Journal of Microbiology

Jong-Chan Chae

7 Articles

Evaluation of a Fosmid-Clone-Based Microarray for Comparative Analysis of Swine Fecal Metagenomes: Soo-Je Park , Dong-Hwan Kim , Man-Young Jung , So-Jeong Kim , Hongik Kim , Yang-Hoon Kim , Jong-Chan Chae , Sung-Keun Rhee; J. Microbiol. 2012;50(4):684-688. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-2115-4

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Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20–100 ng) were observed (r2=0.98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology
Mamoon Rashid, Ulrich Stingl
Biotechnology Advances.2015; 33(8): 1755. CrossRef
Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays
Dieter M. Tourlousse, Futoshi Kurisu, Tomohiro Tobino, Hiroaki Furumai
FEMS Microbiology Letters.2013; 342(1): 70. CrossRef

Metagenomic Assessment of a Sulfur-Oxidizing Enrichment Culture Derived from Marine Sediment: Man-Young Jung , VinhHoa Pham , Soo-Je Park , So-Jeong Kim , Jong-Chan Chae , Yul Roh , Sung-Keun Rhee; J. Microbiol. 2010;48(6):739-747. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0257-9

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Abstract PDF

The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase (sqr) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation (cbbL and cbbM) and denitrification (narG) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr-containing fosmid clones and the relevant gamma-proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic gamma-proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.

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Exogenous sulfide regulates hypoxia/reoxygenation stress through the intrinsic apoptotic pathway in the blood clam (Tegillarca granosa)
Yihang Wang, Feiyu Xia, Shunan Jia, Yang Yang, Xiumei Zhang
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology.2024; 283: 109953. CrossRef
Composition and key-influencing factors of bacterial communities active in sulfur cycling of soda lake sediments
Xiangyuan Li, Maohua Yang, Tingzhen Mu, Delu Miao, Jinlong Liu, Jianmin Xing
Archives of Microbiology.2022;[Epub] CrossRef
Fully aerobic two‐step desulfurization process for purification of highly H2S‐laden biogas
Guillermo Quijano, Ivonne Figueroa‐González, Germán Buitrón
Journal of Chemical Technology & Biotechnology.2018; 93(12): 3553. CrossRef

Isolation, Characterization, and Abundance of Filamentous Members of Caldilineae in Activated Sludge: Dae-No Yoon , Soo-Je Park , So-Jeong Kim , Che Ok Jeon , Jong-Chan Chae , Sung-Keun Rhee; J. Microbiol. 2010;48(3):275-283. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9366-8

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Chloroflexi are currently believed to serve as backbone forming agents in the activated sludge of wastewater treatment plants (WWTPs). In this study, we isolated and characterized filamentous bacteria in the class Caldilineae of the phylum Chloroflexi in municipal WWTPs. Diversity analysis using Chloroflexi-specific 16S rRNA gene clone libraries showed that 97% of the clones belonged to the subdivision Anaerolineae comprising the two classes Anaerolineae (95%) and Caldilineae (2%). Clones of Caldilineae were related to a thermophilic filament Caldilinea aerophila with 93% 16S rRNA gene sequence similarity. We obtained filamentous isolates classified into the class Caldilineae showing the best match to C. aerophila with 89% 16S rRNA gene sequence similarity. Isolates showed no ability to assimilate glucose or N-acetylglucosamine or to degrade biopolymers which were observed in filamentous Chloroflexi of WWTPs. The assessment of relative abundance based on quantitative PCR of the 16S rRNA gene indicated that members of the class Caldilineae comprised 12-19% of the Chloroflexi in the activated sludge. Additionally, fluorescence in situ hybridization experiments showed that diverse filamentous Caldilineae inhabit the activated sludge of municipal WWTPs. These findings yield insight into the role of filamentous mesophilic Caldilinea in stabilizing flocs of activated sludge in a wide range of WWTPs.

