Journal of Microbiology

Journal Articles

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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Abstract: 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.

LAMMER Kinase Governs the Expression and Cellular Localization of Gas2, a Key Regulator of Flocculation in Schizosaccharomyces pombe: Won-Hwa Kang , Yoon-Dong Park , Joo-Yeon Lim , Hee-Moon Park; J. Microbiol. 2024;62(1):21-31. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00097-7

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Abstract: It was reported that LAMMER kinase in Schizosaccharomyces pombe plays an important role in cation-dependent and galactose-specific flocculation. Analogous to other flocculating yeasts, when cell wall extracts of the Δlkh1 strain were treated to the wild-type strain, it displayed flocculation. Gas2, a 1,3-β-glucanosyl transferase, was isolated from the EDTA-extracted cell-surface proteins in the Δlkh1 strain. While disruption of the gas2+ gene was not lethal and reduced the flocculation activity of the Δlkh1 strain, the expression of a secreted form of Gas2, in which the GPI anchor addition sequences had been removed, conferred the ability to flocculate upon the WT strain. The Gas2-mediated flocculation was strongly inhibited by galactose but not by glucose. Immunostaining analysis showed that the cell surface localization of Gas2 was crucial for the flocculation of fission yeast. In addition, we identified the regulation of mbx2+ expression by Lkh1 using RT-qPCR. Taken together, we found that Lkh1 induces asexual flocculation by regulating not only the localization of Gas2 but also the transcription of gas2+ through Mbx2.

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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Abstract

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

Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil: Kyeong Ryeol Kim† , Kyung Hyun Kim† , Shehzad Abid Khan , Hyung Min Kim , Dong Min Han , Che Ok Jeon; J. Microbiol. 2021;59(8):709-718. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1156-y

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Abstract

Two Gram-stain negative, yellow-pigmented, and mesophilic bacteria, designated strains R7T and R19T, were isolated from sandy and forest soil, South Korea, respectively. Both strains were non-motile rods showing catalase- and oxidase-positive activities. Both strains were shown to grow at 10–37°C and pH 6.0–9.0, and in the presence of 0–1.5% (w/v) NaCl. Strain R7T contained iso-C14:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c), whereas strain R19T contained iso-C11:0 3-OH, C16:1 ω7c alcohol, iso-C11:0, iso-C15:0, iso-C16:0, and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1 ω9c) as major cellular fatty acids (> 5%). Both strains contained ubiquinone- 8 as the sole isoprenoid quinone and phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid as the major polar lipids. The DNA G + C contents of strains R7T and R19T calculated from their genomes were 66.9 mol% and 68.9 mol%, respectively. Strains R7T and R19T were most closely related to Lysobacter panacisoli C8-1T and Lysobacter niabensis GH34-4T with 98.7% and 97.8% 16S rRNA sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains R7T and R19T formed distinct phylogenetic lineages within the genus Lysobacter. Based on phenotypic, chemotaxonomic, and molecular features, strains R7T and R19T represent novel species of the genus Lysobacter, for which the names Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. are proposed. The type strains of L. arenosi and L. solisilvae are R7T (= KACC 21663T = JCM 34257T) and R19T (= KACC 21767T = JCM 34258T), respectively.

