Journal of Microbiology

Eungbin Kim

14 Articles

Microbial metabolic responses and CO2 emissions differentiated by soil water content variation in subarctic tundra soils: Dockyu Kim , Namyi Chae , Mincheol Kim , Sungjin Nam , Tai Kyoung Kim , Ki-Tea Park , Bang Yong Lee , Eungbin Kim , Hyoungseok Lee; J. Microbiol. 2022;60(12):1130-1138. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2378-3

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Recent rapid air temperature increases across the northernlatitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature (Ts) and volumetric soil water content (SWC). Under prolonged soil warming at 8°C, Alaskan tundra soils were incubated in a microcosm system and examined for the SWC differential influence on the microbial decomposition activity of large molecular weight (MW) humic substances (HS). When one microcosm soil (AKC1-1) was incubated at a constant SWC of 41% for 90 days (T = 90) and then SWC was gradually decreased from 41% to 29% for another T = 90, the initial HS was partly depolymerized. In contrast, in AKC1-2 incubated at a gradually decreasing SWC from the initial 32% to 10% for T = 90 and then increasing to 27% for another T = 90, HS depolymerization was undetected. Overall, the microbial communities in AKC1-1 could maintain metabolic activity at sufficient and constant SWC during the initial T = 90 incubation. In contrast, AKC1-2 microbes may have been damaged by drought stress during the drying SWC regimen, possibly resulting in the loss of HS decomposition activity, which did not recover even after re-wetting to an optimal SWC range (20–40%). After T = 90, the CO2 production in both treatments was attributed to the increased decomposition of small-MW organic compounds (including aerobic HS-degradative products) within an optimal SWC range. We expect this study to provide new insights into the early effects of warming- and topography-induced SWC variations on the microbial contribution to CO2 emissions via HS decomposition in northern-latitude tundra soil.

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Unidirectional freeze–thaw redistributes water and amplifies soil microbial heterogeneity in a mecrocosm experiment
Huimin Liu, Yaxian Hu, Yuan Song, Xianwen Li, Xiaorong Wei
Geoderma.2025; 453: 117126. CrossRef
Humic substance turnover by bacterial decomposers in the maritime Antarctic soil
Dockyu Kim, Mincheol Kim, Sungho Woo, Eungbin Kim, Hyoungseok Lee, Monika Gorzelak
Soil Research.2025;[Epub] CrossRef
Analysis of CO2 Emission from Urban Soils of the Kola Peninsula (European Arctic)
M. V. Korneykova, V. I. Vasenev, N. V. Saltan, M. V. Slukovskaya, A. S. Soshina, M. S. Zavodskikh, Yu. L. Sotnikova, A. V. Dolgikh
Eurasian Soil Science.2023; 56(11): 1653. CrossRef
Analysis of CO₂ Emission by Urban Soils under the Conditions of the Kola North
M. V. Korneykova, V. I. Vasenev, N. V. Saltan, M. V. Slukovskaya, A. S. Soshina, M. S. Zavodskikh, Y. L. Sotnikova, A. V. Dolgikh
Почвоведение.2023; (11): 1385. CrossRef

Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil: Dockyu Kim , Namyi Chae , Mincheol Kim , Sungjin Nam , Eungbin Kim , Hyoungseok Lee; J. Microbiol. 2020;58(12):1010-1017. Published online December 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0490-9

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Abstract PDF

Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.

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Bacterial community composition and function in different habitats in Antarctic Fildes region revealed by high-throughput sequencing
Yi-He Zhang, Yong-Qiang Hu, Yin-Xin Zeng, Ting Hu, Wei Han, Yu Du, Zhong Hu, Shan-Shan Meng
Frontiers in Microbiology.2025;[Epub] CrossRef
Effect of coal mining subsidence on soil microbial communities in mining areas with high groundwater levels
Ruiping Xu, Junying Li, Xinju Li, Wen Song
Environmental Geochemistry and Health.2025;[Epub] CrossRef
Influence of Composite Amendments on the Characteristics of Sandy Soil
Xinrui Sui, Lingyan Wang, Xinyao Lv, Yanan Liu, Yuqi Zhu, Lingyun Fan, Hanxi Wang
Sustainability.2025; 17(17): 7619. CrossRef
Microbial metabolic responses and CO2 emissions differentiated by soil water content variation in subarctic tundra soils
Dockyu Kim, Namyi Chae, Mincheol Kim, Sungjin Nam, Tai Kyoung Kim, Ki-Tea Park, Bang Yong Lee, Eungbin Kim, Hyoungseok Lee
Journal of Microbiology.2022; 60(12): 1130. CrossRef
Temperature sensitivity of Antarctic soil‐humic substance degradation by cold‐adapted bacteria
Dockyu Kim, Ha Ju Park, Mincheol Kim, Seulah Lee, Soon Gyu Hong, Eungbin Kim, Hyoungseok Lee
Environmental Microbiology.2022; 24(1): 265. CrossRef
Seasonal patterns of rhizosphere microorganisms suggest carbohydrate-degrading and nitrogen-fixing microbes contribute to the attribute of full-year shooting in woody bamboo Cephalostachyum pingbianense
Lushuang Li, Tize Xia, Hanqi Yang
Frontiers in Microbiology.2022;[Epub] CrossRef

