Skip Navigation
Skip to contents

Journal of Microbiology : Journal of Microbiology

OPEN ACCESS
SEARCH
Search

Author index

Page Path
HOME > Browse Articles > Author index
Search
Jeongsu Oh 2 Articles
Bacterial Diversity in Ornithogenic Soils Compared to Mineral Soils on King George Island, Antarctica
Ok-Sun Kim , Namyi Chae , Hyun Soo Lim , Ahnna Cho , Jeong Hoon Kim , Soon Gyu Hong , Jeongsu Oh
J. Microbiol. 2012;50(6):1081-1085.   Published online December 30, 2012
DOI: https://doi.org/10.1007/s12275-012-2655-7
  • 802 View
  • 2 Download
  • 32 Crossref
AbstractAbstract PDF
In the Narębski Point area of King George Island of Antarctica, ornithogenic soils form on land under Chinstrap and Gentoo Penguin rookeries. The purpose of this study was to compare the bacterial community compositions in the gradient of contamination by penguin feces; mineral soil with no contamination, and soils with medium or high contamination. The discrimination between mineral soils and ornithogenic soils by characterization of physicochemical properties and bacterial communities was notable. Physicochemical analyses of soil properties showed enrichment of carbon and nitrogen in ornithogenic soils. Firmicutes were present abundantly in active ornithogenic soils, Bacteroidetes and Proteobacteria in a formerly active one, and several diverse phyla such as Proteobacteria, Actinobacteria, and Acidobacteria in mineral soils. Some predominant species belonging to the Firmicutes and Gammaproteobacteria may play an important role for the mineralization of nutrients in ornithogenic soils. Results of this study indicate that dominant species may play an important role in mineralization of nutrients in these ecosystems.

