AUTHOR=Kim Mirae , Song Jaeho , Shin Seung Yeol , Kogure Kazuhiro , Kang Ilnam , Cho Jang-Cheon 

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

JOURNAL=Frontiers in Marine Science

VOLUME=11

YEAR=2024

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2024.1449548

DOI=10.3389/fmars.2024.1449548

ISSN=2296-7745

ABSTRACT=<p>Despite previous culture-independent studies highlighting the prevalence of the order <italic>Burkholderiales</italic> in deep-sea environments, the cultivation and characterization of deep-sea <italic>Burkholderiales</italic> 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 <italic>Burkholderiales.</italic> Herein, we report the isolation and genome characteristics of strain SAORIC-580<sup>T</sup>, from a depth of 4000 m in the Northwest Pacific Ocean. The strain showed a close phylogenetic relationship with <italic>Limnobacter thiooxidans</italic> CS-K2<sup>T</sup>, sharing 99.9% 16S rRNA gene sequence identity. The complete whole-genome sequence of strain SAORIC-580<sup>T</sup> 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 <italic>Limnobacter</italic> 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<sup>T</sup> 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 <italic>Limnobacter</italic> 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 C<sub>16:0</sub>, C<sub>16:1</sub>, and C<sub>18:1</sub>, and major polar lipids including phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on the polyphasic taxonomic data, it is concluded that strain SAORIC-580<sup>T</sup> (= KACC 21440<sup>T</sup> = NBRC 114111<sup>T</sup>) represents a novel species, for which the name <italic>Limnobacter profundi</italic> sp. nov. is proposed.</p>