Isolation and Characterization of a Rhodococcus Species Strain Able to Grow on ortho- and para-Xylene: Jung Yeon Jang , Dockyu Kim , Hyun Won Bae , Ki Young Choi , Jong-Chan Chae , Gerben J. Zylstra , Young Min Kim , Eungbin Kim; J. Microbiol. 2005;43(4):325-330.; DOI: https://doi.org/2258 [pii]

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Abstract PDF: Rhodococcus sp. strain YU6 was isolated from soil for the ability to grow on o-xylene as the sole carbon and energy source. Unlike most other o-xylene-degrading bacteria, YU6 is able to grow on p-xylene. Numerous growth substrate range experiments, in addition to the ring-cleavage enzyme assay data, suggest that YU6 initially metabolizes o- and p-xylene by direct aromatic ring oxidation. This leads to the formation of dimethylcatechols, which was further degraded largely through meta-cleavage pathway. The gene encoding meta-cleavage dioxygenase enzyme was PCR cloned from genomic YU6 DNA using previously known gene sequence data from the o-xylene-degrading Rhodococcus sp. strain DK17. Subsequent sequencing of the 918-bp PCR product revealed a 98% identity to the gene, encoding methylcatechol 2,3-dioxygenase from DK17. PFGE analysis followed by Southern hybridization with the catechol 2,3-dioxygenase gene demonstrated that the gene is located on an approximately 560-kb megaplasmid, designated pJYJ1 <br>

Identification of Two-Component Regulatory Genes Involved in o-Xylene Degradation by Rhodococcus sp. Strain DK17: Dockyu Kim , Jong-Chan Chae , Gerben J. Zylstra , Ho-Yong Sohn , Gi-Seok Kwon , Eungbin Kim; J. Microbiol. 2005;43(1):49-53.; DOI: https://doi.org/2138 [pii]

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Abstract PDF: Putative genes for a two-component signal transduction system (akbS and akbT) were detected near the alkylbenzene-degrading operon of Rhodococcus sp. DK17. Sequence analysis indicates that AkbS possesses potential ATP-binding and histidine autophosphorylation sites in the N- and C-terminal regions, respectively, and that AkbT has a typical response regulator domain. Mutant analysis combined with RT-PCR experiments further shows that AkbS is required to induce the expression of o-xylene dioxygenase in DK17.

Molecular Cloning and Identification of a Novel Oxygenase Gene Specifically Induced during the Growth of Rhodococcus sp. Strain T104 on Limonene: Ki Young Choi , Dockyu Kim , Sung-Cheol Koh , Jae-Seong So , Jong-Sul Kim , Eungbin Kim; J. Microbiol. 2004;42(2):160-162.; DOI: https://doi.org/2027 [pii]

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Abstract PDF: Rhodococcus sp. strain T104 is able to utilize both limonene and biphenyl as growth substrates.Furthermore, T104 possesses separate pathways for the degradation of limonene and biphenyl. Previously, we found that a gene(s) involved in limonene degradation was also related to indigo-producing ability. To further corroborate this observation, we have cloned and sequenced a 8,842-bp genomic DNA region with four open reading frames, including one for indole oxygenase, which converts indole to indigo (a blue pigment). The reverse transcription PCR data demonstrated that the identified indole oxygenase gene is specifically induced by limonene, thereby implicating this gene in the degradation of limonene by T104.

Monitoring Expression of bphC Gene from Ralstonia eutropha H850 Induced by Plant Terpenes in Soil: Kyung-Ja Jung , Byung-Hyuk Kim , Eungbin Kim , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2002;40(4):340-343.

