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Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan

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Abstract

Two gram-negative, aerobic, brown-pigmented, motile rod-shaped bacteria KMM 9512 and KMM 9513T were isolated from a sediment sample collected from the Sea of Japan seashore, Russia. On the basis of the 16S rRNA gene sequence analysis, novel strains KMM 9512 and KMM 9513T positioned within the genus Rheinheimera (class Gammaproteobacteria) as a separate subline adjacent to Rheinheimera baltica DSM 14885T sharing highest gene sequence similarities of 98.6–97.6 % to their closest phylogenetic relatives, Rheinheimera muenzenbergensis LMG 27269T, R. baltica DSM 14885T, Rheinheimera aquimaris JCM 14331T, Rheinheimera nanhaiensis KACC 14030T, and Rheinheimera pacifica KMM 1406T. Strains KMM 9512 and KMM 9513T belong to the same separate genospecies on the basis of the 16S rRNA gene sequence similarity (99.8 %) and their DNA relatedness to each other (89 %) and to closely related Rheinheimera species (25–53 %). The major isoprenoid quinone was Q-8, polar lipids consisted of phosphatidylserine, phosphatidylglycerol, phosphatidylethanolamine, unknown aminolipids, unknown aminophospholipids, unknown phospholipids, and unknown lipids, and major fatty acid were C16:0, C16:1 ω7c, C17:1 ω8c, C12:0 3-OH followed by C17:0 and C18:1 ω7c in both strains. Strains KMM 9512 and KMM 9513T revealed a remarkable antagonistic activity toward a number of gram-positive and gram-negative microorganisms. On the basis of phylogenetic analysis, DNA–DNA hybridization results, and phenotypic differences, strains KMM 9512 and KMM 9513T are proposed to be classified as a novel species of the genus Rheinheimera, Rheinheimera japonica sp. nov. The type strain of this species is KMM 9513T = NRIC 0918T.

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Acknowledgments

We would like to thank Dr. Moriya Ohkuma, Japan Collection of Microorganisms, JCM, Japan, Dr. Claudine Vereecke, BCCM™/LMG Bacteria Collection, Ghent University, Gent, Belgium, Dr. Soon-Wo Kwon, Korean Agricultural Culture Collection, KACC, Microbial genetics Division, National Institute of Agricultural Biotechnology, RDA, Republic of Korea, for providing Rheinheimera type strains for comparative analyses, to thank Dr. Claudine Vereecke, BCCM™/LMG Bacteria Collection, Ghent University, Gent, Belgium, and Dr. Chantal Bizet, the Collection de l’Institut Pasteur, Institut Pasteur, CIP, Paris, France, for providing indicator strains. This study was supported by a grant from the RSF “Biodiversity and biotechnological potential of marine bacteria and fungi” no. 14-14-00030.

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Authors and Affiliations

  1. G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok, 690022, Russia

    L. A. Romanenko, N. I. Kalinovskaya & V. V. Mikhailov

  2. NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan

    N. Tanaka

  3. Institute of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690041, Russia

    V. I. Svetashev

  4. Far Eastern Federal University, Oktyabr’skaya st., 27, Vladivostok, 690091, Russia

    V. V. Mikhailov

Authors
  1. L. A. Romanenko
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  2. N. Tanaka
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  3. V. I. Svetashev
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  4. N. I. Kalinovskaya
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  5. V. V. Mikhailov
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Correspondence to L. A. Romanenko.

Additional information

Communicated by Erko Stackebrandt.

The DDBJ/GenBank/EMBL accession numbers of the 16S rRNA gene sequences of strains KMM 9513T and KMM 9512 are LC004727 and LC011485, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

203_2015_1095_MOESM1_ESM.pdf

Supplementary material. Online Resource 1. Two-dimensional thin-layer chromatograms of polar lipids of strains: (a) KMM 9512; (b) KMM 9513T; (c) Rheinheimera baltica DSM 14885T; (d) Rheinheimera aquimaris JCM 14331T; (e) Rheinheimera pacifica KMM 1406T; (f) Rheinheimera muenzenbergensis LMG 27269T; (g) Rheinheimera nanhaiensis KACC 14030T. Abbreviations: PS, phosphatidylserine; PE, phosphatidylethanoamine; PG, phosphatidylglycerol; APL1, APL2, unknown aminophospholipids; AL1, AL2, unknown aminolipids; L1, L2, L3, L4, L5, L6, unknown lipids; PL, PL1, PL2, PL3, unknown phospholipids (PDF 441 kb)

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Romanenko, L.A., Tanaka, N., Svetashev, V.I. et al. Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan. Arch Microbiol 197, 613–620 (2015). https://doi.org/10.1007/s00203-015-1095-2

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  • DOI: https://doi.org/10.1007/s00203-015-1095-2

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