Chung Yeon Hwang

Zooplankton in the Southern Ocean represent unique microhabitats for microbial communities that contribute significantly to polar biogeochemical cycles. In this study, we performed a polyphasic and genomic characterization of two Gram-negative, psychrotolerant bacterial strains, HL-MZ7^T and HL-MZ19, isolated from Antarctic zooplankton. Phylogenetic and phylogenomic analyses clearly placed these isolates within the genus Pseudocolwellia, forming a sister clade to Pseudocolwellia agarivorans QM50^T. The complete genomes of HL-MZ7^T (4.5 Mbp) and HL-MZ19 (4.6 Mbp) exhibited DNA G + C contents of 36.0% and 35.9%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values confirmed that both strains represent a novel genomic species, distinct from P. agarivorans QM50^T (79.5% ANI and 24.0% dDDH). Comparative genomic analysis revealed a rich repertoire of genes associated with cold environmental adaptation and host-microbe interactions. Notably, we identified biosynthetic gene clusters of aryl polyenes and homoserine lactones, alongside genes involved in surface adhesion and nutrient acquisition, suggesting a specialized symbiotic potential within the zooplankton micro-niche. Phenotypically, the strains are characterized as strictly aerobic, with optimal growth at 15-20 °C and 3.0% (w/v) sea salts. These findings expand the genomic and ecological understanding of zooplankton-associated bacteria in polar marine ecosystems, and support the proposal of Pseudocolwellia antarctica sp. nov.

Decomposition of bloom-forming organisms often causes coastal hypoxia. To predict hypoxia, the density of a bloom-forming species, its decline rate, and oxygen consumption rate during decomposition should be determined. To determine these parameters, the density of morphologically intact and partially decomposed (PD) cells, and dissolved oxygen (DO) concentrations during a five-day incubation in darkness were measured. Using these data, the decline rate of cell density (k _decline ) and oxygen consumption rate per decomposed cell (OC _{decomposed cell} ) of seven bloom-forming species, including diatoms Skeletonema dohrnii , Thalassiosira minuscula and Chaetoceros peruvianus , dinoflagellates Margalefidinium polykrikoides and Tripos furca , and nanoflagellates Teleaulax amphioxeia and Heterosigma akashiwo were calculated. Among the species, Te . amphioxeia had the highest k _decline , 0.66 d ^− 1 , and M . polykrikoides had the highest OC _{decomposed cell} , 69 pmol O ₂ cell ⁻¹ d ^− 1 . k _decline were species-specific and showed no correlation with cell carbon biomass, whereas OC _{decomposed cell} showed positive correlation with cell carbon biomass. When DO during decomposition of the species were estimated based on k _decline value of (1) intact cells only, (2) intact plus PD _0.5 cells, and (3) intact plus PD ₁ cells, the estimates using intact plus PD _0.5 cells for dinoflagellates and intact plus PD ₁ cells for the others were closest to the measured DO. Furthermore, the Q ₁₀ coefficient calculated from the k _decline for S . dohrnii determined at 15 and 25 °C was 3.1. The present study provides a foundation for understanding phytoplankton bloom dynamics and hypoxia formation at a species level.

LSH1 is a novel lytic siphovirus isolated, together with its host in the genus Alishewanella , from the surface microlayer of a brackish tidal reservoir in South Korea and characterized with respect to growth properties, genome sequence, gene annotation, mass spectrometry, and electron microscopy. Sequence analysis shows that LSH1 shares only distant similarity to other cultured phages, although a closer metagenomic neighborhood can be defined. LSH1 represents the first isolate from a large, previously unsampled family-level sector of the viral tree. Transmission electron microscopy revealed a tail end distinct from the best structurally characterized siphoviral prototypes and similar in appearance to Salmonella phage Jersey, the prototype of a large structurally uncharacterized group named Guernseyvirinae. Therefore, Jersey was included in the comparative analysis with LSH1. A combination of hidden Markov model comparisons and AlphaFold reconstruction was used to clarify the structural relationships of these phages. Both have structural homologs of portions of the canonical bacteriophage lambda tail hub but lack the lambda components associated with receptor recognition linked to ejection triggering in that system. The LSH1 and Jersey tail hubs are of different sequence lineages, but each represents a relatively minimalistic version of the siphoviral tail hub, with distinct candidates for the structural location of their antireceptors. This study explores the capability of AlphaFold to rapidly augment the relatively few structurally characterized phages with models for diverse variants, fleshing out how much variation there is and perhaps leading to a better treatment of how this variation is evolving.

