Journal Articles
- Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake
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Yabing Gu, Junsheng Li, Zhenghua Liu, Min Zhang, Zhaoyue Yang, Huaqun Yin, Liyuan Chai, Delong Meng, Nengwen Xiao
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J. Microbiol. 2024;62(10):829-843. Published online October 22, 2024
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DOI: https://doi.org/10.1007/s12275-024-00171-8
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Abstract
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The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity.
Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH4+-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.
- Antiviral Activity Against SARS‑CoV‑2 Variants Using in Silico and in Vitro Approaches
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Hee-Jung Lee , Hanul Choi , Aleksandra Nowakowska , Lin-Woo Kang , Minjee Kim , Young Bong Kim
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J. Microbiol. 2023;61(7):703-711. Published online June 26, 2023
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DOI: https://doi.org/10.1007/s12275-023-00062-4
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Abstract
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emergence in 2019 led to global health crises and the persistent
risk of viral mutations. To combat SARS-CoV-2 variants, researchers have explored new approaches to identifying
potential targets for coronaviruses. This study aimed to identify SARS-CoV-2 inhibitors using drug repurposing. In silico
studies and network pharmacology were conducted to validate targets and coronavirus-associated diseases to select potential
candidates, and in vitro assays were performed to evaluate the antiviral effects of the candidate drugs to elucidate the
mechanisms of the viruses at the molecular level and determine the effective antiviral drugs for them. Plaque and cytopathic
effect reduction were evaluated, and real-time quantitative reverse transcription was used to evaluate the antiviral activity
of the candidate drugs against SARS-CoV-2 variants in vitro. Finally, a comparison was made between the molecular docking
binding affinities of fenofibrate and remdesivir (positive control) to conventional and identified targets validated from
protein–protein interaction (PPI). Seven candidate drugs were obtained based on the biological targets of the coronavirus,
and potential targets were identified by constructing complex disease targets and PPI networks. Among the candidates,
fenofibrate exhibited the strongest inhibition effect 1 h after Vero E6 cell infection with SARS-CoV-2 variants. This study
identified potential targets for coronavirus disease (COVID-19) and SARS-CoV-2 and suggested fenofibrate as a potential
therapy for COVID-19.
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- Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
- The efficacy of a 2,4-diaminoquinazoline compound as an intranasal vaccine adjuvant to protect against influenza A virus infection in vivo
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Kyungseob Noh , Eun Ju Jeong , Timothy An , Jin Soo Shin , Hyejin Kim , Soo Bong Han , Meehyein Kim
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J. Microbiol. 2022;60(5):550-559. Published online April 18, 2022
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DOI: https://doi.org/10.1007/s12275-022-1661-7
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Abstract
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Adjuvants are substances added to vaccines to enhance antigen-
specific immune responses or to protect antigens from
rapid elimination. As pattern recognition receptors, Toll-like
receptors 7 (TLR7) and 8 (TLR8) activate the innate immune
system by sensing endosomal single-stranded RNA of RNA
viruses. Here, we investigated if a 2,4-diaminoquinazolinebased
TLR7/8 agonist, (S)-3-((2-amino-8-fluoroquinazolin-
4-yl)amino)hexan-1-ol (named compound 31), could be used
as an adjuvant to enhance the serological and mucosal immunity
of an inactivated influenza A virus vaccine. The compound induced
the production of proinflammatory cytokines in macrophages.
In a dose-response analysis, intranasal administration
of 1 μg compound 31 together with an inactivated vaccine
(0.5 μg) to mice not only enhanced virus-specific IgG and
IgA production but also neutralized influenza A virus with
statistical significance. Notably, in a virus-challenge model,
the combination of the vaccine and compound 31 alleviated
viral infection-mediated loss of body weight and increased
survival rates by 40% compared with vaccine only-treated mice.
We suggest that compound 31 is a promising lead compound
for developing mucosal vaccine adjuvants to protect against
respiratory RNA viruses such as influenza viruses and potentially
coronaviruses.
