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Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake
Yabing Gu, Junsheng Li, Zhenghua Liu, Min Zhang, Zhaoyue Yang, Huaqun Yin, Liyuan Chai, Delong Meng, Nengwen Xiao
J. Microbiol. 2024;62(10):829-843.   Published online October 22, 2024
DOI: https://doi.org/10.1007/s12275-024-00171-8
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AbstractAbstract
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
Hee-Jung Lee , Hanul Choi , Aleksandra Nowakowska , Lin-Woo Kang , Minjee Kim , Young Bong Kim
J. Microbiol. 2023;61(7):703-711.   Published online June 26, 2023
DOI: https://doi.org/10.1007/s12275-023-00062-4
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AbstractAbstract
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
Kyungseob Noh , Eun Ju Jeong , Timothy An , Jin Soo Shin , Hyejin Kim , Soo Bong Han , Meehyein Kim
J. Microbiol. 2022;60(5):550-559.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1661-7
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AbstractAbstract
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
Ye Won An , Young Sill Choi , Mi-ran Yun , Chihwan Choi , Su Yeon Kim
J. Microbiol. 2022;60(2):187-191.   Published online January 7, 2022
DOI: https://doi.org/10.1007/s12275-022-1335-5
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AbstractAbstract
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
Soo-Yeon Cho , Soo-Jin Jung , Kyoung-Dong Kim , Jung-Hye Roe
J. Microbiol. 2021;59(12):1075-1082.   Published online October 26, 2021
DOI: https://doi.org/10.1007/s12275-021-1438-4
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AbstractAbstract
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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  • 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
Jae-Hyung Jin , Myung Kyung Choi , Hyun-Soo Cho , Yong-Sun Bahn
J. Microbiol. 2021;59(7):658-665.   Published online July 1, 2021
DOI: https://doi.org/10.1007/s12275-021-1287-1
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AbstractAbstract
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
Yang Hu , Jian Cai , Chengrong Bai , Keqiang Shao , Xiangming Tang , Guang Gao
J. Microbiol. 2018;56(2):104-112.   Published online February 2, 2018
DOI: https://doi.org/10.1007/s12275-018-7244-y
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AbstractAbstract
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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  • 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
Mathur Nadarajan Kathiravan , Geun Ho Gim , Jaewon Ryu , Pyung Il Kim , Chul Won Lee , Si Wouk Kim
J. Microbiol. 2015;53(11):767-775.   Published online October 28, 2015
DOI: https://doi.org/10.1007/s12275-015-5454-0
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AbstractAbstract
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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  • 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
Ruyin Liu , Ke Li , Hongxun Zhang , Junge Zhu , DevRaj Joshi
J. Microbiol. 2014;52(11):898-907.   Published online October 31, 2014
DOI: https://doi.org/10.1007/s12275-014-4075-3
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AbstractAbstract
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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  • 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
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    Journal of Photochemistry and Photobiology B: Biology.2024; : 113083.     CrossRef
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    Jean-Baptiste Ramond, Karen Jordaan, Beatriz Díez, Sandra M. Heinzelmann, Don A. Cowan
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  • 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
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    CATENA.2020; 190: 104559.     CrossRef
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    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
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    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
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    Bingchang Zhang, Weidong Kong, Nan Wu, Yuanming Zhang
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  • 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
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Effects of Elevated CO2 and Pb on the Microbial Community in the Rhizosphere of Pinus densiflora
Sunghyun Kim , Sun Hwa Hong , Kyungsook Cho , Insook Lee , Gayoung Yoo , Hojeong Kang
J. Microbiol. 2012;50(6):895-901.   Published online December 30, 2012
DOI: https://doi.org/10.1007/s12275-012-2207-1
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AbstractAbstract
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
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
J. Microbiol. 2009;47(6):673-681.   Published online February 4, 2010
DOI: https://doi.org/10.1007/s12275-009-0194-7
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AbstractAbstract
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
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
J. Microbiol. 2007;45(2):113-121.
DOI: https://doi.org/2525 [pii]
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AbstractAbstract
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
Shipeng Lu , Minjeong Park , Hyeon-Su Ro , Dae Sung Lee , Woojun Park , Che Ok Jeon
J. Microbiol. 2006;44(2):155-161.
DOI: https://doi.org/2370 [pii]
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AbstractAbstract
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
Chris Freeman , Seon-Young Kim , Seung-Hoon Lee , Hojeong Kang
J. Microbiol. 2004;42(4):267-277.
DOI: https://doi.org/2111 [pii]
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AbstractAbstract
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
Inae Hur , Jongsik Chun
J. Microbiol. 2004;42(1):9-13.
DOI: https://doi.org/2008 [pii]
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AbstractAbstract
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/.

Journal of Microbiology : Journal of Microbiology
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