Gram-stain-negative, aerobic, rod-shaped bacterial strains, designated HL-TH1^T and HL-TH5, were isolated from deep seawater (1127 m depth) of the Amundsen Sea, Antarctica. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strains HL-TH1^T and HL-TH5 were members of the genus Qipengyuania with close relatives Qipengyuania aerophila GH25^T (99.3%), Qipengyuania pacifica NZ-96^T (99.3%), Qipengyuania profundimaris G39^T (99.1%) and Qipengyuania citrea RE35F/1^T (98.8%). The complete genome sequences of strains HL-TH1^T and HL-TH5 comprised a chromosome of 3.2 Mbp and a plasmid of 0.1 Mbp, with DNA G+C content of 64.1%. The whole genome-based comparisons using the average nt identity and digital DNA–DNA hybridization values revealed that both strains belonged to the same genomic species but were clearly discriminated (79.4–85.8% and 21.9–29.3%, respectively) from their close relatives in the genus Qipengyuania. Both strains showed optimal growth at 30 °C, pH 6.5–7.0 and 1.5–2.5% sea salts. The major fatty acids of both strains were C_18:1  ω6c and/or C_18:1  ω7c (37.8–38.4%), C_17:1  ω6c (18.1–19.7%) and C_16:1  ω6c and/or C_16:1  ω7c (12.3–16.7%). The major isoprenoid quinone was ubiquinone-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified lipids. Hence, we propose that strains HL-TH1^T and HL-TH5 are assigned to a novel species belonging to the genus Qipengyuania, for which the name Qipengyuania profunda sp. nov. is proposed. The type strain is HL-TH1^T (=KCCM 90517^T=JCM 36585^T). In addition, Q. aerophila GH25^T and Q. pacifica NZ-96^T were found to be the same species based on a polyphasic approach. Therefore, we propose the reclassification of Q. aerophila as a later heterotypic synonym of Q. pacifica.

Two Gram-stain-negative, facultative anaerobic, rod-shaped and non-gliding bacteria, designated as HL-DH10^T and HL-DH14, were isolated from the halophyte Suaeda japonica in a mudflat, Republic of Korea. Based on the results of 16S rRNA gene pairwise analysis, the two isolates were the members of the family Flavobacteriaceae, and Aestuariibaculum suncheonense SC17^T was the most closely related to strains HL-DH10^T and HL-DH14 with 96.3% and 95.4% sequence similarity, respectively. The average nt identity and digital DNA–DNA hybridization values between strains HL-DH10^T and HL-DH14 and other related species were all less than 79.2% and 21.9%, respectively. The genomic DNA G+C contents of strains HL-DH10^T and HL-DH14 were 32.0% and 31.5%, respectively. Cells of these strains showed optimal growth at 25 °C, pH 6.5–7.0 and 2.5–4.0% (w/v) sea salts. The major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C_15:0 (14.0–16.0%), iso-C_15:1 G (10.0–12.0%), iso-C_17:0 3-OH (12.4–13.9%), iso-C_15:0 3-OH (11.8–14.9%) and anteiso-C_15:0 (9.4–10.6%). The polar lipids consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two to three unidentified aminolipids and three unidentified lipids. The comprehensive phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strains HL-DH10^T and HL-DH14 are considered to represent a novel genus of Flavobacteriaceae. Hence, we propose the novel genus Thalassobellus suaedae gen. nov., sp. nov. The type strain is HL-DH10^T (=KCCM 90512^T=JCM 36598^T).

A Gram-stain-negative, aerobic, rod-shaped and motile strain HL-JVS1(T), was isolated from the gastric tract of a juvenile Pacific white shrimp. Molecular phylogenetic analysis based on 16S rRNA gene sequences of strain HL-JVS1(T) revealed its affiliation with the genus Pleionea, with close relatives including Pleionea mediterranea MOLA115(T) (97.5%) and Pleionea sediminis S1-5-21(T) (96.2%). The complete genome of strain HL-JVS1(T) consisted of a circular 4.4 Mb chromosome and two circular plasmids (6.6 and 35.0 kb) with a G + C content of 43.1%. The average nucleotide identity and digital DNA-DNA hybridization values between strain HL-JVS1(T) and the type strains of described Pleionea species were 69.7-70.4% and 18.3-18.6%, respectively. Strain HL-JVS1(T) grew at 10-40 degrees C (optimum, 30 degrees C) in the presence of 0.5 - 9.0% (w/v) sea salts (optimum, 2.0 - 2.5%), and at pH range of 5.5 - 10.0 (optimum, pH 6.5). The major fatty acids (> 10%) were summed feature 9 (iso-C-17:1 omega 9c and/or C-16:0 10-methyl) (23.3%), iso-C-16:0 (14.5%), iso-C-11:0 3-OH (13.8%) and iso-C-15:0 (11.0%). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, two unidentified aminolipids, and two unidentified lipids. The respiratory quinone was ubiquinone-8. The comprehensive phylogenetic, phylogenomic, phenotypic and chemotaxonomic results showed that strain HL-JVS1(T) is distinct from other Pleionea species. Hence, we propose strain HL-JVS1(T) as a novel species belonging to the genus Pleionea, for which the name Pleionea litopenaei sp. nov. is proposed with HL-JVS1(T) (= KCCM 90514(T) = JCM 36490(T)) as the type strain.

