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Miljaković D, Marinković J, Tamindžić G, Milošević D, Ignjatov M, Karačić V, Jakšić S. Bio-Priming with Bacillus Isolates Suppresses Seed Infection and Improves the Germination of Garden Peas in the Presence of Fusarium Strains. J Fungi (Basel) 2024; 10:358. [PMID: 38786713 PMCID: PMC11122518 DOI: 10.3390/jof10050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Seed infection caused by Fusarium spp. is one of the major threats to the seed quality and yield of agricultural crops, including garden peas. The use of Bacillus spp. with multiple antagonistic and plant growth-promoting (PGP) abilities represents a potential disease control strategy. This study was performed to evaluate the biocontrol potential of new Bacillus spp. rhizosphere isolates against two Fusarium strains affecting garden peas. Six Bacillus isolates identified by 16S rDNA sequencing as B. velezensis (B42), B. subtilis (B43), B. mojavensis (B44, B46), B. amyloliquefaciens (B50), and B. halotolerans (B66) showed the highest in vitro inhibition of F. proliferatum PS1 and F. equiseti PS18 growth (over 40%). The selected Bacillus isolates possessed biosynthetic genes for endoglucanase (B42, B43, B50), surfactin (B43, B44, B46), fengycin (B44, B46), bacillomycin D (B42, B50), and iturin (B42), and were able to produce indole-3-acetic acid (IAA), siderophores, and cellulase. Two isolates, B. subtilis B43 and B. amyloliquefaciens B50, had the highest effect on final germination, shoot length, root length, shoot dry weight, root dry weight, and seedling vigor index of garden peas as compared to the control. Their individual or combined application reduced seed infection and increased seed germination in the presence of F. proliferatum PS1 and F. equiseti PS18, both after seed inoculation and seed bio-priming. The most promising results were obtained in the cases of the bacterial consortium, seed bio-priming, and the more pathogenic strain PS18. The novel Bacillus isolates may be potential biocontrol agents intended for the management of Fusarium seed-borne diseases.
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Affiliation(s)
- Dragana Miljaković
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
| | - Jelena Marinković
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
| | - Gordana Tamindžić
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
| | - Dragana Milošević
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
| | - Maja Ignjatov
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
| | - Vasiljka Karačić
- Faculty of Agriculture, University of Belgrade, 11080 Belgrade, Serbia;
| | - Snežana Jakšić
- Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia; (J.M.); (G.T.); (D.M.); (M.I.); (S.J.)
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Kokila V, Namasivayam SKR, Amutha K, Kumar RR, Bharani RSA, Surya P. Hypocholesterolemic potential of Bacillus amyloliquefaciens KAVK1 modulates lipid accumulation on 3T3-L1 adipose cells and high fat diet-induced obese rat model. World J Microbiol Biotechnol 2024; 40:206. [PMID: 38755297 DOI: 10.1007/s11274-024-04016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
The significance of microorganisms occurring in foods is predominantly targeted due to their application for identifying a novel range of the bacterial spectrum. Diverse microbial species are capable of exhibiting potential pharmacological activities like antimicrobial and anticancer. Microbial strains capable of reducing obesity-related syndromes have also been reported. In the present study, the hypocholesterolemic efficacy of Bacillus amyloliquefaciens isolated from dairy products was scrutinised by in vitro (3T3-L1 adipose cells) and in vivo (high-fat diet-induced obese Wistar albino rats) methods. Potential cholesterol-lowering isolates were screened using a plate assay method and optimised by physical parameters. Molecular identification of the topmost five cholesterol-lowering isolates was acquired by amplification of the 16 S rRNA gene region. Bacillus amyloliquefaciens strain KAVK1, followed by strains KAVK2, KAVK3, KAVK4, and KAVK5 were molecularly determined. Further, cholesterol-lowering strains degraded the spectral patterns determined by the side chain of a cholesterol molecule. The anti-lipase activity was demonstrated using the porcine pancreatic lipase inhibitory method and compared with the reference compound Atorvastatin. Lyophilised strain KAVK1 revealed maximum pancreatic lipase inhibition. Strain KAVK1 attenuated lipid accumulation in 3T3-L1 adipose cell line predicted by Oil Red O staining method. Significant reduction of body weight and change in lipid profile was recognised after the supplement of KAVK1 to obese rats. Histopathological changes in organs were predominantly marked. The result of this study implies that the cholesterol-lowering B. amyloliquefaciens KAVK1 strain was used to treat hypercholesterolemia.
