Abiola C, Gwak JH, Lee UJ, Adigun AO, Rhee SK. Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter. J. Microbiol. 2025;63(4):e2502002. DOI: https://doi.org/10.71150/jm.2502002
Joo-Han Gwak, Adebisi Olabisi, Ui-Ju Lee, Christiana Abiola, Seongjun Lee, Hackwon Do, Yun Ji Choi, Jay-Jung Lee, Man-Young Jung, Nico Jehmlich, Martin von Bergen, Michael Wagner, Samuel Imisi Awala, Zhe-Xue Quan, Sung-Keun Rhee. Hypoosmolarity inhibits archaeal ammonia oxidation. bioRxiv 2025.07.07.663500; doi: https://doi.org/10.1101/2025.07.07.663500
Abiola, C., Gwak, J. H., Lee, U. J., Awala, S. I., Jung, M. Y., Park, W., & Rhee, S. K. (2024). Growth of soil ammonia-oxidizing archaea on air-exposed solid surface. ISME Communications 4(1), ycae129. DOI:10.1093/ismeco/ycae129
Awala, S.I., Gwak, JH., Kim, Y. et al. Nitrous oxide respiration in acidophilic methanotrophs. Nat Commun 15, 4226 (2024). https://doi.org/10.1038/s41467-024-48161-z
Seol-Hee Kim, Jong-Geol Kim, Man-Young Jung, So-Jeong Kim, Joo-Han Gwak, Woon-Jong Yu, Seong Woon Roh, Yang-Hoon Kim, Sung-Keun Rhee (2018); Ketobacter alkanivorans gen. nov., sp. nov., an n-alkane-degrading bacterium isolated from seawater, International Journal of Systematic and Evolutionary Microbiology doi: 10.1099/ijsem.0.002823
Man-Young Jung, Md. Arafat Islam, Joo-Han Gwak , Jong-Geol Kim , Sung-Keun Rhee (2018) Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil, International Journal of Systematic and Evolutionary Microbiology doi: 10.1099/ijsem.0.002926
Ngoc-Loi Nguyen, Woon-Jong Yu, Joo-Han Gwak, So-Jeong Kim, Soo-Je Park, Craig W. Herbold, Jong-Geol Kim, Man-Young Jung and Sung-Keun Rhee (2018), Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils, Front. Microbiol, doi: 10.3389/fmicb.2018.01982
Lee J, Shim D, Moon S, Kim H, Bae W, Kim K, Kim YH, Rhee SK, Hong CP, Hong SY, Lee YJ, Sung J, Ryu H.Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato. (2018). Plant Physiol Biochem. 2018 Jun;127:553-560. doi: 10.1016/j.plaphy.2018.04.031. Epub 2018 Apr 27.
Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX. Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox). (2018) Appl Environ Microbiol. 2018 Nov 30;84(24). pii: e01390-18. doi: 10.1128/AEM.01390-18. Print 2018 Dec 15.
Song GC, Im H, Jung J, Lee S, Jung MY, Rhee SK, Ryu CM. Plant growth-promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae.Environ Microbiol. 2018 Nov 20. doi: 10.1111/1462-2920.14486. [Epub ahead of print]
Kim SJ, Park SJ, Kim JG, Jung MY, Gwak JH, Rhee SK. Draft Genome Sequence of "Candidatus Izimaplasma sp." Strain ZiA1, Obtained from a Toluene-Degrading and Iron-Reducing Enrichment Culture.Microbiol Resour Announc. 2018 Aug 30;7(8). pii: e00861-18. doi: 10.1128/MRA.00861-18. eCollection 2018 Aug
Ok-Ja Si, Hye-Young Yang, Chung Yeon Hwang, So-Jeong Kim, Sun-Bin Choi, Jong-Geol Kim, Man-Young Jung, Song-Gun Kim, Seong Woon Roh, Sung-Keun (2016), Kiloniella antarctica sp. nov., isolated from a polynya of Amundsen Sea in Western Antarctic Sea, International Journal of Systematic and Evolutionary Microbiology 67: 2397-2402
Ngoc-Loi Nguyen,Woon-Jong Yu, Hye-Young Yang, Jong-Geol Kim, Man-Young Jung, Soo-Je Park, Seong-Woon Roh, Sung-Keun Rhee (2017) A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase, Journal of Microbiology, 55: 775
Jian-Gong Wang, Fei Xia, Jemaneh Zeleke, Bin Zou, Sung-Keun Rhee, Zhe-Xue Quan (2017); An improved protocol with a highly degenerate primer targeting copper-containing membrane-bound monooxygenase genes for community analysis of methane- and ammonia-oxidizing bacteria FEMS Microbiology Ecology, Vol 93: 3
Craig W. Herbold, Laura E. Lehtovirta‐Morley, Man‐Young Jung, Nico Jehmlich, Bela Hausmann, Ping Han, Alexander Loy, Michael Pester, Luis A. Sayavedra‐Soto, Sung‐Keun Rhee, James I. Prosser, Graeme W. Nicol, Michael Wagner, Cécile Gubry‐Rangin (2017); Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics, Environmental Microbiology 19(12), 4939–4952
Sundas Rani, Hyeon-Woo Koh, Sung-Keun Rhee, Hirotsugu Fujitani, Soo-Je Park (2017) Detection and Diversity of the Nitrite Oxidoreductase Alpha Subunit (nxrA) Gene of Nitrospina in Marine Sediments; Microbial ecology 73 1 111-122
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 (2016), Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings, Journal of Microbiology, 54,413.
