Journal of Microbiology

Journal Articles

Upgrading Isoquercitrin Concentration via Submerge Fermentation of Mulberry Fruit Extract with Edible Probiotics to Suppress Gene Targets for Controlling Kidney Cancer and Inflammation: Md Rezaul Karim, Safia Iqbal, Shahnawaz Mohammad, Jong-Hoon Kim, Li Ling, Changbao Chen, Abdus Samad, Md Anwarul Haque, Deok-Chun Yang, Yeon Ju Kim, Dong Uk Yang; J. Microbiol. 2024;62(10):919-927. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00163-8

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In recent years, kidney cancer has become one of the most serious medical issues. Kidney cancer is treated with a variety of active compounds that trigger genes that cause cancer. We identified in our earlier research that isoquercitrin (IQ) can activate PIK3CA, IGF1R, and PTGS2. However, it has a very low bioavailability because of its lower solubility in water. So, we utilized sub-merge fermentation technology with two well-known probiotics, Lactobacillus acidophilus and Bacillus subtilis, as a microbial source and mulberry fruit extract as a substrate, which has a high IQ level to improve IQ yield. Furthermore, we compared the total phenolic, flavonoid, and antioxidant contents of fermented and non-fermented samples, and we found that the fermented samples had greater levels than non-fermented sample. In addition, the high-performance liquid chromatography (HPLC) results showed that the fermented mulberry fruit extract from B. subtilis and L. acidophilus showed higher IQ values (190.73 ± 0.004 μg/ml and 220.54 ± 0.007 μg/ml, respectively), compared to the non-fermented samples, which had IQ values (80.12 ± 0.002 μg/ml). Additionally, at 62.5 µg/ml doses of each sample, a normal kidney cell line (HEK 293) showed higher cell viability for fermented and non-fermented samples. Conversely, at the same doses, the fermented samples of L. acidophilus and B. subtilis in a kidney cancer cell line (A498) showed an inhibition of cell growth around 36% and 31%, respectively. Finally, we performed RT and qRT PCR assay, and we found a significant reduction in the expression of the PTGS2, PIK3CA, and IGF1R genes. We therefore can conclude that the fermented samples have a higher concentration of isoquercitrin, and also can inhibit the expression of the genes PTGS2, PIK3CA, and IGF1R, which in turn regulates kidney cancer and inflammation.

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Recent research on the bioactivity of polyphenols derived from edible fungi and their potential in chronic disease prevention
Wenbin Yu, Yufei Zhang, Yi Lu, Zhiwei Ouyang, Jiahua Peng, Yayi Tu, Bin He
Journal of Functional Foods.2025; 124: 106627. CrossRef

Reduction of selenite to elemental Se(0) with simultaneous degradation of phenol by co-cultures of Phanerochaete chrysosporium and Delftia lacustris: Samayita Chakraborty , Eldon R. Rene , Piet N. L. Lens; J. Microbiol. 2019;57(9):738-747. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9042-6

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Abstract

The simultaneous removal of phenol and selenite from synthetic wastewater was investigated by adopting two different co-culturing techniques using the fungus Phanerochaete chrysosporium and the bacterium Delftia lacustris. Separately grown biomass of the fungus and the bacterium (suspended co-culture) was incubated with different concentrations of phenol (0–1,200 mg/L) and selenite (10 mg/L). The selenite ions were biologically reduced to extracellular Se(0) nanoparticles (3.58 nm diameter) with the simultaneous degradation of up to 800 mg/L of phenol. Upon growing the fungus and the bacterium together using an attached growth co-culture, the bacterium grew as a biofilm onto the fungus. The extracellularly produced Se(0) in the attached growth co-culture had a minimum diameter of 58.5 nm. This co-culture was able to degrade completely 50 mg/L phenol, but was completely inhibited at a phenol concentration of 200 mg/L.