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Affiliation(s)
- V Kokila
- Department of Plant Biology and Plant Biotechnology, Shree Chandraprabhu Jain College, Chennai, 601 203, India
- Department of Biotechnology, Vels Institute of Science, Technology & Advanced Studies (VISTAS), Chennai, Tamil Nadu, 600 117, India
| | - S Karthick Raja Namasivayam
- Centre for Applied Research, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, Tamil Nadu, 602105, India.
| | - K Amutha
- Department of Biotechnology, Vels Institute of Science, Technology & Advanced Studies (VISTAS), Chennai, Tamil Nadu, 600 117, India
| | - R Ramesh Kumar
- Department of Anatomy, Dr. A.L.M. Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, Tamil Nadu, 600 113, India
| | - R S Arvind Bharani
- Institute of Obstetrics and Gynaecology, Madras Medical College, Egmore, Chennai, Tamil Nadu, 600 008, India
| | - P Surya
- Centre of Advanced Study in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu, 608 502, India
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Ordon J, Thouin J, Nakano RT, Ma KW, Zhang P, Huettel B, Garrido-Oter R, Schulze-Lefert P. Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota. Nat Microbiol 2024; 9:1117-1129. [PMID: 38503974 PMCID: PMC10994850 DOI: 10.1038/s41564-024-01619-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/22/2024] [Indexed: 03/21/2024]
Abstract
DNA-amplicon-based microbiota profiling can estimate species diversity and abundance but cannot resolve genetic differences within individuals of the same species. Here we report the development of modular bacterial tags (MoBacTags) encoding DNA barcodes that enable tracking of near-isogenic bacterial commensals in an array of complex microbiome communities. Chromosomally integrated DNA barcodes are then co-amplified with endogenous marker genes of the community by integrating corresponding primer binding sites into the barcode. We use this approach to assess the contributions of individual bacterial genes to Arabidopsis thaliana root microbiota establishment with synthetic communities that include MoBacTag-labelled strains of Pseudomonas capeferrum. Results show reduced root colonization for certain mutant strains with defects in gluconic-acid-mediated host immunosuppression, which would not be detected with traditional amplicon sequencing. Our work illustrates how MoBacTags can be applied to assess scaling of individual bacterial genetic determinants in the plant microbiota.
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Affiliation(s)
- Jana Ordon
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Julien Thouin
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ryohei Thomas Nakano
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Ka-Wai Ma
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pengfan Zhang
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Innovative Genomics Institute (IGI), University of California, Berkeley, CA, USA
| | - Bruno Huettel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ruben Garrido-Oter
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Earlham Institute, Norwich, UK
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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Fang L, Zheng X, Sun Z, Li Y, Deng J, Zhou YI. Characterization of a Plant Growth-Promoting Endohyphal Bacillus subtilis in Fusarium acuminatum from Spiranthes sinensis. Pol J Microbiol 2023; 72:29-37. [PMID: 36929887 DOI: 10.33073/pjm-2023-007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
Successful seed germination and seedling growth in orchids require an association with mycorrhizal fungi. An endophytic Fusarium fungal strain YZU 172038 exhibiting plant growth-promoting (PGP) ability was isolated from the roots of Spiranthes sinensis (Orchidaceae). The harboring endohyphal bacteria were detected in the hypha by SYTO-9 fluorescent nucleic acid staining, fluorescence in situ hybridization (FISH), and PCR amplification of the 16S rDNA gene's region. Consequently, one endohyphal bacterium (EHB) - a strain YZSR384 was isolated and identified as Bacillus subtilis based on morphology, phylogenetic analysis, and genomic information. The results indicated that the strain YZSR384 could significantly promote the growth of rice roots and shoots similar to its host fungus. Its indole acetic acid (IAA) production reached a maximum of 23.361 μg/ml on the sixth day after inoculation. The genome annotation revealed several genes involved in PGP traits, including the clusters of genes encoding the IAA (trpABCDEFS), the siderophores (entABCE), and the dissolving phosphate (pstABCS and phoABDHPR). As an EHB, B. subtilis was first isolated from endophytic Fusarium acuminatum from S. sinensis.