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- Efflux-Enhanced Imidazoquinolines To Exploit Chemoresistance
Muhammad Haroon, Sharmin Sultana, Seyedeh A. Najibi, Emily T. Wang, Abbey Michaelson, Pranto S. M. Al Muied, Amy E. Nielsen, Rock J. Mancini
ACS Omega.2025;[Epub] CrossRef - Design, Synthesis, and Biological Evaluation of New 2,6,7-Substituted Purine Derivatives as Toll-like Receptor 7 Agonists for Intranasal Vaccine Adjuvants
Morgan Kim, Kyungseob Noh, Pyeongkeun Kim, Jae Ho Kim, Byeong Wook Choi, Ravi Singh, Jun-Ho Choi, Soo Bong Han, Seong Soon Kim, Eun-Young Lee, Myung Ae Bae, Daeho Shin, Meehyein Kim, Jin Hee Ahn
Journal of Medicinal Chemistry.2024; 67(11): 9389. CrossRef - Evaluation of Antiviral Activity of Gemcitabine Derivatives against Influenza Virus and Severe Acute Respiratory Syndrome Coronavirus 2
Hyeon-Min Cha, Uk-Il Kim, Soo Bin Ahn, Myoung Kyu Lee, Haemi Lee, Hyungtae Bang, Yejin Jang, Seong Soon Kim, Myung Ae Bae, Kyungjin Kim, Meehyein Kim
ACS Infectious Diseases.2023; 9(4): 1033. CrossRef - Identification of broad-spectrum neutralizing antibodies against influenza A virus and evaluation of their prophylactic efficacy in mice
Sumin Son, Soo Bin Ahn, Geonyeong Kim, Yejin Jang, Chunkyu Ko, Meehyein Kim, Sang Jick Kim
Antiviral Research.2023; 213: 105591. CrossRef - Inhibition of KIF20A suppresses the replication of influenza A virus by inhibiting viral entry
Hoyeon Jeon, Younghyun Lim, In-Gu Lee, Dong-In Kim, Keun Pil Kim, So-Hee Hong, Jeongkyu Kim, Youn-Sang Jung, Young-Jin Seo
Journal of Microbiology.2022; 60(11): 1113. CrossRef
- Characterization and validation of an alternative reference bacterium Korean Pharmacopoeia Staphylococcus aureus strain
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Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim
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J. Microbiol. 2022;60(2):187-191. Published online January 7, 2022
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DOI: https://doi.org/10.1007/s12275-022-1335-5
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Abstract
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The National Culture Collection of Pathogens (NCCP) is a
microbial resource bank in Korea that collects pathogen resources
causing infectious disease in human and distributes
them for research and education. The NCCP bank attempts
to discover strains with various characteristics and specific
purposes to provide diverse resources to researchers. Staphylococcus
aureus American Type Culture Collection (ATCC)
6538P is used as a reference strain in the microbial assay for
antibiotics in the Korean and in the United States Pharmacopoeias.
We aimed to analyze domestically isolated microbial
resources from the NCCP to replace the S. aureus reference
strain. Staphylococcus aureus strains were identified using matrix-
assisted laser desorption/ionization time-of-flight mass
spectrometry and the VITEK-2 system and characterized by
multilocus sequence typing, 16S rRNA sequencing, and antibiotic
susceptibility testing. Several candidate strains had similar
characteristics as the reference strain. Among them, the
nucleotide sequence of the 16S rRNA region of NCCP 16830
was 100% identical to that of the reference strain; it was sensitive
to six types of antibiotics and showed results most similar
to the reference strain. A validity evaluation was conducted
using the cylinder-plate method. NCCP 16830 presented
valid results and had the same performance as ATCC
6538P; therefore, it was selected as an alternative candidate
strain.
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- Bacterial composition of refrigerators in households and inactivation of airborne Staphylococcus aureus using a TiO2-UVLED module in a 512 L aerobiology chamber
So-Seum Yong, Jae-Ik Lee, Dong-Hyun Kang
Food Microbiology.2023; 114: 104274. CrossRef
- Non-mitochondrial aconitase regulates the expression of iron-uptake genes by controlling the RNA turnover process in fission yeast
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Soo-Yeon Cho , Soo-Jin Jung , Kyoung-Dong Kim , Jung-Hye Roe
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J. Microbiol. 2021;59(12):1075-1082. Published online October 26, 2021
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DOI: https://doi.org/10.1007/s12275-021-1438-4
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51
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Abstract
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Aconitase, a highly conserved protein across all domains of
life, functions in converting citrate to isocitrate in the tricarboxylic
acid cycle. Cytosolic aconitase is also known to act as
an iron regulatory protein in mammals, binding to the RNA
hairpin structures known as iron-responsive elements within
the untranslated regions of specific RNAs. Aconitase-2 (Aco2)
in fission yeast is a fusion protein consisting of an aconitase
and a mitochondrial ribosomal protein, bL21, residing not
only in mitochondria but also in cytosol and the nucleus. To
investigate the role of Aco2 in the nucleus and cytoplasm of
fission yeast, we analyzed the transcriptome of aco2ΔN mutant
that is deleted of nuclear localization signal (NLS). RNA
sequencing revealed that the aco2ΔN mutation caused increase
in mRNAs encoding iron uptake transporters, such as
Str1, Str3, and Shu1. The half-lives of mRNAs for these genes
were found to be significantly longer in the aco2ΔN mutant
than the wild-type strain, suggesting the role of Aco2 in mRNA
turnover. The three conserved cysteines required for the catalytic
activity of aconitase were not necessary for this role.