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Luteimonas flava sp. nov. and Aquilutibacter rugosus gen. nov., sp. nov., isolated from freshwater environments in China and re-examining the taxonomic status of genera Luteimonas and Lysobacter
Huibin Lu, Li Chen, Yujing Wang, Peng Xing, Qinglong Wu
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Saline soil improvement promotes the transformation of microbial salt tolerance mechanisms and microbial-plant-animal ecological interactions
Keyu Yao, Guanghao Wang, Wen Zhang, Qiang Liu, Jian Hu, Mao Ye, Xin Jiang
Journal of Environmental Management.2024; 372: 123360. CrossRef
Optimal Irrigation and Fertilization Enhanced Tomato Yield and Water and Nitrogen Productivities by Increasing Rhizosphere Microbial Nitrogen Fixation
Hongfei Niu, Tieliang Wang, Yongjiang Dai, Mingze Yao, Bo Li, Jiaqi Zheng, Lizhen Mao, Mingyu Zhao, Zhanyang Xu, Feng Zhang
Agronomy.2024; 14(9): 2111. CrossRef
Short-term effect of reclaimed wastewater quality gradient on soil microbiome during irrigation
V. Moulia, N. Ait-Mouheb, G. Lesage, J. Hamelin, N. Wéry, V. Bru-Adan, L. Kechichian, M. Heran
Science of The Total Environment.2023; 901: 166028. CrossRef
Dyadobacter pollutisoli sp. nov., isolated from plastic waste landfill soil
Kyeong Ryeol Kim, Jeong Min Kim, Jae Kyeong Lee, Dong Min Han, Lujiang Hao, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Physiological and genomic analyses of cobalamin (vitamin B12)-auxotrophy of Lysobacter auxotrophicus sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil
Akihiro Saito, Hideo Dohra, Moriyuki Hamada, Ryota Moriuchi, Yohei Kotsuchibashi, Koji Mori
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Nitratireductor rhodophyticola sp. nov., isolated from marine red algae
Kyung Hyun Kim, Sylvia Kristyanto, Hyung Min Kim, Kyeong Ryeol Kim, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons)
Qian Liu, Guoying Fan, Kui Wu, Xiangning Bai, Xi Yang, Wentao Song, Shengen Chen, Yanwen Xiong, Haiying Chen
Journal of Microbiology.2022; 60(7): 668. CrossRef
Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
Journal of Microbiology.2022; 60(5): 469. CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment
Ju Hye Baek, Woonhee Baek, Sang Eun Jeong, Sung Chul Lee, Hyun Mi Jin, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology.2022;[Epub] CrossRef

Review

[MINIREVIEW]Bacterial bug-out bags: outer membrane vesicles and their proteins and functions: Kesavan Dineshkumar , Vasudevan Aparna , Liang Wu , Jie Wan , Mohamod Hamed Abdelaziz , Zhaoliang Su , Shengjun Wang , Huaxi Xu; J. Microbiol. 2020;58(7):531-542. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0026-3

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Abstract

Among the major bacterial secretions, outer membrane vesicles (OMVs) are significant and highly functional. The proteins and other biomolecules identified within OMVs provide new insights into the possible functions of OMVs in bacteria. OMVs are rich in proteins, nucleic acids, toxins and virulence factors that play a critical role in bacteria-host interactions. In this review, we discuss some proteins with multifunctional features from bacterial OMVs and their role involving the mechanisms of bacterial survival and defence. Proteins with moonlighting activities in OMVs are discussed based on their functions in bacteria. OMVs harbour many other proteins that are important, such as proteins involved in virulence, defence, and competition. Overall, OMVs are a power-packed aid for bacteria, harbouring many defensive and moonlighting proteins and acting as a survival kit in
case
of an emergency or as a defence weapon. In summary, OMVs can be defined as bug-out bags for bacterial defence and, therefore, survival.

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Bacterial membrane vesicles in the pathogenesis and treatment of inflammatory bowel disease
Chinasa Valerie Olovo, Dickson Kofi Wiredu Ocansey, Ying Ji, Xinxiang Huang, Min Xu
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Glycosylphosphatidylinositol-anchored proteins as non- DNA matter of inheritance: from molecular to cell to philosophical biology
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Microbe-host interactions: structure and functions of Gram-negative bacterial membrane vesicles
Min Xiao, Guiding Li, Hefeng Yang
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Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition
Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, Llorenç Cabrera-Bosquet, Thibaut Perez, Cécile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Aliénor Véry, Christian Rolando, Hervé
International Journal of Molecular Sciences.2022; 23(23): 15248. CrossRef
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Extracellular membrane vesicles from Limosilactobacillus reuteri strengthen the intestinal epithelial integrity, modulate cytokine responses and antagonize activation of TRPV1
Yanhong Pang, Ludwig Ermann Lundberg, Manuel Mata Forsberg, David Ahl, Helena Bysell, Anton Pallin, Eva Sverremark-Ekström, Roger Karlsson, Hans Jonsson, Stefan Roos
Frontiers in Microbiology.2022;[Epub] CrossRef
Streptomyces coelicolor Vesicles: Many Molecules To Be Delivered
Teresa Faddetta, Giovanni Renzone, Alberto Vassallo, Emilio Rimini, Giorgio Nasillo, Gianpiero Buscarino, Simonpietro Agnello, Mariano Licciardi, Luigi Botta, Andrea Scaloni, Antonio Palumbo Piccionello, Anna Maria Puglia, Giuseppe Gallo, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
Novel devices for isolation and detection of bacterial and mammalian extracellular vesicles
Shiana Malhotra, Zarinah M. Amin, Garima Dobhal, Sophie Cottam, Thomas Nann, Renee V. Goreham
Microchimica Acta.2021;[Epub] CrossRef
Tracing the origins of extracellular DNA in bacterial biofilms: story of death and predation to community benefit
Davide Campoccia, Lucio Montanaro, Carla Renata Arciola
Biofouling.2021; 37(9-10): 1022. CrossRef
The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages
Leah M. Smith, Simon A. Jackson, Lucia M. Malone, James E. Ussher, Paul P. Gardner, Peter C. Fineran
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Role of extracellular vesicles in liver diseases and their therapeutic potential
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Journal Articles