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Affiliation(s)
- Lan Fang
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Xiao Zheng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengxiang Sun
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Yanyan Li
- 2Tobacco Research Institute of Hubei Province, Wuhan, China
| | - Jianxin Deng
- 1College of Agriculture, Yangtze University, Jingzhou, China
| | - Y I Zhou
- 1College of Agriculture, Yangtze University, Jingzhou, China
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5
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Shin JS, Li S. DNA-Immobilized Fluorescent Polystyrene Nanoparticles as Probes with Tunable Detection Limits. ACS OMEGA 2022; 7:48310-48319. [PMID: 36591202 PMCID: PMC9798753 DOI: 10.1021/acsomega.2c06498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
DNA-immobilized nanoparticle probes show high target specificity; thus, they are employed in various bioengineering and biomedicine applications. When the nanoparticles employed are dye-loaded polymer particles, the resulting probes have the additional benefit of biocompatibility and versatile surface properties. In this study, we construct DNA-immobilized fluorescent polystyrene (PS) nanoparticles through controlled surface reactions. PS nanoparticles with surface carboxyl groups are utilized, and amine-functionalized dye molecules and capture DNAs are covalently immobilized via a one-pot reaction. We show that the surface chemistry employed allows for quantitative control over the number of fluorescent dyes and DNA strands immobilized on the PS nanoparticle surfaces. The nanoparticles thus prepared are then used for DNA detection. The off state of the nanoprobe is achieved by hybridizing quencher-functionalized DNAs (Q-DNAs) to the capture DNAs immobilized on nanoparticle surfaces. Target-DNAs (T-DNAs) are detected by the displacement of the prehybridized Q-DNAs. The nanoprobes show successful detection of T-DNAs with high sequence specificity and long-term stability. They also show excellent detection sensitivity, and the detection limit can be tuned by adjusting the capture DNA-to-dye ratio.
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Duan Y, Li M, Zhang S, Wang Y, Deng J, Wang Q, Yi T, Dong X, Cheng S, He Y, Gao C, Wang Z. Highly Efficient Biotransformation and Production of Selenium Nanoparticles and Polysaccharides Using Potential Probiotic Bacillus subtilis T5. Metabolites 2022; 12:metabo12121204. [PMID: 36557242 PMCID: PMC9784637 DOI: 10.3390/metabo12121204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Selenium is an essential microelement required for human health. The biotransformation of selenium nanoparticles has attracted increasing attention in recent years. However, little of the literature has investigated the comprehensive evaluation of the strains for practical application and the effect on the functional properties in the existence of Se. The present study showed the selenite reduction strain Bacillus subtilis T5 (up to 200 mM), which could produce high yields of selenium polysaccharides and selenium nanoparticles in an economical and feasible manner. Biosynthesized selenium nanoparticles by B. subtilis T5 were characterized systematically using UV-vis spectroscopy, FTIR, Zeta Potential, DLS, and SEM techniques. The biosynthesized SeNPs exhibited high stability with small particle sizes. B. subtilis T5 also possessed a tolerance to acidic pH and bile salts, high aggregation, negative hemolytic, and superior antioxidant activity, which showed excellent probiotic potential and can be recommended as a potential candidate for the selenium biopharmaceuticals industry. Remarkably, B. subtilis T5 showed that the activity of α-amylase was enhanced with selenite treatment to 8.12 U/mL, 2.72-fold more than the control. The genus Bacillus was first reported to produce both selenium polysaccharides with extremely high Se-content (2.302 g/kg) and significantly enhance the activity to promote α-amylase with selenium treatment. Overall, B. subtilis T5 showed potential as a bio-factory for the biosynthesized SeNPs and organ selenium (selenium polysaccharide), providing an appealing perspective for the biopharmaceutical industry.
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Affiliation(s)
- Yuhua Duan
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Mengjun Li
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Sishang Zhang
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yidan Wang
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Jieya Deng
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qin Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Tian Yi
- Institute of Agricultural Quality Standards and Testing Technology Research, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xingxing Dong
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Shuiyuan Cheng
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Chao Gao
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- Correspondence: (C.G.); (Z.W.)
| | - Zhangqian Wang
- National R&D Center for Se-Rich Agricultural Products Processing, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Correspondence: (C.G.); (Z.W.)
