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Chryseobacterium antibioticum sp. nov. with antimicrobial activity against Gram-negative bacteria, isolated from Arctic soil

The Journal of Antibiotics volume 74, pages 115–123 (2021)Cite this article

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Abstract

A yellow-pigmented, non-motile, Gram-stain-negative, pleomorphic bacterium, designated RP-3-3T was obtained from soil sampled at the Arctic region in Cambridge Bay, NU, Canada. The strain is strictly aerobic, psychrotolerant, grow optimally at 15–20 °C and produces flexirubin type pigments. The strain is able to hydrolyse CM-cellulose, casein, starch and DNA. Strain RP-3-3T showed antimicrobial activity against Gram-negative pathogens. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-3-3T formed a lineage within the family Weeksellaceae and clustered as members of the genus Chryseobacterium. The closest members were Chryseobacterium shigense DSM 17126T (98.7% sequence similarity), Chryseobacterium carnipullorum DSM 25581T (98.7%) and Chryseobacterium oncorhychi 701B-08T (98%). The genome is 4,910,468 bp long with 73 scaffolds and 4300 protein-coding genes. The anti-SMASH analysis of whole genome showed ten putative biosynthetic gene clusters responsible for various secondary metabolites. The sole respiratory quinone is MK-6. The major cellular fatty acids are iso-C15:0, iso-C17:1 ω9c, iso-C17:0 3-OH, summed feature 3 (iso-C15 :0 2-OH/C16 :1ω7c) and anteiso-C15:0. The major polar lipid is phosphatidylethanolamine. The DNA G + C content of the type strain is 36.9 mol%. In addition, the average nucleotide identity and in silico DNA–DNA hybridization  relatedness values between strain RP-3-3T and phylogenetically closest members are below the threshold value for species delineation. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RP-3-3T represents novel species in the genus Chryseobacterium, for which the name Chryseobacterium antibioticum sp. nov. is proposed. The type strain is RP-3-3T (=KACC 21620T = NBRC 114360T).

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Acknowledgements

We acknowledge the DASAN, Korean Arctic Station (Korea Polar Research Institute) for providing Arctic soil samples. We greatly appreciate Prof. Aharon Oren (The Hebrew University of Jerusalem, Israel) for his expert suggestions concerning the correct species epithet and etymology.

Funding

This research was supported by Basic Science Research Programme through the National Research Foundation of Korea (NRF-2019R1F1A1058501).

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Authors and Affiliations

  1. Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Kyonggi-Do, 16227, Republic of Korea

    Ram Hari Dahal & Jaisoo Kim

  2. Department of Environmental Engineering, Korea University Sejong Campus, Sejong City, 30019, Republic of Korea

    Dhiraj Kumar Chaudhary

  3. Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, Republic of Korea

    Dong-Uk Kim

  4. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    Ramesh Prasad Pandey

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GenBank/EMBL/DDBJ accession for the 16S rRNA gene sequence of strain RP-3-3T is MN685329 and Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JABBGI000000000. The version described in this paper is version JABBGI010000000.

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Dahal, R.H., Chaudhary, D.K., Kim, DU. et al. Chryseobacterium antibioticum sp. nov. with antimicrobial activity against Gram-negative bacteria, isolated from Arctic soil. J Antibiot 74, 115–123 (2021). https://doi.org/10.1038/s41429-020-00367-1

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