Zur-regulated lipoprotein A contributes to the fitness of Acinetobacter baumannii: Eun Kyung Lee , Chul Hee Choi , Man Hwan Oh; J. Microbiol. 2020;58(1):67-77. Published online January 2, 2020; DOI: https://doi.org/10.1007/s12275-020-9531-7

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Abstract

Acinetobacter baumannii is a notorious nosocomial pathogen that commonly infects severely ill patients. Zinc (Zn) is essential to survive and adapt to different environment and host niches in A. baumannii. Of the Zinc uptake regulator (Zur)-regulated genes in A. baumannii, the A1S_3412 gene encoding a Zur-regulated lipoprotein A (ZrlA) is critical for cell envelope integrity and overcoming antibiotic exposure. This study investigated whether ZrlA contributes to the fitness of A. baumannii in vitro and in vivo using the wildtype A. baumannii ATCC 17978, ΔzrlA mutant, and zrlAcomplemented strains. The ΔzrlA mutant showed reduced biofilm formation, surface motility, and adherence to and invasion of epithelial cells compared to the wild-type strain. In a mouse pneumonia model, the ΔzrlA mutant showed significantly lower bacterial numbers in the blood than the wildtype strain. These virulence traits were restored in the zrlAcomplemented strain. Under static conditions, the expression of csuCDE, which are involved in the chaperone-usher pili assembly system, was significantly lower in the ΔzrlA mutant than in the wild-type strain. Moreover, the expression of the bfmR/S genes, which regulate the CsuA/BABCDE system, was significantly lower in the ΔzrlA mutant under static conditions than in the wild-type strain. Our results indicate that the zrlA gene plays a role in the fitness of A. baumannii by regulating the BfmR/S two-component system and subsequently the CsuA/BABCDE chaperone-usher pili assembly system, suggesting it as a potential target for anti-virulence strategies against A. baumannii.

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Molecular Detection of Pap II, OmpA, and LuxR Genes Responsible for Biofilm Formation in Acinetobacter baumannii Isolated from Hospitalized Patients
Estabraq Ali Maklef, Amal A. Kareem, Susan F. K. Al-Sudani
Medical Journal of Babylon.2024; 21(Suppl 2): S258. CrossRef
Pathogenicity and virulence of Acinetobacter baumannii : Factors contributing to the fitness in healthcare settings and the infected host
Massimiliano Lucidi, Daniela Visaggio, Antonella Migliaccio, Giulia Capecchi, Paolo Visca, Francesco Imperi, Raffaele Zarrilli
Virulence.2024;[Epub] CrossRef
Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii
Minyong Kim, My Tra Le, Lixin Fan, Courtney Campbell, Sambuddha Sen, Daiana A. Capdevila, Timothy L. Stemmler, David P. Giedroc
Biochemistry.2024; 63(5): 660. CrossRef
Acinetobacter Metabolism in Infection and Antimicrobial Resistance
Xiaomei Ren, Lauren D. Palmer, Karen M. Ottemann
Infection and Immunity.2023;[Epub] CrossRef
A response regulator controls Acinetobacter baumannii virulence by acting as an indole receptor
Binbin Cui, Quan Guo, Xia Li, Shihao Song, Mingfang Wang, Gerun Wang, Aixin Yan, Jianuan Zhou, Yinyue Deng, Marenda Wilson-Pham
PNAS Nexus.2023;[Epub] CrossRef
The role of quorum sensing, biofilm formation, and iron acquisition as key virulence mechanisms in Acinetobacter baumannii and the corresponding anti-virulence strategies
Soffi Kei Kei Law, Hock Siew Tan
Microbiological Research.2022; 260: 127032. CrossRef
Carboxy-Terminal Processing Protease Controls Production of Outer Membrane Vesicles and Biofilm in Acinetobacter baumannii
Rakesh Roy, Ren-In You, Chan-Hua Chang, Chiou-Ying Yang, Nien-Tsung Lin
Microorganisms.2021; 9(6): 1336. CrossRef
ppGpp signaling plays a critical role in virulence of Acinetobacter baumannii
Kyeongmin Kim, Maidul Islam, Hye-won Jung, Daejin Lim, Kwangsoo Kim, Sung-Gwon Lee, Chungoo Park, Je Chul Lee, Minsang Shin
Virulence.2021; 12(1): 2122. CrossRef
COG0523 proteins: a functionally diverse family of transition metal-regulated G3E P-loop GTP hydrolases from bacteria to man
Katherine A Edmonds, Matthew R Jordan, David P Giedroc
Metallomics.2021;[Epub] CrossRef
The role of Zur-regulated lipoprotein A in bacterial morphology, antimicrobial susceptibility, and production of outer membrane vesicles in Acinetobacter baumannii
Nayeong Kim, Hyo Jeong Kim, Man Hwan Oh, Se Yeon Kim, Mi Hyun Kim, Joo Hee Son, Seung Il Kim, Minsang Shin, Yoo Chul Lee, Je Chul Lee
BMC Microbiology.2021;[Epub] CrossRef
Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
Jennifer M. Colquhoun, Philip N. Rather
Frontiers in Cellular and Infection Microbiology.2020;[Epub] 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; J. Microbiol. 2019;57(10):852-864. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-8668-8

