Journal of Microbiology

Review

Transmissibility and pathogenicity of SARS-CoV-2 variants in animal models: Young-Il Kim , Mark Anthony B. Casel , Young Ki Choi; J. Microbiol. 2022;60(3):255-267. Published online March 2, 2022; DOI: https://doi.org/10.1007/s12275-022-2033-z

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As of February 2022, SARS-CoV-2 is still one of the most serious public health threats due to its high mortality rate and rapid spread of novel variants. Since the first outbreak in 2019, general understanding of SARS-CoV-2 has been improved through basic and clinical studies; however, knowledge gaps still exist in our understanding of the emerging novel SARSCoV- 2 variants, which impacts the corresponding development of vaccines and therapeutics. Especially, accumulation of mutations in SARS-CoV-2 and rapid spread in populations with previous immunity has resulted in selection of variants that evade the host immune response. This phenomenon threatens to render current SARS-CoV-2 vaccines ineffective for controlling the pandemic. Proper animal models are essential for detailed investigations into the viral etiology, transmission and pathogenesis mechanisms, as well as evaluation of the efficacy of vaccine candidates against recent SARS-CoV-2 variants. Further, the choice of animal model for each research topic is important for researchers to gain better knowledge of recent SARS-CoV-2 variants. Here, we review the advantages and limitations of each animal model, including mice, hamsters, ferrets, and non-human primates, to elucidate variant SARS-CoV-2 etiology and transmission and to evaluate therapeutic and vaccine efficacy.

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Miruthula Tamil Selvan, Sachithra Gunasekara, Ping Xiao, Kristen Griffin, Shannon R. Cowan, Sai Narayanan, Akhilesh Ramachandran, Darren E. Hagen, Jerry W. Ritchey, Jennifer M. Rudd, Craig A. Miller
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Journal Article

Fungal diversity in soils across a gradient of preserved Brazilian Cerrado: Ademir Sergio Ferreira de Araujo , Walderly Melgaço Bezerra , Vilma Maria dos Santos , Luis Alfredo Pinheiro Leal Nunes , Maria do Carmo Catanho Pereira de Lyra , Marcia do Vale Barreto Figueiredo , Vania Maria Maciel Melo; J. Microbiol. 2017;55(4):273-279. Published online January 27, 2017; DOI: https://doi.org/10.1007/s12275-017-6350-6

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Abstract

The preserved Cerrado from Northeastern Brazil presents different physicochemical properties and plant diversity, which can influence the fungal communities. Therefore, we evaluated the fungal diversity in preserved sites, at Sete Ci-dades National Park, across a gradient of vegetation that in-cluded Campo graminoide, Cerrado stricto sensu, Cerradao, and Floresta decidual. Of all of the operational taxonomic units (OTUs) obtained, the Floresta decidual presented the highest richness. Ascomycota were the most abundant phy-lum (45%), followed by Basidiomycota (32%). Basal fungi and other phyla accounted for 23% of the total dataset. Agaricomycetes, Eurotiomycetes, Lecanoromycetes, Basi-diobolus, Dothideomycetes, and Taphrinomycetes were the most abundant classes of fungi found across the gradient of Cerrado vegetation. In conclusion, our study suggests that the Brazilian Cerrado from Sete Cidades National Park pre-sents a high fungal diversity and includes sources of new fungal species for biotechnological purposes.

