- Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica
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Joo-Han Gwak , Samuel Imisi Awala , So-Jeong Kim , Sang-Hoon Lee , Eun-Jin Yang , Jisoo Park , Jinyoung Jung , Sung-Keun Rhee
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J. Microbiol. 2023;61(11):967-980. Published online December 7, 2023
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DOI: https://doi.org/10.1007/s12275-023-00090-0
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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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Citations
Citations to this article as recorded by  - Bulk metagenomics and machine learning unravels nitrogen metabolism patterns in extreme-temperature marine environments
Zheng Guo, Yong-Guang Li, Xiao-Lin Liu, Zhao-Jie Teng, Qi-Long Qin, Qian-Qian Cha, Zhi-Bin Wang, Shou-Qing Ni
Bioresource Technology.2026; 441: 133551. CrossRef - 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
- Ammonia-oxidizing archaea in biological interactions
-
Jong-Geol Kim , Khaled S. Gazi , Samuel Imisi Awala , Man-Young Jung , Sung-Keun Rhee
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J. Microbiol. 2021;59(3):298-310. Published online February 23, 2021
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DOI: https://doi.org/10.1007/s12275-021-1005-z
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357
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16
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The third domain Archaea was known to thrive in extreme or
anoxic environments based on cultivation studies. Recent metagenomics-
based approaches revealed a widespread abundance
of archaea, including ammonia-oxidizing archaea (AOA)
of Thaumarchaeota in non-extreme and oxic environments.
AOA alter nitrogen species availability by mediating the first
step of chemolithoautotrophic nitrification, ammonia oxidation
to nitrite, and are important primary producers in ecosystems,
which affects the distribution and activity of other
organisms in ecosystems. Thus, information on the interactions
of AOA with other cohabiting organisms is a crucial
element in understanding nitrogen and carbon cycles in ecosystems
as well as the functioning of whole ecosystems. AOA
are self-nourishing, and thus interactions of AOA with other
organisms can often be indirect and broad. Besides, there are
possibilities of specific and obligate interactions. Mechanisms
of interaction are often not clearly identified but only inferred
due to limited knowledge on the interaction factors analyzed
by current technologies. Here, we overviewed different types
of AOA interactions with other cohabiting organisms, which
contribute to understanding AOA functions in ecosystems.
-
Citations
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Environmental Science & Technology.2025; 59(18): 8922. CrossRef - Identification of structural and regulatory cell-shape determinants in Haloferax volcanii
Heather Schiller, Yirui Hong, Joshua Kouassi, Theopi Rados, Jasmin Kwak, Anthony DiLucido, Daniel Safer, Anita Marchfelder, Friedhelm Pfeiffer, Alexandre Bisson, Stefan Schulze, Mechthild Pohlschroder
Nature Communications.2024;[Epub] CrossRef - Nitrogen cycling process and application in different prawn culture modes
Zhao Chen, Jian Li, Qianqian Zhai, Zhiqiang Chang, Jitao Li
Reviews in Aquaculture.2024; 16(4): 1580. CrossRef - Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge
Zhaohui Zhang, Lin Bo, Shang Wang, Chenyu Li, Xi Zhang, Bin Xue, Xiaobo Yang, Xinxin He, Zhiqiang Shen, Zhigang Qiu, Chen Zhao, Jingfeng Wang
Environmental Research.2024; 242: 117739. CrossRef - Distinct mechanisms drive plant-nitrifier interactions in topsoil and subsoil
Di Liang, Niuniu Ji, Angela Kent, Wendy H. Yang
Soil Biology and Biochemistry.2024; 192: 109370. CrossRef - Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef - Response of soil microbial community structure and function to the sewage leakage: A case study of a 25-year-old cesspool
Xiaocheng Wei, Jiayin Liang, Tianyang Ning, Chunxue Zhang, Jiarui Wang, Lu Tan, Feng Shen
Chemosphere.2024; 363: 142753. CrossRef - Hiding in plain sight: The discovery of complete genomes of 11 hypothetical spindle‐shaped viruses that putatively infect mesophilic ammonia‐oxidizing archaea
Yimin Ni, Tianqi Xu, Shuling Yan, Lanming Chen, Yongjie Wang
Environmental Microbiology Reports.2024;[Epub] CrossRef - Inulin from halophilic archaeon Haloarcula: Production, chemical characterization, biological, and technological properties
Alejandra Aragón-León, Lorena Moreno-Vilet, Marisela González-Ávila, Pedro Martín Mondragón-Cortez, Guilherme Lanzi Sassaki, Raúl Balam Martínez-Pérez, Rosa María Camacho-Ruíz
Carbohydrate Polymers.2023; 321: 121333. CrossRef - Uncovering the Prokaryotic Diversity of the Bathyal Waters above the Kuril–Kamchatka Trench
Susanna Gorrasi, Angelika Brandt, Francesca Pittino, Andrea Franzetti, Marcella Pasqualetti, Barbara Muñoz-Palazon, Giorgia Novello, Massimiliano Fenice
