• Journal of Microbiology and Biotechnology
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• 제33권10호
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• pp.1292-1298
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• 2023

PAMB 00755^T, 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℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (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 00755^T 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 C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T 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 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• The Plant Pathology Journal
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• 제38권2호
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• pp.167-174
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• 2022

Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.

• Journal of Species Research
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• 제9권4호
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• pp.375-376
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• 2020

A type specimen is the specimen originally used to name a new species; thus, it is one of the most significant materials for taxonomic study. In our study on the inventory and management of endemic species in Korea, we checked the type materials for Pseudolysimachion pusanensis (Y. Lee) Y. Lee, combination name Veronica pusanensis Y. Lee, recorded as deposited at the herbaria of the Ewha Womans University and the National Institute of Biological Resources, and failed to find any specimens. Thus, we concluded that all type specimens of V. pusanensis have since been misplaced. According to articles 9.11 and 9.13 of the International Code of Nomenclature for algae, fungi, and plants, it is necessary to select a neotype if the holotype is missing and no other original material exists. Therefore, we designate the neotype maintained in the herbarium of the National Institute of Biological Resources of the Republic of Korea.

• Journal of Applied Biological Chemistry
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• 제42권3호
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• pp.119-124
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• 1999

About two thirds of the naturally occurring antibiotics have been discovered from actinomycetes. Therefore, the probability of discovering further new antibiotics from actinomycetes is declining as many known metabolites are isolated repeatedly. However, various efforts leave been made in order to enhance the probability of discovering novel compounds. In the present study, we have developed new screening strategies based on the antibiotic biosynthetic pathway, and the genetic information, utilizing polymerase chain reaction. We have selected macrolide type polyketides. In order to divide the ansamycin group antibotic of macrolide type polyketides, we have selected 3-amino-5-hydroxybenzoic acid (AHBA) moiety which contains a biosynthetically unique structural element in the group as a target molecules. Oligonucleotide primers were designed to amplify DNA fragments of macrolide type polyketide synthase and AHBA synthase genes from fourteen actinomycetes species. This method was successfully applied to all three of the known macrolide type polyketide produccing actinomycetes tested. In addition, it also identified the presence of potential macrolide type polyketide producing genes from seven actinomycetes that were known to produce none of macrolide type polyketides, and AHBA biosynthetic genes in one actinomycetes. This technique is potentially useful for the screening of new antibiotices and cloning of their biosynthetic genes.

• Journal of Species Research
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• 제9권3호
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• pp.218-220
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• 2020

A holotype is an element to which the name of a taxon is permanently attached and is key material that facilitates taxonomic research. However, type citation or designation errors due to typographical errors or inadvertent mistakes often exist. When reviewing recently published literature for the type specimens of vascular plants in the herbarium of the National Institute of Biological Resources, we observed that three species, Isoetes laosiensis, Isoetes coreana, and Huperzia jejuensis, had errors, and the actual holotype information and the type descriptions of the protologues did not match. The name Isoetes laosiensis had a collecting number error, while Isoetes coreana and Huperzia jejuensis had collector errors. According to Article 9.2 of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen code), if a holotype designation in the protologue of the name of a taxon is found to contain errors such as collector, collecting number, and illustration errors, the errors are to be corrected. We, therefore, corrected the errors in holotypes of three species, with no alterations made to the intents of the original authors.

• 대한수학회논문집
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• 제24권2호
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• pp.215-226
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• 2009

For a class of Holling type II food chain systems with biological and chemical controls, we give conditions of the local stability of prey-free periodic solutions and of the permanence of the system. Further, we show the system is uniformly bounded.

• 미생물학회지
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• 제24권4호
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• pp.406-410
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• 1986

The isolation and charateriation of a type II restriction endonuclease from Xanthomonas citri IFO 3835 were described. This enzyme (Xci I endonuclease) is an isoschizomer of Sal I endonuclease recognizing 5'-GTCGAC-3' and cleaving at the site indicated by the arrow. Unlike Sal I endonuclease, Xci I endonuclease requries a NaCl concentration of 50mM for its maximum activity.

• Journal of Species Research
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• 제7권1호
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• pp.73-79
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• 2018

The review provides the information about 46 type specimens on 35 taxa of vascular plants from Korea (Fig. 1), kept in the Herbarium of the Komarov Botanical Institute of the Russian Academy of Sciences in addition to 150 taxa published before. Lectotype of Ligustrum patulum Palib is designated here.

• 미생물학회지
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• 제28권4호
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• pp.337-344
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• 1990

미국 뉴저지주에 있는 10개의 회전원판 처리장에서 생물막 시료를 채취하여 사상세균에 대해 현미경적 연구를 실시하였다. 활성오니에서 부유형 성장을 하며 흔히 출현하는 Type 1701, Type 0041. Type 021N, Nocardia, Beggiatoa 및 Sphaerotilus가 회전원판체 생물막에서도 출현하였으나 수도(abundance)는 크게 달랐다. 여기서는 Beggiatoa의 출현빈도가 가장 높았으며, Sphaerotilus, Type 0041, Type 1701, Type 021N, Nocardia의 순이었다. 회전원판 생물막에서 발견된 Beggiatoa는 형태적으로 뚜렷히 구별되는 2가지 Type이 존재하였다. 회전원판체의 중심축으로 100cm 깊이에 존재하는 생물막과 외부의 생물막에 존재하는 사상세균의 군집에 대해 인자분서법에 의한 통계처리를 수행한 결과 대부분의 경우, 내부의 군집과 외부의 군집이 통계적으로 유의하게 달랐으며 장소(내부, 외부)와 단(stage) 사이에도 많은 경우 통계적으로 유의한 상호작용이 있었다.

• 식물분류학회지
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• 제43권2호
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• pp.106-117
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• 2013

한국산 Potentilleae족의 Fragariinae아족과 Potentillinae아족에 포함된 8속 27분류군을 대상으로 주사전자 현미경을 이용하여 잎 양면과 엽병의 털 및 잎 표면의 미세구조를 관찰하였다. 연구결과 한국산 Potentilleae족의 잎과 엽병의 털은 크게 4가지 유형으로 구분되었다(Type I: conical hirtellous, type II: verruculose conical hirtellous, III: crispate villous, IV: floccose villous). Type I은 Fragariinae아족과 Potentillinae아족의 대부분의 분류군에서 관찰되었고, Type II는 유일하게 Potentillinae아족 Potentilla속 Conostylae절의 P. cryptotaeniae에서 나타났다. Type III은 Potentilla속 Conostylae절의 P. chinensis complex와 Leptostylae절의 P. egedii에서 나타났고, type IV는 Conostylae절의 P. discolor와 P. nivea에서 관찰되었다. 융모형인 Type III과 IV를 갖는 분류군들에서는 미세강모가 함께 나타났다. 서로 다른 아족 혹은 절간에 동일한 털 유형을 공유하고 있으며, 한 종에서 두 가지 이상의 털 유형이 관찰되기도 하였다. Type I에 해당하는 Fragariinae아족 다수의 분류군과 Potentillinae아족의 P. centigrana와 P. dickinsii complex에서는 잎 표면에 표피상납질이 발달하였다. 이들의 분포 패턴을 고려하였을 때 아족 간에 표피상납질을 공유하는 특성은 서식지의 생태적 환경과 관련되었을 가능성이 있다. 그러나 분자 계통분류학적인 연구와 비교한 결과 계통적인 영향 또한 관련되었을 것으로 판단된다.