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.

Journal Articles

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea: Wenhui Li, Yu Zhen, Yuhong Yang, Daling Wang, Hui He; J. Microbiol. 2024;62(10):845-858. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00166-5

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This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 10² to 2.17 × 10⁶ copies per gram of sediment and from 6.6 × 10¹ to 7.65 × 10⁴ copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50 °C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

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Metabolism diversification of ammonia-oxidizing archaea and bacteria under different precipitation gradients and land legacies
Soumyadev Sarkar, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, Willow Kessler, Ligia F.T. de Souza, Terry D. Loecke, Marcos V.M. Sarto, Charles W. Rice, Lydia H. Zeglin, Benjamin A. Sikes, Sonny T.M.
Applied Soil Ecology.2025; 206: 105831. CrossRef
Genetic and transcriptional profiles of ammonia oxidizing communities in Bohai sediments: abundance, activity, and environmental correlations
Yining Jiang, Xue Lou, Mingyang Wang, Minggang Zheng, Zhiyao Wang, Hui Chen
Frontiers in Microbiology.2025;[Epub] CrossRef

Pat- and Pta-mediated protein acetylation is required for horizontallyacquired virulence gene expression in Salmonella Typhimurium: Hyojeong Koo , Eunna Choi , Shinae Park , Eun-Jin Lee , Jung-Shin Lee; J. Microbiol. 2022;60(8):823-831. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2095-y

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Abstract PDF

Salmonella Typhimurium is a Gram-negative facultative pathogen that causes a range of diseases, from mild gastroenteritis to severe systemic infection in a variety of animal hosts. S. Typhimurium regulates virulence gene expression by a silencing mechanism using nucleoid-associated proteins such as Histone-like Nucleoid Structuring protein (H-NS) silencing. We hypothesize that the posttranslational modification, specifically protein acetylation, of proteins in gene silencing systems could affect the pathogenic gene expression of S. Typhimurium. Therefore, we created acetylation-deficient mutant by deleting two genes, pat and pta, which are involved in the protein acetylation pathway. We observed that the pat and pta deletion attenuates mouse virulence and also decreases Salmonella’s replication within macrophages. In addition, the Δpat Δpta strain showed a decreased expression of the horizontally-acquired virulence genes, mgtC, pagC, and ugtL, which are highly expressed in low Mg2+. The decreased virulence gene expression is possibly due to higher H-NS occupancy to those promoters because the pat and pta deletion increases H-NS occupancy whereas the same mutation decreases occupancy of RNA polymerase. Our results suggest that Pat- and Pta-mediated protein acetylation system promotes the expression of virulence genes by regulating the binding affinity of H-NS in S. Typhimurium.

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Reversible acetylation of ribosomal protein S1 serves as a smart switch for Salmonella to rapidly adapt to host stress
Yi-Lin Shen, Tian-Xian Liu, Lei Xu, Bang-Ce Ye, Ying Zhou
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Yu Li, Jinyu Zhang, Ke Wei, Di Zhou, Zepeng Wang, Zhiwei Zeng, Yu Han, Weisheng Cao
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CagL polymorphisms between East Asian and Western Helicobacter pylori are associated with different abilities to induce IL-8 secretion: Yun Hui Choi , Jing Lai , Myeong-A Kim , Aeryun Kim , Jinmoon Kim , Hanfu Su , Linhu Ge , Jeong-Heon Cha; J. Microbiol. 2021;59(8):763-770. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1136-2

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Helicobacter pylori colonizes human gastric mucosa. Its infection is associated with gastric diseases including gastric cancer. CagA is one of the most important toxins produced by H. pylori. It is related to gastric cancer which can be injected into host cells via a type IV secretion system (T4SS). CagL is a structural component of T4SS apparatus, which triggers host cell signaling pathway. It has been reported that CagL polymorphisms may influence the severity of disease development. To explore the contribution of CagL polymorphisms between East Asian and Western H. pylori in pathogenesis, cagL gene in G27 H. pylori was swapped by K74 cagL which is identical to East Asian CagL consensus sequence and by Western 26695 H. pylori, resulting in G27ΔcagL/cagLK74 and G27ΔcagL/cagL26695, respectively. Intriguingly, G27ΔcagL/ cagLK74 showed significantly less ability of IL-8 induction than G27ΔcagL/cagL26695 while displayed similar abilities of CagA phosphorylation, and cell elongation. Taken together, this study suggests that the CagL polymorphism may influence IL-8 induction, and K74 CagL has less ability to induce IL-8 secretion than G27 or 26695 CagL. Further research should address how the different capabilities of IL-8 induction between intraspecies-CagL are associated with the large differences of the incidence of gastric cancer between East Asian and Western countries.

