Journal of Microbiology

Journal Articles

Differences in seroprevalence between epicenter and non-epicenter areas of the COVID-19 outbreak in South Korea: Hye Won Jeong , Hyun-Ha Chang , Eun Ji Kim , Yu Kyung Kim , Se-Mi Kim , Eun-Ha Kim , Young-Il Kim , Mark Anthony B. Casel , Seong-Gyu Kim , Rare Rollon , Seung-Gyu Jang , Kwang-Min Yu , Hee-Sung Kim , Hee Sue Park , Su-Jin Park , Yong-Dae Kim , Eung-Gook Kim , Young Ki Choi; J. Microbiol. 2021;59(5):530-533. Published online April 28, 2021; DOI: https://doi.org/10.1007/s12275-021-1095-7

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To compare the standardized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence of high epicenter region with non-epicenter region, serological studies were performed with a total of 3,268 sera from Daegu City and 3,981 sera from Chungbuk Province. Indirect immunofluorescence assay (IFA) for SARS-CoV-2 IgG results showed a high seroprevalence rate in the Daegu City (epicenter) compared with a non-epicenter area (Chungbuk Province) (1.27% vs. 0.91%, P = 0.0358). It is noteworthy that the highest seroprevalence in Daegu City was found in elderly patients (70’s) whereas young adult patients (20’s) in Chungbuk Province showed the highest seroprevalence. Neutralizing antibody (NAb) titers were found in three samples from Daegu City (3/3, 268, 0.09%) while none of the samples from Chungbuk Province were NAb positive. These results demonstrated that even following the large outbreak, the seropositive rate of SARS-CoV-2 in the general population remained low in South Korea.

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Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
The Seroprevalence of SARS-CoV-2 in Children During Early COVID-19 Pandemic in Korea: A Nationwide, Population-Based Study
Jin Lee, Young June Choe, Dohsik Minn, Jong-Hyun Kim
Journal of Korean Medical Science.2022;[Epub] CrossRef

Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment: Ting-Ting Ren , Chun-Zhi Jin , Feng-Jie Jin , Taihua Li , Chang-Jin Kim , Hee-Mock Oh , Hyung-Gwan Lee , Long Jin; J. Microbiol. 2018;56(7):467-471. Published online June 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7567-8

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Abstract

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium, designated strain CHu64- 6-1T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17-m in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the new isolate in the class Sphingobacteriia, and the isolate is notably most closely related to Flavihumibacter sediminis CJ663T (98.1% similarity), Flavihumibacter solisilvae 3-3T (97.8%), Flavihumibacter petaseus T41T (97.5%), Flavihumibacter cheonanensis WS16T (97.4%), and Flavihumibacter stibioxidans YS-17T (97.2%). The cells of strain CHu64-6-1T formed yellow colonies on R2A agar and contained MK-7 as the only menaquinone, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified aminolipids as the major polar lipids, and C15:0 iso, C17:0 iso 3-OH, C15:1 iso G, and C16:1 ω5c as the major fatty acids (> 5%). The DNA G + C content of the genome was determined to be 46.5 mol%. The DNA-DNA hybridization values of strain CHu64-6-1T with F. sediminis CJ663T, F. solisilvae 3-3T, F. petaseus T41T, F. cheonanensis WS16T, and F. stibioxidans YS-17T were 12.4–33.2%. Based on the combined genotypic and phenotypic data, we propose that strain CHu64-6-1T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter profundi sp. nov. is proposed. The type strain is CHu64-6-1T (= KCTC 62290T = CCTCC AB 2018060T).

