- Flavisolibacter aluminii sp. nov., a novel member of the genus Flavisolibacter isolated from an automotive air conditioning system
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Hyosun Lee , Dong-Uk Kim , Suyeon Lee , Song-Gun Kim , A-Young Park , Jae-Hyung Ahn , Jong-Ok Ka
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J. Microbiol. 2019;57(1):18-22. Published online November 19, 2018
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DOI: https://doi.org/10.1007/s12275-019-8219-3
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A Gram-stain-negative, aerobic, non-motile, rod-shaped, and
yellow-pigmented bacterium, designated strain ID1709T, was
isolated from an automotive air conditioning system collected
in Korea. Analysis of 16S rRNA gene sequence similarity
showed that strain ID1709T had 92.2–94.3% similarities with
the type strains of members of the genus Flavisolibacter. The
major cellular fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0
3-OH, and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The
predominant respiratory quinone was MK-7. The polar lipids
comprised phosphatidylethanolamine, aminoglycophospholipid,
two unidentified aminolipids, and three unidentified
lipids. The DNA G + C content of the strain was 35.6 mol%.
Based on phenotypic, chemotaxonomic, and genotypic data,
strain ID1709T represents a novel species in the genus Flavisolibacter,
for which the name Flavisolibacter aluminii sp.
nov. (= KACC 19451T = KCTC 52778T = NBRC 112870T), is
proposed.
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Citations
Citations to this article as recorded by  - Validation List no. 229: valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2026;[Epub] CrossRef - Insights into the Response and Evolution of Microbial Communities During Long-Term Natural Remediation of Contaminated Abandoned Shale Gas Wells
Hongyang Ren, Shuangli Chen, Jiajian Shang, Yujia Gao, Yuanpeng Deng, Zhaoyang Wang, Guojun Hu, Bing Wang
Water, Air, & Soil Pollution.2024;[Epub] CrossRef - Metallococcus carri gen. nov., sp. nov., a novel member of the family Dermacoccaceae isolated from an automotive air conditioning system
Jong Sung Lim, Hyosun Lee, Jigwan Son, Song-Gun Kim, Dong-Uk Kim, Jong-Ok Ka
Archives of Microbiology.2021; 203(7): 4073. CrossRef
- Tardibacter chloracetimidivorans gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from an agricultural soil from Jeju Island in Republic of Korea
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Hyosun Lee , Dong-Uk Kim , Sooyeon Park , Jung-Hoon Yoon , Jae-Hyung Ahn , Jong-Ok Ka
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J. Microbiol. 2018;56(5):324-330. Published online May 2, 2018
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DOI: https://doi.org/10.1007/s12275-018-7455-2
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882
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A pale yellow bacterial strain, designated JJ-A5T, was isolated
form an agricultural soil from Jeju Island in Republic of
Korea. Cells of the strain were Gram-stain-negative, motile,
flagellated and rod-shaped. The strain grew at 15–30°C, pH
6.0–9.0, and in the presence of 0–1.5% (w/v) NaCl. Growth
occurred on R2A, but not on Luria-Bertani agar, nutrient agar,
trypticase soy agar and MacConkey agar. The strain utilized
alachlor as a sole carbon source for growth. The strain JJ-A5T
showed 16S rRNA gene sequence similarities lower than
95.4% with members of the family Sphingomonadaceae. Phylogenetic
analysis showed that the strain belongs to the family
Sphingomonadaceae and strain JJ-A5T was distinctly separated
from established genera of this family. The strain contained
Q-10 as dominant ubiquinone and spermidine as major
polyamine. The predominant cellular fatty acids were
summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), summed feature
3 (C16:1 ω7c and/or C16:1 ω6c), 11-methyl C18:1 ω7c, C16:0
and C14:0 2-OH. The major polar lipids were phosphatidylethanolamine,
phosphatidylglycerol, sphingoglycolipid, and
phosphatidylcholine. The DNA G + C content of the strain
was 62.7 mol%. On the basis of the phenotypic, genomic and
chemotaxonomic characteristics, strain JJ-A5T is considered
to represent a novel genus and species within the family
Sphingomonadaceae, for which the name Tardibacter chloracetimidivorans
gen. nov., sp. nov. is proposed. The type
strain of Tardibacter chloracetimidivorans is JJ-A5T (= KACC
19450T = NBRC 113160T).