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Lee G, Heo S, Kim T, Na HE, Park J, Lee E, Lee JH, Jeong DW. Discrimination of Bacillus subtilis from Other Bacillus Species Using Specific Oligonucleotide Primers for the Pyruvate Carboxylase and Shikimate Dehydrogenase Genes. J Microbiol Biotechnol 2022; 32:1011-1016. [PMID: 35879295 PMCID: PMC9628935 DOI: 10.4014/jmb.2205.05014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022]
Abstract
Bacillus subtilis is a useful bacterium in the food industry with applications as a starter strain for fermented food and as a probiotic. However, it is difficult to discriminate B. subtilis from other Bacillus species because of high phenotypic and genetic similarity. In this study, we employed five previously constructed multilocus sequence typing (MLST) methods for the discrimination of B. subtilis from other Bacillus species and all five MLST assays clearly distinguished B. subtilis. Additionally, the 17 housekeeping genes used in the five MLST assays also clearly distinguished B. subtilis. The pyruvate carboxylase (pyrA) and shikimate dehydrogenase (aroE) genes were selected for the discrimination of B. subtilis because of their high number of polymorphic sites and the fact that they displayed the lowest homology among the 17 housekeeping genes. Specific primer sets for the pyrA and aroE genes were designed and PCR products were specifically amplified from B. subtilis, demonstrating the high specificity of the two housekeeping genes for B. subtilis. This species-specific PCR method provides a quick, simple, powerful, and reliable alternative to conventional methods in the detection and identification of B. subtilis.
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Affiliation(s)
- Gawon Lee
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Sojeong Heo
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Tao Kim
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Hong-Eun Na
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Junghyun Park
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Eungyo Lee
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea
| | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 16227, Republic of Korea
| | - Do-Won Jeong
- Department of Food and Nutrition, Dongduk Women’s University, Seoul 02748, Republic of Korea,Corresponding author Phone: +82-2-940-4463 Fax: +82-2-940-4610 E-mail:
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8
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A sustainable production of lignocellulolytic enzymes and value added metabolites from banana pseudostem waste by Bacillus wakoensis NAULH-4. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Nannan C, Vu HQ, Gillis A, Caulier S, Nguyen TTT, Mahillon J. Bacilysin within the Bacillus subtilis group: gene prevalence versus antagonistic activity against Gram-negative foodborne pathogens. J Biotechnol 2020; 327:28-35. [PMID: 33387595 DOI: 10.1016/j.jbiotec.2020.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/17/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
The Bacillus subtilis group comprises species known for their ability to produce a wide variety of antimicrobial peptides. This work focuses on bacilysin, a broad-spectrum active dipeptide, and its prevalence in the B. subtilis group. In silico genome analysis of strains from Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus licheniformis, Bacillus pumilus and B. subtilis subspecies inaquosorum, spizizenii and subtilis revealed that the bacilysin gene cluster is present in all species except for B. licheniformis. This observation was corroborated by PCR detection of the bacilysin genetic determinants on a collection of 168 food and environmental strains from the B. subtilis group. Phylogenetic analyses also demonstrated that the bacilysin gene cluster sequence showed more than 80 % identity within each species of the B. subtilis group. An in vitro screening of the strain collection was performed against foodborne pathogens. Twenty-three strains were selected for their ability of their Cell-Free Supernatant to inhibit foodborne pathogens. After an ammonium sulphate precipitation of their supernatant, eight strains, all belonging to B. velezensis, exhibited antimicrobial activity against Gram-negative pathogens. Using Ultra High Performance Liquid Chromatography - Mass Spectrometry, the presence of bacilysin was confirmed in these eight precipitates. These findings provide evidence that bacilysin is a major player in the antagonistic activity of B. velezensis against Gram-negative foodborne pathogens.