Citations

Citations to this article as recorded by  
  • Penguin guano shapes Antarctic environmental microbiomes: insights from DNA metabarcoding
    Rodrigo Goldenberg-Barbosa, Anna Luiza dos Santos Donato, Dafne Adriana Abreu dos Anjos, Letícia Bastos Eller, Heitor Evangelista, Cesar Rogerio Leal do Amaral
    Academia Biology.2026;[Epub]     CrossRef
  • Nutrient gradients and environmental filtering drive bacterial assembly and co-occurrence networks across sediment–water habitats during wetland restoration: Contrasting rare and abundant bacteria
    Tingting Luo, Lei Zhang, Yijie An, Ting Song, Feng Xu, Hua Cai
    Journal of Environmental Chemical Engineering.2026; 14(5): 123897.     CrossRef
  • A review on bacterial communities associated with Antarctic penguins
    Rodrigo Goldenberg-Barbosa, Dafne Anjos, Anna Donato, Cesar Rogerio Leal do Amaral
    Polar Biology.2025;[Epub]     CrossRef
  • Bacterial community composition and function in different habitats in Antarctic Fildes region revealed by high-throughput sequencing
    Yi-He Zhang, Yong-Qiang Hu, Yin-Xin Zeng, Ting Hu, Wei Han, Yu Du, Zhong Hu, Shan-Shan Meng
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • From acidophilic to ornithogenic: microbial community dynamics in moss banks altered by gentoo penguins
    Yevheniia Prekrasna-Kviatkovska, Ivan Parnikoza, Anna Yerkhova, Olesia Stelmakh, Mariia Pavlovska, Marta Dzyndra, Oleksandr Yarovyi, Evgen Dykyi
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Recovery of soil organic carbon storage driven by microbial communities during long-term natural restoration in wetland ecosystems
    Shan Zhang, Hui Zhong, Lingling Huang, Zhaoyu Kong, Lan Wu
    Ecological Engineering.2024; 199: 107170.     CrossRef
  • Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments
    Konstantin A. Demin, Evgeniya V. Prazdnova, Tatiana M. Minkina, Andrey V. Gorovtsov, Gemma Reguera
    Applied and Environmental Microbiology.2024;[Epub]     CrossRef
  • Soil chemical properties associated with penguin carrion in Barton Peninsula, King George Island, Antarctica
    Nur Adilla Zaini, Siti Sofo Ismail, Van Lun Low, Mohd Hafizi Mahmud, Jamal Houssaini, Won Young Lee, Chong Chin Heo
    Polar Biology.2024; 47(7): 681.     CrossRef
  • Competitive relationships due to similar nutrient preferences reshape soil bacterial metacommunities
    Heming Han, Hao Liu, Bo Zhang, Yue Li, Chuanhai Li, Hui Cao
    Science of The Total Environment.2024; 933: 172956.     CrossRef
  • Microbial community composition of terrestrial habitats in East Antarctica with a focus on microphototrophs
    Ekaterina Pushkareva, Josef Elster, Sakae Kudoh, Satoshi Imura, Burkhard Becker
    Frontiers in Microbiology.2024;[Epub]     CrossRef
  • Diversity and functionality of soil prokaryotic communities in antarctic volcanic soils: insights from penguin-influenced environments
    Diego Segura, Karen Jordaan, Beatriz Díez, Javier Tamayo-Leiva, Sebastian Doetterl, Daniel Wasner, Jerónimo Cifuentes-Anticevic, Angélica Casanova-Katny
    Polar Biology.2024; 47(9): 945.     CrossRef
  • Plant growth-promoting potential of bacterial isolates from the rhizosphere of Deschampsia antarctica
    Olga Maslovska, Solomiia Komplikevych, Iryna Danylo, Ivan Parnikoza, Svitlana Hnatush
    Ukrainian Antarctic Journal.2024; 22(1(28)): 63.     CrossRef
  • Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats
