1
|
Lee G, Ibal JC, Park TH, Kim MJ, Choi SD, Shin JH. Whole-genome sequencing of Beauveria bassiana KNU-101 using the hybrid assembly approach. Microbiol Resour Announc 2024; 13:e0068123. [PMID: 38236017 PMCID: PMC10868216 DOI: 10.1128/mra.00681-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
In this report, we present the whole-genome sequences of Beauveria bassiana KNU-101, a widely recognized entomopathogenic fungus used as a biopesticide. The genome was assembled using a hybrid assembly approach, resulting in 13 scaffolds with a total size of 35,638,224 bp.
Collapse
Affiliation(s)
- GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- NGS Core Facility, Kyungpook National University, Daegu, Republic of Korea
| | - Tae-Hyung Park
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Min-Ji Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Seung-Dae Choi
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- NGS Core Facility, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
2
|
Sliti A, Singh V, Ibal JC, Jeong M, Shin JH. Impact of propiconazole fungicide on soil microbiome (bacterial and fungal) diversity, functional profile, and associated dehydrogenase activity. Environ Sci Pollut Res Int 2024; 31:8240-8253. [PMID: 38175519 DOI: 10.1007/s11356-023-31643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Pesticides, protect crops but can harm the environment and human health when used without caution. This study evaluated the impact of propiconazole, a fungicide that acts on fungal cell membranes, on soil microbiome abundance, diversity, and functional profile, as well as soil dehydrogenase activity (DHA). The study conducted microcosm experiments using soil samples treated with propiconazole and employed next-generation sequencing (MiSeq) and chromatographic approaches (GC-MS/MS) to analyze the shift in microbial communities and propiconazole level, respectively. The results showed that propiconazole significantly altered the distribution of microbial communities, with notable changes in the abundance of various bacterial and fungal taxa. Among soil bacterial communities, the relative abundance of Proteobacteria and Planctomycetota increased, while that of Acidobacteria decreased after propiconazole treatment. In the fungal communities, propiconazole increased the abundance of Ascomycota and Basidiomycota in the treated soil, while that of Mortierellomycota was reduced. Fungicide application further triggered a significant decrease in DHA over time. Analysis of the functional profile of bacterial communities showed that propiconazole significantly affected bacterial cellular and metabolic pathways. The carbon degradation pathway was upregulated, indicating the microbial detoxification of the contaminant in the treated soil. Our findings suggest that propiconazole application has a discernible impact on soil microbial communities, which could have long-term consequences for soil health, quality, and function.
Collapse
Affiliation(s)
- Amani Sliti
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Vineet Singh
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jerald Conrad Ibal
- Department of Biological Sciences, Idaho State University, Pocatello, ID, 83209, USA
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
- NGS Core Facility, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Department of Integrative Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea.
| |
Collapse
|
3
|
Jo H, Lim K, Ibal JC, Kim MC, Kim HB, Baek C, Heo YM, Lee H, Kang S, Lee DG, Shin JH. Growth Increase in the Herbaceous Plant Centella asiatica by the Plant Growth-Promoting Rhizobacteria Priestia megaterium HyangYak-01. Plants (Basel) 2023; 12:2398. [PMID: 37446960 DOI: 10.3390/plants12132398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023]
Abstract
Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.
Collapse
Affiliation(s)
- HyungWoo Jo
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
| | - Jerald Conrad Ibal
- NGS Core Facility, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
| | - Min-Chul Kim
- NGS Core Facility, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
| | - Hye-Been Kim
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
| | - Chaeyun Baek
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
| | - Young Mok Heo
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
| | - Haeun Lee
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
| | - Seunghyun Kang
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
| | - Dong-Geol Lee
- COSMAX BTI, R&I Center, Seongnam 13486, Republic of Korea
- Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
- NGS Core Facility, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
- Department of Integrative Biotechnology, Kyungpook National University, Daehak-ro 80, Daegu 41566, Republic of Korea
| |
Collapse
|
4
|
Kang GU, Ibal JC, Lee S, Jang MH, Park YJ, Kim MC, Park TH, Kim MS, Kim RH, Shin JH. Alteration of the Soil Microbiota in Ginseng Rusty Roots: Application of Machine Learning Algorithm to Explore Potential Biomarkers for Diagnostic and Predictive Analytics. J Agric Food Chem 2021; 69:8298-8306. [PMID: 34043355 DOI: 10.1021/acs.jafc.1c01314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Conceptualization to utilize microbial composition as a prediction tool has been widely applied in human cohorts, yet the potential capacity of soil microbiota as a diagnostic tool to predict plant phenotype remains unknown. Here, we collected 130 soil samples which are 54 healthy controls and 76 ginseng rusty roots (GRRs). Alpha diversities including Shannon, Simpson, Chao1, and phylogenetic diversity were significantly decreased in GRR (P < 0.05). Moreover, we identified 30 potential biomarkers. The optimized markers were obtained through fivefold cross-validation on a support vector machine and yielded a robust area under the curve of 0.856. Notably, evaluation of multi-index classification performance including accuracy, F1-score, and Kappa coefficient also showed robust discriminative capability (90.99%, 0.903, and 0.808). Taken together, our results suggest that the disease affects the microbial community and offers the potential ability of soil microbiota to identifying farms at the risk of GRR.