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Vegetation degradation dominates over elevation in structuring fungal communities in alpine meadows
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Comparative microbiomes reveal microbial signatures in coffee fermentation and flavor development across distinct Brazilian biomes
Natan Wiele, Gilberto Vinícius de Melo Pereira, Alexander da Silva Vale, Vitória de Mello Sampaio, Ana Isabel Ribeiro-Barros, Agnes de Freitas Diniz de Souza, Diogo Vinícius Nogueira dos Santos, Aristóteles Góes-Neto, Carlos Ricardo Soccol
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Mingfang Jiang, Jiayi Liu, Haoran Sun, Qiubei Chen, Hong Jin, Jingyan Yang, Ke Tao
Environmental Science and Pollution Research.2024; 31(17): 26076. CrossRef
Dynamic responses of endophytic microbial communities of Jerusalem artichoke to the absence of nitrogen fertilizer
Mengjia ZHOU, Ji WANG, Ruixuan YANG, Qian CUI, Xin XU, Jingjing XU, Huijuan ZHANG, Ebru TOKSOY ÖNER, Mingxiang LIANG
Pedosphere.2024;[Epub] CrossRef
Metabarcoding of Soil Fungal Communities in Rupestrian Grassland Areas Preserved and Degraded by Mining: Implications for Restoration
Maurílio Assis Figueiredo, Thamar Holanda da Silva, Otávio Henrique Bezerra Pinto, Mariangela Garcia Praça Leite, Fábio Soares de Oliveira, Maria Cristina Teixeira Braga Messias, Luiz Henrique Rosa, Paulo Eduardo Aguiar Saraiva Câmara, Fabyano Alvares Car
Microbial Ecology.2023; 85(3): 1045. CrossRef
Responses of community traits and soil characteristics of Achnatherum inebrians-type degraded grassland to grazing systems in alpine meadows on the Qinghai-Tibet Plateau
Yanzhu Chen, Changlin Xu, Kaikai Ma, Qingqing Hou, Xiaojun Yu
Frontiers in Plant Science.2023;[Epub] CrossRef
New Insights on Environmental Occurrence of Pathogenic Fungi Based on Metagenomic Data from Brazilian Cerrado Biome
Flávia de Fátima Costa, Renata Carolini Souza, Morgana Ferreira Voidaleski, Amanda Bombassaro, Giovanna Zuzarte Candido, Nickolas Menezes da Silva, Diogo Robl, Leandro Ferreira Moreno, Vinicius Almir Weiss, Roberto Tadeu Raittz, Mauro Antônio Castro, Rena
Brazilian Archives of Biology and Technology.2022;[Epub] CrossRef
Ecosystem functions in different physiognomies of Cerrado through the Rapid Ecosystem Function Assessment (REFA)
ADEMIR S.F. ARAUJO, SANDRA M.B. ROCHA, JADSON E.L. ANTUNES, FABIO F. ARAUJO, LUCAS W. MENDES
Anais da Academia Brasileira de Ciências.2022;[Epub] CrossRef
Abscisic acid-polyacrylamide (ABA-PAM) treatment enhances forage grass growth and soil microbial diversity under drought stress
Xue Tang, Xueting Fei, Yining Sun, Huanhuan Shao, Jinyu Zhu, Xinyi He, Xiaoyan Wang, Bin Yong, Xiang Tao
Frontiers in Plant Science.2022;[Epub] CrossRef
Penicillium polonicum a new isolate obtained from Cerrado soil as a source of carbohydrate-active enzymes produced in response to sugarcane bagasse
Brenda Rabelo de Camargo, Hamille Mey Takematsu, Alonso R. Poma Ticona, Leonardo Assis da Silva, Francilene Lopes Silva, Betania Ferraz Quirino, Pedro R. Vieira Hamann, Eliane Ferreira Noronha
3 Biotech.2022;[Epub] CrossRef
