Jiyoung Lee

Introduction: Genome-based bacterial taxonomy requires standardized and reproducible analytical workflows for species delineation and phylogenomic placement; however, the practical deployment of these workflows remains a significant barrier for experimental biologists and clinical scientists. Widely adopted tools such as Prokka, antiSMASH, and PhyloPhlAn underpin key steps in genome annotation, functional characterization, and phylogenomic reconstruction, but their practical deployment in routine laboratory settings, especially on Windows based systems, remains non trivial due to complex software dependencies and command line centric workflows. Existing solutions, including cloud-based platforms (e.g., Galaxy and KBase) and commercial software suites (e.g., CLC Genomics Workbench), partially alleviate these challenges but may also involve considerations related to data-privacy concerns, upload latency, storage quotas, shared computing resources, and recurring licensing costs. Methods: To address these limitations, we introduce TaxaScope, a graphical-interface-driven desktop workstation designed to support reproducible, genome-based bacterial taxonomy by integrating a curated set of community-validated tools for genome quality assessment, annotation, phylogenomic inference, genome relatedness estimation, and functional profiling within a unified local graphical user interface (GUI). By leveraging Docker- and Podman-based containerization behind a user-friendly frontend, TaxaScope provides version-locked, standardized execution environments across computing platforms without requiring manual dependency management or prior Linux expertise. Result and discussion: We demonstrate the utility of TaxaScope through a comprehensive re-analysis of Pseudomonas putida KCTC 1751T, illustrating how standardized taxonomic workflows can be executed locally while automatically generating high-quality circular genome maps and interactive functional reports suitable for downstream interpretation and figure preparation directly from native tool outputs. Collectively, TaxaScope lowers the technical barrier to standardized and reproducible genome-based bacterial taxonomy by providing a private, locally controlled, containerized workflow that complements cloud-based and commercial infrastructures for routine taxonomic research. By providing a containerized and visualization-oriented desktop environment, TaxaScope facilitates the standardized execution of established genomic tools, thereby bridging the gap between complex bioinformatic workflows and consistent bacterial taxonomy.

Soil salinity is a major abiotic stress that restricts plant growth and agricultural productivity worldwide. Here, we characterized Pseudomonas sp. JBR1, an endophytic bacterium isolated from the halophyte Carex pumila, and evaluated its capacity to enhance salt tolerance in non-halophytic plants. Inoculation with strain JBR1 markedly improved growth of Arabidopsis (Arabidopsis thaliana) and Brassica rapa under saline conditions by reducing reactive oxygen species accumulation, enhancing antioxidant enzyme activity, improving Na⁺/K⁺ ion homeostasis, and stimulating auxin accumulation in roots. In addition to these direct physiological effects, strain JBR1 markedly altered rhizosphere microbial communities. 16S rRNA amplicon sequencing revealed increased microbial diversity and enrichment of beneficial taxa, particularly Streptomyces and Pseudomonas. Predictive functional profiling indicated upregulation of bacterial motility, chemotaxis, and signal transduction pathways in strain JBR1-treated plants, suggesting enhanced microbial colonization and plant–microbe interactions. These results demonstrate that strain JBR1 confers salt tolerance through a dual mechanism: direct modulation of host physiology and indirect restructuring of the rhizosphere microbiome. The synergistic effects of strain JBR1 highlight its potential as a microbial bioinoculant to improve crop resilience in saline soils and support sustainable agriculture.

Halophytic plants harbour salt‐tolerant bacteria that enhance resilience to salinity. In this study, two highly halotolerant Kushneria isolates, K. konosiri (Kk) and K. marisflavi (Km), were obtained from the halophyte Suaeda maritima . Both strains tolerated up to 25% NaCl and promoted Arabidopsis thaliana growth under salt stress by producing indole‐3‐acetic acid, proline, and extracellular polysaccharides that mitigated osmotic stress. Inoculation with Kk or Km increased shoot and root biomass and reduced intracellular Na⁺ and reactive oxygen species. Their agricultural potential was tested in cabbage ( Brassica rapa ), where both isolates alleviated salinity‐induced growth inhibition. A combined inoculum (Kkm) showed enhanced efficacy, significantly increasing shoot biomass (1.26‐fold vs. Kk; 1.23‐fold vs. Km) and dry weight (1.19‐fold vs. Kk; 1.13‐fold vs. Km). Kkm treatment also improved the K⁺/Na⁺ ratio and proline accumulation. Microbial profiling revealed that Kkm enriched Bacillus species in the rhizosphere and promoted greater biofilm formation than single strains. These findings demonstrate that Kushneria isolates function as salt‐tolerant plant growth‐promoting bacteria, enhancing ion homoeostasis, stress protection, and rhizosphere restructuring. This study highlights the potential of halophyte‐derived microbial consortia to improve crop salt tolerance in agriculture.

Two separate bacterial strains, PMTSA4^T and PMR2A8, were isolated from the rhizospheric soils of bell pepper plants grown in a plant nursery. These strains are Gram-negative, non-motile and rod-shaped and grow in aerobic conditions. They exhibit a positive reaction for catalase activity but negative results for oxidase activity. Phylogenetic analysis of the 16S rRNA gene sequences revealed that the strains PMTSA4^T and PMR2A8 are closely related to Flavobacterium piscinae ICH-30^T (95.6%, respectively), Flavobacterium ahnfeltiae 10Alg 130^T (95.5%) and Flavobacterium maris KMM 9535^T (95.3%), aligning them within the genus Flavobacterium. Digital DNA–DNA hybridization (dDDH) values and average nucleotide identities (ANIs) of the whole-genome sequences for the two strains and related Flavobacterium species were significantly below the established thresholds for prokaryotic species delineation (Flavobacterium aquatile LMG 4008^T (dDDH: 19.8% and ANI: 75.5%), F. piscinae ICH-30^T (dDDH: 18.6% and ANI: 73.3%) and F. stagni WWJ 16^T (dDDH: 18.5% and ANI: 72.0%). The strains have genome sizes of 3 068 185 bp and 3 068 330 bp, with a G+C content of 32.5 mol%. In phenotypic characterization, the new strains grew at 10–35 °C and tolerated up to 4% NaCl at pH 5–9 (optimum pH 8). The predominant cellular fatty acids were observed to be iso-C_15:0, iso-C_17:0 3-OH and iso-C_15:0 3-OH. Menaquinone-6 was the predominant quinone. Considering the results from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, it is proposed that the strains PMTSA4^T and PMR2A8 represent a novel species within the genus Flavobacterium.