Collapse
Affiliation(s)
- Gi-Ung Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jerald Conrad Ibal
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seungjun Lee
- Department of Food Science & Nutrition, Pukyong National University, Busan 48513, Republic of Korea
| | - Myeong Hwan Jang
- Punggi Ginseng Research Institute GBARES, Youngju 36023, Republic of Korea
| | - Yeong-Jun Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-Chul Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Tae-Hyung Park
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-Sueng Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ryeong-Hui Kim
- Department of Intergrative Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Department of Intergrative Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
5
|
Jung BK, Ibal JC, Pham HQ, Kim MC, Park GS, Hong SJ, Jo HW, Park CE, Choi SD, Jung Y, Tagele SB, Shin JH. Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2. Front Microbiol 2020; 11:536865. [PMID: 33329415 PMCID: PMC7720635 DOI: 10.3389/fmicb.2020.536865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/12/2020] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.
Collapse
Affiliation(s)
- Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,CJ Blossom Park, Suwon-si, South Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Huy Quang Pham
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Min-Chul Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,Atogen Co., Ltd., Daejeon, South Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,Yeongnam Regional Office, Animal and Plant Quarantine Agency, Busan, South Korea
| | - Hyung Woo Jo
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea.,R&I Center, COSMAX BTI, Seongnam, South Korea
| | - Chang Eon Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Seung-Dae Choi
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Yeongyun Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Setu Bazie Tagele
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, South Korea
| |
Collapse
|
6
|
Jung Y, Tagele SB, Son H, Ibal JC, Kerfahi D, Yun H, Lee B, Park CY, Kim ES, Kim SJ, Shin JH. Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change. Microorganisms 2020; 8:microorganisms8091265. [PMID: 32825401 PMCID: PMC7569816 DOI: 10.3390/microorganisms8091265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.
Collapse
Affiliation(s)
- YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Setu Bazie Tagele
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Department of Applied Plant Sciences, University of Gondar, Gondar 196, Ethiopia
| | - HyunWoo Son
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
| | - Dorsaf Kerfahi
- Department of Biological Sciences, Keimyung University, Daegu 42601, Korea;
| | - Hyunju Yun
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Bora Lee
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Clara Yongjoo Park
- Department of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea; (H.Y.); (B.L.); (C.Y.P.)
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Korea;
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon 51702, Korea;
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea; (Y.J.); (S.B.T.); (H.S.); (J.C.I.)
- Correspondence: ; Tel.: +82-53-950-5716; Fax: +82-53-953-7233
| |
Collapse
|
7
|
Nzila A, Razzak SA, Sankara S, Nazal MK, Al-Momani M, Kang GU, Ibal JC, Shin JH. Characterisation and microbial community analysis of lipid utilising microorganisms for biogas formation. PLoS One 2019; 14:e0224989. [PMID: 31703100 PMCID: PMC6839884 DOI: 10.1371/journal.pone.0224989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
In the anaerobic process, fat-oil-grease (FOG) is hydrolysed to long-chain fatty acids (LCFAs) and glycerol (GLYC), which are then used as substrates to produce biogas. The increase in FOG and LCFAs inhibits methanogenesis, and so far, most work investigating this inhibition has been carried out when FOG or LCFAs were used as co-substrates. In the current work, the inhibition of methanogenesis by FOG, LCFAs and GLYC was investigated when used as sole substrates. To gain more insight on the dynamics of this process, the change of microbial community was analysed using 16S rRNA gene amplicon sequencing. The results indicate that, as the concentrations of cooking olive oil (CO, which represents FOG) and LCFAs increase, methanogenesis is inhibited. For instance, at 0.01 g. L-1 of FOG, the rate of biogas formation was around 8 ml.L-1.day-1, and this decreased to <4 ml.L-1.day-1 at 40 g.L-1. Similar results were observed with the use of LCFAs. However, GLYC concentrations up to 100g.L-1 did not affect the rate of biogas formation. Acidic pH, temperature > = 45°C and NaCl > 3% led to a significant decrease in the rate of biogas formation. Microbial community analyses were carried out from samples from 3 different bioreactors (CO, OLEI and GLYC), on day 1, 5 and 15. In each bioreactor, microbial communities were dominated by Proteobacteria, Firmicutes and Bacteroidetes phyla. The most important families were Enterobacteriaceae, Pseudomonadaceae and Shewanellaceae (Proteobacteria phylum), Clostridiacea and Ruminococcaceae (Firmicutes) and Porphyromonadaceae and Bacteroidaceae (Bacteroidetes). In CO bioreactor, Proteobacteria bacteria decreased over time, while those of OLEI and GLYC bioreactors increased. A more pronounced increase in Bacteroidetes and Firmicutes were observed in CO bioreactor. The methanogenic archaea Methanobacteriaceae and Methanocorpusculaceae were identified. This analysis has shown that a set of microbial population is selected as a function of the substrate.