Influence of the biocontrol agents Trichoderma spp. on the structure and functionality of the edaphic microbial community in common bean cultivars (Phaseolus vulgaris L.) inoculated with Sclerotinia sclerotiorum (Lib.) de Bary
Fábio de Azevedo Silva, Vandinelma de Oliveira Vieira, Rosilaine Carrenho, Vinícius Barros Rodrigues, Murillo Lobo Junior, Gilvan Ferreira da Silva, Marcos Antônio Soares
Applied Soil Ecology.2021; 168: 104190. CrossRef
Diversity, structure, and composition of plant growth-promoting bacteria in soil from Brazilian Cerrado
Jailson do Nascimento Silva, Lucas William Mendes, Jadson Emanuel Lopes Antunes, Vania Maria Maciel Melo, Francisca Andrea da Silva Oliveira, Angela Celis de Almeida Lopes, Veronica Brito da Silva, Arthur Prudêncio de Araujo Pereira, Sergio Emilio Santos
Rhizosphere.2021; 20: 100435. CrossRef
The soil microbiomes of the Brazilian Cerrado
Luciano Procópio, Cristine Barreto
Journal of Soils and Sediments.2021; 21(6): 2327. CrossRef
Arbuscular mycorrhizal community in soil from different Brazilian Cerrado physiognomies
Ademir Sergio Ferreira Araujo, Vania Maria Maciel Melo, Arthur Prudencio de Araujo Pereira, Angela Celis de Almeida Lopes, Sandra Mara Barbosa Rocha, Fabio Fernando Araujo, Lucas William Mendes
Rhizosphere.2021; 19: 100375. CrossRef
The Microbial Community Structure of Rhizosphere Soil was Influenced by Different Sugarcane Varieties with Different Ratooning Abilities
Shasha Luo, Lijun Chen, Yinglin Lu, Sixing Daia, Donglei Sun, Jihu Lia, Yuxing An
Sugar Tech.2021; 23(6): 1306. CrossRef
Biochemical activity and microbial biomass in wetlands (Vereda) and well-drained soils under native vegetation types in Brazilian Cerrado
Cínthia Prates Moreira, Simone Cristina Braga Bertini, Adão Siqueira Ferreira, Lucas Carvalho Basilio Azevedo
Applied Soil Ecology.2021; 160: 103840. CrossRef
Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients
Candice Y Lumibao, Elizabeth R Kimbrough, Richard H Day, William H Conner, Ken W Krauss, Sunshine A Van Bael
FEMS Microbiology Ecology.2020;[Epub] CrossRef
Soil microbial C:N:P ratio across physiognomies of Brazilian Cerrado Soil microbial biomass across a gradient of preserved native Cerrado
SANDRA M.B. ROCHA, JADSON E.L. ANTUNES, FABIO F. DE ARAUJO, LUCAS W. MENDES, RICARDO S. DE SOUSA, ADEMIR S. F. DE ARAUJO
Anais da Academia Brasileira de Ciências.2019;[Epub] CrossRef
Wood-decay fungi (Agaricomycetes, Basidiomycota) in three physiognomies in the Savannah region in Brazil
Maira Cortellini Abrahão, Ricardo Matheus Pires, Adriana de Mello Gugliotta, Eduardo Pereira Cabral Gomes, Vera Lucia Ramos Bononi
Hoehnea.2019;[Epub] CrossRef
Neotropical seasonally dry forests: response of soil fungal communities to anthropogenic actions
Moreno María Virginia, Merlos Cristina Soledad, Pelizza Sebastián Alberto
Biodiversity International Journal.2018; 2(2): 172. CrossRef
Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado
Ademir Sergio Ferreira de Araujo, Lucas William Mendes, Leandro Nascimento Lemos, Jadson Emanuel Lopes Antunes, Jose Evando Aguiar Beserra, Maria do Carmo Catanho Pereira de Lyra, Marcia do Vale Barreto Figueiredo, Ângela Celis de Almeida Lopes, Regina Lu
Communications Biology.2018;[Epub] CrossRef