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Roles of the components of the cag -pathogenicity island encoded type IV secretion system in Helicobacter pylori
Lingzhu Gou, Xiaoping Yang, Jianwei Yun, Zenghui Ma, Xiaofeng Zheng, Hongwei Du, Dekui Zhang
Future Microbiology.2024; 19(14): 1253. CrossRef
Antibacterial and Immunoregulatory Effects of Metformin against Helicobacter pylori Infection in Rat Model
Hassan Valadbeigi, Saeed Khoshnood, Babak Negahdari, Mohd Azmuddin Abdullah, Mohammad Hossein Haddadi, Abhimanyu Abhimanyu
BioMed Research International.2023;[Epub] CrossRef
New CagL Amino Acid Polymorphism Patterns of Helicobacter pylori in Peptic Ulcer and Non-Ulcer Dyspepsia
Reyhan Caliskan, Silva Polat Sari, Bahadir Ercan, Kivanc Derya Peker, Mehtap Omac Sonmez, Ozer Akgul, Burcu Sapmaz, Aliye Soylu, Gokhan Tolga Adas, Yasar Ali Oner, Pelin Yuksel Mayda
Medicina.2022; 58(12): 1738. CrossRef
Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates
Aeryun Kim, Jing Lai, D. Scott Merrell, Ji-Hye Kim, Hanfu Su, Jeong-Heon Cha
Journal of Microbiology.2021; 59(12): 1125. CrossRef

Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae: Jeeeun Park , Young-Sam Kim , Seong-Jin Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Min-Ju Yu , Young Jae Jeon , Kyoung-Ho Kim; J. Microbiol. 2021;59(6):546-551. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-0678-7

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A novel bacterium, designated strain RR4-56T, was isolated from a biofilter of a seawater recirculating aquaculture system. The 16S rRNA gene sequence analysis showed that the isolate was closely related to Halovulum dunhuangense YYQ- 30T (92.6%), Albimonas donghaensis DS2T (91.3%), Pontivivens insulae GYSW-23T (91.3%), and Monaibacterium marinum C7T (90.9%), belonging to the family Rhodobacteraceae. The strain was aerobic, Gram-negative, rod-shaped, oxidasepositive, and catalase-negative. Its optimum temperature, pH, and salinity for growth were 25–30°C, pH 8.5, and 2–3% NaCl (w/v), respectively. Its growth occurred at 15–35°C, pH 5.0–9.5, and 0–7% NaCl (w/v). It contained ubiquinone-10 (Q-10), a respiratory quinone, and the major cellular fatty acids were 11-methyl C18:1 ω7c (31.9%), C18:1 ω6c (30.4%), and C19:0 cyclo ω8c (16.1%). The polar lipids present in the strain were phosphatidylglycerol, an unidentified phospholipid, and an unidentified aminolipid. The strain had one 4,373,045 bp circular chromosome with G + C contents of 65.9 mol% including 4,169 genes, 4,118 coding sequences (CDSs), 3 rRNAs, and 45 tRNAs. Genome annotation predicted some gene clusters related to the degradation of several types of organic matter such as protocatechuate, catechol, and phthalate. Based on the polyphasic characteristics, RR4-56T represents a novel genus and species in the family Rhodobacteraceae, for which the name Pikeienuella piscinae gen. nov., sp. nov. was proposed. The type strain is RR4-56T (= KCTC 52648T = DSM 107918T).

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Lin Lin, Jia Ning, Chunhui Li, Linlin Zhang, Yu Gao, Wang Bo, Ke Shi
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Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

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Reviews

Metaviromics coupled with phage-host identification to open the viral ‘black box’: Kira Moon , Jang-Cheon Cho; J. Microbiol. 2021;59(3):311-323. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-1016-9

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Viruses are found in almost all biomes on Earth, with bacteriophages (phages) accounting for the majority of viral particles in most ecosystems. Phages have been isolated from natural environments using the plaque assay and liquid medium- based dilution culturing. However, phage cultivation is restricted by the current limitations in the number of culturable bacterial strains. Unlike prokaryotes, which possess universally conserved 16S rRNA genes, phages lack universal marker genes for viral taxonomy, thus restricting cultureindependent analyses of viral diversity. To circumvent these limitations, shotgun viral metagenome sequencing (i.e., metaviromics) has been developed to enable the extensive sequencing of a variety of viral particles present in the environment and is now widely used. Using metaviromics, numerous studies on viral communities have been conducted in oceans, lakes, rivers, and soils, resulting in many novel phage sequences. Furthermore, auxiliary metabolic genes such as ammonic monooxygenase C and β-lactamase have been discovered in viral contigs assembled from viral metagenomes. Current attempts to identify putative bacterial hosts of viral metagenome sequences based on sequence homology have been limited due to viral sequence variations. Therefore, culture- independent approaches have been developed to predict bacterial hosts using single-cell genomics and fluorescentlabeling. This review focuses on recent viral metagenome studies conducted in natural environments, especially in aquatic ecosystems, and their contributions to phage ecology. Here, we concluded that although metaviromics is a key tool for the study of viral ecology, this approach must be supplemented with phage-host identification, which in turn requires the cultivation of phage-bacteria systems.

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Carlos Willian Dias Dantas, David Tavares Martins, Wylerson Guimarães Nogueira, Oscar Victor Cardenas Alegria, Rommel Thiago Jucá Ramos
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Zhenyu Liu, Wenhui Jiang, Cholsong Kim, Xiaoya Peng, Cong Fan, Yingliang Wu, Zhixiong Xie, Fang Peng
International Journal of Molecular Sciences.2023; 24(8): 7662. CrossRef
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The functional study of human proteins using humanized yeast: Seho Kim , Juhee Park , Taekyung Kim , Jung-Shin Lee; J. Microbiol. 2020;58(5):343-349. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0136-y

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The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.

