Journal of Microbiology

In-Tae Cha

7 Articles

Optimization of bacterial sporulation using economic nutrient for self-healing concrete: Youngung Ryu , Ki-Eun Lee , In-Tae Cha , Woojun Park; J. Microbiol. 2020;58(4):288-296. Published online February 27, 2020; 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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Raman spectroscopy reveals alteration of spore compositions under different nutritional conditions in Lysinibacillus boronitolerans YS11
Youngung Ryu, Minyoung Hong, Soo Bin Kim, Tae Kwon Lee, Woojun Park
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Influences of different calcium sources on the early age cracks of self-healing cementitious mortar
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Effect and Mechanism of Encapsulation-Based Spores on Self-Healing Concrete at Different Curing Ages
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Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat: In-Tae Cha , Eui-Sang Cho , Yoo Kyung Lee , Seong Woon Roh , Myung-Ji Seo; J. Microbiol. 2019;57(7):569-574. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8666-x

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Strain ML311-T8T was isolated from a glacial retreat area in Svalbard, Norway, and was taxonomically characterized by a polyphasic approach. Upon phylogenetic analysis, strain ML311-T8T was clustered with Paenibacillus arcticus MME2_ R6T and P. contaminans CKOBP-6T with 98.3–98.6 and 93.5– 93.9% 16S rRNA gene sequence similarities, respectively. DNA-DNA hybridization values between strain ML311-T8T and P. arcticus MME2_R6T was 19.9%. The genomic DNA G+C content was 41.1 mol%. The isolated strain was Gramstain- positive, strictly aerobic and rod-shaped, and grew in 0–0.5% (w/v) NaCl, at 4–23°C and pH 6.0–10.0, with optimal growth in 0% (w/v) NaCl, at 20°C and pH 7.0–8.0. The predominant respiratory quinone of strain ML311-T8T was MK- 7 and the major fatty acids were anteiso-C15:0 and C16:0. The polar lipids of strain ML311-T8T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified amino lipids, and three unidentified lipids. On the basis of polyphasic taxonomic analysis, the strain ML311-T8T is proposed to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus psychroresistens sp. nov. is proposed. The type strain is ML311-T8T (= KCCM 43190T = JCM 31243T).

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Maikel Gilberto Fernández-López, Ayixon Sánchez-Reyes, Marcos Eduardo Rosas-Ramírez, Edgar Balcázar-López
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Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp: Juseok Kim , Joon Yong Kim , Hye Seon Song , In-Tae Cha , Seong Woon Roh , Se Hee Lee; J. Microbiol. 2019;57(6):444-449. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8704-8

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A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA- 4604T was observed at 10–40°C (optimum, 37°C), pH 6.0–10.0 (optimum, pH 7.0), and in the presence of 0–8.0% (w/v) NaCl (optimum, 0–2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA- 4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).

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Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Jin-Woo Bae
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Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim , Juseok Kim , In-Tae Cha , Min Young Jung , Hye Seon Song , Yeon Bee Kim , Changsu Lee , Seung-Yeon Kang , Jin-Woo Bae , Yoon-E Choi , Tae-Woon Kim , Seong Woon Roh; J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-019-8487-y

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White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

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Zunongwangia flava sp. nov., belonging to the family Flavobacteriaceae, isolated from Salicornia europaea: Eui-Sang Cho , In-Tae Cha , Hak-Jong Choi , Seong Woon Roh , Young-Do Nam , Sung Man Seo , Myung-Ji Seo; J. Microbiol. 2018;56(12):868-873. Published online October 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8231-z