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Abstract

Recent work suggests that microbial community composition in high-elevation lakes is significantly influenced by microbes entering from upstream terrestrial and aquatic habitats. To test this idea, we conducted 18S and 16S rDNA surveys of microbial communities in a high-alpine lake in the Colorado Rocky Mountains. We compared the microbial community of the lake to water entering the lake and to uphill soils that drain into the lake. Utilizing hydrological and abiotic data, we identified potential factors controlling microbial diversity and community composition. Results show a diverse community entering the lake at the inlet with a strong resemblance to uphill terrestrial and aquatic communities. In contrast, the lake communities (water column and outlet) showed significantly lower diversity and were significantly different from the inlet communities. Assumptions of neutral community assembly poorly predicted community differences between the inlet and lake, whereas “variable selection” and “dispersal limitation” were predicted to dominate. Similarly, the lake communities were correlated with discharge rate, indicating that longer hydraulic residence times limit dispersal, allowing selective pressures within the lake to structure communities. Sulfate and inorganic nitrogen and phosphorus concentrations correlated with community composition, indicating “bottom up” controls on lake community assembly. Furthermore, bacterial community composition was correlated with both zooplankton density and eukaryotic community composition, indicating biotic controls such as “top-down” interactions also contribute to community assembly in the lake. Taken together, these community analyses suggest that deterministic biotic and abiotic selection within the lake coupled with dispersal limitation structures the microbial communities in Green Lake 4.

