- The β‑Lactamase Activity at the Community Level Confers β‑Lactam Resistance to Bloom‑Forming Microcystis aeruginosa Ce
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Yerim Park , Wonjae Kim , Minkyung Kim , Woojun Park
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J. Microbiol. 2023;61(9):807-820. Published online October 18, 2023
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DOI: https://doi.org/10.1007/s12275-023-00082-0
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Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however,
both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested
concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic
NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria
in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic
observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment
of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The
nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin
concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species
and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin
treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXArelated
antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin
toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater
bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where
associated bacteria protect axenic M. aeruginosa cells.
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Citations
Citations to this article as recorded by 
- Public goods-mediated bacterial interplay in aquatic ecosystems
Yerim Park, Wonjae Kim, Jihye Bae, Woojun Park Water Research.2025; 287: 124310. CrossRef - Selective cyanobactericidal activity of Nocardioides convexus MS16 against Microcystis aeruginosa, mediated by direct attack
Seonah Jeong, Ve Van Le, So-Ra Ko, Mingyeong Kang, Min-Seong Kim, Zhun Li, Chi-Yong Ahn Algal Research.2025; 90: 104165. CrossRef - Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts
Wonjae Kim, Yerim Park, Minkyung Kim, Yeji Cha, Jaejoon Jung, Che Ok Jeon, Woojun Park Ecotoxicology and Environmental Safety.2024; 277: 116375. CrossRef - Microcystis abundance is predictable through ambient bacterial communities: A data-oriented approach
Mingyeong Kang, Dong-Kyun Kim, Ve Van Le, So-Ra Ko, Jay Jung Lee, In-Chan Choi, Yuna Shin, Kyunghyun Kim, Chi-Yong Ahn Journal of Environmental Management.2024; 368: 122128. CrossRef - Enhanced mechanical properties of living and regenerative building materials by filamentous Leptolyngbya boryana
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Aabir Banerji, Nichole E. Brinkman, Benjamin Davis, Alison Franklin, Michael Jahne, Scott P. Keely Microorganisms.2024; 12(11): 2121. CrossRef - Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park Journal of Microbiology.2024; 62(11): 933. CrossRef - Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park Journal of Microbiology.2024; 62(3): 249. CrossRef - Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park Harmful Algae.2024; 137: 102680. CrossRef
- [MINIREVIEW]Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective
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Misung Kim , Jaeeun Park , Mingyeong Kang , Jihye Yang , Woojun Park
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J. Microbiol. 2021;59(6):535-545. Published online April 20, 2021
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DOI: https://doi.org/10.1007/s12275-021-1085-9
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The emergence of multidrug resistance (MDR) has become
a global health threat due to the increasing unnecessary use
of antibiotics. Multidrug resistant bacteria occur mainly by
accumulating resistance genes on mobile genetic elements
(MGEs), made possible by horizontal gene transfer (HGT).
Humans and animal guts along with natural and engineered
environments such as wastewater treatment plants and manured
soils have proven to be the major reservoirs and hotspots
of spreading antibiotic resistance genes (ARGs). As those
environments support the dissemination of MGEs through
the complex interactions that take place at the human-animalenvironment
interfaces, a growing One Health challenge is
for multiple sectors to communicate and work together to
prevent the emergence and spread of MDR bacteria. However,
maintenance of ARGs in a bacterial chromosome and/or
plasmids in the environments might place energy burdens
on bacterial fitness in the absence of antibiotics, and those
unnecessary ARGs could eventually be lost. This review highlights
and summarizes the current investigations into the gain
and loss of ARG genes in MDR bacteria among human-animal-
environment interfaces. We also suggest alternative treatments
such as combinatory therapies or sequential use of different
classes of antibiotics/adjuvants, treatment with enzymeinhibitors,
and phage therapy with antibiotics to solve the
MDR problem from the perspective of One Health issues.
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- Raman spectroscopy reveals alteration of spore compositions under different nutritional conditions in Lysinibacillus boronitolerans YS11
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Youngung Ryu , Minyoung Hong , Soo Bin Kim , Tae Kwon Lee , Woojun Park
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J. Microbiol. 2021;59(5):491-499. Published online March 29, 2021
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DOI: https://doi.org/10.1007/s12275-021-0679-6
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Little is known about final spores components when bacteria
undergo sporulation under different nutrient conditions.