Journal of Marine Science and Engineering.2023; 11(11): 2145. CrossRef - Nitrous Oxide Distributions in the Oxygenated Water Column of the Sargasso Sea
Annaliese C. S. Meyer, Jay T. Cullen, Damian S. Grundle
Atmosphere-Ocean.2023; 61(3): 173. CrossRef - An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México
Jesús Barrera-Rojas, Kelly Joel Gurubel-Tun, Emmanuel Ríos-Castro, María Cristina López-Méndez, Belkis Sulbarán-Rangel
Microorganisms.2023; 11(7): 1640. CrossRef - Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions
Choaro D. Dithugoe, Oliver K. I. Bezuidt, Emma L. Cavan, William P. Froneman, Sandy J. Thomalla, Thulani P. Makhalanyane, Barbara J. Campbell
mSphere.2023;[Epub] CrossRef - Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench
Susanna Gorrasi, Andrea Franzetti, Angelika Brandt, Ulrike Minzlaff, Marcella Pasqualetti, Massimiliano Fenice
Environmental Microbiome.2023;[Epub] CrossRef - Examining the Interaction Between Free‐Living Bacteria and Iron in the Global Ocean
Anh Le‐Duy Pham, Olivier Aumont, Lavenia Ratnarajah, Alessandro Tagliabue
Global Biogeochemical Cycles.2022;[Epub] CrossRef - Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. 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
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J. Microbiol. 2018;56(5):365-371. Published online May 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7451-6
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372
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8
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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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Citations
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Jianping Wu, Weidong Zhang, Shanyu Xie, Zhaoshou Wang, Yuanpeng Wang
Journal of Environmental Chemical Engineering.2025; 13(2): 115769. CrossRef - Enclosure restoration regulates epiphytic microbial communities involved in carbon sequestration in a restored urban lake: A new insight from the stability of dissolved organic matter
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 - A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions
Kriti Sengupta, Siddhartha Pal
Environmental Science and Pollution Research.2021; 28(30): 40288. CrossRef - 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
- A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase
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Ngoc-Loi Nguyen , Woon-Jong Yu , Hye-Young Yang , Jong-Geol Kim , Man-Young Jung , Soo-Je Park , Seong-Woon Roh , Sung-Keun Rhee
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J. Microbiol. 2017;55(10):775-782. Published online September 28, 2017
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DOI: https://doi.org/10.1007/s12275-017-7317-3
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385
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15
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Aerobic methane oxidation is a key process in the global carbon
cycle that acts as a major sink of methane. In this study,
we describe a novel methanotroph designated EMGL16-1
that was isolated from a freshwater lake using the floating
filter culture technique. Based on a phylogenetic analysis of
16S rRNA gene sequences, the isolate was found to be closely
related to the genus Methylomonas in the family Methylococcaceae
of the class Gammaproteobacteria with 94.2–97.4%
16S rRNA gene similarity to Methylomonas type strains. Comparison
of chemotaxonomic and physiological properties
further suggested that strain EMGL16-1 was taxonomically
distinct from other species in the genus Methylomonas. The
isolate was versatile in utilizing nitrogen sources such as molecular
nitrogen, nitrate, nitrite, urea, and ammonium. The
genes coding for subunit of the particulate form methane
monooxygenase (pmoA), soluble methane monooxygenase
(mmoX), and methanol dehydrogenase (mxaF) were detected
in strain EMGL16-1. Phylogenetic analysis of mmoX indicated
that mmoX of strain EMGL16-1 is distinct from those
of other strains in the genus Methylomonas. This isolate probably
represents a novel species in the genus. Our study provides
new insights into the diversity of species in the genus
Methylomonas and their environmental adaptations.
-
Citations
Citations to this article as recorded by - Diving into freshwater microbial metabolites: Pioneering research and future prospects
Saloni Sachdeva, Indira P Sarethy
International Journal of Environmental Health Research.2025; 35(2): 282. CrossRef - Recent findings in methanotrophs: genetics, molecular ecology, and biopotential
Fatemeh Ahmadi, Maximilian Lackner
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef - Direct biological fixation provides a freshwater sink for N2O
Yueyue Si, Yizhu Zhu, Ian Sanders, Dorothee B. Kinkel, Kevin J. Purdy, Mark Trimmer
Nature Communications.2023;[Epub] CrossRef -
Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov.