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Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers
Gu Rao, Wen-Long Song, Shu-Zhen Yan, Shuang-Lin Chen, John R. Spear
Applied and Environmental Microbiology.2024;[Epub] CrossRef
The nature of microbial diversity and assembly in the Nebraska Sandhills depends on organismal identity and habitat type
Kaitlin Gattoni, Eli M. S. Gendron, J. Parr McQueen, Kirsten Powers, Thomas O. Powers, Mary J. Harner, Jessica R. Corman, Dorota L. Porazinska
Community Ecology.2024;[Epub] CrossRef
Lakes-scale pattern of eukaryotic phytoplankton diversity and assembly process shaped by electrical conductivity in central Qinghai-Tibet Plateau
Huan Zhu, Xiong Xiong, Benwen Liu, Guoxiang Liu
FEMS Microbiology Ecology.2024;[Epub] CrossRef
Free-Living and Particle-Associated Microbial Communities of Lake Baikal Differ by Season and Nutrient Intake
Maria Bashenkhaeva, Yelena Yeletskaya, Irina Tomberg, Artyom Marchenkov, Lubov Titova, Yuri Galachyants
Diversity.2023; 15(4): 572. CrossRef
Conservation tillage and moderate nitrogen application changed the composition, assembly pattern and interaction network of abundant and rare microbial community on straw surface
Houping Zhang, Yuanpeng Zhu, Chaoyang Yu, Yuze Li, Mei Long, Wei Li, Yuncheng Liao, Weiyan Wang, Xiaoxia Wen
Applied Soil Ecology.2023; 191: 105060. CrossRef
Sediment sulfate content determines assembly processes and network stability of bacteria communities of coastal land-based shrimp aquaculture ponds
Lianzuan Wu, Ping Yang, Linhai Zhang, Liangjuan Luo, Yan Hong, Wanyi Zhu, Lidi Zheng, Guanghui Zhao, Chuan Tong, Josep Peñuelas
Aquaculture.2023; 563: 738953. CrossRef
Microbial predators form a new supergroup of eukaryotes
Denis V. Tikhonenkov, Kirill V. Mikhailov, Ryan M. R. Gawryluk, Artem O. Belyaev, Varsha Mathur, Sergey A. Karpov, Dmitry G. Zagumyonnyi, Anastasia S. Borodina, Kristina I. Prokina, Alexander P. Mylnikov, Vladimir V. Aleoshin, Patrick J. Keeling
Nature.2022; 612(7941): 714. CrossRef
Crossing Treeline: Bacterioplankton Communities of Alpine and Subalpine Rocky Mountain Lakes
Kim Vincent, Hannah Holland-Moritz, Adam J. Solon, Eli M. S. Gendron, Steven K. Schmidt
Frontiers in Microbiology.2022;[Epub] CrossRef
Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes
Qi Yan, Jianming Deng, Feng Wang, Yongqin Liu, Keshao Liu
Frontiers in Microbiology.2021;[Epub] CrossRef
Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes
Javad Sadeghi, Subba Rao Chaganti, Abdolrazagh Hashemi Shahraki, Daniel D. Heath
Science of The Total Environment.2021; 781: 146771. CrossRef
Evidence for phosphorus limitation in high-elevation unvegetated soils, Niwot Ridge, Colorado
Clifton P. Bueno de Mesquita, Laurel M. Brigham, Pacifica Sommers, Dorota L. Porazinska, Emily C. Farrer, John L. Darcy, Katharine N. Suding, Steven K. Schmidt
Biogeochemistry.2020; 147(1): 1. CrossRef

Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China: Pengyu Zhao , Jinxian Liu , Tong Jia , Zhengming Luo , Cui Li , Baofeng Chai; J. Microbiol. 2019;57(6):461-469. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8373-7

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Abstract

Microbial community assembly is affected by trade-offs between deterministic and stochastic processes. However, the mechanisms underlying the relative influences of the two processes remain elusive. This knowledge gap limits our ability to understand the effects of community assembly processes on microbial community structures and functions. To better understand community assembly mechanisms, the community dynamics of bacterial ecological groups were investigated based on niche breadths in 23 soil plots from subalpine coniferous forests on the Loess Plateau in Shanxi, China. Here, the overall community was divided into the ecological groups that corresponded to habitat generalists, ‘other taxa’ and specialists. Redundancy analysis based on Bray-Curtis distances (db-RDA) and multiple regression tree (MRT) analysis indicated that soil organic carbon (SOC) was a general descriptor that encompassed the environmental gradients by which the communities responded to, because it can explain more significant variations in community diversity patterns. The three ecological groups exhibited different niche optima and degrees of specialization (i.e., niche breadths) along the SOC gradient, suggesting the presence of a gradient in tolerance for environmental heterogeneity. The inferred community assembly processes varied along the SOC gradient, wherein a transition was observed from homogenizing dispersal to variable selection that reflects increasing deterministic processes. Moreover, the ecological groups were inferred to perform different community functions that varied with community composition, structure. In conclusion, these results contribute to our understanding of the trade-offs between community assembly mechanisms and the responses of community structure and function to environmental gradients.

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Stochastic Processes Dominate the Assembly of Soil Bacterial Communities of Land Use Patterns in Lesser Khingan Mountains, Northeast China
Junnan Ding, Shaopeng Yu
Life.2024; 14(11): 1407. CrossRef
Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef
Community assembly of bacterial generalists and specialists and their network characteristics in different altitudinal soils on Fanjing Mountain in Southwest China
Zhenming Zhang, Xianliang Wu, Jiachun Zhang, Yingying Liu, Wenmin Luo, Guiting Mou
CATENA.2024; 238: 107863. CrossRef
Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts
Qing Li, Xiaoyu Cheng, Xiaoyan Liu, Pengfei Gao, Hongmei Wang, Chuntian Su, Qibo Huang
Frontiers in Microbiology.2024;[Epub] CrossRef
Full-length 16S rRNA gene sequencing reveals the operating mode and chlorination-aggravated SWRO biofouling at a nuclear power plant
Kaijia Ren, Hongxia Ming, Siyu Liu, Xianlong Lang, Yuan Jin, Jingfeng Fan
Water Science & Technology.2024; 90(1): 1. CrossRef
Kalidium cuspidatum colonization changes the structure and function of salt crust microbial communities
Yaqing Pan, Peng Kang, Yaqi Zhang, Xinrong Li
Environmental Science and Pollution Research.2024; 31(13): 19764. CrossRef