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A Humanized Yeast Model for Studying TRAPP Complex Mutations; Proof-of-Concept Using Variants from an Individual with a TRAPPC1-Associated Neurodevelopmental Syndrome
Erta Zykaj, Chelsea Abboud, Paria Asadi, Simane Warsame, Hashem Almousa, Miroslav P. Milev, Brittany M. Greco, Marcos López-Sánchez, Drago Bratkovic, Aashiq H. Kachroo, Luis Alberto Pérez-Jurado, Michael Sacher
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Humanization reveals pervasive incompatibility of yeast and human kinetochore components
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Journal Article

Rhizocompartments and environmental factors affect microbial composition and variation in native plants: Myung-Suk Kang , Moonsuk Hur , Soo-Je Park; J. Microbiol. 2019;57(7):550-561. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8646-1

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Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

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Reviews

Minireview] Electron microscopic observations of prokaryotic surface appendages: Ki Woo Kim; J. Microbiol. 2017;55(12):919-926. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7369-4

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Abstract PDF

Prokaryotic microbes possess a variety of appendages on their cell surfaces. The most commonly known surface appendages of bacteria include flagella, pili, curli, and spinae. Although archaea have archaella (archaeal flagella) and various types of pili that resemble those in bacteria, cannulae, and hami are unique to archaea. Typically involved in cell motility, flagella, the thickest appendages, are 20–26 nm and 10–14 nm wide in bacteria and archaea, respectively. Bacterial and archaeal pili are distinguished by their thin, short, hair-like structures. Curli appear as coiled and aggregative thin fibers, whereas spinae are tubular structures 50–70 nm in diameter in bacteria. Cannulae are characterized by ~25 nm-wide tubules that enter periplasmic spaces and connect neighboring archaeal cells. Hami are 1–3 μm in length and similar to barbed grappling hooks for attachment to bacteria. Recent advances in specimen preparation methods and image processing techniques have made cryo-transmission electron microscopy an essential tool for in situ structural analysis of microbes and their extracellular structures.

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Minireview] The History of Aerobic Ammonia Oxidizers: from the First Discoveries to Today: Maria Monteiro , Joana Séneca , Catarina Magalhães; J. Microbiol. 2014;52(7):537-547. Published online June 28, 2014; DOI: https://doi.org/10.1007/s12275-014-4114-0

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Abstract PDF

Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilusmaritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In thismini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

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Journal Article

Microbial Community Analysis of a Coastal Hot Spring in Kagoshima, Japan, Using Molecular- and Culture-based Approaches: Minako Nishiyama , Shuichi Yamamoto , Norio Kurosawa; J. Microbiol. 2013;51(4):413-422. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2419-z

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Abstract PDF: Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

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

Characterization of the Bacterial and Archaeal Communities in Rice Field Soils Subjected to Long-Term Fertilization Practices: Jae-Hyung Ahn , Jaekyeong Song , Byung-Yong Kim , Myung-Sook Kim , Jae-Ho Joa , Hang-Yeon Weon; J. Microbiol. 2012;50(5):754-765. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2409-6

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Abstract

The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.