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Abstract PDF: A PCB degrader, Ralstonia eutropha H850 was shown to induce bphC gene encoding 2,3-dihydroxy-biphenyl-1,2-dioxygenase in a carvone-amended pure culture in our previous study (Park et al., 1999). The present study was carried out to examine how plant terpenes, as natural substrates, would cause an expression of a PCB degradative gene in soil that was amended with terpenes. The population of Ralstonia eutropha H850 was maintained at least around 10 8 (CFU/g fresh soil) in the soil amended with carvone or limonene in the presence of succinate as a growth substrate at 50 th day. The gene expression was monitored by RT-PCR using total RNA directly extracted from each soil and bphC gene primers. The bphC gene expression of the seeded strain H850 was observed in the soil amended with biphenyl (4 days) but not with succinate, carvone and limonene. These results indicate that terpenes widely distributed in nature could be a potential inducing substrate for effective PCB biodegration in the soil but their bioavailability and specific induction behavior should be taken into account before PCB bioremediation implementation.

P22-Based Challenge Phage Constructs to Study Protein-Protein Interactions between the [sigma]^54 -Dependent Promoter, dctA, and Its Transcriptional Regulators: Jeong Min Song , Eungbin Kim , Joon H. Lee; J. Microbiol. 2002;40(3):205-210.

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Abstract PDF: To study interactions between C_4 -dicarboxylic acid transport protein D and E[sigma]^54 in the dctA promoter regulatory region, we used the challenge phage system. An ant'-'lac fusion was recombined onto the challenge phage, and this ant'-'lac fusion along with Pant and the R. meliloti dctA promoter regulatory region were cloned onto a plasmid. The plasmid bearing the ant'-'lac fusion was used as a reporter plasmid in a coupled transcription-translation system. Addition of purified [sigma]^54 to the coupled system specifically repressed transcription of the plasmid-borne ant'-'lac fusion. When DCTD was added along with [sigma]^54 to the coupled system, transcription of the ant'-'lac fusion was even further repressed, suggesting that DCTD may stabilize closed complexes between E[sigma]^54 and the dctA promoter.

Reclassification of a Carboxydobacterium, Acinetobacter sp. Strain JC1 DSM3803, as Mycobacterium sp. Strain JC1 DSM 3803: Taeksun Song , Hyeyoung Lee , Yong-Ha Park , Eungbin Kim , Young Ta e Ro , Si Wouk Kim , Young Min Kim; J. Microbiol. 2002;40(3):237-240.

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Abstract PDF: A carboxydotrophic bacterium, isolated from a soil sample in Seoul, was classified initially as Acinetobacter sp. strain JC1 DSM 3803. Chemotaxanomic properties, analysis of the 16s rDNA sequence, fatty acid content, and molecular phylogenetic analysis based on rpoB gene, however, suggested that this bacterium belongs to the genus, Mycobacterium. On the basis of this evidence, it is proposed that Acinetobacter sp. strain JC1 DSM 3803 be reclassified as Mycobacterium sp. strain JC1 DSM 3803.

Three Separate Pathways for the Initial Oxidation of Limonene, Biphenyl, and Phenol by Rhodococcus sp. Strain T104: Dockyu Kim , Min Jung Park , Sung-Cheol Koh , Jae-Seong So , Eungbin Kim; J. Microbiol. 2002;40(1):86-89.

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Abstract PDF: Rhodococcus sp. strain T104, which is able to grow on either biphenyl or limonene, was found to utilize phenol as sole carbon and energy sources. Furthermore, T104 was positively identified to possess three separate pathways for the degradation of limonene, phenol, and biphenyl. The fact that biphenyl and limonene induced almost the same amount of catechol 1,2-dioxygenase activity indicates that limonene can induce both upper and lower pathways for biphenyl degradation by T104.

Stress-shock Response of a Methylotrophic Bacterium Methylovorus sp. strain SS1 DSM 11726: Jong H. Park , Si W. Kim , Eungbin Kim , Young T. Ro , Young M. Kim; J. Microbiol. 2001;39(3):162-167.

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Abstract PDF: Methylovorus sp. strain SS1 DSM 11726 was found to grow continuously when it was transferred from 30 C to 40 C and 43 C. A shift in growth temperature from 30 C to 45 C, 47 C and 50 C reduced the viability of the cell population by more than 10^2 , 10^3 and 10^5 folds, respectively, after 1 h cultivation. Cells transferred to 47 C and 50 C after preincubation for 15 min at 43 C, however, exhibited 10-fold increase in viability. It was found that incubation for 15 min at 40 C of Methylovorus sp. strain SS1 grown at 30 C was sufficient to accelerate the synthesis of a specific subset of proteins. The major heat shock proteins had apparent molecular masses of 90, 70, 66, 60, and 58 kDa. The 60 and 58 kDa proteins were found to cross-react with the antiserum raised against GroEL protein. The heat shock response persisted for over 1 h. The shock proteins were stable for 90 min in the cell. Exposure of the cells to methanol induced proteins identical to the heat shock proteins. Addition of ethanol induced a unique protein with a molecular mass of about 40 kDa in addition to the heat-induced proteins. The proteins induced in paraquat-treated cells were different from the heat shock proteins, except the 70 and 60 kDa proteins.