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Characterization of microbial communities degrading natural organic compounds in activated sludge through 16S rRNA sequencing and mass spectrometry
Zhong-Wei Ke, Chiu-Lan Hsieh, Yen-Yi Liu
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Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses
Patricia Bovio-Winkler, Angela Cabezas, Claudia Etchebehere
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Laibao Ding, Qingwen Tian, Ran Yang, Jinwei Zhu, Qi Guo, Guigan Fang
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Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors
Patricia Bovio-Winkler, Leandro D. Guerrero, Leonardo Erijman, Pía Oyarzúa, María Eugenia Suárez-Ojeda, Angela Cabezas, Claudia Etchebehere
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Reclaimed water use improved polluted water's self-purification capacity --Evidenced by water quality factors and bacterial community structure
Shenqun An, Ying Song, Qiang Fu, Rong Qi, Zehao Wu, Feiyang Ge, Xiaoqian Lu, Wei An, Wenxuan Han
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Analysis of Microbial Communities in Membrane Biofilm Reactors Using a High-Density Microarray
Shilong Li, Liang Duan, Yang Zhao, Fu Gao, Slawomir W. Hermanowicz
Membranes.2023; 13(3): 324. CrossRef
Recent advances in understanding the ecology of the filamentous bacteria responsible for activated sludge bulking
T. Nittami, S. Batinovic
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Study on influence mechanism of biochar on soil nitrogen conversion
Pingnan Zhao, Shen Wang, Dong Liu, Hongxu Li, Song Han, Ming Li
Environmental Pollutants and Bioavailability.2022; 34(1): 419. CrossRef
Regulation of exogenous acyl homoserine lactones on sludge settling performance: Monitoring via ultrasonic time-domain reflectometry
Deyuan Dong, Qiuju Liu, Xiaoyu Wang, Haidong Hu, Bing Wu, Hongqiang Ren, Jinfeng Wang
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Evaluation of the Potential of Sewage Sludge Mycobiome to Degrade High Diclofenac and Bisphenol-A Concentrations
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Long-term effects of maize straw return and manure on the microbial community in cinnamon soil in Northern China using 16S rRNA sequencing
Zhiping Liu, Huaiping Zhou, Wenyan Xie, Zhenxing Yang, Qianqian Lv, Massimiliano Cardinale
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Effect of prolonged sludge retention times on the performance of membrane bioreactor and microbial community for leachate treatment under restricted aeration
Suda Ittisupornrat, Athit Phetrak, Suthida Theepharaksapan, Wuttichai Mhuantong, Tomohiro Tobino
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Anammox bacteria enrich naturally in suspended sludge system during partial nitrification of domestic sewage and contribute to nitrogen removal
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Fouling characterization and aeration performance recovery of fine-pore diffusers operated for 10 years in a full-scale wastewater treatment plant
Lu-Man Jiang, Liuyu Chen, Zhen Zhou, Dongqi Sun, Yunhui Li, Ming Zhang, Yuan Liu, Silu Du, Guang Chen, Jie Yao
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The seasonal changes of core bacterial community decide sewage purification in sub-plateau municipal sewage treatment plants
Xiao-Hu Kang, Yan Leng, Mafiana Macdonald O, Xiao-Ying Zeng, Shi-Weng Li
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Preliminary analysis ofChloroflexipopulations in full-scale UASB methanogenic reactors
P. Bovio, A. Cabezas, C. Etchebehere
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The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge
Lachlan B. M. Speirs, Daniel T. F. Rice, Steve Petrovski, Robert J. Seviour
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Seasonal bacterial community succession in four typical wastewater treatment plants: correlations between core microbes and process performance
Bo Zhang, Quanwei Yu, Guoqi Yan, Hubo Zhu, Xiang yang Xu, Liang Zhu
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Performance and microbial characteristics of biomass in a full-scale aerobic granular sludge wastewater treatment plant
Piotr Świątczak, Agnieszka Cydzik-Kwiatkowska
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Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis
Bo Zhang, Xiangyang Xu, Liang Zhu
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Quantification of Chloroflexi Eikelboom morphotype 1851 for prediction and control of bulking events in municipal activated sludge plants in Japan
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Performance and Microbial Diversity in a Low-Energy ANF-WDSRBC System for the Post-Treatment of Decentralized Domestic Wastewater
Juanhong Li, Xiwu Lu
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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.

Structural Analysis of the fcbABC Gene Cluster Responsible for Hydrolytic Dechlorination of 4-Chlorobenzoate from pJS1 Plasmid of Comamonas sp. P08: Jeong-Soon Lee , Kyoung Lee , Jong-Ok Ka , Jong-Chan Chae , Chi-Kyung Kim; J. Microbiol. 2003;41(2):89-94.

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Abstract PDF: Bacterial strain No. P08 isolated from wastewater at the Cheongju industrial complex was found to be capable of degrading 4-chlorobenzoate under aerobic condition. P08 was identified as Comamonas sp. from its cellular fatty acid composition and 16S rDNA sequence. The fcb genes, responsible for the hydrolytic dechlorination of 4-chlorobenzoate, were cloned from the plasmid pJS1 of Comamonas sp. P08. The fcb gene cluster of comamonas sp. P08 was organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC. This organization of the fcb genes was very similar to that of the fcb genes carried on the chromosomal DNA of Pseudomonas sp. DJ-12. However, it differed from the fcbA-fcbB-fcbC ordering of Arthrobacter sp. SU. The nucleotide sequences of the fcbABC genes of strain P08 showed 98% and 53% identities to those of Pseudomonas sp. DJ-12 and Arthrobacter sp. SU, respectively. This suggests that the fcb genes might have been derived from Pseudomonas sp. DJ-12 to form plasmid pJS1 in Comamonas sp. P08, or that the fcb genes in strain DJ-12 were transposed from Comamonas sp. P08 plasmid.

Cloning and Sequence Analysis of the hpaD Gene Responsible for Homoprotocatechuate 2,3-Dioxygenase from Pseudomonas sp. DJ-12: Sang-Mahn Lee , Jong-Chan Chae , Youngsoo Kim , Chi-Kyung Kim; J. Microbiol. 2001;39(4):334-337.

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Abstract PDF: The degradative pathway of homoprotocatechuate (HPC) is the bacterial route whereby 3,4-dihydroxyphenylacetic acid is catabolized to pyruvate and succinate by a series of sequential reactions. The HPC is catalized by homoprotocatechuate 2,3-dioxygenase (HPC-2,3O) to form 5-carboxymethyl-2-hydroxy-muco semialdehyde. In this study, the hpaD gene encoding HPC-2,3O was cloned from the chromosomal DNA of Pseudomonas sp. DJ-12 and its nucleotide sequence was analyzed. The open reding frame of hpaD gene was found to be composed of 864 nucleotide pairs and to encode a polypeptide with 287 amino acid residues. The deduced amino acid sequence of the HPC-2,3O from Pseudomonas sp. DJ-12 exhibited 60~64% homology with those of the corresponding enzymes from E. coli, Salmonella enterica, and Klebsiella pneumoniae.

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