-
Citations
Citations to this article as recorded by - Interactive effects of maize straw incorporation and improved irrigation on soil physicochemical properties and microbial community structure in saline–alkaline soil
Wenbo Chai, Hanyuan Xu, Chao Yuan, Shufen Li, Hongtao Li, Qing Zhu, Wei Ji, Ming Chi, Jun Wang, Chongxing Xin
Frontiers in Microbiology.2026;[Epub] CrossRef - Removal of alachlor from the water/soil environments: The significance of microbial remediation and its biochemical mechanisms
Zeren Li, Mengyi Chen, Wen-Juan Chen, Mingqiu Liu, Guiling Si, Xixian Zhu, Kalpana Bhatt, Sandhya Mishra, Mohamed A. Ghorab, Shaohua Chen
Journal of Water Process Engineering.2024; 68: 106387. CrossRef - Processes governing the environmental fates of alachlor in soil and aqueous media: a critical review
M. U. Ghani, H. N. Asghar, H. Nadeem, M. Shahid, M. A. Zeshan, A. Niaz, S. Hussain, S. Hussain
International Journal of Environmental Science and Technology.2022; 19(8): 8043. CrossRef - New Associations of Aerobic Bacteria that Actively Decompose Lindane
E. A. Nazarova, D. O. Egorova, L. N. Anan’ina, E. S. Korsakova, E. G. Plotnikova
Applied Biochemistry and Microbiology.2021; 57(5): 643. CrossRef
- Spirosoma metallicus sp. nov., isolated from an automobile air conditioning system
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Hyosun Lee , Dong-Uk Kim , Suyeon Lee , Sooyeon Park , Jung-Hoon Yoon , So Yoon Park , Jong-Ok Ka
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J. Microbiol. 2017;55(9):673-677. Published online August 5, 2017
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DOI: https://doi.org/10.1007/s12275-017-7162-4
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962
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A Gram-stain-negative and orangish yellow-pigmented bacterial
strain, designated PR1014KT, was isolated from an automobile
evaporator core collected in Korea. Phylogenetic
analysis based on 16S rRNA gene sequences indicated that
strain PR1014KT was related with the members of the genus
Spirosoma (94.7–90.2%) and closely related with Spirosoma
lacussanchae CPCC 100624T (94.7%), Spirosoma knui 15J8-
12T (94.3%), and Spirosoma soli MIMBbqt12T (93.3%). The
strain grew at 15–40°C (optimum, 25°C), pH 6.5–7.0 (optimum,
6.5) and 0–1% (w/v) NaCl (optimum, 0%). The predominant
fatty acids were summed feature 3 (C16:1 ω7c and/or
C16:1 ω6c), C16:0, iso-C15:0, C16:1 ω5c, and iso-C17:0 3-OH. The
major menaquinone was MK-7. The polar lipid profile of the
strain indicated that the presence of one phosphatidylethanolamine,
one unidentified aminolipid, two unidentified
aminophospholipids, and three unidentified lipids. The DNA
G+C content of the strain was 47.4 mol%. On the basis of
the phenotypic, genotypic and chemotaxonomic characteristics,
strain PR1014KT represents a novel species in the genus
Spirosoma, for which the name Spirosoma metallicus
sp. nov. (=KACC 17940T =NBRC 110792T) is proposed.
-
Citations
Citations to this article as recorded by -
Spirosoma rhododendri sp. nov., isolated from a flower of royal azalea (Rhododendron schlippenbachii)
Miyoung Won, Seung-Beom Hong, Byeong-Hak Han, Soon-Wo Kwon
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - Spirosoma taeanense sp. nov., a radiation resistant bacterium isolated from a coastal sand dune
Ji Hee Lee, Jong-Hyun Jung, Min-Kyu Kim, Han Na Choe, Chi Nam Seong, Sangyong Lim
Antonie van Leeuwenhoek.2021; 114(2): 151. CrossRef - Spirosoma sordidisoli sp. nov., a propanil-degrading bacterium isolated from a herbicide-contaminated soil
Long Zhang, Xi-Yi Zhou, Xiao-Jing Su, Qiang Hu, Jian-Dong Jiang
Antonie van Leeuwenhoek.2019; 112(10): 1523. CrossRef -
Spirosoma utsteinense sp. nov. isolated from Antarctic ice-free soils from the Utsteinen region, East Antarctica
Guillaume Tahon, Liesbeth Lebbe, Anne Willems
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2018; 68(3): 693. CrossRef
- Pedobacter namyangjuensis sp. nov. Isolated from Soil and Reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.