Salicornia europaea, commonly known as glasswort, thrives in reclaimed land and coastal areas with high salinity, demonstrating remarkable adaptation to the arid conditions of such environments. Two aerobic, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated TR-M5^T and TR-M9, were isolated from the root of Salicornia europaea plants. These bacteria exhibit plant growth-promoting and salt tolerance-enhancing abilities, which have not been reported in other species of the genus. Both strains produce indole-3-acetic acid (IAA), a plant growth hormone, and synthesize proline, which functions as an osmoprotectant. Additionally, they possess gelatinase and cellulase activities. Cells grow in temperatures from 4 to 42°C (optimum 25°C), pH levels from 6.0 to 9.0 (optimum 7.0), and NaCl concentrations from 0 to 8.0% (optimum 6.0%). The average nucleotide identity and digital DNA–DNA hybridization values of strain TR-M5^T with the most closely related type strains for which whole genomes are publicly available were 74.05–77.78% and 18.6–23.1%, respectively. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains TR-M5^T and TR-M9 belong to the genus Algoriphagus. A. locisalis exhibited the highest similarity, sharing a sequence identity of 98.1%. The genomes of TR-M5^T and TR-M9 exhibit a G + C content of 43 mol%. This study specifically focuses on the identification and characterization of strain TR-M5^T as a novel species within the genus Algoriphagus, which we propose to name Algoriphagus halophytocola sp. nov., highlighting its potential role in enhancing plant growth and salt tolerance in saline environments. The type strain is TR-M5^T (KCTC 92720^T = GDMCC 1.3797^T).

Background: Cannabis sativa cultivars can be classified as marijuana or hemp, depending on its amount of the psychoactive cannabinoid Δ⁹‐tetrahydrocannabinolic acid (THCA). Hemp Cheungsam is a non-drug type Cannabis sativa that is characterized by low THCA content. However, the transcripts and expression profile of cannabinoid biosynthesis pathway genes of hemp Cheungsam have not been investigated. Methods: RNA-sequencing (RNA-seq) was performed on three different tissue types (flower, leaf, and stem) of hemp Cheungsam to understand their transcriptomes. The expression of cannabinoid biosynthesis pathway genes was further analyzed in each tissue type. Multiple sequence alignment and conserved domain analyses were used to investigate the homologs of cannbinoid biosynthesis genes. Results: We found that the cannabinoid biosynthesis pathway was mainly expressed in the flowers of hemp Cheungsam, similar to other Cannabis cultivars. However, expression of cannabidiolic acid (CBDA) synthase was much higher than THCA synthase and cannabichromenic acid (CBCA) synthase, suggesting that the transcription profile favors CBDA biosynthesis. Sequence analysis of cannabinoid biosynthesis pathway genes suggested the identity of orthologs in hemp Cheungsam. Conclusions: Cannabinoid biosynthesis in hemp Cheungsam mostly occurs in the flowers, compared to other plant organs. While CBDA synthase expression is high, THCA and CBCA synthase expression is considerably low, indicating lesser THCA biosynthesis and thus low THCA content. Sequence analysis of key genes (CBDA, THCA, and CBCA synthases) of the cannabinoid biosynthetic pathway indicates that orthologs are present in hemp Cheungsam.

Demequina, commonly found in coastal and marine environments, represents a genus of Actinomycetes. In this study, strains Demequina PMTSA13^T and OYTSA14 were isolated from the rhizosphere of Capsicum annuum, leading to the discovery of a novel species, Demequina capsici. Bacteria play a significant role in plant growth, yet there have been no reports of the genus Demequina acting as plant growth-promoting bacteria (PGPB). Comparative genomics analysis revealed ANI similarity values of 74.05–80.63% for PMTSA13^T and 74.02–80.54% for OYTSA14, in comparison to various Demequina species. The digital DNA-DNA hybridization (dDDH) values for PMTSA13^T ranged from 19 to 39%, and 19.1–38.6% for OYTSA14. Genome annotation revealed the presence of genes associated with carbohydrate metabolism and transport, suggesting a potential role in nutrient cycling and availability for plants. These strains were notably rich in genes related to ‘carbohydrate metabolism and transport (G)’, according to their Cluster of Orthologous Groups (COG) classification. Additionally, both strains were capable of producing auxin (IAA) and exhibited enzymatic activities for cellulose degradation and catalase. Furthermore, PMTSA13^T and OYTSA14 significantly induced the growth of Arabidopsis thaliana seedlings primarily attributed to their capacity to produce IAA, which plays a crucial role in stimulating plant growth and development. These findings shed light on the potential roles of Demequina strains in plant–microbe interactions and agricultural applications. The type strain is Demequina capsici PMTSA13^T (= KCTC 59028^T = GDMCC 1.4451^T), meanwhile OYTSA14 is identified as different strains of Demequina capsici.