Review

MINIREVIEW] Modern and Simple Construction of Plasmid: Saving Time and Cost: Hideki Nakayama , Nobuo Shimamoto; J. Microbiol. 2014;52(11):891-897. Published online October 31, 2014; DOI: https://doi.org/10.1007/s12275-014-4501-6

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Abstract

Construction of plasmids has been occupying a significant fraction of laboratory work in most fields of experimental biology. Tremendous effort was made to improve the traditional method for constructing plasmids, in which DNA fragments digested with restriction enzymes were ligated. However, the traditional method remained to be a standard protocol more than 40 years. At last, several recent inventions are rapidly and completely replacing the traditional method, because they are far quicker with less cost, and requiring less material. We here introduce three such methods that cover up most of the cases. Moreover, they are complementary with each other. Our lab protocols are provided for “no strain, no pain” construction of plasmids.

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Tumor biology experimental course design based on the integration of molecular biology and metabolomics
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Research Support, Non-U.S. Gov't

Hepatitis B Virus Core Interacts with the Host Cell Nucleolar Protein, Nucleophosmin 1: Su Jin Lee , Hee Youn Shim , Antony Hsieh , Ji Young Min , Gu hung Jung; J. Microbiol. 2009;47(6):746-752. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-2720-z

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Abstract: Hepatitis B virus (HBV) genome replication requires the packaging of viral factors (pregenomic RNA and polymerase) as well as host factors, including heat shock proteins and protein kinase C. Previous reports have suggested that there are several unidentified host factors that affect this encapsidation step. In this study, we identified a new host factor, nucleophosmin (B23) that interacts with the HBV core protein 149 (Cp149). We analyzed this factor using NHS-activated sepharose resin and MALDI-TOF MS. Using the BIAcore analysis system, we were also able to deduce that the B23.1 residues 259-294 were required for the interaction between Cp149 and B23.1 in vitro.

Genetic Manipulation of Rhabdoviruses : New Insights to Virus Replication, Transcription and Assembly: Michael A. Whitt; J. Microbiol. 1998;36(1):1-8.

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Abstract: Rhabdoviruses, together with the other members of the Rhabdoviridae family, are one of the most widely distributed groups of viruses in nature. Rhabdoviruses have been isolated from virtually all vertebrates, several different species of insects, as well as many plant (65). It is thought that insects were the original hosts for this group of viruses and that rhabdoviruses have since adapted to grow in both vertebrates and invertebrates. This adaptation undoubtedly contributed to one of the disdinguishing features of the prototypic rhabdovirus, vesicular stomatitis virus (VSV), namely the ability to replicate in most primary cell cultures and essentially all established mammalian cell lines, as well as a number of insect and amphibian cell lines. Because VSV has a broad host range, is relatively easy to grow and replicates to high titers in cell culture it has been used extensively as a model system to study many aspects of rhabdovirus entry (32, 69, 70), replication (3, 4) and assembly(36, 55, 58).

Production of the Nucleocapsid Protein of Newcastle Disease Virus in Escherichia coli and its Assembly into Ring- and Nucleocapsid-like Particles: Chiew Ling Kho , Wen Siang Tan , Khatijah Yusoff; J. Microbiol. 2001;39(4):293-299.

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Abstract: The nucleocapsid (NP) protein of Newcastle disease virus (NDV) and its derivative (NP_cfus ) containing the myc region and six histidine residues fused to its C-terminus were expressed abundantly in Escherichia coli. The proteins were purified by sucrose gradient centrifugation. Both the NP and NP_cfus proteins self-assembled into ring-like particles with a diameter of 24 +- 2 nm around a central hole of 7 +- 1 nm. Some of these ring-like particles stacked together to form nucleocapsid-like structures which are heterogeneous in length with a diameter of 20 +- 2 nm and a central hollow of 5 +- 1 nm. Only a very small amount of the monomers in the particles was linked by inter-molecular disulfide bonds. Fusion of the C-terminal end to 29 amino acids inclusive of the myc epitope and His-tag did not impair ring assembly but inhibited the formation of the long herringbone structures. Immunogold labeling of the particles with the anti-myc antibody showed that the C-terminus of the NP_cfus protein is exposed on the surface of these ring-like particles.

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