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Article ; Online: Potato Soft Rot Caused by Psychrotolerant Pseudomonas sp. from Subarctic Tundra Soil

Sungho Woo / Yung Mi Lee / Dockyu Kim

Research in Plant Disease, Vol 29, Iss 4, Pp 399-

2023 Volume 404

Abstract: Agricultural activities and the number of farms in the subarctic regions have been increasing annually after the coronavirus disease 2019 pandemic to achieve food self-sufficiency. Potatoes are vulnerable to soft rot bacteria at all stages of production, ...

Abstract	Agricultural activities and the number of farms in the subarctic regions have been increasing annually after the coronavirus disease 2019 pandemic to achieve food self-sufficiency. Potatoes are vulnerable to soft rot bacteria at all stages of production, storage, and transportation. A novel bacterium, Pseudomonas sp. N3-W, isolated from Alaska tundra soil, grows at 5–25°C and produces extracellular protease(s). N3-W caused necrotic spots (hypersensitivity) in hot pepper leaves and soft rot disease (pathogenicity) in potato tubers. The psychrotolerant N3-W caused significant soft rot symptoms on potatoes at a broad temperature range (5°C, 15°C, and 25°C). In contrast, mesophilic Pectobacterium carotovorum KACC 16999 induced severe rotting symptoms in potatoes at their optimal growth temperature of 15°C and 25°C. However, it barely produced symptoms at 5°C, which is the appropriate storage and transportation temperature for potatoes. The results of pathogenicity testing imply that psychrotolerant soft rot pathogens from polar regions may cause severe soft rot not only during the crop growing season but also during storage and transportation. Our study indicates the possibility of new plant pathogen emergence and transmission due to the expansion of crop cultivation areas caused by permafrost thawing in response to recent polar warming.
Keywords	global warming ; outbreak ; permafrost thawing ; plant pathogen ; soil microbes ; Agriculture (General) ; S1-972
Subject code	571
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Hanrimwon Publishing Company
Document type	Article ; Online
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Article ; Online: Fungal biodegradation of poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based commercial bio-plastic film at ambient conditions.

Ko, Yongseok / Yang, Youri / Kim, Dockyu / Lee, Yong Hwan / Ghatge, Sunil / Hur, Hor-Gil

Chemosphere

2024 Volume 353, Page(s) 141554

Abstract: Microbial biodegradation of commercially available poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based bio-plastic has been pursued at high temperatures exceeding 55 °C. Herein, we first reported three newly isolated fungal ...

Abstract	Microbial biodegradation of commercially available poly(butylene adipate-co-terephthalate)-polylactic acid-thermoplastic starch based bio-plastic has been pursued at high temperatures exceeding 55 °C. Herein, we first reported three newly isolated fungal strains from farmland soil samples of Republic of Korea namely, Pyrenochaetopsis sp. strain K2, Staphylotrichum sp. S2-1, and Humicola sp. strain S2-3 were capable of degrading a commercial bio-plastic film with degradation rates of 9.5, 8.6, and 12.2%, respectively after 3 months incubation at ambient conditions. Scanning electron microscopy (SEM) analyses showed that bio-plastic film was extensively fragmented with severe cracking on the surface structure after incubation with isolated fungal strains. X-ray diffraction (XRD) analysis also revealed that high crystallinity of the commercial bio-plastic film was significantly decreased after degradation by fungal strains. Liquid chromatography-mass spectrometry (LC-MS) analyses of the fungal culture supernatants containing the bio-plastic film showed the peaks for adipic acid, terephthalic acid (TPA), and terephthalate-butylene (TB) as major metabolites, suggesting cleavage of ester bonds and accumulation of TPA. Furthermore, a consortium of fungal strain K2 with TPA degrading bacterium Pigmentiphaga sp. strain P3-2 isolated from the same sampling site exhibited faster degradation rate of the bio-plastic film within 1 month of incubation with achieving complete biodegradation of accumulated TPA. We assume that the extracellular lipase activity presented in the fungal cultures could hydrolyze the ester bonds of PBAT component of bio-plastic film. Taken together, the fungal and bacterial consortium investigated herein could be beneficial for efficient biodegradation of the commercial bio-plastic film at ambient conditions.
MeSH term(s)	Starch/chemistry ; Polyesters/chemistry ; Adipates ; Fungi ; Esters ; Alkenes ; Phthalic Acids
Chemical Substances	poly(lactide) (459TN2L5F5) ; terephthalic acid (6S7NKZ40BQ) ; adipic acid (76A0JE0FKJ) ; butylene (25167-67-3) ; Starch (9005-25-8) ; Polyesters ; Adipates ; Esters ; Alkenes ; Phthalic Acids
Language	English
Publishing date	2024-02-29
Publishing country	England
Document type	Journal Article
ZDB-ID	120089-6
ISSN	1879-1298 ; 0045-6535 ; 0366-7111
ISSN (online)	1879-1298
ISSN	0045-6535 ; 0366-7111
DOI	10.1016/j.chemosphere.2024.141554
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Article ; Online: Microbial metabolic responses and CO