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A yellow pigmented bacterium designated strain MBLN094T within the family Flavobacteriaceae was isolated from a halophyte Salicornia europaea on the coast of the Yellow Sea. This strain was a Gram-stain negative, aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain MBLN094T was found to be related to the genus Zunongwangia, exhibiting 16S rRNA gene sequence similarity values of 97.0, 96.8, 96.4, and 96.3% to Zunongwangia mangrovi P2E16T, Z. profunda SM-A87T, Z. atlantica 22II14-10F7T, and Z. endophytica CPA58T, respectively. Strain MBLN094T grew at 20‒37°C (optimum, 25‒ 30°C), at pH 6.0‒10.0 (optimum, 7.0‒8.0), and with 0.5‒15.0% (w/v) NaCl (optimum, 2.0‒5.0%). Menaquinone MK-6 was the sole respiratory quinone. The polar lipids were phosphatidylethanolamine, two unidentified aminolipids, and four unidentified lipids. Major fatty acids were iso-C17:0 3-OH, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), and iso-C15:0. The genomic DNA G + C content was 37.4 mol%. Based on these polyphasic taxonomic data, strain MBLN094T is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia flava sp. nov. is proposed. The type strain is MBLN094T (= KCTC 62279T = JCM 32262T).

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Citrimicrobium luteum gen. nov., sp. nov., Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Gut of a Sea Cucumber Stichopus japonicus: Hong-Joo Jung , In-Tae Cha , Kyung June Yim , Hye Seon Song , Kichul Cho , Daekyung Kim , Hae-Won Lee , Jae Kook Lee , Myung-Ji Seo , Seong Woon Roh , Sung-Jae Lee; J. Microbiol. 2014;52(10):819-824. Published online August 27, 2014; DOI: https://doi.org/10.1007/s12275-014-4136-7

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A Gram-stain negative, yellow-pigmented, motile, pleomorphic bacterium, designated strain CBA4602T, was isolated from the gut of the sea cucumber Stichopus japonicus, which was collected from Jeju Island in the Republic of Korea. In a phylogenetic analysis based on the 16S rRNA gene, strain CBA4602T belonged to the order Sphingomonadales in the class Alphaproteobacteria. The 16S rRNA gene sequence similarity between strain CBA4602T and ‘Citromicrobium bathyomarinum’ JF-1, the most closely related strain having nonvalidly published name, was 98.4%, followed by 95.2–96.7% identities with sequence of the other closest strains in the genus Erythrobacter. Strain CBA4602T had bacteriochlorophyll a and carotenoids. Strain CBA4602T grew in 0–10% (w/v) NaCl, at 10–42°C and pH 6.0–8.0, with optimal growth in 1–2% NaCl, at 30–37°C and pH 7.0. Strain CBA4602T was positive for catalase and oxidase activities and was able to hydrolyse gelatine and Tween 20 and 40, but not starch, Tween 80 or L-tyrosine. The G+C content of genomic DNA from strain CBA4602T was 68.0 mol% and Q-10 was the major detected isoprenoid quinone. The polar lipids were three unidentified phospholipids, three unidentified glycolipids, and two unidentified lipids. The dominant fatty acids were anteiso-C15:0, C16:0, anteiso-C17:0 and C18:0. As considering the current taxonomic status of the genus ‘Citromicrobium’ and polyphasic taxonomic analyses, strain CBA4602T represents a novel genus and species. The name Citrimicrobium luteum is proposed for the type strain CBA4602T (=KACC 17668T =JCM 19530T).

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Alluvial aquifers are one of the mainwater resources in many countries. Iron reduction in alluvial aquifers is often a major anaerobic process involved in bioremediation or causing problems, including the release of As trapped in Fe(III) oxide. We investigated the distribution of potential iron-reducing bacteria (IRB) in riverine alluvial aquifers (B1, B3, and B6 sites) at the Mankyeong River, Republic of Korea. Inactive iron reduction zones, the diversity and abundance of IRB can be examined using a clone library and quantitative PCR analysis of 16S rRNA genes. Geobacter spp. are potential IRB in the iron-reducing zone at the B6 (9 m) site, where high Fe(II) and arsenic (As) concentrations were observed. At the B3 (16 m) site, where low iron reduction activity was predicted, a dominant clone (10.6%) was 99% identical in 16S rRNA gene sequence with Rhodoferax ferrireducens. Although a major clone belonging to Clostridium spp. was found, possible IRB candidates could not be unambiguously determined at the B1 (18 m) site. Acanonical correspondence analysis demonstrated that, among potential IRB, only the Geobacteraceae were well correlated with Fe(II) and As concentrations. Our results indicate high environmental heterogeneity, and thus high spatial variability, in thedistribution of potential IRB in the riverine alluvial aquifersnear the Mankyeong River.

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