Enzyme Activities Related to the Methanol Oxidation of Mycobacterium sp. strain JC1 DSM 3803: Youngtae Ro , Eungbin Kim , Youngmin Kim; J. Microbiol. 2000;38(4):209-217.

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Abstract PDF: Mycobacterium sp. strain JC1 DSM 3803 grown in methanol showed no methanol dehydrogenase or oxidase activities found in most methylotrophic bacteria and yeasts, respectively. Even though the methanol-grown cells exhibited a little methanol-dependent oxidation by cytochrome c-dependent methanol dehydrogenase and alcohol dehydrogenase, they were not the key enzymes responsible for the methanol oxidation of the cells, in that the cells contained no c-type cytochrome and the methanol oxidizing activity from the partially purified alcohol dehydrogenase was too low, respectively. In substrate switching experiments, we found that only a catalase-peroxidase among the three types of catalase found in glucose-grown cells was highly expressed in the methanol-grown cells and that its activity was relatively high during the exponential growth phase in Mycobacterium sp. JC1. Therefore, we propose that catalase-peroxidase is an essential enzyme responsible for the methanol metabolism directly or indirectly in Mycobacterium sp. JC1.

Roles of the meta- and the ortho-Cleavage Pathways for the Efficient Utilization of Aromatic Hydrocarbons by Sphingomonas yanoikuyae B1: Jeongmin Song , Junghee Sung , Young Min Kim , Gerben J. Zylstra , Eungbin Kim; J. Microbiol. 2000;38(4):245-249.

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Abstract PDF: Catabolic pathways for the degradation of various aromatics by Sphingomonas yanoikuyae B1 are intertwined, joining at the level of substituted benzoates, which are further degraded via ring cleavage reactions. The mutant strain EK497, which was constructed by deleting a large DNA region containing most of the genes for biphenyl, naphthalene, m-xylene, and m-toluate degradation, was unable to grow on all of the aromatics tested except for benzoate as the sole source of carbon and energy. S. yanoikuyae EK497 was found to possess only catechol ortho-ring cleavage activity due to deletion of the genes for the meta-cleavage pathway. Wild-type S. yanoikuyae B1 grown on benzoate has both catechol ortho-and meta-cleavage activity. However, m-xylene and m-toluate, which are metabolized through methylbenzoate, and biphenyl, which is metabolized through benzoate, induce only the meta-cleavage pathway, suggesting the presence of a substrate-dependent induction mechanism.

P22-Based Challenge Phage Constructs to Study DNA-Protein Interactions between the [sigma]^54-Dependent Promoter, dctA, and Its Transcriptional Regulators: Eungbin Kim , Daeyou Kim , Joon Haeng Lee; J. Microbiol. 2000;38(3):176-179.

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Abstract PDF: A challenge phage system was used to study the DNA-protein interaction between C_4 -dicarboylic acid transport protein D (DCTD) or [sigma]^54 , and a [sigma]^54 -dependent promoter, dctAp. R. meliloti dctA promoter regulatory region replaced the O_mnt site on the phage. S. typhimurium strains overproducing either DCTD or [sigma]^54 directed this challenge phage towards lysogeny, indicating that DCTD or E[sigma]^54 recognized the dctA promoter on the phage and repressed transcription of the ant gene. These challenge phage constructs will be useful for examining interactions between DCTD (or [sigma]^54 ) and the dctA promoter region.

Association of a Common Reductase with Multiple Aromatic Terminal Dioxygenases in Sphingomonas yanoikuyae Strain B1: Mihyun Bae , Eungbin Kim; J. Microbiol. 2000;38(1):40-43.

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Abstract PDF: The aromatic dioxygenase system in Sphingomonas yanoikuyae strain B1 consists of three components, an oxygenase, a ferredoxin, and a reductase. The insertional knockout of the bphA4 gene encoding a reductase and subsequent complementation experiments showed that the reductase encoded by bphA4 in S. yanoikuyae strain B1 is associated with multiple dioxygenase components including that of toluate dioxygenase (XylXY).

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