Samuel Imisi Awala, Joo-Han Gwak, Yongman Kim, Chanmee Seo, Andrea Strazzulli, Song-Gun Kim, Sung-Keun Rhee
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef -
Methylococcus mesophilus sp. nov., the first non-thermotolerant methanotroph of the genus Methylococcus, from a rice field
Samuel Imisi Awala, Yongman Kim, Joo-Han Gwak, Chanmee Seo, Seungki Lee, Minseo Kang, Sung-Keun Rhee
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Valorization of Small Alkanes by Biocatalytic Oxyfunctionalization
Durga Mahor, Zhiqi Cong, Martin J. Weissenborn, Frank Hollmann, Wuyuan Zhang
ChemSusChem.2022;[Epub] CrossRef - Assessment of diversity and composition of bacterial community in sludge treatment reed bed systems
Przemysław Kowal, Slawomir Ciesielski, Martyna Godzieba, Karolina Fitobór, Magdalena Gajewska, Katarzyna Kołecka
Science of The Total Environment.2021; 756: 144060. CrossRef - Novel methanotrophic and methanogenic bacterial communities from diverse ecosystems and their impact on environment
Manish Kumar, Ajar Nath Yadav, Raghvendra Saxena, Pankaj Kumar Rai, Diby Paul, Rajesh Singh Tomar
Biocatalysis and Agricultural Biotechnology.2021; 33: 102005. CrossRef - Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea
Samuel Imisi Awala, Lorraine Araza Bellosillo, Joo-Han Gwak, Ngoc-Loi Nguyen, So-Jeong Kim, Byoung-Hee Lee, Sung-Keun Rhee
International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5520. CrossRef - Complete Genome Sequence of Methylomonas koyamae LM6, a Potential Aerobic Methanotroph
Dae-Hee Lee, Lavanya Madhavaraj, Gui Hwan Han, Hyewon Lee, Seung-Goo Lee, Si Wouk Kim, J. Cameron Thrash
Microbiology Resource Announcements.2020;[Epub] CrossRef - Improved methane elimination by methane-oxidizing bacteria immobilized on modified oil shale semicoke
Meng-Ting Sun, Zhi-Man Yang, Xiao-Lei Fan, Fei Wang, Rong-Bo Guo, Dong-Yan Xu
Science of The Total Environment.2019; 655: 915. CrossRef - Acclimated methanotrophic consortia for aerobic co-metabolism of trichloroethene with methane
Chun-Chin Wang, Chen-Huei Li, Chu-Fang Yang
International Biodeterioration & Biodegradation.2019; 142: 52. CrossRef - Complete Genome Sequence of Methylomonas denitrificans Strain FJG1, an Obligate Aerobic Methanotroph That Can Couple Methane Oxidation with Denitrification
Fabini D. Orata, K. Dimitri Kits, Lisa Y. Stein
Genome Announcements.2018;[Epub] CrossRef - Mitigating Methane: Emerging Technologies To Combat Climate Change’s Second Leading Contributor
Chris Pratt, Kevin Tate
Environmental Science & Technology.2018; 52(11): 6084. CrossRef - Factors affecting the selection of PHB accumulating methanotrophs from waste activated sludge while utilizing ammonium as their nitrogen source
Ahmed Fergala, Ahmed AlSayed, Ahmed Eldyasti
Journal of Chemical Technology & Biotechnology.2018; 93(5): 1359. CrossRef
- Calculibacillus koreensis gen. nov., sp. nov., an anaerobic Fe(III)-reducing bacterium isolated from sediment of mine tailings
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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
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J. Microbiol. 2016;54(6):413-419. Published online May 27, 2016
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DOI: https://doi.org/10.1007/s12275-016-6086-8
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381
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3
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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.
-
Citations
Citations to this article as recorded by - 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 - Complete genome sequence of Clostridium perfringens CBA7123 isolated from a faecal sample from Korea
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
- NOTE] 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
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J. Microbiol. 2012;50(4):684-688. Published online July 21, 2012
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DOI: https://doi.org/10.1007/s12275-012-2115-4
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187
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3
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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.