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Using Fungi in Artificial Microbial Consortia to Solve Bioremediation Problems
Elena Efremenko, Nikolay Stepanov, Olga Senko, Aysel Aslanli, Olga Maslova, Ilya Lyagin
Microorganisms.2024; 12(3): 470. CrossRef
Review on environmental selenium: Occurrence, public health implications and biological treatment strategies
Adhena Ayaliew Werkneh, Gebretsadkan Gebremedhin Gebretsadik, Shifare Berhe Gebru
Environmental Challenges.2023; 11: 100698. CrossRef
Simultaneous bioreduction of tellurite and selenite by Yarrowia lipolytica, Trichosporon cutaneum, and their co-culture along with characterization of biosynthesized Te–Se nanoparticles
Firooz Hosseini, Maryam Hadian, Elham Lashani, Hamid Moghimi
Microbial Cell Factories.2023;[Epub] CrossRef
Simultaneous bioremediation of phenol and tellurite by Lysinibacillus sp. EBL303 and characterization of biosynthesized Te nanoparticles
Firooz Hosseini, Elham Lashani, Hamid Moghimi
Scientific Reports.2023;[Epub] CrossRef
Selenium-Containing Nanostructures: Synthesis, Properties, and Agrochemical Aspects of Application (Review)
A. I. Perfileva
Nanobiotechnology Reports.2022; 17(2): 165. CrossRef
Biological selenate and selenite reduction by waste activated sludge using hydrogen as electron donor
Arindam Sinharoy, Piet N.L. Lens
Journal of Environmental Management.2022; 319: 115745. CrossRef
Leucobacter coleopterorum sp. nov., Leucobacter insecticola sp. nov., and Leucobacter viscericola sp. nov., isolated from the intestine of the diving beetles, Cybister brevis and Cybister lewisianus, and emended description of the genus Leucobacter
Dong-Wook Hyun, Hojun Sung, Pil Soo Kim, Ji-Hyun Yun, Jin-Woo Bae
Journal of Microbiology.2021; 59(4): 360. CrossRef
Biological Removal of Selenate and Selenite from Wastewater: Options for Selenium Recovery as Nanoparticles
Arindam Sinharoy, Piet N. L. Lens
Current Pollution Reports.2020; 6(3): 230. CrossRef

Alteration in the ultrastructural morphology of mycelial hyphae and the dynamics of transcriptional activity of lytic enzyme genes during basidiomycete morphogenesis: Elena Vetchinkina , Maria Kupryashina , Vladimir Gorshkov , Marina Ageeva , Yuri Gogolev , Valentina Nikitina; J. Microbiol. 2017;55(4):280-288. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6320-z

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Abstract

The morphogenesis of macromycetes is a complex multilevel process resulting in a set of molecular-genetic, physiological- biochemical, and morphological-ultrastructural changes in the cells. When the xylotrophic basidiomycetes Lentinus edodes, Grifola frondosa, and Ganoderma lucidum were grown on wood waste as the substrate, the ultrastructural morphology of the mycelial hyphal cell walls differed considerably between mycelium and morphostructures. As the macromycetes passed from vegetative to generative development, the expression of the tyr1, tyr2, chi1, chi2, exg1, exg2, and exg3 genes was acti-vated. These genes encode enzymes such as tyrosinase, chi-tinase, and glucanase, which play essential roles in cell wall growth and morphogenesis.