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

Identification of Enriched Conjugated Linoleic Acid Isomers in Cultures of Ruminal Microorganisms after Dosing with 1-13C-Linoleic Acid: Yong-Jae Lee , Thomas C. Jenkins; J. Microbiol. 2011;49(4):622-627. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0415-8

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Abstract: Most studies of linoleic acid biohydrogenation propose that it converts to stearic acid through the production of cis-9 trans-11 CLA and trans-11 C18:1. However, several other CLA have been identified in ruminal contents, suggesting additional pathways may exist. To explore this possibility, this research investigated the linoleic acid biohydrogenation pathway to identify CLA isomers in cultures of ruminal microorganisms after dosing with a 13C stable isotope. The 13C enrichment was calculated as [(M+1/M)×100] in labeled minus unlabeled cultures. After 48 h incubation, significant 13C enrichment was observed in seven CLA isomers, indicating their formation from linoleic acid. All enriched CLA isomers had double bonds in either the 9,11 or 10,12 position except for trans-9 cis-11 CLA. The cis-9 trans-11 CLA exhibited the highest enrichment (30.65%), followed by enrichments from 21.06 to 23.08% for trans-10 cis-12, cis-10 trans-12, trans-9 trans-11, and trans-10 trans-12 CLA. The remaining two CLA (cis-9 cis-11 and cis-10 cis-12 CLA) exhibited enrichments of 18.38 and 19.29%, respectively. The results of this study verified the formation of cis-9 trans-11 and trans-10 cis-12 CLA isomers from linoleic acid biohydrogenation. An additional five CLA isomers also contained carbons originating from linoleic acid, indicating that pathways of linoleic acid biohydrogenation are more complex than previously described.

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

Characterization of a Novel β-Glucosidase-Like Activity from a Soil Metagenome: Chengjian Jiang , Gefei Ma , Shuangxi Li , Tingting Hu , Zhiqun Che , Peihong Shen , Bing Yan , Bo Wu; J. Microbiol. 2009;47(5):542-548. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0024-y

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Abstract

We report the cloning of a novel β-glucosidase-like gene by function-based screening of a metagenomic library from uncultured soil microorganisms. The gene was named bgl1C and has an open reading frame of 1,443 base pairs. It encodes a 481 amino acid polypeptide with a predicted molecular mass of about 57.8 kDa. The deduced amino acid sequence did not show any homology with known β-glucosidases. The putative β-glucosidase gene was subcloned into the pETBlue-2 vector and overexpressed in E. coli Tuner (DE3) pLacІ; the recombinant protein was purified to homogeneity. Functional characterization with a high performance liquid chromatography method demonstrated that the recombinant Bgl1C protein hydrolyzed D-glucosyl-β-(1-4)-D-glucose to glucose. The maximum activity for Bgl1C protein occurred at pH 8.0 and 42°C using p-nitrophenyl-β-D-glucoside as the substrate. A CaCl2 concentration of 1 mM was required for optimal activity. The putative β-glucosidase had an apparent Km value of 0.19 mM, a Vmax value of 4.75 U/mg and a kcat value of 316.7/min under the optimal reaction conditions. The biochemical characterization of Bgl1C has enlarged our understanding of the novel enzymes that can be isolated from the soil metagenome.

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Reductive Dechlorination of Polychlorinated Biphenyls as Affected by Natural Halogenated Aromatic Compounds: Jongseol Kim , Ahmi Lee , Yong-Suk Moon , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2006;44(1):23-28.; DOI: https://doi.org/2341 [pii]

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Abstract: We investigated the effects of halogenated aromatic compounds (HACs) including naturally occurring ones (L-thyroxine, 3-chloro-L-tyrosine, 5-chloroindole, 2-chlorophenol, 4-chlorophenol and chlorobenzene) on polychlorinated biphenyl (PCB) dechlorination in sediment cultures. A PCB-dechlorinating enrichment culture of sediment microorganisms from the St. Lawrence River was used as an initial inoculum. When the culture was inoculated into Aroclor 1248 sediments amended with each of the six HACs, the extent of dechlorination was not enhanced by amendment with HACs. The dechlorination patterns in the HAC-amended sediments were nearly identical to that of the HAC-free sediments except the 3-chloro-L-tyrosine-amended ones where no dechlorination activity was observed. When these sediment cultures were transferred into fresh sediments with the same HACs, the dechlorination specificities remained the same as those of the initial inoculations. Thus, in the present study, the substrate range of the highly selected enrichment culture could not be broadened by the HACs. It appears that HACs affect PCB dechlorination mainly through population selection rather than enzyme induction of single population.