- Molecular Analysis of Spatial Variation of Iron-Reducing Bacteria in Riverine Alluvial Aquifers of the Mankyeong River
-
So-Jeong Kim , Dong-Chan Koh , Soo-Je Park , In-Tae Cha , Joong-Wook Park , Jong-Hwa Na , Yul Roh , Kyung-Seok Ko , Kangjoo Kim , Sung-Keun Rhee
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J. Microbiol. 2012;50(2):207-217. Published online April 27, 2012
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DOI: https://doi.org/10.1007/s12275-012-1342-z
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267
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28
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Abstract
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Alluvial aquifers are one of the mainwater resources in
many countries. Iron reduction in alluvial aquifers is often
a major anaerobic process involved in bioremediation or
causing problems, including the release of As trapped in
Fe(III) oxide. We investigated the distribution of potential
iron-reducing bacteria (IRB) in riverine alluvial aquifers
(B1, B3, and B6 sites) at the Mankyeong River, Republic of
Korea. Inactive iron reduction zones, the diversity and abundance
of IRB can be examined using a clone library and
quantitative PCR analysis of 16S rRNA genes. Geobacter
spp. are potential IRB in the iron-reducing zone at the B6
(9 m) site, where high Fe(II) and arsenic (As) concentrations
were observed. At the B3 (16 m) site, where low iron reduction
activity was predicted, a dominant clone (10.6%) was
99% identical in 16S rRNA gene sequence with Rhodoferax
ferrireducens. Although a major clone belonging to Clostridium
spp. was found, possible IRB candidates could not be
unambiguously determined at the B1 (18 m) site. Acanonical
correspondence analysis demonstrated that, among potential
IRB, only the Geobacteraceae were well correlated with Fe(II)
and As concentrations. Our results indicate high environmental
heterogeneity, and thus high spatial variability, in
thedistribution of potential IRB in the riverine alluvial
aquifersnear the Mankyeong River.
-
Citations
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Guangxue Xie, Qian Hou, Lianzhen Li, Yan Xu, Shaochong Liu, Xilin She
Journal of Hazardous Materials.2024; 465: 133277. CrossRef - Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats
Yongbin Li, Lifang Guo, Max Kolton, Rui Yang, Miaomiao Zhang, Fangjie Qi, Mohsen Soleimani, Xiaoxu Sun, Baoqin Li, Wenlong Gao, Geng Yan, Rui Xu, Weimin Sun
Environmental Science & Technology.2023; 57(1): 231. CrossRef - Bioengineered microbial strains for detoxification of toxic environmental pollutants
Quratulain Maqsood, Aleena Sumrin, Rafia Waseem, Maria Hussain, Mehwish Imtiaz, Nazim Hussain
Environmental Research.2023; 227: 115665. CrossRef - Impacts of straw returning and N application on NH4+-N loss, microbially reducible Fe(III) and bacterial community composition in saline-alkaline paddy soils
Dongmei Liu, Shirong Zhang, Chao Fei, Xiaodong Ding
Applied Soil Ecology.2021; 168: 104115. CrossRef - Nitrogen, water content, phosphorus and active iron jointly regulate soil organic carbon in tropical acid red soil forest
Jinyue Bai, Mingming Zong, Shiyu Li, Haixia Li, Changqun Duan, Yuan Feng, Changhui Peng, Xiaoling Zhang, Di Sun, Chen Lin, Yucheng Shi, Guangyu Zheng, Haidong Wang, Daxiang Liu, Fengrui Li, Wuping Huang
European Journal of Soil Science.2021; 72(1): 446. CrossRef - Phylogenetic diversity contributes more to sediment magnetism than abundance during incubation of iron‐reducing sediment from a non‐active volcanic lake in Northeast China
Y. Zhan, M. R. Yang, S. Zhang, H. Pan, W. D. Wang, L. Yan
Journal of Applied Microbiology.2021; 131(4): 1813. CrossRef - Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling
Martyna Glodowska, Emiliano Stopelli, Daniel Straub, Duyen Vu Thi, Pham T.K. Trang, Pham H. Viet, AdvectAs team members, Michael Berg, Andreas Kappler, Sara Kleindienst
Journal of Hazardous Materials.2021; 407: 124398. CrossRef - 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 - Microbial Community Structures in Terrestrial Subsurface Sediments from the Southern Kanto Plain, Japan
Satoshi Ohkubo, Takeshi Saito, Muhammad Abul Kalam Azad, Hiromitsu Kawai, Wataru Suda, Shin Kore-eda, Shoichiro Hamamoto, Hirotaka Saito, Takato Takemura, Toshiko Komatsu, Jun-ichi Ohnishi
Geomicrobiology Journal.2020; 37(7): 595. CrossRef - The effects of the soil environment on soil organic carbon in tea plantations in Xishuangbanna, southwestern China
Sun Di, Mingming Zong, Shiyu Li, Haixia Li, Changqun Duan, Changhui Peng, Yonggui Zhao, Jinyue Bai, Chen Lin, Yuan Feng, Wuping Huang, Di Wang
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Wenzhen Yuan, Xiaosi Su, Jing Bai, Wei Xu, Huang Wang, Dong Su
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Man-Young Jung , VinhHoa Pham , Soo-Je Park , So-Jeong Kim , Jong-Chan Chae , Yul Roh , Sung-Keun Rhee
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J. Microbiol. 2010;48(6):739-747. Published online January 9, 2011
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DOI: https://doi.org/10.1007/s12275-010-0257-9
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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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Citations