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Dong-Uk Kim , Yoo-Jeong Kim , Dong-Hyeon Shin , Hang-Yeon Weon , Soon-Wo Kwon , Chi-Nam Seong , Jong-Ok Ka
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J. Microbiol. 2013;51(1):25-30. Published online March 2, 2013
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DOI: https://doi.org/10.1007/s12275-013-2231-9
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974
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18
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A Gram-stain-negative, non-motile, strictly aerobic, yellowpigmented bacterium, designated strain 5G38T, was isolated from a field cultivated with Chinese cabbage in Korea. The strain grew at 5–40°C and at pH 6.0–8.0. 16S rRNA gene sequence analysis revealed that strain 5G38T represented a distinct lineage within the family Sphingobacteriaceae and showed the highest 16S rRNA gene sequence similarity of 95.2% with Pedobacter koreensis WPCB189T, followed by Pedobacter agri PB92T (94.6%), Pedobacter suwonensis 15-52T (94.4%), Pedobacter rhizosphaerae 01-96T (94.4%), Pedobacter sandarakinus DS-27T (94.4%), and Nubsella zeaxanthinifaciens TDMA-5T (94.3%). Strain 5G38T formed monophyletic clade with Nubsella zeaxanthinifaciens in the cluster comprised of species of the genus Pedobacter. Chemotaxonomic characteristics of the novel strains, including DNA G+C content of genomic DNA (37.0 mol%), the predominant respiratory quinine (MK-7), and the major fatty acids which were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or iso-C15:0 2-OH) and iso-C17:0 3-OH, are similar to those of the genus Pedobacter. However, the novel strains can be distinguished from the other species of Pedobacter by physiological properties. The name Pedobacter namyangjuensis sp. nov. is therefore proposed for strain 5G38T (KACC 13938T =NBRC 107692T) as the type strain. Furthermore, the reclassification of Nubsella zeaxanthinifaciens as Pedobacter zeaxanthinifaciens comb. nov. is proposed.
-
Citations
Citations to this article as recorded by - Validation list no. 225: valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Validation List no. 226: valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2025;[Epub] CrossRef - Microaerobic methane-driven denitrification in a biotrickle bed – Investigating the active microbial biofilm community composition using RNA-stable isotope probing
Emmanuel O. Egbadon, Kathryn Wigley, Sunday T. Nwoba, Carlo R. Carere, Louise Weaver, Kim Baronian, Lee Burbery, Peter A. Gostomski
Chemosphere.2024; 346: 140528. CrossRef - Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer
Thijs Van Gerrewey, Christophe El-Nakhel, Stefania De Pascale, Jolien De Paepe, Peter Clauwaert, Frederiek-Maarten Kerckhof, Nico Boon, Danny Geelen
Microorganisms.2021; 9(6): 1326. CrossRef - Screening and Characterization of Two Extracellular Polysaccharide-Producing Bacteria from the Biocrust of the Mu Us Desert
Zhanfang Xue, Shuting Zhao, Nomin Bold, Jianguo Zhang, Zhimin Hu, Xiaofeng Hu, Ying Gao, Shaolin Chen, Yahong Wei
Molecules.2021; 26(18): 5521. CrossRef -
Pedobacter yulinensis sp. nov., isolated from sandy soil, and emended description of the genus Pedobacter
Yahong Wei, Baodan Wang, Limei Zhang, Jianguo Zhang, Shaolin Chen
International Journal of Systematic and Evolutionary Microbiology.2018; 68(8): 2523. CrossRef -
Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue
Ling-Li Zhang, Long-Zhan Gan, Zhi-Bin Xu, Feng Yang, Yan Li, Xiao-Li Fan, Xiao-Feng Liu, Yong-Qiang Tian, Yu-Mei Dai
International Journal of Systematic and Evolutionary Microbiology.2018; 68(12): 3713. CrossRef - Molecular identification of bacterial endosymbionts of Sappinia strains
Daniele Corsaro, Claudia Wylezich, Julia Walochnik, Danielle Venditti, Rolf Michel
Parasitology Research.2017; 116(2): 549. CrossRef -
Pedobacter solisilvae sp. nov., isolated from forest soil
Dong Jin Yang, Jin-Kyung Hong
International Journal of Systematic and Evolutionary Microbiology