Jong-Geol Kim, Soo-Je Park, Jaap S Sinninghe Damsté, Stefan Schouten, W Irene C Rijpstra, Man-Young Jung, So-Jeong Kim, Joo-Han Gwak, Heeji Hong, Ok-Ja Si, SangHoon Lee, Eugene L Madsen, Sung-Keun Rhee (2016) Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea, Proceedings of the National Academy of Sciences Jul 2016, 113 (28) 7888-7893; DOI:10.1073/pnas.1605501113
Man‐Young Jung, Jong‐Geol Kim, Jaap S. Sinninghe, Damsté W. Irene, C. Rijpstra Eugene, L. Madsen, So‐Jeong Kim, Heeji Hong, Ok‐Ja Si, Melina Kerou, Christa Schleper ,Sung‐Keun Rhee (2016), A hydrophobic ammonia‐oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar‐contaminated sediment, Environmental Microbiology Reports 8(6), 983–992
Sundas Rani, Hyeon-Woo Koh, Hongik Kim, Sung-Keun Rhee, Soo-Je Park (2016) Marinobacter salinus sp. nov., a moderately halophilic bacterium isolated from a tidal flat environment, International Journal of Systematic and Evolutionary Microbiology 67: 205-211
Heyon-Woo Koh, Sundas Rani, So-Jeong Kim, Eunyoung Moon, Seung Won Nam, Sung-Keun Rhee, Soo-Je Park (2016), Halomonas aestuarii sp. nov., a moderately halophilic bacterium isolated from a tidal flat, International Journal of Systematic and Evolutionary Microbiology 67: 4298-4303
Heeji Hong, So-Jeong Kim, Ui-Gi Min, Yong-Jae Lee, Song-Gun Kim, Seong Woon Roh, Jong-Geol Kim, Jeong-Geol Na, and Sung-Keun Rhee, (2015), Anaerosolibacter carboniphilus sp. nov., a strictly anaerobic iron-reducing bacterium isolated from a coal-contaminated soil, International journal of systematic and evolutionary microbiology, 65, 1480-1485.
Heeji Hong, So-Jeong Kim, Ui-Gi Min, Yong-Jae Lee, Song-Gun Kim, Man-Young Jung, Yong-Seok Seo, and Sung-Keun Rhee, (2015), Geosporobacter ferrireducens sp. nov., an anaerobic iron-reducing bacterium isolated from an oil-contaminated site, Antonie van Leeuwenhoek, 107, 971-77.
Joo-Han Gwak, So-Jeong Kim, Man-Young Jung, Jong-Geol Kim, Seong Woon Roh, Kyung June Yim, Yong-Jae Lee, Song-Gun Kim, Soo-Je Park, and Sung-Keun Rhee, (2015), Draconibacterium filum sp. nov., a new species of the genus of Draconibacterium from sediment of the east coast of the Korean Peninsula, Antonie van Leeuwenhoek, 107, 1049-56.
Ok-Ja Si, So-Jeong Kim, Man-Young Jung, Seon-Bin Choi, Jong-Geol Kim, Song-Gun Kim, Seong Woon Roh, SangHoon Lee, and Sung-Keun Rhee, (2015), Leeuwenhoekiella polynyae sp. nov., isolated from a polynya of Amundsen Sea in western Antarctica, International journal of systematic and evolutionary microbiology, 65, 1694-1699.
Seon-Bin Choi, Jong-Geol Kim, Man-Young Jung, So-Jeong Kim, Ui-Gi Min, Ok-Ja Si, Soo-Je Park, Chung Yeon Hwang, Jisoo Park, SangHoon Lee, and Sung-Keun Rhee, (2015), Cultivation and biochemical characterization of heterotrophic bacteria associated with phytoplankton bloom in the Amundsen Sea polynya, Antarctica, Deep Sea Research Part II: Topical Studies in Oceanography, Vol 123, 2016, 126-134.
Olga I. Nedashkovskaya, Andrey D. Kukhlevskiy, Natalia V. Zhukova, So-Jeong Kim, Sung-Keun Rhee, Valery V. Mikhailov (2015), Winogradskyella litoriviva sp. nov., isolated from coastal seawater, International Journal of Systematic and Evolutionary Microbiology 65: 3652-3657.