Citations to this article as recorded by - 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
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- Detection of Representative Enteropathogenic Bacteria, Vibrio spp., Pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, Using a Virulence Factor Gene-Based Oligonucleotide Microarray§
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Dong-Hun Kim , Bok-Kwon Lee , Yong-Dae Kim , Sung-Keun Rhee , Young-Chang Kim
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J. Microbiol. 2010;48(5):682-688. Published online November 3, 2010
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DOI: https://doi.org/10.1007/s12275-010-0119-5
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188
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Rapid identification of enteropathogenic bacteria in stool samples is critical for clinical diagnosis and antimicrobial therapy. In this study, we describe the development of an approach that couples multiplex PCR with hybridization to a DNA microarray, to allow the simultaneous detection of the 10 pathogens. The microarray was synthesized with 20-mer oligonucleotide probes that were designed to be specific for virulencefactor genes of each strain. The detection limit for genomic DNA from a single strain was approximately 10 fg. In the presence of heterogeneous non-target DNA, the detection sensitivity of the array decreased to approximately 100 fg. We did not observe any non-specific hybridization. In addition, we successfully used this oligonucleotide-based DNA microarray to identify the causative agents in clinical stool samples from patients with food-borne enteritis.
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Dae-No Yoon , Soo-Je Park , So-Jeong Kim , Che Ok Jeon , Jong-Chan Chae , Sung-Keun Rhee
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J. Microbiol. 2010;48(3):275-283. Published online June 23, 2010
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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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- Microeukaryotic Diversity in Marine Environments, an Analysis of Surface Layer Sediments from the East Sea
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Soo-Je Park , Byoung-Joon Park , Vinh Hoa Pham , Dae-No Yoon , Si-Kwan Kim , Sung-Keun Rhee
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J. Microbiol. 2008;46(3):244-249. Published online July 5, 2008
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DOI: https://doi.org/10.1007/s12275-007-0237-x
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Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.
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- Characterization of the Depth-Related Changes in the Microbial Communities in Lake Hovsgol Sediment by 16S rRNA Gene-Based Approaches
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Young-Do Nam , Youlboong Sung , Ho-Won Chang , Seong Woon Roh , Kyoung-Ho Kim , Sung-Keun Rhee , Jung-Chan Kim , Joo-Yong Kim , Jung-Hoon Yoon , Jin-Woo Bae
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J. Microbiol. 2008;46(2):125-136. Published online June 11, 2008
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DOI: https://doi.org/10.1007/s12275-007-0189-1
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Abstract
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The undisturbed sediment of Lake Hovsgol (Mongolia) is scientifically important because it represents a record of the environmental changes that took place between the Holocene (the present age) and Pleistocene (the last ice age; 12,000 14C years before present day). Here, we investigated how the current microbial
<br>communities change as the depth increases by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes of the microbial communities. The microbial diversity, as estimated by the Shannon index, decreased as the depth increased. In particular, significant changes in archaeal diversity were observed in the middle depth (at 39~42 cm depth of total 60 cm depth) that marks the border between the Holocene and Pleistocene. Phylotype belonging to Beta- and Gamma-Proteobacteria were the predominant bacteria and most of these persisted throughout the depth examined. However, as the depth increased, some bacteria
<br>(some genera belonging to Beta-Proteobacteria, Nitrospira, and OP8-9) were not detectable while others (some genera belonging to Alpha-, Beta-, Gamma-Proteobacteria) newly deteced by DGGE. Crenarchaea were the predominant archaea and only one phylotype belonging to Euryarchaea was found. Both the
<br>archaeal and bacterial profiles revealed by the DGGE band patterns could be grouped into four and three subsets, respectively, subsets that were largely divided by the border between the Holocene and Pleistocene. Thus, the diversity of the current microbial communities in Lake Hovsgol sediments decreases with increasing
<br>depth. These changes probably relate to the environmental conditions in the sediments, which were shaped by the paleoclimatic events taking place between the Holocene and Pleistocene.
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