Collapse
Affiliation(s)
- Alexis Nzila
- Department of Life Sciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Shaikh Abdur Razzak
- Departments of Chemical Engineering, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Saravanan Sankara
- Department of Life Sciences, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Mazen K. Nazal
- Research Institute, Center for Environment and Water, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Marwan Al-Momani
- Departments of Mathematics & Statistics, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Gi-Ung Kang
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
8
|
Park YJ, Park CE, Jung BK, Park MK, Ibal JC, Kim SJ, Lee SH, Sook Ko H, Shin JH. The first complete mitochondrial genome sequence of the mud crab Macrophthalmus japonicus (arthropoda, decapoda, macrophthalmidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1501300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yeong-Jun Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Min-Kyu Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang-Jun Kim
- Department of Natural Sciences, Republic of Korea Naval Academy, Changwon, Republic of Korea
| | - Seok Hyun Lee
- Department of Life Science, Silla University, Busan, Republic of Korea
| | - Hyun Sook Ko
- Department of Life Science, Silla University, Busan, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
9
|
Park YJ, Jung BK, Hong SJ, Park GS, Ibal JC, Pham H, Shin JH. Expression and Characterization of Calcium- and Zinc-Tolerant Xylose Isomerase from Anoxybacillus kamchatkensis G10. J Microbiol Biotechnol 2018; 28:606-612. [DOI: 10.4014/jmb.1712.12021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
10
|
Jung BK, Hong SJ, Jo HW, Jung Y, Park YJ, Park CE, Kim MC, Ibal JC, Roh DH, Shin JH. Genome sequencing to develop Paenibacillus donghaensis strain JH8 T (KCTC 13049 T=LMG 23780 T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype. Mar Genomics 2018; 37:39-42. [PMID: 33250125 DOI: 10.1016/j.margen.2017.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/16/2017] [Accepted: 11/18/2017] [Indexed: 11/29/2022]
Abstract
Paenibacillus donghaensis JH8T (KCTC 13049T=LMG 23780T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.
Collapse
Affiliation(s)
- Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyung Woo Jo
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - YeonGyun Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeong-Jun Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-Chul Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dong-Hyun Roh
- Department of Microbiology, Chungbuk National Univeristy, Cheongju 28644, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; Institute of Agricultural Science & Technology, Kyungpook National University, Daegu 41566, Republic of Korea.
| |
Collapse
|
11
|
Park YJ, Park CE, Jung BK, Ibal JC, Jung Y, Hong SJ, Park GS, Lee SH, Sook Ko H, Shin JH. The first complete mitochondrial genome sequence of the leucosiid crab Pyrhila pisum (Arthropoda, Decapoda, Leucosiidae). Mitochondrial DNA B Resour 2017; 2:885-886. [PMID: 33474023 PMCID: PMC7799897 DOI: 10.1080/23802359.2017.1407717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pyrhila pisum is known as leucosiid crab. So far, there is no study about whole mitochondrial genome in Leucosiidae family. Here, we report first the complete sequence of the mitochondrial genome from P. pisum, which is composed of 15,516 base pair encoding 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and A + T-rich region. The nucleotide composition of P. pisum was G + C: 25.5%, A + T: 74.5%, with a strong AT bias. In phylogenetic analysis using whole mitogenome, it was figured out that P. pisum was closely related to Sesarma neglectum but their family is different.
Collapse
Affiliation(s)
- Yeong-Jun Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - YeonGyun Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Gun-Seok Park
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Seok Hyun Lee
- Department of Life Science, Silla University, Busan, Republic of Korea
| | - Hyun Sook Ko
- Department of Life Science, Silla University, Busan, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|
12
|
Park YJ, Park CE, Hong SJ, Jung BK, Ibal JC, Park GS, Shin JH. The complete mitochondrial genome sequence of the greater wax moth Galleria mellonella (Insecta, Lepidoptera, Pyralidae): sequence and phylogenetic analysis comparison based on whole mitogenome. Mitochondrial DNA B Resour 2017; 2:714-715. [PMID: 33473956 PMCID: PMC7800018 DOI: 10.1080/23802359.2017.1390418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The larva of Galleria mellonella is widely used as a model organism for in vivo toxicology and pathogenicity testing. Here, we report complete sequence of the mitochondrial genome (mitogenome) from G. mellonella, which is comprised of 15,320 base pairs encoding 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an A + T rich region. The overall base composition was G + C: 19.6%, A + T: 80.4%, with an apparent AT bias. Phylogenetic analysis using whole mitogenome revealed that G. mellonella was closely related to Corcyra cephalonica, which is in the same Pyralidae family.
Collapse
Affiliation(s)
- Yeong-Jun Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Eon Park
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jerald Conrad Ibal
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Gun-Seok Park
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jae-Ho Shin
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea
| |
Collapse
|