    Hanbyul Lee, Yong-Joon Cho, Ahnna Cho, Ok-Sun Kim
    Journal of Microbiology.2023; 61(7): 663.     CrossRef
  • Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach
    Vesselin V. Doytchinov, Svetoslav G. Dimov
    Life.2022; 12(6): 916.     CrossRef
  • Optimization of plant harvest and management patterns to enhance the carbon sink of reclaimed wetland in the Yangtze River estuary
    Wenxuan Mei, Qiuxiao Yin, Xiaoping Tian, Xiaohua Fu, Yongjian Guan, Lei Wang
    Journal of Environmental Management.2022; 312: 114954.     CrossRef
  • Source and acquisition of rhizosphere microbes in Antarctic vascular plants
    Sergio Guajardo-Leiva, Jaime Alarcón, Florence Gutzwiller, Jorge Gallardo-Cerda, Ian S. Acuña-Rodríguez, Marco Molina-Montenegro, Keith A. Crandall, Marcos Pérez-Losada, Eduardo Castro-Nallar
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • Highly specialized bacterial communities within three distinct rhizocompartments of Antarctic hairgrass (Deschampsia antarctica Desv.)
    Anna Znój, Jakub Grzesiak, Jan Gawor, Robert Gromadka, Katarzyna J. Chwedorzewska
    Polar Biology.2022; 45(5): 833.     CrossRef
  • Correlation between molecular microbial community and nitrogen cycling on ornithogenic soil affected by tsunami in Japan
    Akifumi Hosoda, Mao Kurosaki, Kentaro Kazama, Hirotatsu Murano, Chitoshi Mizota, Yasuaki Niizuma
    Ecological Genetics and Genomics.2022; 23: 100114.     CrossRef
  • Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes
    Lia Ramírez-Fernández, Luis H. Orellana, Eric R. Johnston, Konstantinos T. Konstantinidis, Julieta Orlando
    Science of The Total Environment.2021; 788: 147693.     CrossRef
  • A smelly business: Microbiology of Adélie penguin guano (Point Thomas rookery, Antarctica)
    Jakub Grzesiak, Agata Kaczyńska, Jan Gawor, Karolina Żuchniewicz, Tamara Aleksandrzak-Piekarczyk, Robert Gromadka, Marek K. Zdanowski
    Science of The Total Environment.2020; 714: 136714.     CrossRef
  • Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica
    Lía Ramírez-Fernández, Nicole Trefault, Margarita Carú, Julieta Orlando, Adrian Zwolicki
    PLOS ONE.2019; 14(1): e0209887.     CrossRef
  • Local-scale variation of soil bacterial communities in ice-free regions of maritime Antarctica
    Mincheol Kim, Hyun-Soo Lim, Chang-Uk Hyun, Ahnna Cho, Hyun-Ju Noh, Soon Gyu Hong, Ok-Sun Kim
    Soil Biology and Biochemistry.2019; 133: 165.     CrossRef
  • Links between bacteria derived from penguin guts and deposited guano and the surrounding soil microbiota
    Wen Chyin Yew, David Anthony Pearce, Michael James Dunn, Stacey Adlard, Siti Aisyah Alias, Azizan Abu Samah, Peter Convey
    Polar Biology.2018; 41(2): 269.     CrossRef
  • Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkia purinilytica comb.
    Anja Poehlein, Natalya Yutin, Rolf Daniel, Michael Y. Galperin
    International Journal of Systematic and Evolutionary Microbiology .2017; 67(8): 2711.     CrossRef
  • Transfer of ornithogenic influence through different trophic levels of the Arctic terrestrial ecosystem of Bjørnøya (Bear Island), Svalbard
    Katarzyna Zmudczyńska-Skarbek, Mateusz Barcikowski, Szymon M. Drobniak, Dariusz J. Gwiazdowicz, Pierre Richard, Piotr Skubała, Lech Stempniewicz
    Soil Biology and Biochemistry.2017; 115: 475.     CrossRef
  • Microbial diversity at Mitchell Peninsula, Eastern Antarctica: a potential biodiversity “hotspot”