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Flavihumibacter fluminis sp. nov., a novel thermotolerant bacterium isolated from river silt
Bai Guo, Weidong Mu, Sidi Mao, Shucheng Li, Shaomei Yang, Aijv Liu, Shuzhen Wei, Xiuyun Li, Feng Sang, Hongkuan Deng, Yuling Dong, Hongliang Liu, Zhiwei Chen
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Lacibacter sediminis sp. nov., isolated from contaminated freshwater sediment
Ye Zhuo, Chun-Zhi Jin, Feng-Jie Jin, Hee-Mock Oh, Hyung-Gwan Lee, Taihua Li, Long Jin
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Flavihumibacter fluminis sp. nov. and Flavihumibacter rivuli sp. nov., isolated from a freshwater stream
Miri S. Park, Hyeonuk Sa, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2022; 60(8): 806. CrossRef
Responses of bacterial communities and organic matter degradation in surface sediment to Macrobrachium nipponense bioturbation
Yiran Hou, Bing Li, Gongcheng Feng, Chengfeng Zhang, Jie He, Haidong Li, Jian Zhu
Science of The Total Environment.2021; 759: 143534. CrossRef
Description of desferrioxamine-producing bacterium Chitinophaga agrisoli sp. nov., isolated from soil
Chun-Zhi Jin, Long Jin, Dong Hyo Kang, Min-Jiao Liu, Jong Min Lee, Dong-Jin Park, Chang-Jin Kim
Antonie van Leeuwenhoek.2021; 114(6): 741. CrossRef
Reactivation of Frozen Stored Microalgal-Bacterial Granular Sludge under Aeration and Non-Aeration Conditions
Yao Shen, Lin Zhu, Bin Ji, Siqi Fan, Yabin Xiao, Yingqun Ma
Water.2021; 13(14): 1974. CrossRef
Positive effects of zeolite powder on aerobic granulation: Nitrogen and phosphorus removal and insights into the interaction mechanisms
Huihua Lin, Rui Ma, Junhao Lin, Shichang Sun, Xiangli Liu, Peixin Zhang
Environmental Research.2020; 191: 110098. CrossRef
Caulobacter soli sp. nov., isolated from soil sampled at Jiri Mountain, Republic of Korea
Yuanyuan Yang, Chun-Zhi Jin, Feng-Jie Jin, Taihua Li, Jong-Min Lee, Chang-Jin Kim, Hyung-Gwan Lee, Long Jin
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4158. CrossRef
Lysobacter profundi sp. nov., isolated from freshwater sediment and reclassification of Lysobacter panaciterrae as Luteimonas panaciterrae comb. nov.
Chun-Zhi Jin, Xiuli Song, Yun Ju Sung, Feng-Jie Jin, Taihua Li, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
International Journal of Systematic and Evolutionary Microbiology .2020; 70(6): 3878. CrossRef
Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment
Ye Zhuo, Chun-Zhi Jin, Feng-Jie Jin, Taihua Li, Dong Hyo Kang, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin
Antonie van Leeuwenhoek.2020; 113(3): 365. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments: Shiling Zheng , Bingchen Wang , Fanghua Liu , Oumei Wang; J. Microbiol. 2017;55(11):862-870. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7104-1

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Abstract

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNAbased terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The
results
also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