.2017; 67(11): 4814. CrossRef - Pedobacter psychrotolerans sp. nov., isolated from soil
Pooja Manandhar, Gengxin Zhang, Arun Lama, Yilun Hu, Feng Gao
International Journal of Systematic and Evolutionary Microbiology.2016; 66(11): 4560. CrossRef -
Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil
Hien T. T. Ngo, MooChang Kook, Tae-Hoo Yi
International Journal of Systematic and Evolutionary Microbiology
.2015; 65(Pt_3): 1008. CrossRef -
Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica
Xuyang Da, Fan Jiang, Xulu Chang, Lvzhi Ren, Xia Qiu, Wenjing Kan, Yumin Zhang, Sangsang Deng, Chengxiang Fang, Fang Peng
International Journal of Systematic and Evolutionary Microbiology
.2015; 65(Pt_11): 3841. CrossRef - Pedobacter bambusae sp. nov., isolated from soil of a bamboo plantation
Kyung Hwa Won, MooChang Kook, Tae-Hoo Yi
Antonie van Leeuwenhoek.2015; 107(2): 565. CrossRef -
Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil
Hao Zhang, Jing Zhang, Man Song, Ming-gen Cheng, Ya-dong Wu, Su-hui Guo, Qiang Li, Qing Hong, Xing Huang
International Journal of Systematic and Evolutionary Microbiology
.2015; 65(Pt_10): 3517. CrossRef -
Pedobacter xixiisoli sp. nov., isolated from bank soil
Yanhua Zeng, Hao Feng, Yili Huang
International Journal of Systematic and Evolutionary Microbiology
.2014; 64(Pt_11): 3683. CrossRef - Pedobacter nutrimenti sp. nov., isolated from chilled food
Julia Derichs, Peter Kämpfer, André Lipski
International Journal of Systematic and Evolutionary Microbiology.2014; 64(Pt_4): 1310. CrossRef - Pedobacter seoulensis sp. nov., isolated from soil of a bamboo field
Hien T. T. Ngo, Heung-Min Son, Sang-Yong Park, Ki-Young Kim, Tae-Hoo Yi
Antonie van Leeuwenhoek.2014; 105(5): 961. CrossRef - Infection of cells by Sindbis virus at low temperature
Gongbo Wang, Raquel Hernandez, Keith Weninger, Dennis T. Brown
Virology.2007; 362(2): 461. CrossRef
- Growth Promotion of Xanthium italicum by Application of Rhizobacterial Isolates of Bacillus aryabhattai in Microcosm Soil
-
Sol Lee , Jong-Ok Ka , Hong-Gyu Song
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J. Microbiol. 2012;50(1):45-49. Published online February 27, 2012
-
DOI: https://doi.org/10.1007/s12275-012-1415-z
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965
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58
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Abstract
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This study was conducted using rhizobacteria, which are
able to exert beneficial effects upon plant growth in the infertile
soil collected from barren lakeside areas. Four strains
of plant growth promoting bacteria were isolated from the
rhizosphere of a common wild plant, Erigeron canadensis.
Isolated strains LS9, LS11, LS12, and LS15 were identified
as Bacillus aryabhattai by 16S rDNA sequence analysis. B.
aryabhattai LS9, LS11, LS12, and LS15 could solubilize
577.9, 676.8, 623.6, and 581.3 mg/L of 0.5% insoluble calcium
phosphate within 2 days of incubation. Production of indole
acetic acid, a typical growth promoting phytohormone
auxin, by strain LS15 was 471.3 mg/L in 2 days with the addition
of auxin precursor L-tryptophan. All the strains also
produced other phytohormones such as indole butyric acid,
gibberellins, and abscisic acid, and strain LS15 showed the
highest production rate of gibberellin (GA3), 119.0 μg/mg
protein. Isolated bacteria were used in a microcosm test for
growth of wild plant Xanthium italicum, which can be utilized
as a pioneer plant in barren lands. Seed germination
was facilitated, and the lengths of roots, and shoots and the
dry weights of germinated seedlings after 16 days were
higher than those of the uninoculated control plants. Root
lengths of seedlings of X. italicum increased by 121.1% in
LS11-treated samples after 16 days. This plant growth-promoting
capability of B. aryabhattai strains may be utilized
as an environmentally friendly means of revegetating barren
lands, especially sensitive areas such as lakeside lands.