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Varying nitrogen fertilization and soil bacterial community dynamics at three growth phases of winter wheat production
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Long-term maintenance rate fertilisation increases soil bacterial-archaeal community diversity in the subsoil and N-cycling potentials in a humid crop season
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Bacterial communities in cropland soils: Taxonomy and functions
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Differential effects of fresh and composted organic wastes on soil bacterial community and maize growth
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Effect of Rice Straw and Stubble Burning on Soil Physicochemical Properties and Bacterial Communities in Central Thailand
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Biology.2023; 12(4): 501. CrossRef
Soil microbial diversity under different types of interference in birch secondary forest in the Greater Khingan Mountains in China
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Global biogeographic distribution of Bathyarchaeota in paddy soils
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mSystems.2023;[Epub] CrossRef
Response of soils properties and archaea community to saline-sodic soils under long-term rice-based cropping system
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Archives of Agronomy and Soil Science.2023; 69(4): 533. CrossRef
Response of microbial community diversity and subsoil properties to cow manure amendment in mollisols
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Evaluation of a subtropical maize-rice rotation system maintained under long-term fertilizer inputs for sustainable intensification of agriculture
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Applied Soil Ecology.2023; 184: 104772. CrossRef
Effects of shining pondweed (Potamogeton lucens) on fungal communities in water and rhizosphere sediments in Nansi Lake, China
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Effects of tillage practice on fungal and actinobacterial cellulolytic community with different humified particle‐size fractions in a double‐cropping paddy field
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Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem
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Continuous straw return for 8 years mitigates the negative effects of inorganic fertilisers on C‐cycling soil bacteria
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Effects of shining pondweed (Potamogeton lucens) on bacterial communities in water and rhizosphere sediments in Nansi Lake, China
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Effects of N Application Rate and Dicyandiamide on the Fate of 15N Fertilizer and the Abundance of Microbial Genes in a Sandy Soil Amended with Sugarcane Litter
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Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis
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Effects of Land Reclamation on Soil Bacterial Community and Potential Functions in Bauxite Mining Area
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International Journal of Environmental Research and Public Health.2022; 19(24): 16921. CrossRef
Long-Term Organic–Inorganic Fertilization Regimes Alter Bacterial and Fungal Communities and Rice Yields in Paddy Soil
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Long-term cultivation alter soil bacterial community in a forest-grassland transition zone
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Frontiers in Microbiology.2022;[Epub] CrossRef
The effect of environmental parameters and fertilization practices on yield and soil microbial diversity in a Kenyan paddy rice field
Markus Gorfer, Luigimaria Borruso, Evi Deltedesco, Emily W. Gichuhi, Daniel M. Menge, Daigo Makihara, Nadine Praeg, Stefano Cesco, Tanja Mimmo, Lutz Merbold, Sonja Leitner
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Higher pH is associated with enhanced co‐occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome
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Manure Application Increases Soil Bacterial and Fungal Network Complexity and Alters Keystone Taxa
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Pre-flooding soil used in monocropping increased strawberry biomass and altered bacterial community composition
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Research Progress on the Effects of Logging and Burning on Forest Soil Microorganisms
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International Journal of Ecology.2021; 10(04): 472. CrossRef
Alternation of soil bacterial and fungal communities by tomato–rice rotation in Hainan Island in Southeast of China
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Balanced fertilization over four decades has sustained soil microbial communities and improved soil fertility and rice productivity in red paddy soil
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Long-Term Manure Application Changes Bacterial Communities in Rice Rhizosphere and Arsenic Speciation in Rice Grains
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Comparison of bacterial and archaeal communities in two fertilizer doses and soil compartments under continuous cultivation system of garlic
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Relationship between Plant Roots, Rhizosphere Microorganisms, and Nitrogen and Its Special Focus on Rice
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Long‐term inorganic nitrogen application changes the ammonia‐oxidizing archaeal community composition in paddy soils
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Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria
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Different responses of soil carbon chemistry to fertilization regimes in the paddy soil and upland soil were mainly reflected by the opposite shifts of OCH and alkyl C
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Responses of archaeal, bacterial, and functional microbial communities to growth season and nitrogen fertilization in rice fields
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Shifts in microbial communities and networks are correlated with the soil ionome in a kiwifruit orchard under different fertilization regimes
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Applied Soil Ecology.2020; 149: 103517. CrossRef
Phosphorus Input Alters the Assembly of Rice (Oryza sativa L.) Root-Associated Communities
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Microbial Ecology.2020; 79(2): 357. CrossRef
Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition
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Rice.2020;[Epub] CrossRef
