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Adeniji AA, Loots DT, Babalola OO. Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation. Appl Microbiol Biotechnol 2019; 103:3669-3682. [PMID: 30911788 DOI: 10.1007/s00253-019-09710-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/06/2023]
Abstract
Some members of the Bacillus velezensis (Bv) group (e.g., Bv FZB42T and AS3.43) were previously assigned grouping with B. subtilis and B. amyloliquefaciens, based on the fact that they shared a 99% DNA-DNA percentage phylogenetic similarity. However, hinging on current assessments of the pan-genomic reassignments, the differing phylogenomic characteristics of Bv from B. subtilis and B. amyloliquefaciens are now better understood. Within this re-grouping/reassignment, the various strains within the Bv share a close phylogenomic resemblance, and a number of these strains have received a lot of attention in recent years, due to their genomic robustness, and the growing evidence for their possible utilization in the agricultural industry for managing plant diseases. Only a few applications for their use medicinally/pharmaceutically, environmentally, and in the food industry have been reported, and this may be due to the fact that the majority of those strains investigated are those typically occurring in soil. Although the intracellular unique biomolecules of Bv strains have been revealed via in silico genome modeling and investigated using transcriptomics and proteomics, a further inquisition into the Bv metabolome using newer technologies such as metabolomics could elucidate additional applications of this economically relevant Bacillus species, beyond that of primarily the agricultural sector.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Faculty of Natural and Agricultural Science, North-West University, Food Security and Safety, Private Bag X2046, Mmabatho, 2735, South Africa.,Faculty of Natural and Agricultural Science, North-West University, Human Metabolomics Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa
| | - Du Toit Loots
- Faculty of Natural and Agricultural Science, North-West University, Human Metabolomics Private Bag X6001, Box 269, Potchefstroom, 2531, South Africa
| | - Olubukola Oluranti Babalola
- Faculty of Natural and Agricultural Science, North-West University, Food Security and Safety, Private Bag X2046, Mmabatho, 2735, South Africa.
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Grady EN, MacDonald J, Ho MT, Weselowski B, McDowell T, Solomon O, Renaud J, Yuan ZC. Characterization and complete genome analysis of the surfactin-producing, plant-protecting bacterium Bacillus velezensis 9D-6. BMC Microbiol 2019; 19:5. [PMID: 30621587 PMCID: PMC6325804 DOI: 10.1186/s12866-018-1380-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/25/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Bacillus velezensis is an endospore-forming, free-living soil bacterium with potential as a biopesticide against a broad spectrum of microbial pathogens of plants. Its potential for commercial development is enhanced by rapid replication and resistance to adverse environmental conditions, typical of Bacillus species. However, the use of beneficial microbes against phytopathogens has not gained dominance due to limitations that may be overcome with new biopesticidal strains and/or new biological knowledge. RESULTS Here, we isolated B. velezensis strain 9D-6 and showed that it inhibits the in vitro growth of prokaryotic and eukaryotic pathogens, including the bacteria Bacillus cereus , Clavibacter michiganensis, Pantoea agglomerans, Ralstonia solanacearum, Xanthomonas campestris, and Xanthomonas euvesicatoria; and the fungi Alternaria solani, Cochliobolus carbonum, Fusarium oxysporum, Fusarium solani, Gibberella pulicaris, Gibberella zeae, Monilinia fructicola, Pyrenochaeta terrestris and Rhizoctonia solani. Antimicrobial compounds with activity against Clavibacter michiganensis were isolated from B. velezensis 9D-6 and characterized by high resolution LC-MS/MS, yielding formulae of C52H91N7O13 and C53H93N7O13, which correspond to [Leu7] surfactins C14 and C15 (also called surfactin B and surfactin C), respectively. We further sequenced the B. velezensis 9D-6 genome which consists of a single circular chromosome and revealed 13 gene clusters expected to participate in antimicrobial metabolite production, including surfactin and two metabolites that have not typically been found in this species - ladderane and lantipeptide. Despite being unable to inhibit the growth of Pseudomonas syringae DC3000 in an in vitro plate assay, B. velezensis 9D-6 significantly reduced root colonization by DC3000, suggesting that 9D-6 uses methods other than antimicrobials to control phytopathogens in the environment. Finally, using in silico DNA-DNA hybridization (isDDH), we confirm previous findings that many strains currently classified as B. amyloliquefaciens are actually B. velezensis. CONCLUSIONS The data presented here suggest B. velezensis 9D-6 as a candidate plant growth promoting bacterium (PGPB) and biopesticide, which uses a unique complement of antimicrobials, as well as other mechanisms, to protect plants against phytopathogens. Our results may contribute to future utilization of this strain, and will contribute to a knowledge base that will help to advance the field of microbial biocontrol.