The UV cross-linking RNA immunoprecipitation analysis
revealed that Aco2 directly bound to the mRNAs of iron uptake
transporters. Aco2-mediated degradation of iron-uptake
mRNAs appears to utilize exoribonuclease pathway that involves
Rrp6 as evidenced by genetic interactions. These results
reveal a novel role of non-mitochondrial aconitase protein
in the mRNA turnover in fission yeast to fine-tune iron
homeostasis, independent of regulation by transcriptional
repressor Fep1.
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Citations
Citations to this article as recorded by

- Iron-mediated post-transcriptional regulation in Toxoplasma gondii
Megan A. Sloan, Adam Scott, Dana Aghabi, Lucia Mrvova, Clare R. Harding, Dominique Soldati-Favre
PLOS Pathogens.2025; 21(2): e1012857. CrossRef - The Key Enzymes of Carbon Metabolism and the Glutathione Antioxidant System Protect Yarrowia lipolytica Yeast Against pH-Induced Stress
Tatyana I. Rakhmanova, Natalia N. Gessler, Elena P. Isakova, Olga I. Klein, Yulia I. Deryabina, Tatyana N. Popova
Journal of Fungi.2024; 10(11): 747. CrossRef - The intricate link between iron, mitochondria and azoles in Candida species
Wouter Van Genechten, Rudy Vergauwen, Patrick Van Dijck
The FEBS Journal.2024; 291(16): 3568. CrossRef - Non-Mitochondrial Aconitase-2 Mediates the Transcription of Nuclear-Encoded Electron Transport Chain Genes in Fission Yeast
Ho-Jung Kim, Soo-Yeon Cho, Soo-Jin Jung, Yong-Jun Cho, Jung-Hye Roe, Kyoung-Dong Kim
Journal of Microbiology.2024; 62(8): 639. CrossRef - Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress
Tatyana I. Rakhmanova, Varvara Yu. Sekova, Natalya N. Gessler, Elena P. Isakova, Yulia I. Deryabina, Tatyana N. Popova, Yevgeniya I. Shurubor, Boris F. Krasnikov
International Journal of Molecular Sciences.2023; 24(8): 7670. CrossRef
- Zinc-binding domain mediates pleiotropic functions of Yvh1 in Cryptococcus neoformans
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Jae-Hyung Jin , Myung Kyung Choi , Hyun-Soo Cho , Yong-Sun Bahn
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J. Microbiol. 2021;59(7):658-665. Published online July 1, 2021
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DOI: https://doi.org/10.1007/s12275-021-1287-1
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Abstract
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Yvh1 is a dual-specificity phosphatase (DUSP) that is evolutionarily
conserved in eukaryotes, including yeasts and humans.
Yvh1 is involved in the vegetative growth, differentiation,
and virulence of animal and plant fungal pathogens.
All Yvh1 orthologs have a conserved DUSP catalytic domain
at the N-terminus and a zinc-binding (ZB) domain with two
zinc fingers (ZFs) at the C-terminus. Although the DUSP domain
is implicated in the regulation of MAPK signaling in
humans, only the ZB domain is essential for most cellular
functions of Yvh1 in fungi. This study aimed to analyze the
functions of the DUSP and ZB domains of Yvh1 in the human
fungal pathogen Cryptococcus neoformans, whose Yvh1
(CnYvh1) contains a DUSP domain at the C-terminus and
a ZB domain at the N-terminus. Notably, CnYvh1 has an extended
internal domain between the two ZF motifs in the ZB
domain. To elucidate the function of each domain, we constructed
individual domain deletions and swapping strains
by complementing the yvh1Δ mutant with wild-type (WT)
or mutated YVH1 alleles and examined their Yvh1-dependent
phenotypes, including growth under varying stress conditions,
mating, and virulence factor production. Here, we found
that the complementation of the yvh1Δ mutant with the mutated
YVH1 alleles having two ZFs of the ZB domain, but not
the DUSP and extended internal domains, restored the WT
phenotypic traits in the yvh1Δ mutant. In conclusion, the
ZB domain, but not the N-terminal DUSP domain, plays a
pivotal role in the pathobiological functions of cryptococcal
Yvh1.
- Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China
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Yang Hu , Jian Cai , Chengrong Bai , Keqiang Shao , Xiangming Tang , Guang Gao
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J. Microbiol. 2018;56(2):104-112. Published online February 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7244-y
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Abstract
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The patterns of macrobiota in lotic ecosystems have been
extensively explored, however, the dynamics of microbiota
remain poorly investigated, especially in the high-elevation
region. To address this deficit, we collected eight samples to
unveil the bacterial and archaeal community in the Kaidu
river, located at the arid region of northwestern China (an
average of 2,500 m a.s.l.). For the bacterial community, phylogenetically
Betaproteobacteria prevailed, followed by Alphaproteobacteria
and Actinobacteria; at the finer genus level,
Limnohabitans and Variovorax were prominent. Along the
river, the bacterial community showed a continuous succession.
Specifically, their α- and β-diversity gradually increased,
suggesting a distance-decay pattern. Additionally, there was
an ecological transition between the dominant and the rare
sub-community along the river: the relative abundance of the
dominant members gradually decreased as the rare members
increased. We report that temperature and spatial distance
were significantly related to the variation of bacterial community.
Variance partitioning analysis showed that the environmental
factors contributed more to the bacterial community
than did the spatial distance. In the case of the archaeal
community, the methanogenic groups, mainly Methanosaeta
and Methanosarcina, were prominent within the Kaidu
river. Unlike the continuous change in the patterns of the
bacterial community, the archaeal community showed a constant
pattern along the river. Our results showed that the archaeal
community was independent of the environmental and
spatial factors. We propose that the inoculation of soil-derived
archaea is responsible for the archaeal community in
the Kaidu river. Together, our study demonstrated that the
bacterial community in the high-elevation Kaidu river is a
continuum, whereas the archaeal community is not.
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Citations
Citations to this article as recorded by

- Planktonic archaea reveal stronger dispersal limitation and more network connectivity than planktonic bacteria in the Jinsha River of southwestern China
Ge Cui, Juan Chen, Chao Wang, Peifang Wang, Bo Zhang, Han Gao, Rui Fu
Freshwater Biology.2023; 68(11): 1995. CrossRef - Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event
Mégane Noyer, Maria Bernard, Olivier Verneau, Carmen Palacios
Environmental Science and Pollution Research.2023; 30(17): 49685. CrossRef - Using the health index of the environmental microbiota to predict the health status of aquatic wildlife
Haile Yang, Qiong Zhou, Xia Guo, Zhigang Liu, Hui Zhang, Hao Du
Ecological Indicators.2023; 151: 110346. CrossRef - Phytoplankton dynamics and implications for eutrophication management in an urban river with a series of rubber dams
Linlin Bao, Jie Chen, Hongjin Tong, Jun Qian, Xuyong Li
Journal of Environmental Management.2022; 311: 114865. CrossRef - Effect of Water Chemistry, Land Use Patterns, and Geographic Distances on the Spatial Distribution of Bacterioplankton Communities in an Anthropogenically Disturbed Riverine Ecosystem
Jun Zhao, Wang Peng, Mingjun Ding, Minghua Nie, Gaoxiang Huang
Frontiers in Microbiology.2021;[Epub] CrossRef - Bacterial community composition shaped by water chemistry and geographic distance in an anthropogenically disturbed river
Peng Wang, Jun Zhao, Hanyu Xiao, Wenjing Yang, Xiaofang Yu
Science of The Total Environment.2019; 655: 61. CrossRef - Structure of bacterial and eukaryote communities reflect in situ controls on community assembly in a high-alpine lake
Eli Michael S. Gendron, John L. Darcy, Katherinia Hell, Steven K. Schmidt
Journal of Microbiology.2019; 57(10): 852. CrossRef
Research Support, Non-U.S. Gov'ts
- Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil
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Mathur Nadarajan Kathiravan , Geun Ho Gim , Jaewon Ryu , Pyung Il Kim , Chul Won Lee , Si Wouk Kim
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J. Microbiol. 2015;53(11):767-775. Published online October 28, 2015
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DOI: https://doi.org/10.1007/s12275-015-5454-0
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47
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Abstract
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In this study, novel DNA extraction and purification methods
were developed to obtain high-quantity and reliable quality
DNA from the microbial community of agricultural yellow
loess soil samples. The efficiencies of five different soil DNAextraction
protocols were evaluated on the basis of DNA
yield, quality and DNA shearing. Our suggested extraction
method
, which used CTAB, EDTA and cell membrane lytic
enzymes in the extraction followed by DNA precipitation
using isopropanol, yielded a maximum DNA content of 42.28
± 5.59 μg/g soil. In addition, among the five different purification
protocols, the acid-treated polyvinyl polypyrrolidone
(PVPP) spin column purification method yielded high-quality
DNA and recovered 91% of DNA from the crude DNA.