Land use change from upland to paddy field in Mollisols drives soil aggregation and associated microbial communities
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Combined Application of Organic and Inorganic Nitrogen Fertilizers Affects Soil Prokaryotic Communities Compositions
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Agronomy.2020; 10(1): 132. CrossRef
Effects of rice straw and rice straw ash on rice growth and α-diversity of bacterial community in rare-earth mining soils
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Scientific Reports.2020;[Epub] CrossRef
Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard
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Scientific Reports.2020;[Epub] CrossRef
Nitrogen leaching greatly impacts bacterial community and denitrifiers abundance in subsoil under long-term fertilization
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Agriculture, Ecosystems & Environment.2020; 294: 106885. CrossRef
Diversity and structure of bacterial community in rhizosphere of lima bean
Regina Maria Silva Sousa, Lucas William Mendes, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Antonia Maria de Cassia Batista Sousa, Regina Lucia Ferreira Gomes, Angela Celis de Almeida Lopes, Fábio Fernando Araújo, Vania Maria Maciel Melo,
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Comparison of soil bacterial diversity and community composition between clear-cut logging and control sites in a temperate deciduous broad-leaved forest in Mt. Sambong, South Korea
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Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System
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Frontiers in Microbiology.2020;[Epub] CrossRef
Biochar Effects on Bacterial Community and Metabolic Pathways in Continuously Cotton-Cropped Soil
Guangming Han, Quanqiu Chen, Shengxi Zhang, Guorong Li, Xianda Yi, Changhui Feng, Xiaogang Wang, Cui Yu, Jiayang Lan
Journal of Soil Science and Plant Nutrition.2019; 19(2): 249. CrossRef
The 19-years inorganic fertilization increased bacterial diversity and altered bacterial community composition and potential functions in a paddy soil
Qiong Huang, Jianlei Wang, Cong Wang, Qing Wang
Applied Soil Ecology.2019; 144: 60. CrossRef
Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies
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Agronomy.2019; 9(1): 14. CrossRef
Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long‐term fertilization management
Haiming Tang, Xiaoping Xiao, Yilan Xu, Chao Li, Kaikai Cheng, Xiaochen Pan, Weiyan Li
Journal of Basic Microbiology.2019; 59(6): 621. CrossRef
Taking insight into the gut microbiota of three spider species: No characteristic symbiont was found corresponding to the special feeding style of spiders
Guowen Hu, Lihua Zhang, Yueli Yun, Yu Peng
Ecology and Evolution.2019; 9(14): 8146. CrossRef
Long-term application of manure over plant residues mitigates acidification, builds soil organic carbon and shifts prokaryotic diversity in acidic Ultisols
Guiping Ye, Yongxin Lin, Deyan Liu, Zengming Chen, Jiafa Luo, Nanthi Bolan, Jianbo Fan, Weixin Ding
Applied Soil Ecology.2019; 133: 24. CrossRef
Short-term response of the soil bacterial community to differing wildfire severity in Pinus tabulaeformis stands
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Scientific Reports.2019;[Epub] CrossRef
Integrating environmental parameters and economic benefits to analyze the ecological agriculture (EA) application in the mountain rice paddy system of Chongqing, China
Ying Shao, Zhongli Chen, Hongyan Xiao, Zihan Zhu, Bo Li
Environmental Sciences Europe.2019;[Epub] CrossRef
Effects of Long-Term Application of Vinasse on Physicochemical Properties, Heavy Metals Content and Microbial Diversity in Sugarcane Field Soil
Juan Yin, Chao-Bing Deng, Xiao-Fei Wang, Gan-lin Chen, Viktor Gábor Mihucz, Gui-Ping Xu, Qu-Cheng Deng
Sugar Tech.2019; 21(1): 62. CrossRef
Long-term N fertilization altered 13C-labeled fungal community composition but not diversity in wheat rhizosphere of Chinese black soil
Qingfeng Wang, Mingchao Ma, Xin Jiang, Baoku Zhou, Dawei Guan, Fengming Cao, Sanfeng Chen, Jun Li
Soil Biology and Biochemistry.2019; 135: 117. CrossRef
Decrease in diversity and shift in composition of the soil bacterial community were closely related to high available phosphorus in agricultural Fluvisols of North China
Chenxu Liu, Xiaorong Zhao, Qimei Lin, Guitong Li
Acta Agriculturae Scandinavica, Section B — Soil & Plant Science.2019; 69(7): 618. CrossRef
Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress
Andrew P. Madigan, Eleonora Egidi, Frank Bedon, Ashley E. Franks, Kim M. Plummer
Frontiers in Microbiology.2019;[Epub] CrossRef
The stabilizing mechanism of cadmium in contaminated soil using green synthesized iron oxide nanoparticles under long-term incubation
Jiajiang Lin, Fengxin He, Binglin Su, Mengqiang Sun, Gary Owens, Zuliang Chen
Journal of Hazardous Materials.2019; 379: 120832. CrossRef
Application of phosphate-containing materials affects bioavailability of rare earth elements and bacterial community in soils
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Science China Technological Sciences.2019; 62(9): 1616. CrossRef
Long-term silicate fertilization increases the abundance of Actinobacterial population in paddy soils
Sandipan Samaddar, Jaak Truu, Poulami Chatterjee, Marika Truu, Kiyoon Kim, Sukjin Kim, Sundaram Seshadri, Tongmin Sa
Biology and Fertility of Soils.2019; 55(2): 109. CrossRef
Shifts in bacterial community composition increase with depth in three soil types from paddy fields in China
Xu Li, Huanhuan Wang, Xiang Li, Xinyu Li, Huiwen Zhang
Pedobiologia.2019; 77: 150589. CrossRef
Continuous application of inorganic and organic fertilizers over 47 years in paddy soil alters the bacterial community structure and its influence on rice production
Upendra Kumar, Amaresh Kumar Nayak, Mohammad Shahid, Vadakattu V.S.R. Gupta, P. Panneerselvam, Sangita Mohanty, Megha Kaviraj, Anjani Kumar, Dibyendu Chatterjee, B. Lal, P. Gautam, Rahul Tripathi, B.B. Panda
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Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays
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Frontiers in Microbiology.2018;[Epub] CrossRef
Differences in rice rhizosphere bacterial community structure by application of lignocellulolytic plant-probiotic bacteria with rapid composting traits
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Ecological Engineering.2018; 120: 209. CrossRef
Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols
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AMB Express.2018;[Epub] CrossRef
Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere of Chinese Mollisols