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Affiliation(s)
- Elliot Nicholas Grady
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Margaret T. Ho
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ori Solomon
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
| | - Justin Renaud
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, Dental Science Building Rm. 3014, University of Western Ontario, London, ON N6A 5C1 Canada
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
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Zhao Y, Xiong Z, Wu G, Bai W, Zhu Z, Gao Y, Parmar S, Sharma VK, Li H. Fungal Endophytic Communities of Two Wild Rosa Varieties With Different Powdery Mildew Susceptibilities. Front Microbiol 2018; 9:2462. [PMID: 30386316 PMCID: PMC6198141 DOI: 10.3389/fmicb.2018.02462] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022] Open
Abstract
Powdery mildew (PM) is one of the most devastating and wide spread fungal diseases of rose, which seriously decrease its productivity and commercial value. In the present study, the endophytic fungal communities of two wild Rosa varieties (Rosa multiflora Thunb and R. multiflora var. carnea Redouté and Thory) with different PM susceptibilities were studied through Illumina MiSeq sequencer. A total of 14,000,424 raw reads were obtained from 60 samples, and 6,862,953 tags were produced after merging paired-end reads. 4462 distinct OTUs were generated at a 97% similarity level. It was found that only 34.2% of OTUs shared between two plant varieties. All of the OTUs were assigned into four fungal phyla, 17 classes, 43 orders, 86 families, 157 genera, and 208 species. Members of Ascomycota were found to be the most common fungal endophytes (EF) among all plant samples (93.7% relative abundance), followed by Basidiomycota (4.7% relative abundance), while Zygomycota and Glomeromycota were found to be rare and incidental. At each developmental stage of plants, the diversity and community structure of EF between two Rosa varieties showed significant differences. Both PCoA plots and PERMANOVA analyses indicated that developmental stage was the major factor contributing to the difference between the Rosa varieties (R2 = 0.348, p < 0.001). In addition, plant varieties and tissues were also important factors contributing to the difference (R2 = 0.031, p < 0.05; R2 = 0.029, p < 0.05). Moreover, Neofusicoccum, Rhodosporidium, and Podosphaera, etc., were found to be significantly different between two Rosa varieties, and some of the endophytes may play a role in PM resistance. These finding are encouraging to testify the potential use of these fungi in the biocontrol of PM in future studies.
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Affiliation(s)
- Yi Zhao
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Zhi Xiong
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Guangli Wu
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Weixiao Bai
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Zhengqing Zhu
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Yonghan Gao
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Shobhika Parmar
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Vijay K Sharma
- Medical School of Kunming University of Science and Technology, Kunming, China
| | - Haiyan Li
- Medical School of Kunming University of Science and Technology, Kunming, China
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Complete genome sequence of Bacillus velezensis QST713: A biocontrol agent that protects Agaricus bisporus crops against the green mould disease. J Biotechnol 2018; 278:10-19. [DOI: 10.1016/j.jbiotec.2018.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022]
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Ye M, Tang X, Yang R, Zhang H, Li F, Tao F, Li F, Wang Z. Characteristics and Application of a Novel Species of Bacillus: Bacillus velezensis. ACS Chem Biol 2018; 13:500-505. [PMID: 29309732 DOI: 10.1021/acschembio.7b00874] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacillus velezensis has been investigated and applied more and more widely recently because it can inhibit fungi and bacteria and become a potential biocontrol agent. In order to provide more clear and comprehensive understanding of B. velezensis for researchers, we collected the recent relevant articles systematically and reviewed the discovery and taxonomy, secondary metabolites, characteristics and application, gene function, and molecular research of B. velezensis. This review will give some direction to the research and application of this strain for the future.
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Affiliation(s)
- Miao Ye
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ru Yang
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fangshu Li
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Fangzheng Tao
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Fei Li
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
| | - Zaigui Wang
- College of Life Science, Anhui Agricultural University, Anhui Hefei 230036, Peoples’ Republic of China
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Lim SM, Yoon MY, Choi GJ, Choi YH, Jang KS, Shin TS, Park HW, Yu NH, Kim YH, Kim JC. Diffusible and Volatile Antifungal Compounds Produced by an Antagonistic Bacillus velezensis G341 against Various Phytopathogenic Fungi. THE PLANT PATHOLOGY JOURNAL 2017; 33:488-498. [PMID: 29018312 PMCID: PMC5624491 DOI: 10.5423/ppj.oa.04.2017.0073] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/31/2017] [Accepted: 06/14/2017] [Indexed: 05/25/2023]
Abstract
The aim of this study was to identify volatile and agar-diffusible antifungal metabolites produced by Bacillus sp. G341 with strong antifungal activity against various phytopathogenic fungi. Strain G341 isolated from four-year-old roots of Korean ginseng with rot symptoms was identified as Bacillus velezensis based on 16S rDNA and gyrA sequences. Strain G341 inhibited mycelial growth of all phytopathogenic fungi tested. In vivo experiment results revealed that n-butanol extract of fermentation broth effectively controlled the development of rice sheath blight, tomato gray mold, tomato late blight, wheat leaf rust, barley powdery mildew, and red pepper anthracnose. Two antifungal compounds were isolated from strain G341 and identified as bacillomycin L and fengycin A by MS/MS analysis. Moreover, volatile compounds emitted from strain G341 were found to be able to inhibit mycelial growth of various phytopathogenic fungi. Based on volatile compound profiles of strain G341 obtained through headspace collection and analysis on GC-MS, dimethylsulfoxide, 1-butanol, and 3-hydroxy-2-butanone (acetoin) were identified. Taken together, these results suggest that B. valezensis G341 can be used as a biocontrol agent for various plant diseases caused by phytopathogenic fungi.
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Affiliation(s)
- Seong Mi Lim
- Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
| | - Mi-Young Yoon
- Eco-friendly New Material Research Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Gyung Ja Choi
- Eco-friendly New Material Research Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Yong Ho Choi
- Eco-friendly New Material Research Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Kyoung Soo Jang
- Eco-friendly New Material Research Group, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Teak Soo Shin
- Crop Protection Research Center, Farm Hannong Company, Ltd., Chungnam 33010,
Korea
| | - Hae Woong Park
- R&D Division, World Institute of Kimchi, Gwangju 61755,
Korea
| | - Nan Hee Yu
- Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
| | - Young Ho Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jin-Cheol Kim
- Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186,
Korea
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Carro L, Nouioui I. Taxonomy and systematics of plant probiotic bacteria in the genomic era. AIMS Microbiol 2017; 3:383-412. [PMID: 31294168 PMCID: PMC6604993 DOI: 10.3934/microbiol.2017.3.383] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.
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Affiliation(s)
- Lorena Carro
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Imen Nouioui
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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