-
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Mexican Journal of Biotechnology.2025; 3(2): 47. CrossRef - Enhanced biological nitrogen fixation and nodulation in alfalfa through the synergistic interactions between Sinorhizobium meliloti and Priestia aryabhattai
Rui Liu, Chang Li, Yunjun Zhang, Chunli Liu, Jinai Xue, Yanning Zheng
World Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef - Agronomic feasibility of bacterial consortium with Bacillus species and its effects on the productivity of some important crops
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Australian Journal of Crop Science.2025; 19(10): 994. CrossRef - Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism
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Gongronella
sp. w5 hydrolyzes plant sucrose and releases fructose to recruit phosphate-solubilizing bacteria to provide plants with phosphorus
Xiaojie Wang, Junnan Fang, Li Li, Xing Li, Pu Liu, Bin Song, Jonathan Adams, Yazhong Xiao, Zemin Fang, Gladys Alexandre
Applied and Environmental Microbiology.2024;[Epub] CrossRef - Phytoremediation Prospects for Restoration of Contamination in the Natural Ecosystems
Shaista Khan, Tariq H. Masoodi, Nazir A. Pala, Shah Murtaza, Javeed A. Mugloo, Parvez A. Sofi, Musaib U. Zaman, Rupesh Kumar, Amit Kumar
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Yubin Zhao, Dawei Guan, Xu Liu, Gui-Feng Gao, Fangang Meng, Bingqiang Liu, Pengfei Xing, Xin Jiang, Mingchao Ma, Fengming Cao, Li Li, Jun Li
Frontiers in Microbiology.2022;[Epub] CrossRef - Probing into the unique relationship between a soil bacterium, Pseudomonas putida AKMP7 and Arabidopsis thaliana: A case of “conditional pathogenesis”
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Plant Physiology and Biochemistry.2022; 183: 46. CrossRef - Volatile Organic Compounds of Streptomyces sp. TOR3209 Stimulated Tobacco Growth by Up-Regulating the Expression of Genes Related to Plant Growth and Development
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Agriculture.2022; 12(11): 1890. CrossRef - Microbial application in remediation of heavy metals: an overview
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Current Research in Microbial Sciences.2022; 3: 100133. CrossRef - Compost-derived indole-3-acetic-acid-producing bacteria and their effects on enhancing the secondary fermentation of a swine manure-corn stalk composting
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Chemosphere.2022; 291: 132750. CrossRef - Characterization of rhizospheric bacteria isolated from soil cultivated with sugarcane in Tamaulipas state, Mexico
Jesús García, Martín Reyes, Juan Flores, Jesús Quiroz, Israel García, José Reyes, Homar Gill
Revista de la Facultad de Agronomía, Universidad del Zulia.2021; 38(4): 951. CrossRef - Bacillus as a source of phytohormones for use in agriculture
Jorge Poveda, Fernando González-Andrés
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Yang Zhang, Jieshi Tang, Gang Ren, Kaixin Zhao, Xianfang Wang
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Yanjiang Zhang, Tian Zhang, Zhijing Xue, Yifan Liu, Yongzhe Li, Yulong Li, Qin Chen
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- Effects of Phosphate Addition on Biofilm Bacterial Communities and Water Quality in Annular Reactors Equipped with Stainless Steel and Ductile Cast Iron Pipes
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Hyun-Jung Jang , Young-June Choi , Hee-Myong Ro , Jong-Ok Ka
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J. Microbiol. 2012;50(1):17-28. Published online February 27, 2012
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DOI: https://doi.org/10.1007/s12275-012-1040-x
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Abstract
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The impact of orthophosphate addition on biofilm formation
and water quality was studied in corrosion-resistant
stainless steel (STS) pipe and corrosion-susceptible ductile cast
iron (DCI) pipe using cultivation and culture-independent
approaches. Sample coupons of DCI pipe and STS pipe
were installed in annular reactors, which were operated for
9 months under hydraulic conditions similar to a domestic
plumbing system. Addition of 5 mg/L of phosphate to the
plumbing systems, under low residual chlorine conditions,
promoted a more significant growth of biofilm and led to a
greater rate reduction of disinfection by-products in DCI pipe
than in STS pipe. While the level of THMs (trihalomethanes)
increased under conditions of low biofilm concentration,
the levels of HAAs (halo acetic acids) and CH (chloral hydrate)
decreased in all cases in proportion to the amount of
biofilm. It was also observed that chloroform, the main species
of THM, was not readily decomposed biologically and
decomposition was not proportional to the biofilm concentration;
however, it was easily biodegraded after the addition
of phosphate. Analysis of the 16S rDNA sequences of 102
biofilm isolates revealed that Proteobacteria (50%) was the
most frequently detected phylum, followed by Firmicutes
(10%) and Actinobacteria (2%), with 37% of the bacteria
unclassified. Bradyrhizobium was the dominant genus on
corroded DCI pipe, while Sphingomonas was predominant
on non-corroded STS pipe. Methylobacterium and Afipia
were detected only in the reactor without added phosphate.