Qingfeng Wang, Xin Jiang, Dawei Guan, Dan Wei, Baisuo Zhao, Mingchao Ma, Sanfeng Chen, Li Li, Fengming Cao, Jun Li
Applied Soil Ecology.2018; 125: 88. CrossRef
Agriculturally relevant microbial community structure in long-term fertilized paddy soils as revealed by phospholipid fatty acid (PLFA) and pyrosequencing analyses
Saranya Kuppusamy, Aillen Rose Daquiado, Song Yeob Kim, Young-Eun Yoon, Jang Hwan Kim, Sook Jin Kim, Yong Bok Lee
Archives of Agronomy and Soil Science.2018; 64(10): 1379. CrossRef
Insight into the Aggregation Capacity of Anammox Consortia during Reactor Start-Up
Yunpeng Zhao, Ying Feng, Jianqi Li, Yongzhao Guo, Liming Chen, Sitong Liu
Environmental Science & Technology.2018; 52(6): 3685. CrossRef
Effects of reclaimed water irrigation and nitrogen fertilization on the chemical properties and microbial community of soil
Wei GUO, Mathias N Andersen, Xue-bin QI, Ping LI, Zhong-yang LI, Xiang-yang FAN, Yuan ZHOU
Journal of Integrative Agriculture.2017; 16(3): 679. CrossRef
Effect of fertilization on soil microorganisms in paddy rice systems – A meta-analysis
Daniel Geisseler, Bruce A. Linquist, Patricia A. Lazicki
Soil Biology and Biochemistry.2017; 115: 452. CrossRef
The effect of different organic materials amendment on soil bacteria communities in barren sandy loam soil
Hongcui Dai, Yuanquan Chen, Xiaolei Yang, Jixiao Cui, Peng Sui
Environmental Science and Pollution Research.2017; 24(30): 24019. CrossRef
Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand
Andreas Reim, Marcela Hernández, Melanie Klose, Amnat Chidthaisong, Monthira Yuttitham, Ralf Conrad
Frontiers in Microbiology.2017;[Epub] CrossRef
Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China
Jing Zhou, Xin Jiang, Dan Wei, Baisuo Zhao, Mingchao Ma, Sanfeng Chen, Fengming Cao, Delong Shen, Dawei Guan, Jun Li
Scientific Reports.2017;[Epub] CrossRef
Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review
Hussnain Mukhtar, Yu-Pin Lin, Johnathen Anthony
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Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France)
Jorge R. Osman, Gustavo Fernandes, Michael S. DuBow
Rhizosphere.2017; 3: 112. CrossRef
Evident variations of fungal and actinobacterial cellulolytic communities associated with different humified particle-size fractions in a long-term fertilizer experiment
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Soil Biology and Biochemistry.2017; 113: 1. CrossRef
Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil
Annika Vaksmaa, Theo A. van Alen, Katharina F. Ettwig, Elisabetta Lupotto, Giampiero Valè, Mike S. M. Jetten, Claudia Lüke
Frontiers in Microbiology.2017;[Epub] CrossRef
Silica fertilization and nano-MnO2 amendment on bacterial community composition in high arsenic paddy soils
Jihai Shao, Yaxian He, Huiling Zhang, Anwei Chen, Ming Lei, Junfeng Chen, Liang Peng, Ji-Dong Gu
Applied Microbiology and Biotechnology.2016; 100(5): 2429. CrossRef
Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices
Jae-Hyung Ahn, Shin Ae Lee, Jeong Myeong Kim, Myung-Sook Kim, Jaekyeong Song, Hang-Yeon Weon
Journal of Microbiology.2016; 54(11): 724. CrossRef
Wheat and Rice Growth Stages and Fertilization Regimes Alter Soil Bacterial Community Structure, But Not Diversity
Jichen Wang, Chao Xue, Yang Song, Lei Wang, Qiwei Huang, Qirong Shen
Frontiers in Microbiology.2016;[Epub] CrossRef
Thirty four years of nitrogen fertilization decreases fungal diversity and alters fungal community composition in black soil in northeast China
Jing Zhou, Xin Jiang, Baoku Zhou, Baisuo Zhao, Mingchao Ma, Dawei Guan, Jun Li, Sanfeng Chen, Fengming Cao, Delong Shen, Jie Qin
Soil Biology and Biochemistry.2016; 95: 135. CrossRef
Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil
A. Vaksmaa, C. Lüke, T. van Alen, G. Valè, E. Lupotto, M. S. M Jetten, K. F. Ettwig, Gary King
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Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community
Björn Breidenbach, Martin B. Blaser, Melanie Klose, Ralf Conrad
Environmental Microbiology.2016; 18(9): 2868. CrossRef
Pyrosequencing analysis of bacterial community diversity in long-term fertilized paddy field soil
Aileen Rose Daquiado, Saranya Kuppusamy, Song Yeob Kim, Jang Hwan Kim, Young-Eun Yoon, Pil Joo Kim, Sung-Hwan Oh, Youn-Sig Kwak, Yong Bok Lee
Applied Soil Ecology.2016; 108: 84. CrossRef
Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China
Jing Zhou, Dawei Guan, Baoku Zhou, Baisuo Zhao, Mingchao Ma, Jie Qin, Xin Jiang, Sanfeng Chen, Fengming Cao, Delong Shen, Jun Li
Soil Biology and Biochemistry.2015; 90: 42. CrossRef
Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw
Ruibo Sun, Xue-Xian Zhang, Xisheng Guo, Daozhong Wang, Haiyan Chu
Soil Biology and Biochemistry.2015; 88: 9. CrossRef
Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water
Min Sun, Tangfu Xiao, Zengping Ning, Enzong Xiao, Weimin Sun
Applied Microbiology and Biotechnology.2015; 99(6): 2911. CrossRef
Impact of long-term fertilizer treatment on the microeukaryotic community structure of a rice field soil
Jun Murase, Azusa Hida, Kaori Ogawa, Toshihiro Nonoyama, Nanako Yoshikawa, Katsuhiko Imai
Soil Biology and Biochemistry.2015; 80: 237. CrossRef
Patterns of Bacterial Diversity Along a Long-Term Mercury-Contaminated Gradient in the Paddy Soils
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Microbial Ecology.2014; 68(3): 575. CrossRef
Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem
Hyo Jung Lee, Sang Yoon Kim, Pil Joo Kim, Eugene L. Madsen, Che Ok Jeon
FEMS Microbiology Ecology.2014; 88(1): 195. CrossRef
Ammonia oxidizer abundance in paddy soil profile with different fertilizer regimes
Jichen Wang, Li Zhang, Qiang Lu, Waseem Raza, Qiwei Huang, Qirong Shen
Applied Soil Ecology.2014; 84: 38. 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
Analysis of Community Structure of Metabolically Active Bacteria in a Rice Field Subjected to Long-Term Fertilization Practices
Jae-Hyung Ahn, Min-Young Choi, Hye-Won Lee, Byung-Yong Kim, Jaekyeong Song, Myung-Sook Kim, Hang-Yeon Weon
Korean Journal of Soil Science and Fertilizer.2013; 46(6): 585. CrossRef
Structure and function of the methanogenic microbial communities in Uruguayan soils shifted between pasture and irrigated rice fields
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Environmental Microbiology.2013; 15(9): 2588. CrossRef
Comparative Analysis of Endophytic Bacterial Communities in the Roots of Rice Grown under Long-term Fertilization Practice using Pyrosequencing Method
Byung-Yong Kim, Jae-Hyung Ahn, Jaekyeong Song, Myung-Sook Kim, Hang-Yeon Weon
Korean Journal of Soil Science and Fertilizer.2012; 45(6): 1100. CrossRef
Application of Amplicon Pyrosequencing in Soil Microbial Ecology
Jae-Hyung Ahn, Byung-Yong Kim, Dae-Hoon Kim, Jaekyeong Song, Hang-Yeon Weon
Korean Journal of Soil Science and Fertilizer.2012; 45(6): 1073. CrossRef

