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Singhvi N, Talwar C, Nagar S, Verma H, Kaur J, Mahato NK, Ahmad N, Mondal K, Gupta V, Lal R. Insights into the radiation and oxidative stress mechanisms in genus Deinococcus. Comput Biol Chem 2024; 112:108161. [PMID: 39116702 DOI: 10.1016/j.compbiolchem.2024.108161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.
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Affiliation(s)
- Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun 248007, India
| | - Chandni Talwar
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Shekhar Nagar
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi 110019, India
| | - Helianthous Verma
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Jasvinder Kaur
- Department of Zoology, Gargi College, University of Delhi, New Delhi 110049, India
| | - Nitish Kumar Mahato
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand, India
| | - Nabeel Ahmad
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun 248007, India
| | - Krishnendu Mondal
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun 248001, India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun 248001, India.
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, New Delhi 110019, India.
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Lee JH, Jung JH, Kim MK, Lim S. Deinococcus taeanensis sp. nov., a Radiation-Resistant Bacterium Isolated from a Coastal Dune. Curr Microbiol 2022; 79:334. [PMID: 36161362 PMCID: PMC9510100 DOI: 10.1007/s00284-022-03044-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/14/2022] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, nonspore-forming, nonmotile, aerobic, rod-shaped, and very pale orange-colored bacterial strain, designated TS293T, was isolated from a sand sample obtained from a coastal dune after exposure to 3kGy of gamma (γ)-radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Deinococcus and clustered with D. deserti VCD115T. The genome of strain TS293T was 4.62 Mbp long (68.2% G + C content and 4124 predicted genes) divided into a 2.86Mb main chromosome and five plasmids. Many genes considered to be important to the γ-radiation and oxidative stress resistance of Deinococcus were conserved in TS293T, but genome features that could differentiate TS293T from D. deserti and D. radiodurans, the type species of the Deinococcus genus, were also detected. Strain TS293T showed resistance to γ-radiation with D10 values (i.e., the dose required to reduce the bacterial population by tenfold) of 3.1kGy. The predominant fatty acids of strain TS293T were summed feature 3 (C16:1ω6c and/or C16:1ω7c) and iso-C16:0. The major polar lipids were two unidentified phosphoglycolipids and one unidentified glycolipid. The main respiratory quinone was menaquinone-8. Based on the phylogenetic, genomic, physiological, and chemotaxonomic characteristics, strain TS293T represents a novel species, for which the name Deinococcus taeanensis sp. nov. is proposed. The type strain is TS293T (= KCTC 43191T = JCM 34027T).
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Affiliation(s)
- Ji Hee Lee
- Division of Pathogen Resource Management, Korea Disease Control and Prevention Agency, Cheongju, 28160, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
- Department of Radiation Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Bae S, Kang H, Kim H, Joh K. Deinococcus betulae sp. nov. and Deinococcus arboris sp. nov., novel bacteria isolated from bark of birch tree (Betula platyphylla). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two reddish-coloured bacterial strains (HMF7604T and HMF7620T) were isolated from bark of birch tree (Betula platyphylla) together with two strains (designed as HMF7603 and HMF7618). Cells were observed to be Gram-stain-negative, oval- to short rod-shaped and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four isolates belonged to the genus
Deinococcus
, family
Deinococcaceae
. They had the highest similarities (95.4–95.6 %) to
Deinococcus multiflagellatus
ID1504T, with which they formed a clade in phylogenetic trees. Menaquinone-8 was the only respiratory quinone. The predominant fatty acids were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), C15 : 1
ω6c, C17 : 0 and C16 : 0. Strain HMF7604T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, one unidentified aminolipid, three unidentified phospholipids and three unidentified polar lipids, while strain HMF7620T contained one unidentified phosphoglycolipid, four unidentified glycolipids, one unidentified aminophospholipid, one unidentified phospholipid and one unidentified polar lipid. The DNA G+C contents of strains HMF7604T and HMF7620T were 65.6 and 65.7 mol%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between the two isolates and their close relative
D. multiflagellatus
were 81.1–95.3 and 24.5–61.6 %, respectively. Based on the results of phenotypic and phylogenetic characterizations, the four isolates are considered to represent two novel species of the genus
Deinococcus
, for which the names Deinococcus betulae sp. nov. and Deinococcus arboris sp. nov. are proposed. The type strains are HMF7604T (=KCTC 43354T=NBRC 115489T) and HMF7620T (=KCTC 43051T=NBRC 113959T).