Different degrees of resistance and germination rates were
observed in the three types of spores of Lysinibacillus boronitolerans
YS11 (SD, Spores formed in Difco sporulation
mediumTM; SC and SF, Spores formed in an agricultural byproduct
medium with 10 mM CaCl2 and with 10 mM FeSO4,
respectively). Stronger UV resistance was recorded for SF
with 1.8–2.3-fold greater survival than SC and SD under UV
treatment. The three spore types showed similar heat resistances
at 80°C, but survival rates of SC and SD were much
higher (~1,000 times) than those of SF at 90°C. However,
germination capacity of SF was 20% higher than those of
SD and SC on Luria-Bertani agar plates for 24 h. SF germinated
more rapidly in a liquid medium with high NaCl concentrations
than SC and SD, but became slower under alkaline
conditions. Raman spectroscopy was used to analyze the
heterogeneities in the three types of vegetative cells and their
spores under different nutritional conditions. Exponentially
grown-each vegetative cells had different overall Raman peak
values. Raman peaks of SC, SD, and SF also showed differences
in adenine and amide III compositions and nucleic acid
contents. Our data along with Raman spectroscopy provided
the evidence that spores formed under under different growth
conditions possess very different cellular components, which
affected their survival and germination rates.
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Xiao Hu, Pengfei Ge, Xiaomeng Wang, Xinyu Liao, Jinsong Feng, Ruiling Lv, Tian Ding Food Research International.2024; 196: 115058. CrossRef - Alleviation of H2O2 toxicity by extracellular catalases in the phycosphere of Microcystis aeruginosa
Yerim Park, Wonjae Kim, Yeji Cha, Minkyung Kim, Woojun Park Harmful Algae.2024; 137: 102680. CrossRef - Effects of sporulation conditions on the growth, germination, and resistance of Clostridium perfringens spores
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- Optimization of bacterial sporulation using economic nutrient for self-healing concrete
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Youngung Ryu , Ki-Eun Lee , In-Tae Cha , Woojun Park
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J. Microbiol. 2020;58(4):288-296. Published online February 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-9580-y
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The use of heat- and alkali-resistant bacteria is essential for
the biological repair of damaged concrete. Lysinibacillus boronitolerans
YS11 was isolated from the rhizosphere of Miscanthus
sacchariflorus. The increased pH in the urea-minus
condition during the growth of the YS11 strain promoted calcium
carbonate (CaCO3) formation. To identify the optimum
medium that promoted the growth of the YS11 strain, a Plackett-
Burman design was conducted for the screening process.
Consequently, malt powder, rice bran, (NH4)2SO4, and corn
syrup were chosen to enhance YS11 growth. The optimization
of these four useful factors was carried out using a central
composite design. To obtain higher survivability in mortar,
the sporulation process is essential, and additional factors
such as Mn2+, Fe2+, and Ca2+ were found to contribute
to sporulation. A mixture of L. boronitolerans YS11 spore
powder, cement, paste, sand, yeast extract, calcium lactate,
and water showed a healing effect on a 0.3 mm mortar crack
in 7 days. Furthermore, calcium carbonate precipitation was
observed over the crack surface. Thus, we confirmed that mortar
treated with YS11 spore powder was effective in healing
micro-cracks in concrete.
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Manpreet Bagga, Charlotte Hamley-Bennett, Aleena Alex, Brubeck L Freeman, Ismael Justo-Reinoso, Iulia C Mihai, Susanne Gebhard, Kevin Paine, Anthony D Jefferson, Enrico Masoero, Irina D Ofiţeru Construction and Building Materials.2022; 358: 129412. CrossRef - Review of autonomous self-healing cementitious material
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Minyoung Hong, Indong Jang, Yongjun Son, Chongku Yi, Woojun Park AMB Express.2021;[Epub] CrossRef - Raman spectroscopy reveals alteration of spore compositions under different nutritional conditions in Lysinibacillus boronitolerans YS11
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- Sterilization efficiency of pathogen-contaminated cottons in a laundry machine
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Yoonjae Shin , Jungha Park , Woojun Park
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J. Microbiol. 2020;58(1):30-38. Published online November 25, 2019
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DOI: https://doi.org/10.1007/s12275-020-9391-1
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438
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12
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12
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Abstract
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Pathogenic bacteria on abiotic surfaces such as fabrics, bedding,
patient wears, and surgical tools are known to increase
the risk of bacterial diseases in infants and the elderly. The
desiccation tolerance of bacteria affects their viability in cotton.
