:0. The major respiratory quinone was menaquinone MK-7. The polar lipid profile contained the major lipids phosphatidylethanolamine, five unidentified aminolipids, two lipids lacking a functional group and two minor glycolipids and one lipid lacking a functional group. An alkali-stable lipid was present. The polyamine pattern contained the predominant compound sym-homospermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, polar lipid, and fatty acid composition revealed that strain 36B243T represents a new species of the genus Pedobacter. For this reason, we propose the name Pedobacter nototheniae sp. nov. with the type strain 36B243T (= LMG 30634T = CCM 8855T = CIP 111622T).

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Acknowledgements

We thank Gundula Will, Maria Sowinsky and Katja Grebing for excellent technical assistance and Prof. Aharon Oren for his advice on the specific epithet. We are also grateful to Dr. Marcelo Cortez-San Martín for his valuable help in the fieldwork in Antarctica. This work was supported by the Chilean Antarctic Institute (Grant INACH 86_13); CONICYT/FONDAP/15110027 and FONDECYT 1190283, both awarded by the Comisión Nacional de Investigación Científica y Tecnológica (CONICYT, Chile).

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Authors and Affiliations

  1. Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany

    Peter Kämpfer & Stefanie P. Glaeser

  2. Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile

    Rute Irgang, Matías Poblete-Morales & Ruben Avendaño-Herrera

  3. Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile

    Rute Irgang & Ruben Avendaño-Herrera

  4. Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, Chile

    Guillermo Fernández-Negrete

  5. Institut für Mikrobiologie, Veterinärmedizinische Universität, Vienna, Austria

    Hans-Jürgen Busse

  6. Aquaculture and Marine Ecosystems Division, Fraunhofer Chile Research Foundation, Santiago, Chile

    Derie Fuentes-Messina

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  1. Peter Kämpfer
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Contributions

PK, RI and RA-H planned the study. RI, SG, MP-M and PK provided the data on physiology, fatty acids and the 16S rRNA gene sequence. GF-N and DF-M provided the genome sequence data and the comparative analysis. H-JB provided data on the quinone type, lipids and polyamines. PK, SG and RA-H wrote the paper.

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Correspondence to Peter Kämpfer or Ruben Avendaño-Herrera.

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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain 36B243T is MH065727. This Whole Genome sequence (WGS) project has been deposited as a genome assembly at the DDBJ/ENA/GenBank under the accession RQRS00000000.

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Kämpfer, P., Irgang, R., Fernández-Negrete, G. et al. Proposal of Pedobacter nototheniae sp. nov., isolated from the spleen of a black rock cod (Notothenia coriiceps, Richardson 1844) from the Chilean Antarctica. Antonie van Leeuwenhoek 112, 1465–1475 (2019). https://doi.org/10.1007/s10482-019-01275-7

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