A novel Gram-stain-negative, aerobic, rod-shaped bacterium, designated as HL-NP1T, was isolated from the surface water of the northwestern Pacific Ocean after enrichment cultivation using the organic phosphorous compound of 2-aminoethylphosphonate. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Jiella , with the highest similarity to Jiella pacifica 40Bstr34T (98.7 %). The complete genome sequence of strain HL-NP1T comprised a circular chromosome of 5.58 Mbp and two circular plasmids of 0.15 and 0.22 Mbp. Comparison of the genome sequences between strains HL-NP1T and J. pacifica 40Bstr34T revealed that average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values (88.0, 86.4 and 33.9 %, respectively) were below the recommended cut-off levels for delineating bacterial species. Strain HL-NP1T showed optimal growth at 30 °C, pH 6.5–7.0, with 2.0–2.5 % (w/v) NaCl. The sole respiratory quinone was ubiquinone-10. The predominant fatty acid was summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid and four unidentified lipids. The G+C content of the genomic DNA was 65.1 %. Based on phylogenetic, genotypic, phenotypic and chemotaxonomic data, strain HL-NP1T is proposed to represent a novel species of the genus Jiella , for which the name Jiella pelagia sp. nov. is proposed. The type strain is HL-NP1T (= KCCM 90499T = JCM 35838T).

Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage–host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, ACA1 and ACA2, were isolated from sediment core samples of the continental shelf in the western Arctic Ocean. These phages exhibited successful propagation at a low temperature of 1 °C and displayed typical myovirus morphology with isometric icosahedral heads and contractile tails. The complete genome sequences of phages ACA1 and ACA2 were 36,825 bp and 36,826 bp in size, respectively, sharing almost the same gene content. These are temperate phages encoding lysogeny-related proteins such as anti-repressor, immunity repressor and integrase. The absence of cross-infection between the host strains, which were genomically distinct Pseudoalteromonas species, can likely be attributed to heavy divergence in the anti-receptor apparently mediated by an associated diversity-generating retroelement. HHpred searching identified genes for all of the structural components of a P2-like phage (family Peduoviridae), although the whole of the Peduoviridae family appeared to be divided between two anciently diverged tail modules. In contrast, Blast matching and whole genome tree analysis are dominated by a nonstructural gene module sharing high similarity with Pseudoalteromonas phage C5a (founder of genus Catalunyavirus). This study expands the knowledge of diversity of P2-like phages known to inhabit Peudoalteromonas and demonstrates their presence in the Arctic niche.

A Gram-negative, strictly aerobic, non-motile, slightly curved rod-shaped bacterial strain, designated as HL-RS19^T, was isolated from a sea surface microlayer (SML) sample of the brackish Lake Shihwa. Here, we characterized the new strain HL-RS19^T using a polyphasic approach to determine its taxonomic position. A phylogenetic analysis of its 16S rRNA gene sequence revealed that strain HL-RS19^T belonged to the genus Lacinutrix and was closely related to L. mariniflava AKS432^T (97.9%), L. algicola AKS293^T (97.8%), and other Lacinutrix species (5%) of strain HL-RS19^T were identified as iso-C_15:1 G (16.5%), iso-C_16:0 3-OH (12.9%), anteiso-C_15:1 A (9.9%), anteiso-C_15:0 (9.7%), iso-C_15:0 (9.0%), and iso-C_15:0 3-OH (8.3%). The polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid, and two unidentified lipids. The major respiratory quinone was MK-6. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic data, strain HL-RS19^T represents a novel species belonging to the genus Lacinutrix, for which the name Lacinutrix neustonica sp. nov. is proposed. The type strain is HL-RS19^T (=KCCM 90497^T = JCM 35710^T). The genome sequence analysis of strain HL-RS19^T suggests that it may be well adapted to a harsh SML environment and is likely involved in arsenic cycling, potentially contributing to the bioremediation of anthropogenic arsenic pollution.