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Processing pathways of organic matter under methanogenic conditions and its influence on arsenic mobilization in aquifers
Xiaofang Yuan, Yamin Deng, Yao Du, Jiangkai Xue, Kunfu Pi, Yijun Yang, Yuxiao Xu, Xianjun Xie, Yanxin Wang
Journal of Hydrology.2025; 647: 132367. CrossRef
Fermentative iron reduction buffers acidification and promotes microbial metabolism in marine sediments
Yuechao Zhang, Qinqin Hao, Oumei Wang, Xiao-Hua Zhang, Fanghua Liu
Journal of Environmental Chemical Engineering.2023; 11(5): 110922. CrossRef
Biogenic Fe Incorporation into Anaerobic Granular Sludge Assisted by Shewanella oneidensis MR-1 Enhanced Interspecies Electron Transfer and Methane Production
Meihui Zhuo, Xiangchun Quan, Zhiqi Gao, Ruoyu Yin, Yanping Quan
ACS Sustainable Chemistry & Engineering.2023; 11(7): 3001. CrossRef
Assessing the enhanced reduction effect with the addition of sulfate based P inactivating material during algal bloom sedimentation
Xin Liu, Xuan Sun, Rui Liu, Leilei Bai, Peixin Cui, Huacheng Xu, Changhui Wang
Chemosphere.2022; 300: 134656. CrossRef
Complete Genome Sequence of Methanobacterium electrotrophus Strain YSL, Isolated from Coastal Riverine Sediments
Shiling Zheng, Fanghua Liu, Frank J. Stewart
Microbiology Resource Announcements.2021;[Epub] CrossRef
The differences in the corrosion product compositions of Methanogen-induced microbiologically influenced corrosion (Mi-MIC) between static and dynamic growth conditions
Biwen Annie An, Eric Deland, Oded Sobol, Jizheng Yao, Torben Lund Skovhus, Andrea Koerdt
Corrosion Science.2021; 180: 109179. CrossRef
Organic matter stabilized Fe in drinking water treatment residue with implications for environmental remediation
Changhui Wang, Zhanling Wang, Huacheng Xu, Leilei Bai, Cheng Liu, Helong Jiang, Peixin Cui
Water Research.2021; 189: 116688. CrossRef
Methanobacterium Capable of Direct Interspecies Electron Transfer
Shiling Zheng, Fanghua Liu, Bingchen Wang, Yuechao Zhang, Derek R. Lovley
Environmental Science & Technology.2020; 54(23): 15347. CrossRef
Formation of Zerovalent Iron in Iron-Reducing Cultures of Methanosarcina barkeri
Haitao Shang, Mirna Daye, Orit Sivan, Caue S. Borlina, Nobumichi Tamura, Benjamin P. Weiss, Tanja Bosak
Environmental Science & Technology.2020; 54(12): 7354. CrossRef
Tackling antibiotic inhibition in anaerobic digestion: The roles of Fe3+ and Fe3O4 on process performance and volatile fatty acids utilization pattern
Fetra J. Andriamanohiarisoamanana, Ikko Ihara, Gen Yoshida, Kazutaka Umetsu
Bioresource Technology Reports.2020; 11: 100460. CrossRef
A potential contribution of a Fe(III)-rich red clay horizon to methane release: Biogenetic magnetite-mediated methanogenesis
Leilei Xiao, Wenchao Wei, Min Luo, Hengduo Xu, Dawei Feng, Jiafeng Yu, Jiafang Huang, Fanghua Liu
CATENA.2019; 181: 104081. CrossRef
Methanogenic Activity and Microbial Community Structure in Response to Different Mineralization Pathways of Ferrihydrite in Paddy Soil
Li Zhuang, Ziyang Tang, Zhen Yu, Jian Li, Jia Tang
Frontiers in Earth Science.2019;[Epub] CrossRef
A new insight into the strategy for methane production affected by conductive carbon cloth in wetland soil: Beneficial to acetoclastic methanogenesis instead of CO2 reduction
Jiajia Li, Leilei Xiao, Shiling Zheng, Yuechao Zhang, Min Luo, Chuan Tong, Hengduo Xu, Yang Tan, Juan Liu, Oumei Wang, Fanghua Liu
Science of The Total Environment.2018; 643: 1024. CrossRef

Research Support, Non-U.S. Gov'ts

Microbial Communities in Semi-consolidated Carbonate Sediments of the Southwest Indian Ridge: Jiwei Li , Xiaotong Peng , Huaiyang Zhou , Jiangtao Li , Zhilei Sun , Shun Chen; J. Microbiol. 2014;52(2):111-119. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3133-1