    Mukan Ji, Josie van Dorst, Andrew Bissett, Mark V. Brown, Anne S. Palmer, Ian Snape, Steven D. Siciliano, Belinda C. Ferrari
    Polar Biology.2016; 39(2): 237.     CrossRef
  • Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula
    Igor S. Pessi, César Osorio-Forero, Eric J. C. Gálvez, Felipe L. Simões, Jefferson C. Simões, Howard Junca, Alexandre J. Macedo
    FEMS Microbiology Ecology.2015; 91(1): 1.     CrossRef
  • Distribution and Interaction Patterns of Bacterial Communities in an Ornithogenic Soil of Seymour Island, Antarctica
    Pabulo Henrique Rampelotto, Anthony Diego Muller Barboza, Antônio Batista Pereira, Eric W. Triplett, Carlos Ernesto G. R. Schaefer, Flávio Anastácio de Oliveira Camargo, Luiz Fernando Wurdig Roesch
    Microbial Ecology.2015; 69(3): 684.     CrossRef
  • Edifisols—a new soil unit of technogenic soils
    Przemysław Charzyński, Piotr Hulisz, Renata Bednarek, Agnieszka Piernik, Marta Winkler, Marcin Chmurzyński
    Journal of Soils and Sediments.2015; 15(8): 1675.     CrossRef
  • Penguin activity influences soil biogeochemistry and soil respiration in rookeries on Ross Island, Antarctica
    Becky A. Ball, Chelsey R. Tellez, Ross A. Virginia
    Polar Biology.2015; 38(9): 1357.     CrossRef
  • Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing
    Neng Fei Wang, Tao Zhang, Fang Zhang, En Tao Wang, Jian Feng He, Hui Ding, Bo Tao Zhang, Jie Liu, Xiang Bin Ran, Jia Ye Zang
    Frontiers in Microbiology.2015;[Epub]     CrossRef
  • Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines
    Edward Alain B. Pajarillo, Jong Pyo Chae, Marilen P. Balolong, Hyeun Bum Kim, Kang-Seok Seo, Dae-Kyung Kang
    Journal of Microbiology.2014; 52(8): 646.     CrossRef
PyroTrimmer: a Software with GUI for Pre-Processing 454 Amplicon Sequences
Jeongsu Oh , Byung Kwon Kim , Wan-Sup Cho , Soon Gyu Hong , Kyung Mo Kim
J. Microbiol. 2012;50(5):766-769.   Published online November 4, 2012
DOI: https://doi.org/10.1007/s12275-012-2494-6
  • 802 View
  • 2 Download
  • 22 Crossref
AbstractAbstract PDF
The ultimate goal of metagenome research projects is to understand the ecological roles and physiological functions of the microbial communities in a given natural environment. The 454 pyrosequencing platform produces the longest reads among the most widely used next generation sequencing platforms. Since the relatively longer reads of the 454 platform provide more information for identification of microbial sequences, this platform is dedicated to microbial community and population studies. In order to accurately perform the downstream analysis of the 454 multiplex datasets, it is necessary to remove artificially designed sequences located at either ends of individual reads and to correct lowquality sequences. We have developed a program called Pyro-Trimmer that removes the barcodes, linkers, and primers, trims sequence regions with low quality scores, and filters out low-quality sequence reads. Although these functions have previously been implemented in other programs as well, PyroTrimmer has novelty in terms of the following features: i) more sensitive primer detection using Levenstein distance and global pairwise alignment, ii) the first stand-alone software with a graphic user interface, and iii) various options for trimming and filtering out the low-quality sequence reads. PyroTrimmer, written in JAVA, is compatible with multiple operating systems and can be downloaded free at http://pyrotrimmer.kobic.re.kr.