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Affiliation(s)
| | - Huong Quynh Vu
- Laboratory of Food and Environmental Microbiology, Belgium; Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Belgium
| | - Simon Caulier
- Laboratory of Food and Environmental Microbiology, Belgium; Phytopathology-Applied Microbiology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Thuy Thanh Thi Nguyen
- Faculty of Food Science and Technology, Vietnam National University of Agriculture, Hanoi, Viet Nam
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Bahuguna A, Joe AR, Kumar V, Lee JS, Kim SY, Moon JY, Cho SK, Cho H, Kim M. Study on the Identification Methods for Effective Microorganisms in Commercially Available Organic Agriculture Materials. Microorganisms 2020; 8:microorganisms8101568. [PMID: 33053711 PMCID: PMC7599497 DOI: 10.3390/microorganisms8101568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/23/2022] Open
Abstract
The identification of microorganisms in closely related groups is challenging. The present work focused on the different molecular methodology for the accurate microbial identification in the five commercially available organic agriculture materials enriched with effective microorganisms. From the tested five organic agricultural materials, a total of seven distinct bacterial colonies (A-1, B-1, C-1, D-1, E-1, E-2, and E-3) were isolated and processed for sequential identification utilizing HiCrome™ Bacillus agar, biochemical tests with API CHB50, 16S rRNA gene analysis, random amplified polymorphic DNA (RAPD), and species-specific PCR analysis. All the isolated microorganisms were Gram-positive rods and spore former belonging to Bacillus group and appeared as a differential characteristic feature on HiCrome™ Bacillus agar. All isolates showed high-percentage similarities with the different members of Bacillus species in biochemical testing and 16S rRNA gene analysis. The collective identification results revealed isolates, A-1, B-1, and C-1, close to B. velezensis. Further RAPD-PCR and species-specific PCR discriminated and provided confirmatory evidence for D-1 as B. thuringiensis and E-1, E-2, and E-3 as B. licheniformis, respectively. In addition, presence of B. thuringiensis was also confirmed by toxin crystal protein staining. In conclusion, the species-specific primers could be used as a rapid and accurate identification tool to discriminate closely related Bacillus species such as B. subtilis, B. licheniformis, and B. thuringiensis.
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Affiliation(s)
- Ashutosh Bahuguna
- Department of Food Science and Technology, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541, Korea; (A.B.); (A.-r.J.); (V.K.)
| | - Ah-ryeong Joe
- Department of Food Science and Technology, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541, Korea; (A.B.); (A.-r.J.); (V.K.)
| | - Vishal Kumar
- Department of Food Science and Technology, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541, Korea; (A.B.); (A.-r.J.); (V.K.)
| | - Jong Suk Lee
- Division of Food and Nutrition and Cook, Taegu Science University, Daegu 41453, Korea;
| | - Sung-Youn Kim
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon 39660, Korea; (S.-Y.K.); (S.-K.C.); (H.C.)
| | - Ji-Young Moon
- Gyeonggi Provincial Office, National Agricultural Products Quality Management Service, Anyang 14035, Korea;
| | - Soon-Kil Cho
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon 39660, Korea; (S.-Y.K.); (S.-K.C.); (H.C.)
| | - Hyunjeong Cho
- Experiment Research Institute, National Agricultural Products Quality Management Service, Gimcheon 39660, Korea; (S.-Y.K.); (S.-K.C.); (H.C.)
| | - Myunghee Kim
- Department of Food Science and Technology, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 38541, Korea; (A.B.); (A.-r.J.); (V.K.)
- Correspondence: ; Tel.: +82-53-810-2958
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11
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Cho MS, Jin YJ, Kang BK, Park YK, Kim C, Park DS. Understanding the ontogeny and succession of Bacillus velezensis and B. subtilis subsp. subtilis by focusing on kimchi fermentation. Sci Rep 2018; 8:7045. [PMID: 29728638 PMCID: PMC5935750 DOI: 10.1038/s41598-018-25514-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 04/23/2018] [Indexed: 12/30/2022] Open
Abstract
Bacillus subtilis and B. velezensis are frequently isolated from various niches, including fermented foods, water, and soil. Within the Bacillus subtilis group, B. velezensis and B. subtilis subsp. subtilis have received significant attention as biological resources for biotechnology-associated industries. Nevertheless, radical solutions are urgently needed to identify microbes during their ecological succession to accurately confirm their action at the species or subspecies level in diverse environments, such as fermented materials. Thus, in this study, previously published genome data of the B. subtilis group were compared to exploit species- or subspecies-specific genes for use as improved qPCR targets to detect B. velezensis and B. subtilis subsp. subtilis in kimchi samples. In silico analyses of the selected genes and designed primer sequences, in conjunction with SYBR Green real-time PCR, confirmed the robustness of this newly developed assay. Consequently, this study will allow for new insights into the ontogeny and succession of B. velezensis and B. subtilis subsp. subtilis in various niches. Interestingly, in white kimchi without red pepper powder, neither B. subtilis subsp. subtilis nor B. velezensis was detected.
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Affiliation(s)
- Min Seok Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Yong Ju Jin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Bo Kyoung Kang
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Yu Kyoung Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - ChangKug Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Dong Suk Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea.
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