Hyeon-Woo Koh, Heeji Hong, Ui-Gi Min, Myung-Suk Kang, Song-Gun Kim, Jeong-Geol Na, Sung-Keun Rhee, Soo-Je Park (2015), Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater, International Journal of Systematic and Evolutionary Microbiology 65: 4574-4579, doi: 10.1099/ijsem.0.000614
14. In-Tae Cha, Kyung June Yim, Hye Seon Song, Hae-Won Lee, Dong-Wook Hyun, Kil-Nam Kim, Jong-Soon Choi, Daekyung Kim, Sung-Jae Lee, and Myung-Ji Seo, (2014), Halolamina rubra sp. nov., a haloarchaeon isolated from non-purified solar salt, Antonie van Leeuwenhoek, 105, 907-14.
13. In-Tae Cha, Kyung June Yim, Hye Seon Song, Hae-Won Lee, Dong-Wook Hyun, Kil-Nam Kim, Myung-Ji Seo, Daekyung Kim, Jong-Soon Choi, and Sung-Jae Lee, (2014), Halobellus rufus sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt, Antonie van Leeuwenhoek, 105, 925-32.
12. Man-Young Jung, Soo-Je Park, So-Jeong Kim, Jong-Geol Kim, Jaap S Sinninghe Damsté, Che Ok Jeon, and Sung-Keun Rhee, (2014), A mesophilic, autotrophic, ammonia-oxidizing archaeon of Thaumarchaeal Group I. 1a cultivated from a deep oligotrophic soil horizon, Applied and environmental microbiology, 80, 3645-55.
11. Man-Young Jung, Reinhard Well, Deullae Min, Anette Giesemann, Soo-Je Park, Jong-Geol Kim, So-Jeong Kim, and Sung-Keun Rhee, (2014), Isotopic signatures of N2O Produced by Ammonia-Oxidizing Archaea from soils, The ISME journal, 8, 1115-25.
10. Jong-Geol Kim, Soo-Je Park, Zhe-Xue Quan, Man-Young Jung, In-Tae Cha, So-Jeong Kim, Kyoung-Ho Kim, Eun-Jin Yang, Young-Nam Kim, and Sang-Hoon Lee, (2014), Unveiling Abundance and Distribution of Planktonic Bacteria and Archaea in a Polynya in Amundsen Sea, Antarctica, Environmental microbiology, 16, 1566-78.
9. So-Jeong Kim, Soo-Je Park, Man-Young Jung, Jong-Geol Kim, Eugene L Madsen, and Sung-Keun Rhee, (2014), An Uncultivated Nitrate-Reducing Member of the Genus Herminiimonas Degrades Toluene, Applied and environmental microbiology, 80, 3233-43.
8. So-Jeong Kim, Soo-Je Park, Man-Young Jung, Jong-Geol Kim, Ui-Gi Min, Hee-Ji Hong, and Sung-Keun Rhee, (2014), Draft genome sequence of an aromatic compound-degrading bacterium, Desulfobacula sp. Ts, belonging to the Deltaproteobacteria, FEMS microbiology letters, 360, 9-12.
7. So-Jeong Kim, Soo-Je Park, In-Tae Cha, Deullae Min, Jin-Seog Kim, Won-Hyung Chung, Jong-Chan Chae, Che Ok Jeon, and Sung-Keun Rhee, (2014), Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis, Environmental microbiology, 16, 189-204.
6. Olga I Nedashkovskaya, Larissa A Balabanova, Natalia V Zhukova, So-Jeong Kim, Irina Y Bakunina, and Sung-Keun Rhee, (2014), Flavobacterium Ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga, Archives of microbiology, 196, 745-52.
5. Soo-Je Park, Rohit Ghai, AB Martın-Cuadrado, F Rodrıguez-Valera, Won-Hyong Chung, K Kwon, Jung-Hyun Lee, Eugene L Madsen, and Sung-Keun Rhee, (2014), Genomes of two new Ammonia-Oxidizing Archaea enriched from deep marine sediments, PloS one, 9, e96449
4. Soo-Je Park, Jinu Kim, Jong-Soo Lee, Sung-Keun Rhee, and Hongik Kim, (2014), Characterization of the fecal microbiome in different swine groups by high-throughput sequencing, Anaerobe, 28, 157-62
3. Hye Seon Song, In-Tae Cha, Kyung June Yim, Hae-Won Lee, Dong-Wook Hyun, Sung-Jae Lee, Sung-Keun Rhee, Kil-Nam Kim, Daekyung Kim, and Jong-Soon Choi, (2014), Halapricum salinum gen. nov., sp. nov., an extremely halophilic archaeon isolated from non-purified solar salt, Antonie van Leeuwenhoek, 105, 979-86.
2. Kyung June Yim, In-Tae Cha, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Sung-Jae Lee, Young-Do Nam, Dong-Wook Hyun, Jin-Woo Bae, and Sung-Keun Rhee, (2014), Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood, Antonie van Leeuwenhoek, 105, 603-12.
1. Kyung June Yim, In-Tae Cha, Tae Woong Whon, Hae-Won Lee, Hye Seon Song, Kil-Nam Kim, Young-Do Nam, Sung-Jae Lee, Jin-Woo Bae, and Sung-Keun Rhee, (2014), Halococcus sediminicola sp. nov., an extremely halophilic archaeon isolated from a marine sediment, Antonie van Leeuwenhoek, 105, 73-79.