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ORIGINAL RESEARCH article

Front. Mar. Sci.
Sec. Aquatic Microbiology
Volume 11 - 2024 | doi: 10.3389/fmars.2024.1449548
This article is part of the Research Topic The Biological Pump: A Hunt For Microbial Key Players Involved in Ocean Carbon and Nutrient Fluxes View all 3 articles

Cultivation of deep-sea bacteria from the Northwest Pacific Ocean and characterization of Limnobacter profundi sp. nov., a phenol-degrading bacterium

Provisionally accepted
Mirae Kim Mirae Kim 1Jaeho Song Jaeho Song 2Seung Yeol Shin Seung Yeol Shin 2Kazuhiro Kogure Kazuhiro Kogure 3Ilnam Kang Ilnam Kang 1Jang-Cheon Cho Jang-Cheon Cho 1*
  • 1 Inha University, Incheon, Republic of Korea
  • 2 Honam National Institute of Biological Resources (HNIBR), Jeollanamdo, Republic of Korea
  • 3 University of the Ryukyus, Nishihara, Okinawa, Japan

The final, formatted version of the article will be published soon.

    Despite previous culture-independent studies highlighting the prevalence of the order Burkholderiales in deep-sea environments, the cultivation and characterization of deep-sea Burkholderiales have been infrequent. A total of 243 deep-sea bacterial strains were isolated from various depths in the Northwest Pacific Ocean, with 33 isolates (13.6%) from a depth of 4000 m classified into Burkholderiales. Herein, we report the isolation and genome characteristics of strain SAORIC-580 T , from a depth of 4000 m in the Northwest Pacific Ocean. The strain showed a close phylogenetic relationship with Limnobacter thiooxidans CS-K2 T , sharing 99.9% 16S rRNA gene sequence identity. The complete whole-genome sequence of strain SAORIC-580 T comprised 3.3 Mbp with a DNA G+C content of 52.5%. Comparative genomic analysis revealed average nucleotide identities between 79.4-85.7% and digital DNA-DNA hybridization values of 19.9-29.5% when compared to other Limnobacter genomes, indicating that the strain represents a novel species within the genus. Genomic analysis revealed unique adaptations to deep-sea conditions, including genes associated with phenol degradation, stress responses, cold adaptation, heavy metal resistance, signal transduction, and carbohydrate metabolism. The SAORIC-580 T genome was found to be more abundant in the deep sea than at the surface in the trenches of the Northwest Pacific Ocean, suggesting adaptations to the deep-sea environment. Phenotypic characterization highlighted distinct differences from other Limnobacter species, including variations in growth conditions, enzyme activities, and phenol degradation capabilities. Chemotaxonomic markers of the strain included ubiquinone-10, major fatty acids such as C16:0, C16:1, and C18:1, and major polar lipids including phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on the polyphasic taxonomic data, it is concluded that strain SAORIC-580 T (= KACC 21440 T = NBRC 114111 T ) represents a novel species, for which the name Limnobacter profundi sp. nov. is proposed.

    Keywords: Limnobacter profundi, deep sea, Burkholderiales, Genome, Novel species, phenol degradation

    Received: 15 Jun 2024; Accepted: 15 Oct 2024.

    Copyright: © 2024 Kim, Song, Shin, Kogure, Kang and Cho. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Jang-Cheon Cho, Inha University, Incheon, Republic of Korea

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