Thus, washing and drying machines are required to use
conditions that ensure the sterilization of bacteria in cotton.
The objective of this study is to determine the effects of various
sterilization conditions of washing and drying machines
on the survival of three pathogenic bacteria (Acinetobacter
baumannii, Pseudomonas aeruginosa, and Staphylococcus
aureus) commonly presented in contaminated cotton and two
non-pathogenic bacteria (Bacillus subtilis and Escherichia coli)
in cotton. High survival rates of A. baumannii and S. aureus
in desiccated cotton were observed based on scanning electron
microscope and replicate organism direct agar contact
assay. The survival rates of A. baumannii and S. aureus exposed
in desiccated cotton for 8 h were higher (14.4 and 5.0%,
respectively) than those of other bacteria (< 0.5%). All tested
bacteria were eradicated at low-temperature (< 40°C) washing
with activated oxygen bleach (AOB). However, bacterial
viability was shown in low temperature washing without AOB.
High-temperature (> 60°C) washing was required to achieve
99.9% of the sterilization rate in washing without AOB. The
sterilization rate was 93.2% using a drying machine at 60°C
for 4 h. This level of sterilization was insufficient in terms
of time and energy efficiency. High sterilization efficiency
(> 99.9%) at 75°C for 3 h using a drying machine was confirmed.
This study suggests standard conditions of drying
machines to remove bacterial contamination in cotton by
providing practical data.
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- EDITORIAL] Gut microbiomes and their metabolites shape human and animal health
-
Woojun Park
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J. Microbiol. 2018;56(3):151-153.
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DOI: https://doi.org/10.1007/s12275-018-0577-8
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410
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45
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Abstract
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The host genetic background, complex surrounding environments,
and gut microbiome are very closely linked to human
and animal health and disease. Although significant correlations
between gut microbiota and human and animal health
have been revealed, the specific roles of each gut bacterium
in shaping human and animal health and disease remain
unclear. However, recent omics-based studies using experimental
animals and surveys of gut microbiota from unhealthy
humans have provided insights into the relationships among
microbial community, their metabolites, and human and animal
health. This editorial introduces six review papers that
provide new discoveries of disease-associated microbiomes
and suggest possible microbiome-based therapeutic approaches
to human disease.
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- [Minireview] Antibiotic resistance of pathogenic Acinetobacter species and emerging combination therapy
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Bora Shin , Woojun Park
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J. Microbiol. 2017;55(11):837-849. Published online October 27, 2017
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DOI: https://doi.org/10.1007/s12275-017-7288-4
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347
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Abstract
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The increasing antibiotic resistance of Acinetobacter species
in both natural and hospital environments has become a serious
problem worldwide in recent decades. Because of both
intrinsic and acquired antimicrobial resistance (AMR) against
last-resort antibiotics such as carbapenems, novel therapeutics
are urgently required to treat Acinetobacter-associated infectious
diseases. Among the many pathogenic Acinetobacter
species, A. baumannii has been reported to be resistant to all
classes of antibiotics and contains many AMR genes, such as
blaADC (Acinetobacter-derived cephalosporinase). The AMR
of pathogenic Acinetobacter species is the result of several
different mechanisms, including active efflux pumps, mutations
in antibiotic targets, antibiotic modification, and low
antibiotic membrane permeability. To overcome the limitations
of existing drugs, combination theraphy that can increase
the activity of antibiotics should be considered in the
treatment of Acinetobacter infections. Understanding the
molecular mechanisms behind Acinetobacter AMR resistance
will provide vital information for drug development and
therapeutic strategies using combination treatment. Here,
we summarize the classic mechanisms of Acinetobacter AMR,
along with newly-discovered genetic AMR factors and currently
available antimicrobial adjuvants that can enhance drug
efficacy in the treatment of A. baumannii infections.