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Abstract

White semi-consolidated carbonate sediments attached to black ferromanganese oxide films were collected approximately 50 km west of a newly discovered hydrothermal field near the Southwest Indian Ridge (SWIR). The biodiversity of the prokaryotic communities within the field was examined using clone library-based culture-independent analysis of the exterior black oxides and the interior white carbonates. Subsequent 16S rRNA gene analysis suggested that Gammaproteobacteria, Acidobacteria, and Thaumarchaeota members dominated the bacterial and archaeal clone libraries. To further characterize the metabolic processes within the microbial community, analyses of the amoA (coding the alpha subunit of the ammonia monooxygenase for Archaea) and aprA (coding the alpha subunit of the dissimilatory adenosine-5'-phosphosulfate reductase for the sulfate-reducing and sulfur-oxidizing prokaryotes) functional genes were conducted. The functional gene analysis results suggested that Thaumarchaeota and Alphaproteobacteria members were the potential players that participated in N and S cycles in this marine carbonate sedimentary environment. This paper is the first to describe the microbial communities and their potential metabolic pathways within the semi-consolidated carbonate sediments of the SWIR.

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An insight into the prokaryotic diversity from a polymetallic nodule-rich region in the Central Indian Ocean Basin using next generation sequencing approach
Shruti Shah, Samir R. Damare, Maria Brenda Luzia Mascarenhas-Pereira, Jayesh Patil, Sneha Parab, Sushil Nair, Arpita Ghosh
Frontiers in Microbiology.2024;[Epub] CrossRef
Biogeography and potential ecological functions of prokaryotes in the hydrothermal and non-hydrothermal field sediments of the Indian Ocean Ridges
Jing Huang, Ping Chen, Yaxin Zhu, Jian Wang, Lei Song, Xiqiu Han, Ying Huang
Frontiers in Marine Science.2023;[Epub] CrossRef
Spatiotemporal dynamics of high and low nucleic acid-content bacterial communities in Chinese coastal seawater: assembly process, co-occurrence relationship and the ecological functions
Wei Hu, Ningning Zheng, Yadi Zhang, Mark Bartlam, Yingying Wang
Frontiers in Microbiology.2023;[Epub] CrossRef
Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India
Himadri Bose, Rajendra Prasad Sahu, Pinaki Sar
Science of The Total Environment.2022; 841: 156486. CrossRef
Microbial diversity and community structure in deep-sea sediments of South Indian Ocean
Daochen Zhu, Sivasamy Sethupathy, Lu Gao, Muhammad Zohaib Nawaz, Weimin Zhang, Jianxiong Jiang, Jianzhong Sun
Environmental Science and Pollution Research.2022; 29(30): 45793. CrossRef
Spatial patterns and co-occurrence networks of microbial communities related to environmental heterogeneity in deep-sea surface sediments around Yap Trench, Western Pacific Ocean
Chenru Zhang, Qian Liu, Xianrong Li, Min Wang, Xiaoshou Liu, Jinpeng Yang, Jishang Xu, Yong Jiang
Science of The Total Environment.2021; 759: 143799. CrossRef
Bacterial and Fungal Diversity in Sediment and Water Column From the Abyssal Regions of the Indian Ocean
Natasha Maria Barnes, Samir R. Damare, Belle Damodara Shenoy
Frontiers in Marine Science.2021;[Epub] CrossRef
High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge
Beiyu Hu, Bingxue Xu, Juanli Yun, Jian Wang, Bingliang Xie, Caiming Li, Yanghuan Yu, Ying Lan, Yaxin Zhu, Xin Dai, Ying Huang, Li Huang, Jianzhang Pan, Wenbin Du
Lab on a Chip.2020; 20(2): 363. CrossRef
Polyphasic approach revealed complex bacterial community structure and function in deep sea sediment of ultra-slow spreading Southwest Indian Ridge
Rupesh Kumar Sinha, K.P. Krishnan, Femi Anna Thomas, M.B. Binish, Mahesh Mohan, P. John Kurian
Ecological Indicators.2019; 96: 40. CrossRef
Macrofaunal burrowing enhances deep-sea carbonate lithification on the Southwest Indian Ridge
Hengchao Xu, Xiaotong Peng, Shun Chen, Jiwei Li, Shamik Dasgupta, Kaiwen Ta, Mengran Du
Biogeosciences.2018; 15(21): 6387. CrossRef
Lipid Biomarkers Reveal Microbial Communities in Hydrothermal Chimney Structures from the 49.6°E Hydrothermal Vent Field at the Southwest Indian Ocean Ridge
Jijiang Lei, Fengyou Chu, Xiaoguo Yu, Xiaohu Li, Chunhui Tao
Geomicrobiology Journal.2017; 34(6): 557. CrossRef
Fungal communities from the calcareous deep-sea sediments in the Southwest India Ridge revealed by Illumina sequencing technology
Likui Zhang, Manyu Kang, Yangchao Huang, Lixiang Yang
World Journal of Microbiology and Biotechnology.2016;[Epub] CrossRef
Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge
Likui Zhang, Manyu Kang, Jiajun Xu, Jian Xu, Yinjie Shuai, Xiaojian Zhou, Zhihui Yang, Kesen Ma
Scientific Reports.2016;[Epub] CrossRef
Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge
Ping Chen, Limin Zhang, Xiaoxuan Guo, Xin Dai, Li Liu, Lijun Xi, Jian Wang, Lei Song, Yuezhu Wang, Yaxin Zhu, Li Huang, Ying Huang
Frontiers in Microbiology.2016;[Epub] CrossRef