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Flow modeling and structural characterization in fungal pellets
J. Sánchez-Vargas, F.J. Valdés-Parada, L. Peraza-Reyes, D. Lasseux, M.A. Trujillo-Roldán
Journal of Theoretical Biology.2024; 590: 111853. CrossRef
Transcriptome analysis provides insight into gamma irradiation delaying quality deterioration of postharvest Lentinula edodes during cold storage
Hong Gao, Shuang Ye, Yani Liu, Xiuzhi Fan, Chaomin Yin, Ying Liu, Jingyu Liu, Yu Qiao, Xueling Chen, Fen Yao, Defang Shi
Food Chemistry: Molecular Sciences.2023; 6: 100172. CrossRef
Improvement of natamycin production by controlling the morphology of Streptomyces gilvosporeus Z8 with microparticle talc in seed preculture
Chaoping Yue, Haitao Xu, Yingying Yu, Xin Yu, Min Yu, Chen Zhang, Qian You, Shaofan Xia, Zixian Ding, Hao Fu, Xin Zeng, Feng Li
Journal of Chemical Technology & Biotechnology.2021; 96(6): 1533. CrossRef
The molecular mechanism of stipe cell wall extension for mushroom stipe elongation growth
Cuicui Liu, Jingjing Bi, Liqin Kang, Jiangsheng Zhou, Xiao Liu, Zhonghua Liu, Sheng Yuan
Fungal Biology Reviews.2021; 35: 14. CrossRef
UDP-glucose pyrophosphorylase gene affects mycelia growth and polysaccharide synthesis of Grifola frondosa
Xin-Yi Zan, Xi-Hong Wu, Feng-Jie Cui, Hong-An Zhu, Wen-Jing Sun, Li-Hua Jiang, Ting-Lei Tao, Xiu Zhao
International Journal of Biological Macromolecules.2020; 161: 1161. CrossRef
Chitinases Play a Key Role in Stipe Cell Wall Extension in the Mushroom Coprinopsis cinerea
Jiangsheng Zhou, Liqin Kang, Cuicui Liu, Xin Niu, Xiaojun Wang, Hailong Liu, Wenming Zhang, Zhonghua Liu, Jean-Paul Latgé, Sheng Yuan, Marie A. Elliot
Applied and Environmental Microbiology.2019;[Epub] CrossRef
Comparative Study of Pleurotus ostreatus Mushroom Grown on Modified PAN Nanofiber Mats
Lilia Sabantina, Franziska Kinzel, Thomas Hauser, Astrid Többer, Michaela Klöcker, Christoph Döpke, Robin Böttjer, Daria Wehlage, Anke Rattenholl, Andrea Ehrmann
Nanomaterials.2019; 9(3): 475. CrossRef
Algorithm for Physiological Interpretation of Transcriptome Profiling Data for Non-Model Organisms
R. F. Gubaev, V. Y. Gorshkov, L. M. Gapa, N. E. Gogoleva, E. P. Vetchinkina, Y. V. Gogolev
Molecular Biology.2018; 52(4): 497. CrossRef
Improved mycelia and polysaccharide production of Grifola frondosa by controlling morphology with microparticle Talc
Ting-Lei Tao, Feng-Jie Cui, Xiao-Xiao Chen, Wen-Jing Sun, Da-Ming Huang, Jinsong Zhang, Yan Yang, Di Wu, Wei-Min Liu
Microbial Cell Factories.2018;[Epub] CrossRef

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

Inhibition of quorum sensing, biofilm, and spoilage potential in Shewanella baltica by green tea polyphenols: Junli Zhu , Xuzheng Huang , Fang Zhang , Lifang Feng , Jianrong Li; J. Microbiol. 2015;53(12):829-836. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5123-3

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Abstract

We investigated the quorum sensing (QS) system of Shewanella baltica and the anti-QS related activities of green tea polyphenols (TP) against spoilage bacteria in refrigerated large yellow croaker. Autoinducer-2 (AI-2) and the diketopiperazines (DKPs) cyclo-(L-Pro-L-Leu) and cyclo-(L-Pro-L-Phe) were detected in the culture extract of S. baltica XH2, however, no N-acylhomoserine lactones (AHLs) activity was observed. Green TP at sub-inhibitory concentrations interfered with AI-2 and DKPs activities of S. baltica without inhibiting cell growth and promoted degradation of AI-2. The green TP treatment inhibited biofilm development, exopolysaccharide production and swimming motility of S. baltica in a concentration- dependent manner. In addition, green TP decreased extracellular protease activities and trimethylamine production in S. baltica. A transcriptional analysis showed that green TP repressed the luxS and torA genes in S. baltica, which agreed with the observed reductions in QS activity and the spoilage phenotype. Epigallocatechin gallate (EGCG)-enriched in green TP significantly inhibited AI-2 activity of S.baltica. These findings strongly suggest that green TP could be developed as a new QS inhibitor for seafood preservation to enhance shelf life.