Effects of Sulfate Concentration on the Anaerobic Dechlorination of Polychlorinated Biphenyls in Estuarine Sediments: Young-Cheol Cho , Kyoung-Hee Oh; J. Microbiol. 2005;43(2):166-171.; DOI: https://doi.org/2167 [pii]

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Abstract: In order to determine the effects of sulfate concentration on the anaerobic dechlorination of polychlorinated biphenyls, sediments spiked with Aroclor 1242 were made into slurries using media which had various sulfate concentrations ranging from 3 to 23 mM. The time course of dechlorination clearly demonstrated that dechlorination was inhibited at high concentration of sulfate due to less dechlorination of meta-substituted congeners. When the dechlorination patterns were analyzed by the calculation of Euclidean distance, the dechlorination pathway in the 3 mM sulfate samples was found to be different from that observed in the 13 mM samples, although the extent of dechlorination in these two samples was similar. It is possible that the dechlorination in the high sulfate concentration samples is inhibited by the suppression of growth of methanogen, which have been shown to be meta-dechlorinating microorganisms.

Introductory Journal Article

[Editorial]Omics-based microbiome analysis in microbial ecology: from sequences to information: Jang-Cheon Cho; J. Microbiol. 2021;59(3):229-232.; DOI: https://doi.org/10.1007/s12275-021-0698-3

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Abstract

Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics
methods
triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.

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Advancing early warning and surveillance for zoonotic diseases under climate change: Interdisciplinary systematic perspectives
Chen-Xi Wang, Le-Shan Xiu, Qin-Qin Hu, Tung-Chun Lee, Jia Liu, Leilei Shi, Xiao-Nong Zhou, Xiao-Kui Guo, Liyuan Hou, Kun Yin
Advances in Climate Change Research.2023; 14(6): 814. CrossRef
Mercury methylation in boreal aquatic ecosystems under oxic conditions and climate change: a review
Juanjo Rodríguez
Frontiers in Marine Science.2023;[Epub] CrossRef
Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review
Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez, Pilar Hernández
Biomolecules.2021; 11(8): 1111. CrossRef
Microbial diversity analysis of two full-scale seawater desalination treatment trains provides insights into detrimental biofilm formation
Mircea Podar, Amanda L. May, Weiliang Bai, Kellie Peyton, Dawn M. Klingeman, Cynthia M. Swift, Devan A.F. Linson, Jacques Mathieu, Daniel Siljeström, Ignacio Beneyto, Lauren B. Stadler, Yosef Pinhas, Frank E. Löffler, Pedro J.J. Alvarez, Manish Kumar
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Removal of PCR inhibitors from soil DNA by chemical flocculation
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Distribution of airborne microorganisms in yellow sands of Korea: Choi, Dae Sung , Park, Yong Keun , Oh, Sang Kon , Yoon, Hee Ju , Kim, Jee Cheon , Seo, Won Jun , Cha, Seung Hee; J. Microbiol. 1997;35(1):1-9.

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Abstract: Distribution of airborne microorganisms was determined with two different types of air samplers, the Anderson cascade sampler and the Aerobioscope sampler, in the vicinity of Taejon. The size distribution of particles carrying bacteria and fungi was concurrently measured. The concentration of detected viable airborne particles was greatly varied. It was observed that the number of microbial particles increased in April and October. The most size of particles carrying bacteria was larger than 4.7 um in mean aerodiameter, which made up 69.8% of the total particle fraction. About 63.2% of fungi-carrying particles were smaller than 4.7 um in aerodiameter. The distribution of particles on Yellow Sand Phenomena days was also analyzed. The number of fine particles having mass median aero-diameter from 1.0 to 10.mu.m increased on Yellow Sand Phenomena days to about 6 times that on normal days and the n umber of colony forming unit (CFU/㎥) of airborne bacteria also increased by 4.3 times in April. The results from the Anderson sampler showed that the concentration of bacteria increased greatly on the fraction of fine particles ranging from 0.6 um to 4.7 um in diameter. Unlike the increase in bacterial floraon Yellow Sand Phenomena days, the fungal concentration slightly decreased and showed a normal size distribution pattern. This study suggests that a long-range transmission of bacteria results form bacteria adsorbing onto the fine particles during the Yellow Sand Phenomena.