Spectrophotometry revealed that the ultraviolet A260/A230
and A260/A280 absorbance ratios of the purified DNA were
1.82 ± 0.03 and 1.94 ± 0.05, respectively. PCR-based 16S rRNA
amplification showed clear bands at ~1.5 kb with acid-treated
PVPP–purified DNA templates. In conclusion, our suggested
extraction and purification protocols can be used to recover
high concentration, high purity, and high-molecular-weight
DNA from clay and silica-rich agricultural soil samples.
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Citations
Citations to this article as recorded by

- TACKLING THE SOIL MICROBIOME – CHALLENGES AND OPORTUNITIES
Andreea-Mihaela Mlesnita
Journal of Experimental and Molecular Biology.2024;[Epub] CrossRef - Effects of sodium sulfide application on the growth of Robinia pseudoacacia, heavy metal immobilization, and soil microbial activity in Pb–Zn polluted soil
Xiangyu Zhang, Xiao Lou, Haoqiang Zhang, Wei Ren, Ming Tang
Ecotoxicology and Environmental Safety.2020; 197: 110563. CrossRef - Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi
Zhuoran Han, Jingfeng Sun, Aijun Lv, Anli Wang
MicrobiologyOpen.2019;[Epub] CrossRef - Isolation of PCR-quality Genomic DNA from Soils Impacted with Extra Heavy Crude Oil
Laynet Angerlyn Puentes , Yusibeska Ramos, Ysvic Inojosa, César Rivera, Angela De Sisto
BIO-PROTOCOL.2019;[Epub] CrossRef - Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei
Boyun Jiang, Jingfeng Sun, Aijun Lv, Xiucai Hu, Hongyue Shi, YeongYik Sung, Qingkui Wang, Yang Wang
FEMS Microbiology Letters.2019;[Epub] CrossRef - Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples
Mariam Hassan, Tamer Essam, Salwa Megahed
Brazilian Journal of Microbiology.2018; 49: 1. CrossRef - A modified method for genomic DNA extraction from the fish intestinal microflora
Zhuoran Han, Jingfeng Sun, Aijun Lv, YeongYik Sung, Xueliang Sun, Hongyue Shi, Xiucai Hu, Anli Wang, Kezhi Xing
AMB Express.2018;[Epub] CrossRef - Isolation of nematode DNA from 100 g of soil using Fe3O4 super paramagnetic nanoparticles
Adrienne M. Gorny, Frank S. Hay, Xiaohong Wang, Sarah J. Pethybridge
Nematology.2018; 20(3): 271. CrossRef - Evaluation of the Punch-it™ NA-Sample kit for detecting microbial DNA in blood culture bottles using PCR-reverse blot hybridization assay
Jungho Kim, Hye-young Wang, Seoyong Kim, Soon Deok Park, Kwangmin Yu, Hyo Youl Kim, Young Uh, Hyeyoung Lee
Journal of Microbiological Methods.2016; 128: 24. CrossRef
- Spatial Distribution of Microbial Communities Associated with Dune Landform in the Gurbantunggut Desert, China
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Ruyin Liu , Ke Li , Hongxun Zhang , Junge Zhu , DevRaj Joshi
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J. Microbiol. 2014;52(11):898-907. Published online October 31, 2014
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DOI: https://doi.org/10.1007/s12275-014-4075-3
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Abstract
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The microbial community compositions and potential ammonia oxidation in the topsoil at different positions of sand dune (stoss slope, crest, lee slope, and interdune) from the Gurbantunggut Desert, the largest semi-fixed desert in China, were investigated using several molecular methods. Actinobacteria and Proteobacteria (especially Alphaproteobacteria) were commonly the dominant taxa across all soil samples. Bacterial communities were similar in soils collected from the stoss slopes and interdunes (HC-BSCs, biological soil crusts with a high abundance of cyanobacteria), containing more abundant cyanobacterial populations (16.9–24.5%)
than those (0.2–0.7% of Cyanobacteria) in the crests and lee slopes (LC-BSCs, biological soil crusts with a low abundance of cyanobacteria). The Cyanobacteria were mainly composed of Microcoleus spp., and quantitative PCR analysis revealed
that 16S rRNA gene copy numbers of Cyanobacteria (especially genus Microcoleus) were at least two orders of magnitude higher in HC-BSCs than in LC-BSCs. Heterotrophic Geodermatophilus spp. frequently occurred in HC-BSCs (2.5–8.0%), whereas genera Arthrobacter, Bacillus, and Segetibacter were significantly abundant in LC-BSC communities. By comparison, the desert archaeal communities were less complex, and were dominated by Nitrososphaera spp. The amoA gene abundance of ammonia-oxidizing archaea (AOA) was higher than that of ammonia-oxidizing bacteria (AOB) in all soil samples, particularly in the interdunal soils (106–108 archaeal amoA gene copies per gram dry soil), indicating that AOA possibly dominate the ammonia oxidation at the interdunes.