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The hrp pathogenicity island of Pseudomonas syringae pv. tomato DC3000 is induced by plant phenolic acids: Jun Seung Lee , Hye Ryun Ryu , Ji Young Cha , Hyung Suk Baik; J. Microbiol. 2015;53(10):725-731. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5256-4

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Abstract

Plants produce a wide array of antimicrobial compounds, such as phenolic compounds, to combat microbial pathogens. The hrp PAI is one of the major virulence factors in the plant pathogen, Pseudomonas syringae. A major role of hrp PAI is to disable the plant defense system during bacterial invasion. We examined the influence of phenolic compounds on hrp PAI gene expression at low and high concentrations. There was approximately 2.5 times more hrpA and hrpZ mRNA in PtoDC3000 that was grown in minimal media (MM) supplemented with 10 μM of ortho-coumaric acid than in PtoDC3000 grown in MM alone. On the other hand, a significantly lower amount of hrpA mRNA was observed in bacteria grown in MM supplemented with a high concentration of phenolic compounds. To determine the regulation pathway for hrp PAI gene expression, we performed qRTPCR using gacS, gacA, and hrpS deletion mutants.

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Global Analysis of Type Three Secretion System and Quorum Sensing Inhibition of Pseudomonas savastanoi by Polyphenols Extracts from Vegetable Residues
Carola Biancalani, Matteo Cerboneschi, Francesco Tadini-Buoninsegni, Margherita Campo, Arianna Scardigli, Annalisa Romani, Stefania Tegli, Boris Alexander Vinatzer
PLOS ONE.2016; 11(9): e0163357. CrossRef

Characterization of Recombinant β-Glucosidase from Arthrobacter chlorophenolicus and Biotransformation of Ginsenosides Rb1, Rb2, Rc, and Rd: Myung Keun Park , Chang-Hao Cui , Sung Chul Park , Seul-Ki Park , Jin-Kwang Kim , Mi-Sun Jung , Suk-Chae Jung , Mi-Sun Jung , Suk-Chae Jung , Sun-Chang Kim , Wan-Taek Im; J. Microbiol. 2014;52(5):399-406. Published online May 9, 2014; DOI: https://doi.org/10.1007/s12275-014-3601-7

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Abstract

The focus of this study was the cloning, expression, and characterization of recombinant ginsenoside hydrolyzing β-glucosidase from Arthrobacter chlorophenolicus with an ultimate objective to more efficiently bio-transform ginse-nosides. The gene bglAch, consisting of 1,260 bp (419 amino acid residues) was cloned and the recombinant enzyme, over-expressed in Escherichia coli BL21 (DE3), was characterized. The GST-fused BglAch was purified using GST·Bind agarose resin and characterized. Under optimal conditions (pH 6.0 and 37°C) BglAch hydrolyzed the outer glucose and arabino-pyranose moieties of ginsenosides Rb1 and Rb2 at the C20 position of the aglycone into ginsenoside Rd. This was fol-lowed by hydrolysis into F2 of the outer glucose moiety of ginsenoside Rd at the C3 position of the aglycone. Additio-nally, BglAch more slowly transformed Rc to F2 via C-Mc1 (compared to hydrolysis of Rb1 or Rb2). These results in-dicate that the recombinant BglAch could be useful for the production of ginsenoside F2 for use in the pharmaceutical and cosmetic industries.

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International Journal of Biological Macromolecules.2024; 256: 127915. CrossRef
Progress in the Conversion of Ginsenoside Rb1 into Minor Ginsenosides Using β-Glucosidases
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Enzymatic biotransformation of ginsenoside Rb1 by recombinant β-glucosidase of bacterial isolates from Indonesia
Almando Geraldi, Ni'matuzahroh, Fatimah, Chang-Hao Cui, Thi Thuy Nguyen, Sun Chang Kim
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Characterization of a Novel Ginsenoside MT1 Produced by an Enzymatic Transrhamnosylation of Protopanaxatriol-Type Ginsenosides Re
Byeong-Min Jeon, Jong-In Baek, Min-Sung Kim, Sun-Chang Kim, Chang-hao Cui
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In silico Approach to Elucidate Factors Associated with GH1 β-Glucosidase Thermostability
Amer Ahmed, Ayesha Sumreen, Aasia Bibi, Faiz ul Hassan Nasim, Kashfa Batool
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A literature update elucidating production of Panax ginsenosides with a special focus on strategies enriching the anti-neoplastic minor ginsenosides in ginseng preparations
Tanya Biswas, A. K. Mathur, Archana Mathur
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Molecular Characterization of the Alpha Subunit of Multicomponent Phenol Hydroxylase from 4-Chlorophenol-Degrading Pseudomonas sp. Strain PT3: Wael S. El-Sayed , Mohamed K. Ibrahim , Salama A. Ouf; J. Microbiol. 2014;52(1):13-19. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3250-x

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Abstract

Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)- degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with λmax 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs.