Microbial Degradation of Monohydroxybenzoic Acids: Timmanagouda B. Karegoudar , Chi-Kyung Kim; J. Microbiol. 2000;38(2):53-61.

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Abstract: Hydroxybenzoic acids are the most important intermediates in the degradative pathways of various aromatic compounds. Microorganisms catabolize aromatic compounds by converting them to hydroxylated intermediates and then cleave the benzene nucleus with ring dioxygenases. Hydroxylation of the benzene nucleus of an aromatic compound is an essential step for the initiation and subsequent disintegration of the benzene ring. The incorporation of two hydroxyl groups is essential for the labilization of the benzene nucleus. Monohydroxybenzoic acids such as 2-hydroxybenzoic acid, 3-hydroxybenzoic acid, and 4-hydroxybenzoic acid through hydroxylation yield terminal aromatic intermediates like catechol, protocatechuic acid, gentisic acid, or pyrocatechuic acid that are susceptible for subsequent oxygenative cleavage of the benzene ring. These terminal aromatic intermediates are further degraded to cellular components through ortho-and /or meta-cleavage pathways and finally lead to the formation of constituents of the TCA cycle. Many groups of microorganisms have been isolated as degraders of hydroxybenzoic acids with diverse degradative routes and specific enzymes involved in their metabolic pathways. Various microorganisms carry out unusual non-oxidative decarboxylation of aromatic acids and convert them to respective phenols which have been documented. Further, Pseudomonas and Bacillus spp. are the most ubiquitous microorganisms, being the principal components of microflora of most soil and water environments.

Effect of Moisture Content on Reductive Dechlorination of Polychlorinated Biphenyls and Population Dynamics of Dechlorinating Microorganisms: O-Seob Kwon , Young Eui Kim , Jong Gyu Park; J. Microbiol. 2001;39(3):195-201.

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Abstract: The effect of moisture content on the reductive dechlorination of polychlorinated biphenyls and population dynamics of dechlorinating microorganisms was investigated in sediments spiked with Aroclor 1248. In sediment slurry with an overlying water layer, dechlorination ensued after a 4-week lag period and reduced the average number of chlorines per biphenyl from 3.91 to 3.15 after 48 weeks. In the sediments of reduced moisture content, however, dechlorination occurred after a lag period of 12 weeks and decreased the average number of chlorines per biphenyl to only 3.62, and the dechlorination rate was also slower. When the population size of dechlorinators, methanogens, and sulfate-reducing bacteria was determined by the most probable number techniques, however, no difference was found between the slurry and the low-moisture sediments, except for methanogens. The growth of dechlorinating populations coincided with the end of the lag period and they then increased by 3 orders of magnitude in two conditions. Specific growth rate of dechlorinators showed little difference between the slurry and the low-moisture sediments; however, growth yield was high in the sediments of reduced moisture content. The reduction of sediment moisture decreased the dechlorination rate and extent of PCBs but did not inhibit the growth of PCB dechlorinators.

Morphological Diversity of Marine Microorganisms on Different Isolation Media: Shin Hye Park , Kae Kyoung Kwon , Deuk-Soo Lee , Hong Kum Lee; J. Microbiol. 2002;40(2):161-165.

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Abstract: Isolation frequency of microorganisms from marine sources was examined with different media and samples collected from the coastal area of Cheju Island. From sea water samples, about 1% of microorganisms from the total number of bacteria were recovered. Microorganisms were cultured at the much lower frequency of 10^-4 ?0^-6 from other marine sources, such as sediment, sponges and corals. The frequency of duplicated isolation was examined with 140 morphologically different colonies isolated on different media. Fourteen percent of them exhibited the same morphology on two different media. The duplication frequency of the isolates among three different media was 33%.

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