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Acinetobacter baumannii
with synergism and additivity when combined with polymyxin B
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- Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus
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Yun Suk Lee , Hyun Jung Kim , Woojun Park
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J. Microbiol. 2017;55(6):440-447. Published online May 28, 2017
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DOI: https://doi.org/10.1007/s12275-017-7086-z
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Abstract
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Although microbially induced calcium carbonate precipita-tion (MICP) through ureolysis has been widely studied in en-vironmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium car-bonate-precipitating bacteria that induced an alkaline envi-ronment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to pre-cipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy disper-sive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning elec-tron microscopy analysis indicated the formation of morpho-logically distinct minerals around cells under these condi-tions. Monitoring of bacterial growth, pH changes, and Ca2+ concentrations under aerobic, hypoxia, and anaerobic con-ditions suggested that strain YS11 could induce alkaline con-ditions up to a pH of 8.9 and utilize 95% of free Ca2+ only under aerobic conditions. Unusual Ca2+ binding and its re-lease from cells were observed under hypoxia conditions. Bio-film and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore- forming ability, which supports its potential application for self-healing concrete.
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- MINIREVIEW] Indole: a signaling molecule or a mere metabolic byproduct that alters bacterial physiology at a high concentration?
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Jisun Kim , Woojun Park
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J. Microbiol. 2015;53(7):421-428. Published online June 27, 2015
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DOI: https://doi.org/10.1007/s12275-015-5273-3
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Abstract
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Indole is an organic compound that is widespread in microbial
communities inhabiting diverse habitats, like the soil
environment and human intestines. Measurement of indole
production is a traditional method for the identification of
microbial species. Escherichia coli can produce millimolar
concentrations of indole in the stationary growth phase under
nutrient-rich conditions. Indole has received considerable
attention because of its remarkable effects on various
biological functions of the microbial communities, for example,
biofilm formation, motility, virulence, plasmid stability,
and antibiotic resistance. Indole may function as an
intercellular signaling molecule, like a quorum-sensing signal.
Nevertheless, a receptor system for indole and the function
of this compound in coordinated behavior of a microbial population
(which are requirements for a true signaling molecule)
have not yet been confirmed. Recent findings suggest
that a long-known quorum-sensing regulator, E. coli’s SdiA,
cannot recognize indole and that this compound may simply
cause membrane disruption and energy reduction, which
can lead to various changes in bacterial physiology including
unstable folding of a quorum-sensing regulator. Indole
appears to be responsible for acquisition of antibiotic resistance
via the formation of persister cells and activation of an
exporter. This review highlights and summarizes the current
knowledge about indole as a multitrophic molecule among
bacteria, together with recently identified new avenues of
research.
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- Effects of Nutritional Input and Diesel Contamination on Soil Enzyme Activities and Microbial Communities in Antarctic Soils
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Jiwon Han , Jaejoon Jung , Seunghun Hyun , Hyun Park , Woojun Park
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J. Microbiol. 2012;50(6):916-924. Published online December 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-2636-x
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Abstract
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Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel
contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction.
Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance
of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act
as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.