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Citations
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- Streptomycetes in the Gurbantunggut Desert of Xinjiang: from culturable resource diversity to exploring the biosynthetic potential of antimicrobial natural products
Shuai LI, Lei DONG, JiaRui HAN, GuoYuan SHI, WenHui LIAN, YongHong LIU, BoHan LI, Abdalla Abdelshafy Mohamad Osama, WenJun LI
SCIENTIA SINICA Vitae.2024;[Epub] CrossRef - Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae
Sergey V. Tarlachkov, Irina P. Starodumova, Olga V. Boueva, Sergei V. Chernyshov, Lyudmila I. Evtushenko
Journal of Photochemistry and Photobiology B: Biology.2024; : 113083. CrossRef - Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems
Jean-Baptiste Ramond, Karen Jordaan, Beatriz Díez, Sandra M. Heinzelmann, Don A. Cowan
Microbiology and Molecular Biology Reviews.2022;[Epub] CrossRef - Spatial Diversity in Bacterial Communities across Barren and Vegetated, Native and Invasive, Coastal Dune Microhabitats
Brianna L. Boss, Bianca R. Charbonneau, Javier A. Izquierdo
Diversity.2021; 13(11): 525. CrossRef - Effect of substrate types on contaminant removals, electrochemical characteristics and microbial community in vertical flow constructed wetlands for treatment of urban sewage
Shaoyuan Bai, Lanqian Qin, Liheng Liu, Xutao Gao, Yanli Ding, Yanhong Li
Journal of Environmental Management.2021; 280: 111682. CrossRef - The driving effect of nitrogen-related functional microorganisms under water and nitrogen addition on N2O emission in a temperate desert
Ping Yue, Xiaoan Zuo, Kaihui Li, Xiaoqing Cui, Shaokun Wang, Tom Misselbrook, Xuejun Liu
Science of The Total Environment.2021; 772: 145470. CrossRef - Induced biological soil crusts and soil properties varied between slope aspect, slope gradient and plant canopy in the Hobq desert of China
Xiangjun Zhou, Tan Ke, Shuangxi Li, Songqiang Deng, Xiaoliang An, Xiao Ma, Roberto De Philippis, Lanzhou Chen
CATENA.2020; 190: 104559. CrossRef - Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems
Pok Man Leung, Sean K. Bay, Dimitri V. Meier, Eleonora Chiri, Don A. Cowan, Osnat Gillor, Dagmar Woebken, Chris Greening, James C. Stegen
mSystems.2020;[Epub] CrossRef - Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri, Ana R. Lopes
PLOS ONE.2020; 15(1): e0227639. CrossRef - Growth of cyanobacterial soil crusts during diurnal freeze-thaw cycles
Steven K. Schmidt, Lara Vimercati
Journal of Microbiology.2019; 57(4): 243. CrossRef - Effects of indigenous soil cyanobacteria on seed germination and seedling growth of arid species used in restoration
M. Muñoz-Rojas, A. Chilton, G. S. Liyanage, T. E. Erickson, D. J. Merritt, B. A. Neilan, M. K. J. Ooi
Plant and Soil.2018; 429(1-2): 91. CrossRef - Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing
Roland C. Wilhelm, Erick Cardenas, Hilary Leung, András Szeitz, Lionel D. Jensen, William W. Mohn
Frontiers in Microbiology.2017;[Epub] CrossRef - Changes in desert steppe soil culturable bacteria from northwestern China and correlation with physicochemical parameters
Yanlin Li, Jixiang Chen, Zhi Yang, Yonggang Wang, Yan Zhang, Yongtao Zhou
Toxicological & Environmental Chemistry.2017; 99(5-6): 809. CrossRef - Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China
Bingchang Zhang, Weidong Kong, Nan Wu, Yuanming Zhang
Journal of Basic Microbiology.2016; 56(6): 670. CrossRef - Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes
Haïtham Sghaier, Karima Hezbri, Faten Ghodhbane-Gtari, Petar Pujic, Arnab Sen, Daniele Daffonchio, Abdellatif Boudabous, Louis S Tisa, Hans-Peter Klenk, Jean Armengaud, Philippe Normand, Maher Gtari
The ISME Journal.2016; 10(1): 21. CrossRef - Microbial Characterization of Qatari Barchan Sand Dunes
Sara Abdul Majid, Michael F. Graw, Aspassia D. Chatziefthimiou, Hanh Nguyen, Renee Richer, Michel Louge, Ali A. Sultan, Patrick Schloss, Anthony G. Hay, Stefan J. Green
PLOS ONE.2016; 11(9): e0161836. CrossRef - Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities
Sandra Ronca, Jean-Baptiste Ramond, Brian E. Jones, Mary Seely, Don A. Cowan
Frontiers in Microbiology.2015;[Epub] CrossRef
- Effects of Elevated CO2 and Pb on the Microbial Community in the Rhizosphere of Pinus densiflora