PCR-DGGE analysis showed that the diversity of species in
biofilm tended to increase when phosphate was added regardless
of the pipe material, indicating that phosphate addition
upset the biological stability in the plumbing systems.
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Citations
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DOI: https://doi.org/10.1007/s12275-011-0530-6
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719
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27
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Abstract
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It is important to know the comprehensive microbial communities of fecal pollution sources and receiving
water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of
the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities
in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities
in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest
value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting
for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram
analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and
Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia
coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and
enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected
in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis,
and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the
pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple
fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for
multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of
fecal pollution source tracking.
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J. Microbiol. 2011;49(3):340-348. Published online June 30, 2011
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DOI: https://doi.org/10.1007/s12275-011-0302-3
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Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to
evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples
were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria
(4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion,
this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.
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- Diversity of Bacterial Community in Freshwater of Woopo Wetland
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Keun Sik Baik , Seong Chan Park , Eun Mi Kim , Kyung Sook Bae , Jae-Hyung Ahn , Jong-Ok Ka , Jongsik Chun , Chi Nam Seong
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J. Microbiol. 2008;46(6):647-655. Published online December 24, 2008
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DOI: https://doi.org/10.1007/s12275-008-0135-x
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Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.
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- Molecular Identification of Fecal Pollution Sources in Water Supplies by Host-Specific Fecal DNA Markers and Terminal Restriction Fragment Length Polymorphism Profiles of 16S rRNA Gene
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Ju-Yong Jeong , Kyung-Ik Gil , Kyong-Hee Lee , Jong-Ok Ka
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J. Microbiol. 2008;46(6):599-607. Published online December 24, 2008
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DOI: https://doi.org/10.1007/s12275-008-0174-3
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Specific fecal DNA markers were investigated for major pollution sources, cow, human, and pig, and occurrence of the identified markers was analyzed in river waters using Terminal Restriction Fragment Length Polymorphism (T-RFLP) techniques and sequencing of 16S rDNA of Bacteroides-Prevotella. The unique and specific DNA markers for cow and human were identified as a 222 bp and 60 bp peak in HaeIII T-RFLP profiles, respectively, and the pig-specific marker was not identified but the unique T-RFLP profile of pig could be used as a substitution. Human-specific marker was detected in most of the river waters tested (92.1%) and T-RFLP profiles of river waters were shown to be similar to those of human feces. Cluster analysis of T-RFLP data showed that the fecal sources were multiple (human plus cow and human plus dairy cow) in most of the river waters. The phylogenetic analysis for the clones recovered from the fecal and water samples showed that the clones from cow formed a discreet cluster from those of other sources. The other clones from human, pig, and river water formed two groups all together. The results of this study could be used to identify and control the fecal pollution source in the bodies of water in Korea.
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Citations
Citations to this article as recorded by - Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing
Ju-Yong Jeong, Hee-Deung Park, Kyong-Hee Lee, Hang-Yeon Weon, Jong-Ok Ka
The Journal of Microbiology.2011; 49(4): 585. CrossRef - Application of an Integrated Community Analysis Approach for Microbial Source Tracking in a Coastal Creek
Yiping Cao, Laurie C. Van De Werfhorst, Bram Sercu, Jill L. S. Murray, Patricia A. Holden
Environmental Science & Technology.2011; 45(17): 7195. CrossRef
- Revegetation of a Lakeside Barren Area by the Application of Plant Growth-promoting Rhizobacteria
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Tae-Seok Ahn , Jong-Ok Ka , Geon-Hyoung Lee , Hong-Gyu Song
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J. Microbiol. 2007;45(2):171-174.