- NOTE] Pedobacter jeongneungensis sp. nov., Isolated from Forest Soil
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Jaejoon Jung , Woojun Park
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J. Microbiol. 2012;50(4):660-664. Published online July 21, 2012
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DOI: https://doi.org/10.1007/s12275-012-1629-0
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309
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Strain BH45T was isolated from forest soil of Mt. Bukhan in Jeongneung, Seoul, Korea. The Gram-staining-negative strain BH45T grows at 4–30°C (optimum of 25–30°C) and between pH 5–8 (optimum of pH 6–8). Its major cellular fatty acids are C18:3 ω6c (6,9,12) and C10:0. The G+C content of genomic DNA was 40.2 mol%. The major respiratory quinone system in strain BH45T is menaquinone-7. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain BH45T is closely related to the genus Pedobacter. Sequence similarities with P. terrae KCTC 12762T, P. suwonensis KACC 11317T, P. soli KACC 14939T, P. alluvionis DSM 19624T, P. roseus KCCM 42272T, P. yonginense KCTC 22721T were 97.5, 97.1, 97.0, 97.0, 97.0, and 96.0%, respectively. DNA-DNA hybridization results distinguish strain BH45T from two Pedobacter species with high 16S rRNA gene sequence similarities. According to the phenotypic and molecular data, the strain BH45T clearly represents a novel species within the genus Pedobacter; thus, the name Pedobacter jeongneungensis sp. nov. is proposed for this strain. The type strain is BH45T (=KACC 15514T =JCM 17626T).
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Citations
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International Journal of Systematic and Evolutionary Microbiology
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Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx
Yerim Park, Jihyeon Min, Bitnara Kim, Woojun Park
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Minkyung Kim, Wonjae Kim, Woojun Park
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Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa
Minkyung Kim, Byoung-Hee Lee, Ki-Eun Lee, Woojun Park
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef - Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine
Zhiyong Wang, Yuanqing Tan, Ding Xu, Gejiao Wang, Jihong Yuan, Shixue Zheng International Journal of Systematic and Evolutionary Microbiology.2016; 66(12): 5112. CrossRef
- Seasonal Changes in Nitrogen-Cycle Gene Abundances and in Bacterial Communities in Acidic Forest Soils
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Jaejoon Jung , Jinki Yeom , Jiwon Han , Jisun Kim , Woojun Park
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J. Microbiol. 2012;50(3):365-373. Published online June 30, 2012
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DOI: https://doi.org/10.1007/s12275-012-1465-2
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277
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The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.
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- Physiological and Metabolic Responses for Hexadecane Degradation in Acinetobacter oleivorans DR1
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Jaejoon Jung , Jaemin Noh , Woojun Park
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J. Microbiol. 2011;49(2):208-215. Published online May 3, 2011
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DOI: https://doi.org/10.1007/s12275-011-0395-8
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The hexadecane degradation of Acinetobacter oleivorans DR1 was evaluated with changes in temperature and ionic salt contents. Hexadecane degradation of strain DR1 was reduced markedly by the presence of sodium chloride (but not potassium chloride). High temperature (37°C) was also shown to inhibit the motility, biofilm formation, and hexadecane biodegradation. The biofilm formation of strain DR1 on the oil-water interface might prove to be a critical physiological feature for the degradation of hexadecane. The positive relationship between biofilm formation and hexadecane degradation could be observed at 30°C, but not at low temperatures (25°C). Alterations in cell hydrophobicity and EPS production by temperature and
salts were not correlated with biofilm formation and hexadecane degradation. Our proteomic analyses have demonstrated that metabolic changes through the glyoxylate pathway are important for efficient degradation of hexadecane. Proteins involved in fatty acid metabolism, gluconeogenesis, and oxidative stress defense
proteins appear to be highly expressed during biodegradation of hexadecane. These results suggested that biofilm formation and oxidative stress defense are important physiological responses for hexadecane degradation along with metabolic switch to glyoxylate pathway in strain DR1.
- Acinetobacter oleivorans sp. nov. Is Capable of Adhering to and Growing on Diesel-Oil
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Yoon-Suk Kang , Jaejoon Jung , Che Ok Jeon , Woojun Park
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J. Microbiol. 2011;49(1):29-34. Published online March 3, 2011
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DOI: https://doi.org/10.1007/s12275-011-0315-y
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360
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A diesel-oil and n-hexadecane-degrading novel bacterial strain, designated DR1T, was isolated from a rice paddy in Deok-So, South Korea. The strain DR1T cells were Gram-negative, aerobic coccobacilli, and grew at 20-37°C with the optimal temperature of 30°C, and an optimal pH of 6-8. Interestingly, strain DR1T was highly motile (swimming and swarming motility) using its fimbriae, and generated N-acyl homoserine lactones as quorum-sensing signals. The predominant respiratory quinone as identified as ubiquinone-9 (Q-9) and DNA G+C content was 41.4 mol%. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species A. calcoaceticus, A. haemolyticus, A. baumannii, A. baylyi, and A. beijerinckii, with which it evidenced sequence similarities of 98.2%, 97.4%, 97.2%, 97.1%, and 97.0%, respectively. DNA-DNA hybridization values between strain DR1T and other Acinetobacter spp. were all less than 20%. The physiological and taxonomic characteristics with the DNA-DNA hybridization data supported the identification of strain DR1T in the genus Acinetobacter as a novel species, for which the name Acinetobacter oleivorans sp. nov. is proposed. The type strain is DR1T (=KCTC 23045T =JCM 16667T).