Kim, Dockyu / Chae, Namyi / Kim, Mincheol / Nam, Sungjin / Kim, Tai Kyoung / Park, Ki-Tea / Lee, Bang Yong / Kim, Eungbin / Lee, Hyoungseok

Journal of microbiology (Seoul, Korea)

2022 Volume 60, Issue 12, Page(s) 1130–1138

Abstract: Recent rapid air temperature increases across the northern-latitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature ( ... ...

Abstract	Recent rapid air temperature increases across the northern-latitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature (T
MeSH term(s)	Soil ; Water ; Carbon Dioxide ; Tundra ; Humic Substances
Chemical Substances	Soil ; Water (059QF0KO0R) ; Carbon Dioxide (142M471B3J) ; Humic Substances
Language	English
Publishing date	2022-11-24
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2012399-1
ISSN	1976-3794 ; 1225-8873
ISSN (online)	1976-3794
ISSN	1225-8873
DOI	10.1007/s12275-022-2378-3
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Article ; Online: Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment.

Yu, Jihyeon / Lee, Hyoungseok / Cho, Sung Mi / Lee, Yelim / Kim, Dockyu / Hong, Soon Gyu / Park, Sang-Jong / Kim, Sang-Gyu / Jin, Hongshi / Lee, Jungeun

Plant, cell & environment

2024 Volume 47, Issue 3, Page(s) 976–991

Abstract: Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial ... ...

Abstract	Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial lifecycles involving growth and dormancy alternation. This study explores genetic controls and molecular mechanisms enabling S. uncinata to cope with seasonality of the Antarctic environment. We analysed the seasonal transcriptome dynamics of S. uncinata collected monthly from February 2015 to January 2016 in King George Island, Antarctica. Findings indicate that genes involved in plant growth were predominantly upregulated in Antarctic summer, while those associated with protein synthesis and cell cycle showed marked expression during the winter-to-summer transition. Genes implicated in cellular stress and abscisic acid signalling were highly expressed in winter. Further, validation included a comparison of the Antarctic field transcriptome data with controlled environment simulation of Antarctic summer and winter temperatures, which revealed consistent gene expression patterns in both datasets. This proposes a seasonal gene regulatory model of S. uncinate to understand moss adaptation to extreme environments. Additionally, this data set is a valuable resource for predicting genetic responses to climatic fluctuations, enhancing our knowledge of Antarctic flora's resilience to global climate change.
MeSH term(s)	Bryophyta/genetics ; Ecosystem ; Antarctic Regions ; Snow ; Extreme Environments ; Gene Expression Profiling
Language	English
Publishing date	2024-01-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	391893-2
ISSN	1365-3040 ; 0140-7791
ISSN (online)	1365-3040
ISSN	0140-7791
DOI	10.1111/pce.14793
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Article ; Online: Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil.

Chaudhary, Dhiraj Kumar / Kim, Dong-Uk / Kim, Dockyu / Kim, Jaisoo

Scientific reports

2019 Volume 9, Issue 1, Page(s) 4134

Abstract: This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri- ... ...