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Affiliation(s)
| | | | | | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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Fahrion J, Fink C, Zabel P, Schubert D, Mysara M, Van Houdt R, Eikmanns B, Beblo-Vranesevic K, Rettberg P. Microbial Monitoring in the EDEN ISS Greenhouse, a Mobile Test Facility in Antarctica. Front Microbiol 2020; 11:525. [PMID: 32296408 PMCID: PMC7137377 DOI: 10.3389/fmicb.2020.00525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
The EDEN ISS greenhouse, integrated in two joined containers, is a confined mobile test facility in Antarctica for the development and optimization of new plant cultivation techniques for future space programs. The EDEN ISS greenhouse was used successfully from February to November 2018 for fresh food production for the overwintering crew at the Antarctic Neumayer III station. During the 9 months of operation, samples from the different plants, from the nutrition solution of the aeroponic planting system, and from diverse surfaces within the three different compartments of the container were taken [future exploration greenhouse (FEG), service section (SS), and cold porch (CP)]. Quantity as well as diversity of microorganisms was examined by cultivation. In case of the plant samples, microbial quantities were in a range from 102 to 104 colony forming units per gram plant material. Compared to plants purchased from a German grocery, the produce hosted orders of magnitude more microorganisms than the EDEN ISS plants. The EDEN ISS plant samples contained mainly fungi and a few bacteria. No classical food associated pathogenic microorganism, like Escherichia and Salmonella, could be found. Probably due to the used cultivation approach, Archaea were not found in the samples. The bioburden in the nutrition solutions increased constantly over time but never reached critical values like 102-103 cfu per 100 mL in irrigation water as it is stated, e.g., for commercial European plant productions. The surface samples revealed high differences in the microbial burden between the greenhouse part of the container and the SS and CP part. However, the numbers of organisms (bacteria and fungi) found in the planted greenhouse were still not critical. The microbial loaded surfaces showed strong temporal as well as spatial fluctuations. In samples of the nutrition solution and the surface, the amount of bacteria exceeded the amount of fungi by many times. For identification, 16S rRNA gene sequencing was performed for the isolated prokaryotic organisms. Phylogenetic analyses revealed that the most abundant bacterial phyla were Firmicutes and Actinobacteria. These phyla include plant- and human-associated bacterial species. In general, it could be shown that it is possible to produce edible fresh food in a remote environment and this food is safe for consumption from a microbiological point of view.
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Affiliation(s)
- Jana Fahrion
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | - Carina Fink
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Paul Zabel
- Institute for Space Systems, German Aerospace Center (DLR), Bremen, Germany
| | - Daniel Schubert
- Institute for Space Systems, German Aerospace Center (DLR), Bremen, Germany
| | - Mohamed Mysara
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Bernhard Eikmanns
- Institute of Microbiology and Biotechnology, Faculty of Natural Sciences, University of Ulm, Ulm, Germany
| | | | - Petra Rettberg
- Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
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Deinococcus arcticus sp. nov., isolated from Silene acaulis rhizosphere soil of the Arctic tundra. Int J Syst Evol Microbiol 2019; 69:3437-3442. [DOI: 10.1099/ijsem.0.003636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Carbonero F, Mayta A, Bolea M, Yu JZ, Lindeblad M, Lyubimov A, Neri F, Szilagyi E, Smith B, Halliday L, Bartholomew A. Specific Members of the Gut Microbiota are Reliable Biomarkers of Irradiation Intensity and Lethality in Large Animal Models of Human Health. Radiat Res 2018; 191:107-121. [PMID: 30430918 DOI: 10.1667/rr14975.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The development of effective biomarkers for detecting the magnitude of radiation exposure and resiliency of host response is crucial to identifying appropriate treatment strategies after radiation exposure. We hypothesized that the gastrointestinal resident bacteria would demonstrate predictable, dose-dependent changes after radiation exposure across two large animal models of acute radiation syndrome. Here, Göttingen minipigs (GMP) (n = 50) and rhesus macaques (n = 48) were exposed to five dose levels (resulting in mortality rates of 33-100% and 25-68.7%, respectively). Fecal samples taken prior to and after irradiation (day 0 for GMP; day 0, 3 and 14 for macaques) were used for 16S rRNA gene sequence amplicon high-throughput sequencing. Baseline gut microbiota profiles were dissimilar between GMP and macaques, however, radiation appeared to have similar effect at the phylum level, resulting in Bacteroidetes decrease and Firmicutes increase in both models. The abundance of the main Bacteroidetes genus ( Bacteroides for GMP, Prevotella for macaques) was profoundly decreased by irradiation. Intracellular symbionts [Elusimicrobia in GMP, Treponema (Spirochaetes) in macaques] consistently increased after irradiation, suggesting their use as potential biomarkers of intestinal injury, and potential negative effect on health. Prevotella, Lactobacillus, Clostridium XIVa, Oscillibacter and Elusimicrobium/ Treponema abundances were found to be very significantly correlated with radiation intensity. Furthermore, Prevotella, Enterorhabdus and Ruminococcus and Enterorhabdus maintenance was strongly associated with survival in GMP, while Prevotella, Oscillibacter and Treponema were strongly associated with survival and Streptococcus with death in macaques. Overall, we found that a wide range of gut bacterial genera known to be abundant in the human gut microbiota are excellent biomarkers of radiation intensity and resilience in animal models, and that detrimental effects can be monitored, and potentially prevented, by targeting selected genera.