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Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes
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Molecular Characterization of Chloranilic Acid Degradation in Pseudomonas putida TQ07: Luis G. Treviño-Quintanilla , Julio A. Freyre-González , Rosa A. Guillén-Garcés , Clarita Olvera; J. Microbiol. 2011;49(6):974-980. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1507-1

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Abstract: Pentachlorophenol is the most toxic and recalcitrant chlorophenol because both aspects are directly proportional to the halogenation degree. Biological and abiotic pentachlorophenol degradation generates p-chloranil, which in neutral to lightly alkaline environmental conditions is hydrolyzed to chloranilic acid that present a violet-reddish coloration in aqueous solution. Several genes of the degradation pathway, cadR-cadCDX, as well as other uncharacterized genes (ORF5 and 6), were isolated from a chloranilic acid degrading bacterium, Pseudomonas putida strain TQ07. The disruption by random mutagenesis of the cadR and cadC genes in TQ07 resulted in a growth deficiency in the presence of chloranilic acid, indicating that these genes are essential for TQ07 growth with chloranilic acid as the sole carbon source. Complementation assays demonstrated that a transposon insertion in mutant CAD82 (cadC) had a polar effect on other genes contained in cosmid pLG3562. These results suggest that at least one of these genes, cadD and cadX, also takes part in chloranilic acid degradation. Based on molecular modeling and function prediction, we strongly suggest that CadC is a pyrone dicarboxylic acid hydrolase and CadD is an aldolase enzyme like dihydrodipicolinate synthase. The results of this study allowed us to propose a novel pathway that offers hypotheses on chloranilic acid degradation (an abiotic by-product of pentachlorophenol) by means of a very clear phenotype that is narrowly related to the capability of Pseudomonas putida strain TQ07 to degrade this benzoquinone.

Degradation of Endocrine Disrupting Chemicals by Genetic Transformants with Two Lignin Degrading Enzymes in Phlebia tremellosa: Hyunwoo Kum , Sungsuk Lee , Sunhwa Ryu , Hyoung T. Choi; J. Microbiol. 2011;49(5):824-827. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1230-y

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Abstract: A white rot fungus Phlebia tremellosa produced lignin degrading enzymes, which showed degrading activity against various recalcitrant compounds. However, manganese peroxidase (MnP) activity, one of lignin degrading enzymes, was very low in this fungus under various culture conditions. An expression vector that carried both the laccase and MnP genes was constructed using laccase genomic DNA of P. tremellosa and MnP cDNA from Polyporus brumalis. P. tremellosa was genetically transformed using the expression vector to obtain fungal transformants showing increased laccase and MnP activity. Many transformants showed highly increased laccase and MnP activity at the same time in liquid medium, and three of them were used to degrade endocrine disrupting chemicals. The transformant not only degraded bisphenol A and nonylphenol more rapidly but also removed the estrogenic activities of the chemicals faster than the wild type strain.

Review

Minireview] Alpine Microorganisms: Useful Tools for Low-Temperature Bioremediation: Rosa Margesin; J. Microbiol. 2007;45(4):281-285.; DOI: https://doi.org/2572 [pii]

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Abstract: Cold environments, including polar and alpine regions, are colonized by a wide diversity of microorganisms able to thrive at low temperatures. There is evidence of a wide range of metabolic activities in alpine cold ecosystems. Like polar microorganisms, alpine microorganisms play a key ecological role in their natural habitats for nutrient cycling, litter degradation, and many other processes. A number of studies have demonstrated the capacity of alpine microorganisms to degrade efficiently a wide range of hydrocarbons, including phenol, phenol-related compounds and petroleum hydrocarbons, and the feasibility of low-temperature bioremediation of European alpine soils by stimulating the degradation capacity of indigenous microorganisms has also been shown.