Microbial Community Response to a Simulated Hydrocarbon Spill in Mangrove Sediments: Rodrigo Gouvêa Taketani , Natália Oliveira Franco , Alexandre Soares Rosado , Jan Dirk van Elsas; J. Microbiol. 2010;48(1):7-15. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0147-1

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Abstract: In this study, we examined the hypothesis that the microbial communities in mangrove sediments with different chemical and historical characteristics respond differently to the disturbance of a hydrocarbon spill. Two different mangrove sediments were sampled, one close to an oil refinery that had suffered a recent oil spill and another that had not been in contact with oil. Based on the sampled sediment, two sets of mesocosms were built, and oil was added to one of them. They were subjected to mimicked mangrove conditions and monitored for 75 days. Archaeal and bacterial communities were evaluated through PCRDGGE. Both communities showed the emergence of small numbers of novel bands in response to oil pollution. 16S rRNA gene clone libraries were constructed from both mesocosms before the addition of oil and at day 75 after oil addition. LIBSHUFF analysis showed that both mangrove-based mesocosms contained similar communities at the start of the experiment and that they were different from the initial one, as well as from each other, after 75 days. These results hint at a role of environmental history that is not obvious from community diversity indicators, but is apparent from the response to the applied stress.

Effect of Moisture Content on Reductive Dechlorination of Polychlorinated Biphenyls and Population Dynamics of Dechlorinating Microorganisms: O-Seob Kwon , Young Eui Kim , Jong Gyu Park; J. Microbiol. 2001;39(3):195-201.

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Abstract: The effect of moisture content on the reductive dechlorination of polychlorinated biphenyls and population dynamics of dechlorinating microorganisms was investigated in sediments spiked with Aroclor 1248. In sediment slurry with an overlying water layer, dechlorination ensued after a 4-week lag period and reduced the average number of chlorines per biphenyl from 3.91 to 3.15 after 48 weeks. In the sediments of reduced moisture content, however, dechlorination occurred after a lag period of 12 weeks and decreased the average number of chlorines per biphenyl to only 3.62, and the dechlorination rate was also slower. When the population size of dechlorinators, methanogens, and sulfate-reducing bacteria was determined by the most probable number techniques, however, no difference was found between the slurry and the low-moisture sediments, except for methanogens. The growth of dechlorinating populations coincided with the end of the lag period and they then increased by 3 orders of magnitude in two conditions. Specific growth rate of dechlorinators showed little difference between the slurry and the low-moisture sediments; however, growth yield was high in the sediments of reduced moisture content. The reduction of sediment moisture decreased the dechlorination rate and extent of PCBs but did not inhibit the growth of PCB dechlorinators.

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