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Sunghyun Kim , Sun Hwa Hong , Kyungsook Cho , Insook Lee , Gayoung Yoo , Hojeong Kang
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J. Microbiol. 2012;50(6):895-901. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2207-1
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Abstract
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Rising levels of atmospheric CO2 may stimulate forest productivity in the future, resulting in increased carbon storage in terrestrial ecosystems. However, heavy metal contamination may interfere with this, though the response is not yet known. In this study, we investigated the effect of elevated CO2 and Pb contamination on microorganisms and decomposition in pine tree forest soil. Three-year old pine trees
(Pinus densiflora) were planted in Pb contaminated soils (500 mg/kg-soil) and uncontaminated soils and cultivated for three months in a growth chamber where the CO2 concentration was controlled at 380 or 760 mg/kg. Structures of the microbial community were comparatively analyzed in bulk and in rhizosphere soil samples using community-level physiological profiling (CLPP) and 16S rRNA gene PCRDGGE
(denaturing gradient gel electrophoresis). Additionally, microbial activity in rhizospheric soil, growth and the C/N ratio of the pine trees were measured. Elevated CO2 significantly increased microbial activities and diversity in Pb contaminated soils due to the increase in carbon sources, and this increase was more distinctive in rhizospheric soil than in bulk soils. In addition, increased plant growth and C/N ratios of pine needles at elevated CO2 resulted in an increase in cation exchange capacity (CEC) and dissolved organic carbon (DOC) of the rhizosphere in Pb contaminated soil. Taken together, these findings indicate that elevated CO2 levels and heavy metals can affect the soil carbon cycle by
changing the microbial community and plant metabolism.
Research Support, U.S. Gov't, Non-P.H.S.
- Functional Shifts in Unvegetated, Perhumid, Recently-Deglaciated Soils Do Not Correlate with Shifts in Soil Bacterial Community Composition
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Sarah R. Sattin , Cory C. Cleveland , Eran Hood , Sasha C. Reed , Andrew J. King , Steven K. Schmidt , Michael S. Robeson , Nataly Ascarrunz , Diana R. Nemergut
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J. Microbiol. 2009;47(6):673-681. Published online February 4, 2010
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DOI: https://doi.org/10.1007/s12275-009-0194-7
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Past work in recently deglaciated soils demonstrates that microbial communities undergo shifts prior to plant colonization. To date, most studies have focused on relatively ‘long’ chronosequences with the ability to sample plant-free sites over at least 50 years of development. However, some recently deglaciated soils feature rapid plant colonization and questions remain about the relative rate of change in the microbial community in the unvegetated soils of these chronosequences. Thus, we investigated the forelands of the Mendenhall Glacier near Juneau, AK, USA, where plants rapidly establish. We collected unvegetated samples representing soils that had been ice-free for 0, 1, 4, and 8 years. Total nitrogen (N) ranged from 0.00~0.14 mg/g soil, soil organic carbon pools ranged from 0.6~2.3 mg/g soil, and both decreased in concentration between the 0 and 4 yr soils. Biologically available phosphorus (P) and pH underwent similar dynamics. However, both pH and available P increased in the 8 yr soils. Nitrogen fixation was nearly undetectable in the most recently exposed soils, and increased in the 8 yr soils to ~5 ng N fixed/cm2/h, a trend that was matched by the activity of the soil N-cycling enzymes urease and β-1,4-N-acetyl-glucosaminidase. 16S rRNA gene clone libraries revealed no significant differences between the 0 and 8 yr soils; however, 8 yr soils featured the presence of cyanobacteria, a division wholly absent from the 0 yr soils. Taken together, our results suggest that microbes are consuming allochtonous organic matter sources in the most recently exposed soils. Once this carbon source is depleted, a competitive advantage may be ceded to microbes not reliant on in situ nutrient sources.