Abstract	This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42
MeSH term(s)	Arctic Regions ; Biotransformation ; Flavobacterium/classification ; Flavobacterium/genetics ; Flavobacterium/metabolism ; Gasoline/microbiology ; Genome, Bacterial ; Phylogeny ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Soil Pollutants/metabolism
Chemical Substances	Gasoline ; Soil Pollutants
Language	English
Publishing date	2019-03-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-40667-7
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Article: Temperature sensitivity of Antarctic soil‐humic substance degradation by cold‐adapted bacteria

Kim, Dockyu / Park, Ha Ju / Kim, Mincheol / Lee, Seulah / Hong, Soon Gyu / Kim, Eungbin / Lee, Hyoungseok

Environmental microbiology. 2022 Jan., v. 24, no. 1

2022

Abstract: Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct ... ...

Abstract	Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of −3.8°C to 9.6°C) for 90 days (average Antarctic summer period). This continuous 3‐month artificial incubation maintained a higher total soil temperature than that in natural conditions. The long‐term warming effects rapidly decreased HS content during the initial incubation, with no significant difference between 5°C and 8°C. In the presence of Antarctic tundra soil heterogeneity, the relative abundance of Proteobacteria (one of the major bacterial phyla in cold soil environments) increased during HS decomposition, which was more significant at 8°C than at 5°C. Contrasting this, the relative abundance of Actinobacteria (another major group) did not exhibit any significant variation. This microcosm study indicates that higher temperatures or prolonged thawing periods affect the relative abundance of cold‐adapted bacterial communities, thereby promoting the rate of microbial HS decomposition. The resulting increase in HS‐derived small metabolites will possibly accelerate warming‐induced changes in the Antarctic tundra ecosystem.
Keywords	Actinobacteria ; Proteobacteria ; cold soils ; ecosystems ; metabolites ; microbial growth ; soil heterogeneity ; soil organic matter ; soil temperature ; summer ; tundra ; tundra soils ; Antarctic region
Language	English
Dates of publication	2022-01
Size	p. 265-275.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.15849
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Article ; Online: Flavobacterium dasani sp. nov., a psychrotolerant bacterium isolated from Arctic soil.

Chaudhary, Dhiraj Kumar / Kim, Dockyu / Kim, Jaisoo

Archives of microbiology

2018 Volume 201, Issue 1, Page(s) 81–86

Abstract: A novel yellow-colored, Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, and rod-shaped psychrotolerant bacterium, designated strain PLR-18- ... ...

Abstract	A novel yellow-colored, Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, and rod-shaped psychrotolerant bacterium, designated strain PLR-18-3
MeSH term(s)	Arctic Regions ; Bacterial Typing Techniques ; Base Composition ; Cold Temperature ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Flavobacterium/classification ; Flavobacterium/genetics ; Flavobacterium/isolation & purification ; Ice Cover/microbiology ; Phosphatidylethanolamines/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil ; Soil Microbiology ; Vitamin K 2/analysis
Chemical Substances	DNA, Bacterial ; Fatty Acids ; Phosphatidylethanolamines ; RNA, Ribosomal, 16S ; Soil ; Vitamin K 2 (11032-49-8) ; phosphatidylethanolamine (39382-08-6)
Language	English
Publishing date	2018-09-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	124824-8
ISSN	1432-072X ; 0302-8933
ISSN (online)	1432-072X
ISSN	0302-8933
DOI	10.1007/s00203-018-1574-3
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Article ; Online: Soil water content as a critical factor for stable bacterial community structure and degradative activity in maritime Antarctic soil.

Kim, Dockyu / Chae, Namyi / Kim, Mincheol / Nam, Sungjin / Kim, Eungbin / Lee, Hyoungseok

Journal of microbiology (Seoul, Korea)

2020 Volume 58, Issue 12, Page(s) 1010–1017

Abstract: Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature ( ... ...

Abstract	Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (T
MeSH term(s)	Antarctic Regions ; Bacteria/classification ; Bacteria/genetics ; Bacteria/metabolism ; Biomass ; Carbon/metabolism ; Ecosystem ; Fatty Acids ; Microbiota ; Phospholipids ; RNA, Ribosomal, 16S ; Soil/chemistry ; Soil Microbiology ; Temperature ; Tundra ; Water/chemistry ; Water Microbiology ; Water Supply
Chemical Substances	Fatty Acids ; Phospholipids ; RNA, Ribosomal, 16S ; Soil ; Water (059QF0KO0R) ; Carbon (7440-44-0)
Language	English
Publishing date	2020-12-02
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2012399-1
ISSN	1976-3794 ; 1225-8873
ISSN (online)	1976-3794
ISSN	1225-8873
DOI	10.1007/s12275-020-0490-9
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Article ; Online: Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil

Dhiraj Kumar Chaudhary / Dong-Uk Kim / Dockyu Kim / Jaisoo Kim

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 9

Abstract: Abstract This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42T and Kopri-43, isolated during screening of oil-degrading psychrotrophs from oil-contaminated Arctic soil. A preliminary 16S rRNA gene ... ...

