Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds

Lingmin Jiang,Chan Ju Lim,김성건,Jae Cheol Jeong,Cha Young Kim,Dae-Hyuk Kim,Suk Weon Kim,Jiyoung Lee 한국미생물학회 2020 The journal of microbiology Vol.58 No.1

Strain ATSA2T was isolated from surface-sterilized kimchi cabbage (Brassica rapa subsp. pekinensis) seeds and represents a novel bacterium based on the polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ATSA2T formed a lineage within genus Saccharibacillus and was most closely to Saccharibacillus deserti WLG055T (98.1%) and Saccharibacillus qingshengii H6T (97.9%). The whole-genome of ATSA2T comprised a 5,619,468 bp of circular chromosome with 58.4% G + C content. The DNA-DNA relatedness values between strain ATSA2T and its closely related type strains S. deserti WLJ055T and S. qingshengii H6T were 26.0% and 24.0%, respectively. Multiple gene clusters associated with plant growth promotion activities (stress response, nitrogen and phosphorus metabolism, and auxin biosynthesis) were annotated in the genome. Strain ATSA2T was Gram-positive, endospore-forming, facultatively anaerobic, and rod-shaped. It grew at 15–37°C (optimum 25°C), pH 6.0–10.0 (optimum pH 8.0), and in the presence of 0–5% (w/v) NaCl (optimum 1%). The major cellular fatty acids (> 10%) of strain ATSA2T were anteiso- C15:0 and C16:0. MK-7 was the major isoprenoid quinone. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, and three unknown glycolipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, strain ATSA2T is proposed to represent a novel species of genus Saccharibacillus, for which the name is Saccharibacillus brassicae sp. nov. The type strain is ATSA2T (KCTC 43072T = CCTCC AB 2019223T).

Cohnella abietis sp. nov., isolated from Korean fir (Abies koreana) rhizospheric soil of Halla mountain

Lingmin Jiang,Sophea Pheng,Keun Chul Lee,Se Won Kang,Jae Cheol Jeong,Cha Young Kim,Hyeong Cheol Park,Dae-Hyuk Kim,Suk Weon Kim,Song-Gun Kim,이지영 한국미생물학회 2019 The journal of microbiology Vol.57 No.11

A strictly aerobic, motile, endospore-forming, rod-shaped bacterium, designated HS21T, was isolated from rhizospheric soil of the Korean fir tree (Abies koreana) from Halla mountain on Jeju island, Korea. Growth of strain HS21T was observed at pH 6.0–8.0 (optimum: pH 7.0), 0–2% (w/v) NaCl and 4–30°C (optimum: 25°C). A comparative analysis of 16S rRNA gene sequences showed that strain HS21T was most closely related to Cohnella luojiensis HY-22RT (97.6%), followed by C. lupini RLAHU4BT (97.4%) and C. collisoli NKM- 5T (97.2%). The genome of strain HS21T comprised a circular chromosome of 7,059,027 bp with 44.8% G + C content. The DNA-DNA relatedness values between strain HS21T and C. luojiensis HY-22RT and C. lupini RLAHU4BT were 18.1% and 13.8%, respectively. The major cellular fatty acids (> 5%) of the isolate were anteiso-C15:0, iso-C16:0, C16:0, and iso-C15:0. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, lysylphosphatidylglycerol, and three unidentified aminophospholipids. Based on its phenotypic, phylogenetic, genomic, and chemotaxonomic properties, strain HS21T represents a novel species of the genus Cohnella, for which the name Cohnella abietis sp. nov. is proposed. The type strain is HS21T (= KCTC 43028T = CCTCC AB 2019010T).

Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory

Lingmin Jiang,Dexin Wang,이정숙,Dae-Hyuk Kim,Jae Cheol Jeong,Cha Young Kim,Suk Weon Kim,Jiyoung Lee 한국미생물학회 2020 The journal of microbiology Vol.58 No.5

Strain KSNA2T, a Gram-negative, moderately halophilic, facultatively anaerobic, motile, rod-shaped bacterium, was isolated from the surface-sterilized stem tissue of a beach morning glory (Calystegia soldanella) plant in Chuja Island, Jejudo, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that strain KSNA2T formed a distinct lineage within the family Enterobacteriaceae, with the highest 16S rRNA gene sequence similarity to Izhakiella australiensis KCTC 72143T (96.2%) and Izhakiella capsodis KCTC 72142T (96.0%), exhibited 95.5– 95.9% similarity to other genera in the family Enterobacteriaceae and Erwiniaceae. Conserved signature indels analysis elucidated that strain KSNA2T was delimited into family Enterobacteriaceae. KSNA2T genome comprises a circular chromosome of 5,182,800 bp with 56.1% G + C content. Digital DNA-DNA relatedness levels between strain KSNA2T and 18 closely related species were 19.3 to 21.1%. Average nucleotide identity values were between 72.0 and 76.7%. Growth of strain KSNA2T was observed at 4 to 45°C (optimum, 25°C) and pH 5.0 to 12.0 (optimum, pH 7.0) in the presence of 0 to 11% (w/v) NaCl (optimum, 0–7%). The major cellular fatty acids (> 10%) were C16:0 followed by summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C17:0 cyclo, and C14:0. The major isoprenoid quinone was ubiquinone-8 (Q-8). With combined phylogenetic, genomic, phenotypic, and chemotaxonomic features, strain KSNA2T represents a novel species of a new genus in the family Enterobacteriaceae, for which the name Jejubacter calystegiae gen. nov., sp. nov. is proposed. The type strain is KSNA2T (= KCTC 72234T = CCTCC AB 2019098T).

Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir

Jiang Lingmin,Choe Hanna,Peng Yuxin,Jeon Doeun,Cho Donghyun,Jiang Yue,Lee Ju Huck,Kim Cha Young,Lee Jiyoung 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.10

PAMB 00755T , a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20°C, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755T was most closely related to Sphingomonas chungangi MAH-6T (97.7%) and Sphingomonas polyaromaticivorans B2-7T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9–81.3%), average amino acid identity (73.3–75.9%), and digital DNA–DNA hybridization (73.3– 75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C18:1ω7c and/or C18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755T as the type strain (= KCTC 92781T = GDMCC 1.3779T ).

Genome-Based Insights into the Thermotolerant Adaptations of Neobacillus endophyticus BRMEA1T

Lingmin Jiang,Ho Le Han,Yuxin Peng,Doeun Jeon,Donghyun Cho,Cha Young Kim,Jiyoung Lee 한국식물병리학회 2023 식물병연구 Vol.29 No.3

The bacterium Neobacillus endophyticus BRMEA1T, isolated from the medicinal plant Selaginella involvens, known as its thermotolerant can grow at 50°C. To explore the genetic basis for its heat tolerance response and its potential for producing valuable natural compounds, the genomes of two thermotolerant and four mesophilic strains in the genus Neobacillus were analyzed using a bioinformatic software platform. The whole genome was annotated using RAST SEED and OrthVenn2, with a focus on identifying potential heattolerance- related genes. N. endophyticus BRMEA1T was found to possess more stress response genes compared to other mesophilic members of the genus, and it was the only strain that had genes for the synthesis of osmoregulated periplasmic glucans. This study sheds light on the potential value of N. endophyticus BRMEA1T, as it reveals the mechanism of heat resistance and the application of secondary metabolites produced by this bacterium through whole-genome sequencing and comparative analysis.

A graphene‑based highly sensitive aptasensor for the detection of lung cancer marker CA125

Junnan Chen,Lingmin Yu,Wenzhen Xu,Tao Lin,Sicong Jiang,Caijin Jin 한국탄소학회 2023 Carbon Letters Vol.33 No.6

Graphene-based sensors have emerged as significant tools for biosensing applications due to their unique electrical, mechanical, and thermal properties. In this study, we have developed an innovative and sensitive aptasensor based on the surfacemodified graphene for the detection of lung cancer biomarker CA125. The sensor leverages the combination of graphene surface and gold nanoparticles (AuNPs) electrodeposition to achieve a high level of sensitivity and selectivity for the biomarker detection. A noticeable decrease in electron transfer resistance was observed upon the AuNPs deposition, demonstrating the enhancement of electrochemical performance. Our experimental findings showed a strong linear relationship between the sensor response and CA125 concentrations, ranging from 0.2 to 15.0 ng/mL, with a detection limit of 0.085 ng/ mL. This study presents a novel approach to lung cancer detection, surpassing the traditional methods in terms of invasiveness, cost, and accuracy. The results from this work could pave the way for the development of graphene-based sensors in various other biosensing applications.

Complete genome sequence of Cohnella sp. HS21 isolated from Korean fir (Abies koreana) rhizospheric soil

지앙 링민,강세원,김성건,정재철,김차영,김대혁,김석원,이지영,Jiang, Lingmin,Kang, Se Won,Kim, Song-Gun,Jeong, Jae Cheol,Kim, Cha Young,Kim, Dae-Hyuk,Kim, Suk Weon,Lee, Jiyoung The Microbiological Society of Korea 2019 미생물학회지 Vol.55 No.2

Paenibacillaceae계의 Cohnella 속은 다양한 환경 속에서 서식한다. 여기에 우리는 한국 한라산 꼭대기의 구상나무(Abies koreana) 근권 토양으로부터 분리된 Cohnella sp. HS21의 전체 게놈 서열을 보고한다. 균주 HS21은 원형 염색체 7,059,027 bp와 44.8%의 GC 함량을 가지고 있다. 5,939개의 단백질 코딩 유전자와 78개의 트랜스퍼 (tRNA) 유전자, 27개의 리보솜 RNA (rRNA) 유전자, 4개의 비 코딩 RNA 유전자(ncRNA), 90개의 위 유전자가 존재했다. 박테리아는 항생제 관련 유전자 클러스터와 식물 세포벽 분해 효소를 코딩하는 유전자를 포함하고 있다. The genus Cohnella, which belongs to the family Paenibacillaceae, inhabits a wide range of environmental niches. Here, we report the complete genome sequence of Cohnella sp. HS21, which was isolated from the rhizospheric soil of Korean fir (Abies koreana) on the top of Halla Mountain in the Republic of Korea. Strain HS21 features a 7,059,027 bp circular chromosome with 44.8% GC-content. Its genome contains 5,939 protein-coding genes, 78 transfer RNA (tRNA) genes, 27 ribosomal RNA (rRNA) genes, 4 noncoding RNA genes (ncRNA), and 90 pseudogenes. The bacterium contains antibiotic-related gene clusters and genes encoding plant cell wall-degrading enzymes.