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DOI: https://doi.org/2516 [pii]
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The growth stimulation of wild plants by several bacterial species showing plant growth-promoting capabilities was examined in a barren lakeside area at Lake Paro, Korea. Microbial numbers and activities in the field soil were monitored for 73 days after inoculation of the bacteria. The acridine orange direct counts for the total soil bacterial populations ranged between 2.0-2.3×109 cells/g soil and 1.4-1.8×109 cells/g soil in the inoculated and uninoculated soils, respectively. The numbers of Pseudomonas spp., which is known as a typical plant growth-promoting rhizobacteria, and the total microbial activity were higher in the inoculated soil compared to those in the uninoculated soil. The average shoot and root lengths of the wild plants grown in the inoculated soil were 17.3 cm and 12.4 cm, respectively, and longer than those of 11.4 cm and 8.5 cm in the uninoculated soil. The total dry weight of the harvested wild plants was also higher in the inoculated soil (42.0 g) compared to the uninoculated soil (35.1 g). The plant growth-promoting capabilities of the inoculated bacteria may be used for the rapid revegetation of barren or disturbed land, and as biofertilizer in agriculture.
- Genetic and Phenotypic Diversity of (R/S)-Mecoprop [2-(2-Methyl-4-Chlorophenoxy)Propionic Acid]-Degrading Bacteria Isolated fromSoils
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Jong-Sung Lim , Mee-Kum Jung , Mi-Soon Kim , Jae-Hyung Ahn , Jong-Ok Ka
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J. Microbiol. 2004;42(2):87-93.
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DOI: https://doi.org/2040 [pii]
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Twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. Analysis of 16S rDNA sequences indicated that the isolates were related to members of the genus Sphingomonas. Ten different chromosomal DNA patterns were obtained by polymerase-chain-reaction (PCR) amplification of repetitive extragenic palindromic (REP) sequences from the 12 isolates. The isolates were found to be able to utilize the chiral herbicide mecoprop as a sole source of carbon and energy. While seven of the isolates were able to degrade both (R)- and (S)-mecoprop, four isolates exhibited enantioselective degradation of the (S)-type and one isolate could degrade only the (R)-enantiomer. All of the isolates were observed to possess plasmid DNAs. When certain plasmids were removed from isolates MP11, MP15, and MP23, those strains could no longer degrade mecoprop. This compelling result suggests that plasmid DNAs, in this case, conferred the ability to degrade the herbicide. The isolates MP13, MP15, and MP24 were identified as the same strain; however, they exhibited different plasmid profiles. This indicates that these isolates acquired different mecoprop-degradative plasmids in different soils through natural gene transfer.
- Structural Analysis of the fcbABC Gene Cluster Responsible for Hydrolytic Dechlorination of 4-Chlorobenzoate from pJS1 Plasmid of Comamonas sp. P08
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Jeong-Soon Lee , Kyoung Lee , Jong-Ok Ka , Jong-Chan Chae , Chi-Kyung Kim
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J. Microbiol. 2003;41(2):89-94.
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Bacterial strain No. P08 isolated from wastewater at the Cheongju industrial complex was found to be capable of degrading 4-chlorobenzoate under aerobic condition. P08 was identified as Comamonas sp. from its cellular fatty acid composition and 16S rDNA sequence. The fcb genes, responsible for the hydrolytic dechlorination of 4-chlorobenzoate, were cloned from the plasmid pJS1 of Comamonas sp. P08. The fcb gene cluster of comamonas sp. P08 was organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC. This organization of the fcb genes was very similar to that of the fcb genes carried on the chromosomal DNA of Pseudomonas sp. DJ-12. However, it differed from the fcbA-fcbB-fcbC ordering of Arthrobacter sp. SU. The nucleotide sequences of the fcbABC genes of strain P08 showed 98% and 53% identities to those of Pseudomonas sp. DJ-12 and Arthrobacter sp. SU, respectively. This suggests that the fcb genes might have been derived from Pseudomonas sp. DJ-12 to form plasmid pJS1 in Comamonas sp. P08, or that the fcb genes in strain DJ-12 were transposed from Comamonas sp. P08 plasmid.