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Affiliation(s)
- Franck Carbonero
- a Department of Food Science, University of Arkansas, Fayetteville, Arkansas 72704
| | - Alba Mayta
- a Department of Food Science, University of Arkansas, Fayetteville, Arkansas 72704
| | - Mathilde Bolea
- a Department of Food Science, University of Arkansas, Fayetteville, Arkansas 72704
| | - Jiang-Zhou Yu
- b Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Matt Lindeblad
- c Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Alex Lyubimov
- c Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | - Flavia Neri
- b Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Erzsebet Szilagyi
- b Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Brett Smith
- d Department of Radiation Oncology, University of Illinois at Chicago, Chicago, Illinois
| | - Lisa Halliday
- e Department of Primatology, Biologic Resources Laboratory, University of Illinois at Chicago, Chicago, Illinois
| | - Amelia Bartholomew
- b Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
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Wang Q, Song Y, Choi L, Liu H, Wang G, Li M. Deinococcus rufus sp. nov., isolated from soil near an iron factory. Int J Syst Evol Microbiol 2018; 68:1622-1626. [PMID: 29561256 DOI: 10.1099/ijsem.0.002724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A Gram-stain-negative, non-motile, rod-shaped, red-pigmented strain, designated W37T, was isolated from soil near an iron factory in Busan (Republic of Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W37T was most closely related to Deinococcus yunweiensis YIM 007T (98.3 %) and Deinococcus radioresistens 8AT (96.3 %). The DNA-DNA relatedness between strain W37T and D. yunweiensis YIM 007T was 50.5 %. The predominant respiratory quinone was MK-8. The major polar lipids were an unidentified phosphoglycolipid, an unidentified aminophospholipid, four unidentified glycolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids (>5 %) of strain W37T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and iso-C17 : 1ω9c. The DNA G+C content was 69.0 mol%. Moreover, the chemo-physical characteristics of strain W37T clearly differed from those of related species, including ranges of growth temperature and pH, positive activity for 4-hydroxybenzoate and negative activity for cystine arylamidase. Phenotypic, chemotaxonomic and genotypic analyses indicated that strain W37T represents a novel species of the genus Deinococcus, for which the name Deinococcus rufus sp. nov., is proposed. The type strain is W37T (=KCTC 33913T=CCTCC AB 2017081T).
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yali Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Lina Choi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hongyu Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 66:4299-4305. [PMID: 27928990 DOI: 10.1099/ijsem.0.001585] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Lee JJ, Lee YH, Park SJ, Lee SY, Park S, Lee DS, Kang IK, Ten LN, Jung HY. Deinococcus knuensis sp. nov., a bacterium isolated from river water. Antonie Van Leeuwenhoek 2016; 110:407-414. [PMID: 28000055 DOI: 10.1007/s10482-016-0813-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/26/2016] [Indexed: 11/25/2022]
Abstract
Strain 16F3HT, a Gram-negative, aerobic, non-motile, and oval-shaped bacterium, was isolated from river water collected from the Han River in South Korea. Growth of strain 16F3HT was observed at 10-42 °C (optimum at 25-30 °C), but no growth occurred at 4 °C. The strain is able to grow at pH 4-10 (optimum at pH 7-8) and tolerates up to 4% NaCl (w/v), with optimum growth at 0.5% NaCl. The isolate was found to be resistant to UV irradiation. Based on 16S rRNA gene sequence analysis, it is closely related to 'Deinococcus seoulensis' 16F1E (98.8%), Deinococcus aquaticus PB314T (98.1%) and Deinococcus caeni Ho-08T (98.0%). The level of DNA-DNA homology between the novel strain and the three related strains was 57.4, 41.2, and 35.8%, respectively. Chemotaxonomic data revealed that strain 16F3HT possesses MK-8 as the predominant respiratory quinone, an unidentified phosphoglycolipid as the major polar lipid, and C15:1 ω6c and C16:1 ω7c as the major fatty acids. The DNA G + C content was determined to be 65.7 mol%. Based on polyphasic evidence, strain 16F3HT (=KCTC 33794T = JCM 31406T) should be classified as the type strain of a novel Deinococcus species, for which the name Deinococcus knuensis sp. nov. is proposed.
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Affiliation(s)
- Jae-Jin Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Yeon-Hee Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Su-Jin Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Seung-Yeol Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangkyu Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - In-Kyu Kang
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Leonid N Ten
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Young Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea.
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