Seasonal Changes in Nitrogen-Cycle Gene Abundances and in Bacterial Communities in Acidic Forest Soils: Jaejoon Jung , Jinki Yeom , Jiwon Han , Jisun Kim , Woojun Park; J. Microbiol. 2012;50(3):365-373. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1465-2

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The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.

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Diversity of Bovine Rumen Methanogens In Vitro in the Presence of Condensed Tannins, as Determined by Sequence Analysis of 16S rRNA Gene Library: Hui Yin Tan , Chin Chin Sieo , Chin Mei Lee , Norhani Abdullah , Juan Boo Liang , Yin Wan Ho; J. Microbiol. 2011;49(3):492-498. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-0319-7

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Molecular diversity of rumen archaeal populations from bovine rumen fluid incubated with or without condensed tannins was investigated using 16S rRNA gene libraries. The predominant order of rumen archaea in the 16S rRNA gene libraries of the control and condensed tannins treatment was found to belong to a novel group of rumen archaea that is distantly related to the order Thermoplasmatales, with 59.5% (15 phylotypes) and 81.43% (21 phylotypes) of the total clones from the control and treatment clone libraries, respectively. The 16S rRNA gene library of the control was found to have higher proportions of methanogens from the orders Methanomicrobiales (32%) and Methanobacteriales (8.5%) as compared to those found in the condensed tannins treatment clone library in both orders (16.88% and 1.68% respectively). The phylotype distributed in the order Methanosarcinales was only found in the control clone library. The study indicated that condensed tannins could alter the diversity of bovine rumen methanogens.

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Characterization of Hyperthermostable Fructose-1,6-Bisphosphatase from Thermococcus onnurineus NA1: Yeol Gyun Lee , Sung Gyun Kang , Jung-Hyun Lee , Seung Il Kim , Young-Ho Chung; J. Microbiol. 2010;48(6):803-807. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0377-2

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To understand the physiological functions of thermostable fructose-1,6-bisphosphatase (TNA1-Fbp) from Thermococcus onnurineus NA1, its recombinant enzyme was overexpressed in Escherichia coli, purified, and the enzymatic properties were characterized. The enzyme showed maximal activity for fructose-1,6- bisphosphate at 95°C and pH 8.0 with a half-life (t1/2) of about 8 h. TNA1-Fbp had broad substrate specificities for fructose-1,6-bisphosphate and its analogues including fructose-1-phosphate, glucose-1-phosphate, and phosphoenolpyruvate. In addition, its enzyme activity was increased five-fold by addition of 1 mM Mg2+, while Li+ did not enhance enzymatic activity. TNA1-Fbp activity was inhibited by ATP, ADP, and phosphoenolpyruvate, but AMP up to 100 mM did not have any effect. TNA1-Fbp is currently defined as a class V fructose-1,6-bisphosphatase (FBPase) because it is very similar to FBPase of Thermococcus kodakaraensis KOD1 based on sequence homology. However, this enzyme shows a different range of substrate specificities. These results suggest that TNA1-Fbp can establish new criterion for class V FBPases.

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Pcal_0111, a highly thermostable bifunctional fructose-1,6-bisphosphate aldolase/phosphatase from Pyrobaculum calidifontis
Iram Aziz, Naeem Rashid, Raza Ashraf, Qamar Bashir, Tadayuki Imanaka, Muhammad Akhtar
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Application of Quantitative Real-Time PCR for Enumeration of Total Bacterial, Archaeal, and Yeast Populations in Kimchi: Eun-Jin Park , Ho-Won Chang , Kyoung-Ho Kim , Young-Do Nam , Seong Woon Roh , Jin-Woo Bae; J. Microbiol. 2009;47(6):682-685. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0297-1

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Abstract PDF: Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.