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

Green Fluorescent Protein as a Marker for Monitoring a Pentachlorophenol Degrader Sphingomonas chlorophenolica ATCC39723: Eun-Taex Oh , Jae-Seong So , Byung-Hyuk Kim , Jong-Sul Kim , Sung-Cheol Koh; J. Microbiol. 2004;42(3):243-247.; DOI: https://doi.org/2081 [pii]

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Abstract: Sphingomonas chlorophenolica ATCC39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpB gene by homologous recombination. As the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. Their population density dropped from 108 to 106 (cfu/ml) in the non-sterilized soil microcosms during the first 6 days. Moreover, the gfp recombinant was not detected even at lower dilution rates after a certain time period. The recombinant, however, survived for at least 28 days in the sterilized soil microcosms. Although the gfp recombinant did not degrade pentachlorophenol (PCP), this experiment showed the possibility of using gfp as a monitoring reporter system for S. chlorophenolica ATCC39723 and potentially other species of Sphingomonas.

Synthesis and Requirement of Escherichia coli Heat Shock Proteins GroEL and DnaK for Survival under Phenol Stress Conditions: Jeon, Taeck Joong , Lee, Kil Jae; J. Microbiol. 1998;36(1):26-33.

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Abstract: Exposure of Escherichia coli strain MC4100 to various concentrations of phenol at temperatures higher than 20℃ led to induction of stress proteins such as GroEL and DnaK, as analyzed by SDS-PAGE and Western blotting methods. The optimum range of phenol concentration for the induction of GroEL and DnaK was slightly different at each temperature of bacterial growth and phenol treatment. The level of GroEL increased as the temperatures of growth and phenol treatment were increased from 30℃ to 40℃. The level of induced FroEL was maximal in the wild type cells which had been grown and treated by 2000㎍/㎖ phenol at 40℃. In contrast to GroEL, the level of DnaK decreased as the temperatures of growth and phenol treatment were increased from 25℃ to 40℃. Dnak was maximally induced in the cells grown and exposed to 1000㎍/㎖ phenol at 25℃. In rpoH mutant cells KY1601, GroEL was not additionally induced by phenol treatment and DnaK was not even detectable under normal and phenol stress conditions. Viability of cells under the same conditions of phenol treatment showed that the phenol resistance in much more induced in wild type cells than rpoH mutant cells. These results suggest that the induction of GroEL and DnaK is required for the enhanced viability of cells under conditions of phenol stress.

Development of Molecular Biological Methods to Analyze Bacterial Species Diversity in Freshwater and Soil Ecosystems: Dong-Hun Lee , Sung-Ae Noh , Chi-Kyung Kim; J. Microbiol. 2000;38(1):11-17.

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Abstract: A new method was developed for the rapid analysis of diverse bacterial species in the natural envi-ronment. Our method is based on PCR-single-strands-conformation polymorphism (PCR-SSCP) and selective isolation technique of single-stranded DNA. Variable V3 fragments of 16S rDNA were amplified by PCR with bacterial 16S rDNA primers, where one of the primers was biotinylated at the 5'-end. The biotinylated strands of the PCR products were selectively isolated by using streptavidin paramagnetic particles and a magnetic stand, to prevent SSCP analysis producing heteroduplexes from heterogeneous DNA samples. The selected strands were separated by electrophoresis on a polyacrylamide gel, and detected by silver staining. Analysis of PCR products from 8 bacterial strains demonstrated their characteristic DNA band patterns. In addition, changes in the structure of the bacterial community and species diversity in the microcosm treated with phenol could be monitored. After 3 weeks of incubation, phenol and its intermediate, 2-hydroxy-muconic-semialdehyde, were degraded by indig-enous bacteria. These dominating bacterial populations were identified as strong bands on an SSCP gel. Therefore, this study provides useful tools for microbial community analysis of natural habitats.

Three Separate Pathways for the Initial Oxidation of Limonene, Biphenyl, and Phenol by Rhodococcus sp. Strain T104: Dockyu Kim , Min Jung Park , Sung-Cheol Koh , Jae-Seong So , Eungbin Kim; J. Microbiol. 2002;40(1):86-89.

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Abstract: Rhodococcus sp. strain T104, which is able to grow on either biphenyl or limonene, was found to utilize phenol as sole carbon and energy sources. Furthermore, T104 was positively identified to possess three separate pathways for the degradation of limonene, phenol, and biphenyl. The fact that biphenyl and limonene induced almost the same amount of catechol 1,2-dioxygenase activity indicates that limonene can induce both upper and lower pathways for biphenyl degradation by T104.

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