Journal of Microbiology

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Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter: Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee; J. Microbiol. 2025;63(4):e2502002. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2502002

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Abstract PDF Supplementary Material: Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera “Candidatus Nitrosocosmicus” and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.

Research Article

Comprehensive genomic and functional analysis of Leuconostoc lactic acid bacteria in alcohol and acetaldehyde metabolism: Joo-Han Gwak, Yun Ji Choi, Hina Ayub, Min Kyeong Seol, Hongik Kim, Man-Young Jung; J. Microbiol. 2025;63(2):e2410026. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2410026

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Abstract PDF Supplementary Material: Alcohol consumption can lead to the accumulation of harmful metabolites, such as acetaldehyde, contributing to various adverse health effects, including hangovers and liver damage. This study presents a comprehensive genomic and functional analysis of Leuconostoc suionicum VITA-PB2, a lactic acid bacterial strain isolated from kimchi, to elucidate its role in enhancing alcohol and acetaldehyde metabolism. Genomic characterization revealed key genes encoding alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), providing insights into the metabolic capabilities of strain VITA-PB2. Phylogenomic analyses confirmed its taxonomic classification and genetic similarity to other Leuconostoc species. Functional validation through in vitro and in vivo experiments demonstrated superior ethanol and acetaldehyde decomposition abilities of strain VITA-PB2, with significant reductions in blood ethanol and acetaldehyde levels observed in rats administered with the strain. Further analysis indicated that while hepatic ADH activity did not significantly increase; however, ALDH expression was elevated. This suggests that the microbial ADH of strain VITA-PB2 contributed to ethanol breakdown, while both microbial and host ALDH facilitated acetaldehyde detoxification. These findings highlight the potential of strain VITA-PB2 as a functional probiotic for mitigating the toxic effects of alcohol consumption.

Journal Articles

Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica: Joo-Han Gwak , Samuel Imisi Awala , So-Jeong Kim , Sang-Hoon Lee , Eun-Jin Yang , Jisoo Park , Jinyoung Jung , Sung-Keun Rhee; J. Microbiol. 2023;61(11):967-980. Published online December 7, 2023; DOI: https://doi.org/10.1007/s12275-023-00090-0

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Abstract

Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the “Candidatus Nitrosomarinus”-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.

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Alleviated photoinhibition on nitrification in the Indian Sector of the Southern Ocean
Lingfang Fan, Min Chen, Zifei Yang, Minfang Zheng, Yusheng Qiu
Acta Oceanologica Sinica.2024; 43(7): 52. CrossRef

Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism: Man-Young Jung , So-Jeong Kim , Jong-Geol Kim , Heeji Hong , Joo-Han Gwak , Soo-Je Park , Yang-Hoon Kim , Sung-Keun Rhee; J. Microbiol. 2018;56(5):365-371. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7451-6

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Abstract

Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H+ and Na+ ions, respectively. Strain IRF9 harbored two different types of ATPases (Na+-dependent F-type ATPase and H+- dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions.

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Promoting effects and mechanisms of common iron oxides on corrosion of carbon steel induced by methanogenic microbiota
Jianping Wu, Weidong Zhang, Shanyu Xie, Zhaoshou Wang, Yuanpeng Wang
Journal of Environmental Chemical Engineering.2025; 13(2): 115769. CrossRef
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Siwen Hu, Dayong Zhao, Rujia He, Xiaojian Sun, Jin Zeng
Journal of Cleaner Production.2025; 501: 145295. CrossRef
Co-exposure of microplastics and polychlorinated biphenyls strongly influenced the cycling processes of typical biogenic elements in anoxic soil
Guangxue Xie, Qian Hou, Lianzhen Li, Yan Xu, Shaochong Liu, Xilin She
Journal of Hazardous Materials.2024; 465: 133277. CrossRef
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Kriti Sengupta, Siddhartha Pal
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Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China
Yue Zhan, Mengran Yang, Yu Zhang, Jian Yang, Weidong Wang, Lei Yan, Shuang Zhang
World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef
Maize straw biochar addition inhibited pentachlorophenol dechlorination by strengthening the predominant soil reduction processes in flooded soil
Min Zhu, Xiaofei Lv, Ashley E. Franks, Philip C. Brookes, Jianming Xu, Yan He
Journal of Hazardous Materials.2020; 386: 122002. CrossRef
New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era
Krisztián Laczi, Ágnes Erdeiné Kis, Árpád Szilágyi, Naila Bounedjoum, Attila Bodor, György Erik Vincze, Tamás Kovács, Gábor Rákhely, Katalin Perei
Frontiers in Microbiology.2020;[Epub] CrossRef
Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool
Manal F. Alqahtani, Suman Bajracharya, Krishna P. Katuri, Muhammad Ali, Ala’a Ragab, Grégoire Michoud, Daniele Daffonchio, Pascal E. Saikaly
Frontiers in Microbiology.2019;[Epub] CrossRef

Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings: Ui-Gi Min , So-Jeong Kim , Heeji Hong , Song-Gun Kim , Joo-Han Gwak , Man-Young Jung , Jong-Geol Kim , Jeong-Geol Na , Sung-Keun Rhee; J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6086-8

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Abstract

A strictly anaerobic bacterium, strain B5T, was isolated from sediment of an abandoned coal mine in Taebaek, Republic of Korea. Cells of strain B5T were non-spore-forming, straight, Gram-positive rods. The optimum pH and temperature for growth were pH 7.0 and 30°C, respectively, while the strain was able to grow within pH and temperature ranges of 5.5– 7.5 and 25–45°C, respectively. Growth of strain B5T was observed at NaCl concentrations of 0 to 6.0% (w/v) with an optimum at 3.0–4.0% (w/v). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown phospholipid and three unknown polar lipids. Strain B5T grew anaerobically by reducing nitrate, nitrite, ferric-citrate, ferric-nitrilotriacetate, elemental sulfur, thiosulfate, and anthraquinone- 2-sulfonate in the presence of proteinaceous compounds, organic acids, and carbohydrates as electron donors. The isolate was not able to grow by fermentation. Strain B5T did not grow under aerobic or microaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B5T is most closely related to the genus Tepidibacillus (T. fermentans STGHT; 96.3%) and Vulcanibacillus (V. modesticaldus BRT; 94.6%). The genomic DNA G+C content (36.9 mol%) of strain B5T was higher than those of T. fermentans STGHT (34.8 mol%) and V. modesticaldus BRT (34.5 mol%). Based on its phenotypic, chemotaxonomic, and phylogenetic properties, we describe a new species of a novel genus Calculibacillus, represented by strain B5T (=KCTC 15397T =JCM 19989T), for which we propose the name Calculibacillus koreensis gen. nov., sp. nov.

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Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives
Sharareh Harirchi, Taner Sar, Mohaddaseh Ramezani, Habibu Aliyu, Zahra Etemadifar, Seyed Ali Nojoumi, Fatemeh Yazdian, Mukesh Kumar Awasthi, Mohammad J. Taherzadeh
Microorganisms.2022; 10(12): 2355. 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
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Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Changsu Lee, Joseph Kwon, Jisu Kang, Jin-Kyu Rhee, Myeong Seon Jeong, Young-Do Nam, Seong Woon Roh
Gut Pathogens.2017;[Epub] CrossRef

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