Journal Article

Monitoring Nutrient Impact on Bacterial Community Composition during Bioremediation of Anoxic PAH-Contaminated Sediment: Myungsu Kim , Seung Seob Bae , Mijin Seol , Jung-Hyun Lee , Young-Sook Oh; J. Microbiol. 2008;46(6):615-623. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0097-z

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Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

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

Bacterial, Archaeal, and Eukaryal Diversity in the Intestines of Korean People: Young-Do Nam , Ho-Won Chang , Kyoung-Ho Kim , Seong Woon Roh , Min-Soo Kim , Mi-Ja Jung , Si-Woo Lee , Jong-Yeol Kim , Jung-Hoon Yoon , Jin-Woo Bae; J. Microbiol. 2008;46(5):491-501. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0199-7

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The bacterial, archaeal, and eukaryal diversity in fecal samples from ten Koreans were analyzed and compared by using the PCR-fingerprinting method, denaturing gradient gel electrophoresis (DGGE). The bacteria all belonged to the Firmicutes and Bacteroidetes phyla, which were known to be the dominant bacterial species in the human intestine. Most of the archaeal sequences belonged to the methane-producing archaea but several halophilic archarea-related sequences were also detected unexpectedly. While a small number of eukaryal sequences were also detected upon DGGE analysis, these sequences were related to fungi and stramenopiles (Blastocystis hominis). With regard to the bacterial and archaeal DGGE analysis, all ten samples had one and two prominent bands, respectively, but many individual-specific bands were also observed. However, only five of the ten samples had small eukaryal DGGE bands and none of these bands was observed in all five samples. Unweighted pair group method and arithmetic averages clustering algorithm (UPGMA) clustering analysis revealed that the archaeal and bacterial communities in the ten samples had relatively higher relatedness (the average Dice coefficient values were 68.9 and 59.2% for archaea and bacteria, respectively) but the eukaryal community showed low relatedness (39.6%).

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Archaeal Communities in Mangrove Soil Characterized by 16S rRNA Gene Clones: Bing Yan , Kui Hong , Zi-Niu Yu; J. Microbiol. 2006;44(5):566-571.; DOI: https://doi.org/2439 [pii]

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Abstract PDF: An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

Archaeal Diversity in Tidal Flat Sediment as Revealed by 16S rDNA Analysis: Bong-Soo Kim , Huyn-Myung Oh , Hojeong Kang , Jongsik Chun; J. Microbiol. 2005;43(2):144-151.; DOI: https://doi.org/2170 [pii]

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Abstract PDF: During the past ten years, Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages. More recently, the presence of novel archaeal phylogenetic lineages has been discovered in coastal marine environments, freshwater lakes, polar seas, and deep-sea hydrothermal vents. Therefore, we conducted an investigation into the archaeal community existing in tidal flat sediment collected from Ganghwa Island, Korea. Phylogenetic analysis of archaeal 16S rDNA amplified directly from tidal flat sediment DNA revealed the presence of two major lineages, belonging to the Crenarchaeota (53.9%) and Euryarchaeota (46.1%) phyla. A total of 102 clones were then sequenced and analyzed by comprehensive phylogenetic analysis. The sequences determined in our samples were found to be closely related to the sequences of clones which had been previously obtained from a variety of marine environments. Archaeal clones exhibited higher similarities (83.25 - 100%) to sequences from other environments in the public database than did those (75.22 - 98.46%) of previously reported bacterial clones obtained from tidal flat sediment. The results of our study suggest that the archaeal community in tidal flat sediment is remarkably diverse.

Research Support, U.S. Gov't, Non-P.H.S.

A Novel Archaeal Group in the Phylum Crenarchaeota Found Unexpectedly in an Eukaryotic Survey in the Cariaco Basin: Sun-Ok Jeon , Tae-Seok Ahn , Sun-Hee Hong; J. Microbiol. 2008;46(1):34-39.; DOI: https://doi.org/10.1007/s12275-007-0247-8

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Abstract PDF: Archaea have been found in many more diverse habitats than previously believed due in part to modern molecular approaches to discovering microbial diversity. We report here an unexpected expansion of the habitat diversity of the Archaea in the Cariaco Basin we found using a primer set designed for 18S eukaryotic rDNA sequence analysis. The results presented here expand the originally identified 9 archaeal clones reported in this environment using bacterial/archaeal primers to 152 archaeal clones: 67 (18 OTU) of these clones were found at a depth of 900 m of station A while 71 (9 OTU) of them were at a depth of between 300~335 m of station B&C depending upon which location the samples were taken. We used three phylogenetic analysis methods and detected 20 phylotypes belonging to a single previously unreported group distantly related to the Crenarchaeota. Also, we determined that the original nine sequences did not fall into any of the known phyla of the Archaea suggesting that they may represent a novel group within the Kingdom Archaea. Thus, from these two studies, we suggest that Archaea in the Cariaco Basin could be unique; however, further studies using archaeal-specific primers and the design of new primers as well as the systematic use of several different primer combinations may improve the chances of understanding the archeal diversity in the Cariaco Basin.

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