Citations

Citations to this article as recorded by  
  • Linking biogeochemical signatures to archaeal community structure at active methane seeps in the Tatar trough, far eastern Russia
    Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Helge Niemann, Carme Huguet, Young-Keun Jin, Hirotsugu Minami, Akihiro Hachikubo, Kyung-Hoon Shin
    Marine Chemistry.2026; : 104677.     CrossRef
  • Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
    Bilal Wajid, Faria Anwar, Imran Wajid, Haseeb Nisar, Sharoze Meraj, Ali Zafar, Mustafa Kamal Al-Shawaqfeh, Ali Riza Ekti, Asia Khatoon, Jan S. Suchodolski
    Functional & Integrative Genomics.2022; 22(1): 3.     CrossRef
  • Microbiome in Cladonia squamosa Is Vertically Stratified According to Microclimatic Conditions
    Hyun-Ju Noh, Yung Mi Lee, Chae Haeng Park, Hong Kum Lee, Jang-Cheon Cho, Soon Gyu Hong
    Frontiers in Microbiology.2020;[Epub]     CrossRef
  • DNA Sequencing Technologies
    Ka-Chun Wong, Jiao Zhang, Shankai Yan, Xiangtao Li, Qiuzhen Lin, Sam Kwong, Cheng Liang
    ACM Computing Surveys.2020; 52(5): 1.     CrossRef
  • Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments
    Yung Mi Lee, Kyuin Hwang, Jae Il Lee, Mincheol Kim, Chung Yeon Hwang, Hyun-Ju Noh, Hakkyum Choi, Hong Kum Lee, Jongsik Chun, Soon Gyu Hong, Seung Chul Shin
    Frontiers in Microbiology.2018;[Epub]     CrossRef
  • Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea
    Dong-Hun Lee, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, Kyung-Hoon Shin
    Biogeosciences.2018; 15(24): 7419.     CrossRef
  • Niche specialization of bacteria in permanently ice‐covered lakes of the McMurdo Dry Valleys, Antarctica
    Miye Kwon, Mincheol Kim, Cristina Takacs‐Vesbach, Jaejin Lee, Soon Gyu Hong, Sang Jong Kim, John C Priscu, Ok‐Sun Kim
    Environmental Microbiology.2017; 19(6): 2258.     CrossRef
  • Geographical structure of endosymbiotic bacteria hosted by Bathymodiolus mussels at eastern Pacific hydrothermal vents
    Phuong-Thao Ho, Eunji Park, Soon Gyu Hong, Eun-Hye Kim, Kangchon Kim, Sook-Jin Jang, Robert C. Vrijenhoek, Yong-Jin Won
    BMC Evolutionary Biology.2017;[Epub]     CrossRef
  • Succession of bacterial community structure during the early stage of biofilm development in the Antarctic marine environment
    Yung Mi Lee, Kyung Hee Cho, Kyuin Hwang, Eun Hye Kim, Mincheol Kim, Soon Gyu Hong, Hong Kum Lee
    The Korean Journal of Microbiology.2016; 52(1): 49.     CrossRef
  • Aboveground Whitefly Infestation-Mediated Reshaping of the Root Microbiota
    Hyun G. Kong, Byung K. Kim, Geun C. Song, Soohyun Lee, Choong-Min Ryu
    Frontiers in Microbiology.2016;[Epub]     CrossRef
  • CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment
    Jeongsu Oh, Chi-Hwan Choi, Min-Kyu Park, Byung Kwon Kim, Kyuin Hwang, Sang-Heon Lee, Soon Gyu Hong, Arshan Nasir, Wan-Sup Cho, Kyung Mo Kim, Christophe Antoniewski
    PLOS ONE.2016; 11(3): e0151064.     CrossRef
  • Bacterial communities in Antarctic lichens
    Chae Haeng Park, Kyung Mo Kim, Ok-Sun Kim, Gajin Jeong, Soon Gyu Hong
    Antarctic Science.2016; 28(6): 455.     CrossRef
  • Soil development and bacterial community shifts along the chronosequence of the Midtre Lovénbreen glacier foreland in Svalbard
    Hye Young Kwon, Ji Young Jung, Ok-Sun Kim, Dominique Laffly, Hyoun Soo Lim, Yoo Kyung Lee
    Journal of Ecology and Environment.2015; 38(4): 461.     CrossRef
  • Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
    Yoon-Seong Jeon, Sang-Cheol Park, Jeongmin Lim, Jongsik Chun, Bong-Soo Kim
    Journal of Microbiology.2015; 53(1): 60.     CrossRef
  • Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica
    Mincheol Kim, Ahnna Cho, Hyoun Soo Lim, Soon Gyu Hong, Ji Hee Kim, Joohan Lee, Taejin Choi, Tae Seok Ahn, Ok-Sun Kim, Jack Anthony Gilbert
    PLOS ONE.2015; 10(3): e0119966.     CrossRef
  • Algal and Fungal Diversity in Antarctic Lichens
    Chae Haeng Park, Kyung Mo Kim, Arve Elvebakk, Ok‐Sun Kim, Gajin Jeong, Soon Gyu Hong
    Journal of Eukaryotic Microbiology.2015; 62(2): 196.     CrossRef
  • Bacterial community of sediments from the Australian-Antarctic ridge
    Yung Mi Lee, Doshik Hahm, You-Jung Jung, Sung Hyun Park, Jongsik Chun, Soon Gyu Hong
    Polar Biology.2014; 37(4): 587.     CrossRef
  • Deodorization of pig slurry and characterization of bacterial diversity using 16S rDNA sequence analysis
    Ok-Hwa Hwang, Sebastian Raveendar, Young-Ju Kim, Ji-Hun Kim, Tae-Hun Kim, Dong-Yoon Choi, Che Ok Jeon, Sung-Back Cho, Kyung-Tai Lee
    Journal of Microbiology.2014; 52(11): 918.     CrossRef
  • Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash
    Jae Ho Joa, Hang Yeon Weon, Hae Nam Hyun, Young Chull Jeun, Sang Wook Koh
    Journal of Microbiology.2014; 52(12): 995.     CrossRef
  • A metagenomics‐based approach to the top‐down effect on the detritivore food web: a salamanders influence on fungal communities within a deciduous forest
    Donald M. Walker, Brandy R. Lawrence, Dakota Esterline, Sean P. Graham, Michael A. Edelbrock, Jessica A. Wooten
    Ecology and Evolution.2014; 4(21): 4106.     CrossRef
  • Differences in Gastric Mucosal Microbiota Profiling in Patients with Chronic Gastritis, Intestinal Metaplasia, and Gastric Cancer Using Pyrosequencing Methods
    Chang Soo Eun, Byung Kwon Kim, Dong Soo Han, Seon Young Kim, Kyung Mo Kim, Bo Youl Choi, Kyu Sang Song, Yong Sung Kim, Jihyun F. Kim
    Helicobacter.2014; 19(6): 407.     CrossRef
  • Bacterial diversity in ornithogenic soils compared to mineral soils on King George Island, Antarctica
    Ok-Sun Kim, Namyi Chae, Hyun Soo Lim, Ahnna Cho, Jeong Hoon Kim, Soon Gyu Hong, Jeongsu Oh
    Journal of Microbiology.2012; 50(6): 1081.     CrossRef

Journal of Microbiology : Journal of Microbiology
TOP