Abstract	Abstract This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42T and Kopri-43, isolated during screening of oil-degrading psychrotrophs from oil-contaminated Arctic soil. A preliminary 16S rRNA gene sequence and phylogenetic tree analysis indicated that these Arctic strains belonged to the genus Flavobacterium, with the nearest relative being Flavobacterium psychrolimnae LMG 22018T (98.9% sequence similarity). The pairwise 16S rRNA gene sequence identity between strains Kopri-42T and Kopri-43 was 99.7%. The DNA-DNA hybridization value between strain Kopri-42T and Kopri-43 was 88.6 ± 2.1% indicating that Kopri-42T and Kopri-43 represents two strains of the same genomospecies. The average nucleotide identity and in silico DNA-DNA hybridization values between strain Kopri-42T and nearest relative F. psychrolimnae LMG 22018T were 92.4% and 47.9%, respectively. These values support the authenticity of the novel species and confirmed the strain Kopri-42T belonged to the genus Flavobacterium as a new member. The morphological, physiological, biochemical and chemotaxonomic data also distinguished strain Kopri-42T from its closest phylogenetic neighbors. Based on the polyphasic data, strains Kopri-42T and Kopri-43 represents a single novel species of the genus Flavobacterium, for which the name Flavobacterium petrolei sp. nov. is proposed. The type strain is Kopri-42T (=KEMB 9005-710T = KACC 19625T = NBRC 113374T).
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-03-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article: Improvement of moss photosynthesis by humic acids from Antarctic tundra soil

Byun, Mi Young / Kim, Dockyu / Youn, Ui Joung / Lee, Seulah / Lee, Hyoungseok

Plant physiology and biochemistry. 2021 Feb., v. 159

2021

Abstract: There have been several published reports regarding the growth promoting effect of humic acids (HA) on vascular plants; however, the effect of HA on bryophytes is still unknown. Due to the ecological importance of mosses, which dominate the Antarctic ... ...

Abstract	There have been several published reports regarding the growth promoting effect of humic acids (HA) on vascular plants; however, the effect of HA on bryophytes is still unknown. Due to the ecological importance of mosses, which dominate the Antarctic flora, we assessed the effectiveness of HA as a biostimulant using three moss species: Antarctic Ceratodon purpureus KMA5038, Arctic Bryum sp. KMR5045, and Physcomitrella patens which inhabits temperate regions. Natural HA (KS1-3_HA) were extracted through acidic precipitation of alkaline extracts from Antarctic tundra soil. Spectroscopic structural properties of KS1-3_HA were characterized and determined to possess several functional groups such as hydroxyl (R–OH) and carboxyl (R–COOH), implying they could have a growth-related biological function. For two polar mosses, increasing HA concentrations correlated with increased growth and photosynthesis. The efficiency for temperate moss increased at lower concentrations tested, but rather began to reduce at the highest HA concentration, indicating that effective concentrations of HA vary depending on the moss species and habitat. Based on these results, Antarctic HA may have ecological role in enhancing the growth and photosynthesis of Antarctic mosses. We believe this is the first study to establish a positive physiological effect of HA on mosses and hope it may serve as a basis for studying the role of HA in preserving the terrestrial ecosystem of Antarctica.
Keywords	Bryum ; Ceratodon purpureus ; flora ; habitats ; mosses and liverworts ; photosynthesis ; plant physiology ; spectroscopy ; terrestrial ecosystems ; tundra soils ; Antarctic region ; Antarctica ; Arctic region
Language	English
Dates of publication	2021-02
Size	p. 37-42.
Publishing place	Elsevier Masson SAS
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	742978-2
ISSN	1873-2690 ; 0981-9428
ISSN (online)	1873-2690
ISSN	0981-9428
DOI	10.1016/j.plaphy.2020.12.007
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