Research Support, Non-U.S. Gov'ts
- Dominance of Endospore-forming Bacteria on a Rotating Activated Bacillus Contactor Biofilm for Advanced Wastewater Treatment
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Seong Joo Park , Jerng Chang Yoon , Kwang-Soo Shin , Eung Ho Kim , Soobin Yim , Yeon-Je Cho , Gi Moon Sung , Dong-Geun Lee , Seung Bum Kim , Dong-Uk Lee , Sung-Hoon Woo , Ben Koopman
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J. Microbiol. 2007;45(2):113-121.
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DOI: https://doi.org/2525 [pii]
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Abstract
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The bacterial diversity inherent to the biofilm community structure of a modified rotating biological contactor wastewater treatment process, referred to as the Rotating Activated Bacillus Contactor (RABC) process, was characterized in this study, via both culture-dependent and culture-independent methods. On the basis of culture-dependent methods, Bacillus sp. were found to exist in large numbers on the biofilm (6.5% of the heterotrophic bacteria) and the microbial composition of the biofilms was quite simple. Only three phyla were identified-namely, the Proteobacteria, the Actinobacteria (High G+C Gram-positive bacteria), and the Firmicutes (Low G+C Gram-positive bacteria). The culture-independent partial 16S rDNA sequence analysis revealed a considerably more diverse microbial composition within the biofilms. A total of eight phyla were recovered in this case, three of which were major groups: the Firmicutes (43.9%), the Proteobacteria (28.6%), and the Bacteroidetes (17.6%). The remaining five phyla were minor groups: the Planctomycetes (4.4%), the Chlorobi (2.2%), the Actinobacteria (1.1%), the Nitrospirae (1.1%), and the Verrucomicrobia (1.1%). The two most abundant genera detected were the endospore-forming bacteria (31.8%), Clostridium and Bacillus, both of which are members of the Firmicutes phylum. This finding indicates that these endospore-forming bacteria successfully colonized and dominated the RABC process biofilms. Many of the colonies or clones recovered from the biofilms evidenced significantly high homology in the 16S rDNA sequences of bacteria stored in databases associated with advanced wastewater treatment capabilities, including nitrification and denitrification, phosphorus accumulation, the removal of volatile odors, and the removal of chlorohydrocarbons or heavy metals. The microbial community structures observed in the biofilms were found to correlate nicely with the enhanced performance of advanced wastewater treatment protocols.
- Analysis of Microbial Communities Using Culture-dependent and Culture-independent Approaches in an Anaerobic/Aerobic SBR Reactor
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Shipeng Lu , Minjeong Park , Hyeon-Su Ro , Dae Sung Lee , Woojun Park , Che Ok Jeon
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J. Microbiol. 2006;44(2):155-161.
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DOI: https://doi.org/2370 [pii]
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Abstract
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Comparative analysis of microbial communities in a sequencing batch reactor which
performed enhanced biological phosphorus removal (EBPR) was carried out using a
cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: α, β, γ- Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivationbased method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.
Review
- Effects of Elevated Atmospheric CO_2 Concentrations on Soil Microorganisms
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Chris Freeman , Seon-Young Kim , Seung-Hoon Lee , Hojeong Kang
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J. Microbiol. 2004;42(4):267-277.
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DOI: https://doi.org/2111 [pii]
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Abstract
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Effects of elevated CO_2 on soil microorganisms are known to be mediated by various interactions with plants, for which such effects are relatively poorly documented. In this review, we summarize and synthesize results from studies assessing impacts of elevated CO_2 on soil ecosystems, focusing primarily on plants and a variety the of microbial processes. The processes considered include changes in microbial biomass of C and N, microbial number, respiration rates, organic matter decomposition, soil enzyme activities, microbial community composition, and functional groups of bacteria mediating trace gas emission such as methane and nitrous oxide. Elevated CO_2 in atmosphere may enhance certain microbial processes such as CH_4 emission from wetlands due to enhanced carbon supply from plants. However, responses of extracellular enzyme activities and microbial community structure are still controversy, because interferences with other factors such as the types of plants, nutrient availabilitial in soil, soil types, analysis methods, and types of CO_2 fumigation systems are not fully understood.
Research Support, Non-U.S. Gov't
- A Method for Comparing Multiple Bacterial Community Structures from 16S rDNA Clone Library Sequences
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Inae Hur , Jongsik Chun
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J. Microbiol. 2004;42(1):9-13.
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DOI: https://doi.org/2008 [pii]
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Abstract
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Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.