- Cloning and Sequence Analysis of Two Catechol-degrading Gene Clusters from a Phenol-utilizing Bacterium Pseudomonas putida SM25
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Young-Hee Jung , Jong-Ok Ka , Choong-Ill Cheon , Myeong-Sok Lee , Eun-Sook Song , Soon-Young Choi , Daeho Cho , Sang-Ho Choi , Kwon-Soo Ha , Young Mok Park , Jong-Soon Choi , Kyung-Hee Min
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J. Microbiol. 2003;41(2):102-108.
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A 6.1 kb Sph I fragment from the genomic DNA of Pseudomonas putida SM 25 was cloned into the vector pUC19. The open reading frame of catB was found to consist of 1,122 nucleotides. The sequence alignment of the catB gene products from different kinds of bacteria revealed an overall identity ranging from 40 to 98%. The catC gene contained an open reading frame of 96 codons, from which a protein with a molecular mass of about 10.6 kDa was predicted. The amino acids in the proposed activesite region of CatC were found to be almost conserved, including the charged residues. Since the catBC genes in P. putida SM25 were tightly linked, they could be regulated under coordinate transcription, and transcribed from a single promoter located upstream of the catB gene, as in P. putida RB1.
- Cloning and Sequence Analysis of the xylL Gene Responsible for 4CBA-Dihydrodiol Dehydrogenase from Pseudomonas sp. S-47
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Dong-Woo Park , Youngsoo Kim , Sang-Mahn Lee , Jong-Ok Ka , Chi-Kyung Kim
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J. Microbiol. 2000;38(4):275-280.
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Pseudomonas sp. S-47 is capable of catabolizing 4-chlorobenzoate (4CBA) as carbon and energy sources under aerobic conditions via the meta-cleavage pathway. 4CBA-dioxygenase and 4CBA-dihydrodiol dehydrogenase (4CBA-DD) catalyzed the degradation of 4CBA to produce 4-chlorocatechol in the pathway. In this study, the xylL gene encoding 4CBA-DD was cloned from the chromosomal DNA of Pseudomonas sp. S-47 and its nucleotide sequence was analyzed. The xylL gene was found to be composed of 777 nucleotide pairs and to encode a polypeptide of 28 kDa with 258 amino acid residues. The deduced amino acid sequence of the dehydrogenase (XylL) from strain S-47 exhibited 98% and 60% homologies with those of the corresponding enzymes, Pseudomonas putida mt-2 (XylL) and Acinetobacter calcoaceticus (BenD), respectively. However, the amino acid sequences show 30% or less homology with those of Pseudomonas putida (BnzE), Pseudomonas putida F1 (TodD), Pseudomonas pseudoalcaligenes KF707 (BphB), and Pseudomonas sp. C18 (NahB). Therefore, the 4CBA-dihydrodiol dehydrogenase of strain S-47 belongs to the group I dehydrogenase involved in the degradation of mono-aryls with a carboxyl group
- Assessing Survival and Detection of Catechol-bidegrading Strains in Waste Water microcosms
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Soo-Jin Choi , Min-Sup Song , Soo-youn Lee , Seong-Karp Hong , Kyung-Hee Min , Jong-Ok Ka , Chi-Kyung Kim , Young-Keun Park
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J. Microbiol. 1998;36(4):239-248.
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Catechol-degrading bacteria, Escherichia coli JM101 carrying pIB1343 (strain pIB1343) and Flavimonas orizihabitans KHi (strain KH1), were chosen as model bacteria to estimate the sur vival and catechol-degradability in waste water microcosms. Before their application to ecosystem, survival and catechol degradation of these bacteria were investigated in waste water microcosms. It was found that strain pIB1343 adapted much faster to waste water environments and degraded catechol in the case of Namdong samples, whereas the strain KH1 degraded catechol much faster in Sihwa samples. When catechol was added to the microcosms, indigenous microorganisms in Sihwa samples used catechol as a carbon and energy source much better than those in Namdong samples. A modified filter extraction technique was used to obtain the high-yield purified DNA from 50 ml of waste water samples and the extracted DNA (polymorphic DNA [20~23 kb]) was of sufficient quantity and quality for the amplification. PCR was performed with catA-specicic promers, C120U and C120L, which specifically detected the catA gene encoding catechol 1,2-dioxygenase in waste water microcosms, and then the 320 bp PCR products were amplified. PCR products were quantified by densitomenter. Using the standard curve of detection limit by catA-specific PCR products, the number of catA genes for their corresponding intensities of PCR products was obtained. the number of total catA genes PCR in waste water microcosms was correalated with catechol degradation.
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