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Sujin Yeom , Jinki Yeom , Woojun Park
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J. Microbiol. 2010;48(2):153-159. Published online May 1, 2010
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DOI: https://doi.org/10.1007/s12275-010-0075-0
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The zwf, which encodes glucose-6-phosphate dehydrogenase, is repressed by NtrC under nitrogen-limited condition. Previously, we demonstrated that induction of zwf-1 is required for protecting Pseudomonas putida cells under oxidative stress, which could be possible probably because of derepression of HexR on the zwf-1 gene under oxidative stress. These findings led us investigate that NtrC still represses the zwf-1 under nitrogen-limited oxidative stress condition, which makes cells more sensitive under such condition. Interestingly, deletion of the ntrC gene significantly reduces growth rate, but renders cells more resistant to oxidative stress, under nitrogen limited condition in P. putida. More vitality of the ntrC mutant under oxidative stress condition was also confirmed by the fluorogenic redox dye using flow cytometry. The results of transcriptome analysis demonstrated that the derepression of several oxidative stress genes along with the zwf-1 gene might confer high resistance to oxidative stress in the ntrC mutant. Here, we presented the data for the first time, showing that different sets of genes are involved in nitrogen-rich and nitrogen-limited oxidative stress conditions and NtrC-sensed nitrogen availability is one of the most important prerequisite for full cellular defense against oxidative stress in P. putida.
- Analysis of Microbial Communities Using Culture-dependent and Culture-independent Approaches in an Anaerobic/Aerobic SBR Reactor
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Shipeng Lu , Minjeong Park , Hyeon-Su Ro , Dae Sung Lee , Woojun Park , Che Ok Jeon
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J. Microbiol. 2006;44(2):155-161.
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DOI: https://doi.org/2370 [pii]
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Abstract
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Comparative analysis of microbial communities in a sequencing batch reactor which
performed enhanced biological phosphorus removal (EBPR) was carried out using a
cultivation-based technique and 16S rRNA gene clone libraries. A standard PCR protocol and a modified PCR protocol with low PCR cycle was applied to the two clone libraries of the 16S rRNA gene sequences obtained from EBPR sludge, respectively, and the resulting 424 clones were analyzed using restriction fragment length polymorphisms (RFLPs) on 16S rRNA gene inserts. Comparison of two clone libraries showed that the modified PCR protocol decreased the incidence of distinct fragment patterns from about 63% (137 of 217) in the standard PCR method to about 34% (70 of 207) under the modified protocol, suggesting that just a low level of PCR cycling (5 cycles after 15 cycles) can significantly reduce the formation of chimeric DNA in the final PCR products. Phylogenetic analysis of 81 groups with distinct RFLP patterns that were obtained using the modified PCR method revealed that the clones were affiliated with at least 11 phyla or classes of the domain Bacteria. However, the analyses of 327 colonies, which were grouped into just 41 distinct types by RFLP analysis, showed that they could be classified into five major bacterial lineages: α, β, γ- Proteobacteria, Actinobacteria, and the phylum Bacteroidetes, which indicated that the microbial community yielded from the cultivationbased method was still much simpler than that yielded from the PCR-based molecular method. In this study, the discrepancy observed between the communities obtained from PCR-based and cultivation-based methods seems to result from low culturabilities of bacteria or PCR bias even though modified culture and PCR methods were used. Therefore, continuous development of PCR protocol and cultivation techniques is needed to reduce this discrepancy.
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