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Ali MA, Ahmed T, Ibrahim E, Rizwan M, Chong KP, Yong JWH. A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities. Heliyon 2024; 10:e31573. [PMID: 38841467 PMCID: PMC11152693 DOI: 10.1016/j.heliyon.2024.e31573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/08/2024] [Accepted: 05/19/2024] [Indexed: 06/07/2024] Open
Abstract
Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.
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Affiliation(s)
- Md. Arshad Ali
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Temoor Ahmed
- Xianghu Laboratory, Hangzhou, 311231, China
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- MEU Research Unit, Middle East University, Amman, Jordan
| | - Ezzeldin Ibrahim
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Department of Vegetable Diseases Research, Plant Pathology Research Institute, Agriculture Research Centre, Giza, Egypt
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Khim Phin Chong
- Biotechnology Programme, Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu, 88400, Sabah, Malaysia
| | - Jean Wan Hong Yong
- Department of Biosystems and Technology, Swedish University of Agricultural Sciences, 23456, Alnarp, Sweden
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Shih SY, Huang YS, Chou KR, Wu HY, Tsai H. Isolation and genome characterization of Paenibacillus polymyxa 188, a potential biocontrol agent against fungi. J Appl Microbiol 2024; 135:lxae075. [PMID: 38509027 DOI: 10.1093/jambio/lxae075] [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: 11/15/2023] [Revised: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
AIMS In this work, we aimed to isolate marine bacteria that produce metabolites with antifungal properties. METHODS AND RESULTS Paenibacillus polymyxa 188 was isolated from a marine sediment sample, and it showed excellent antifungal activity against many fungi pathogenic to plants (Fusarium tricinctum, Pestalotiopsis clavispora, Fusarium oxysporum, F. oxysporum f. sp. Cubense (Foc), Curvularia plantarum, and Talaromyces pinophilus) and to humans (Aspergillus terreus, Penicillium oxalicum, and Microsphaeropsis arundinis). The antifungal compounds produced by P. polymyxa 188 were extracted and analyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The complete genome sequence and biosynthetic gene clusters of P. polymyxa 188 were characterized and compared with those of other strains. A total of 238 carbohydrate-active enzymes (CAZymes) were identified in P. polymyxa 188. Two antibiotic gene clusters, fusaricidin and tridecaptin, exist in P. polymyxa 188, which is different from other strains that typically have multiple antibiotic gene clusters. CONCLUSIONS Paenibacilluspolymyxa 188 was identified with numerous biosynthetic gene clusters, and its antifungal ability against pathogenic fungi was verified.
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Affiliation(s)
- Sra-Yh Shih
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - You-Syu Huang
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
- Eastern Marine Biology Research Center, Taitung City, 950, Taiwan
| | - Ker-Rui Chou
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - Hung-Yi Wu
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
| | - HsinYuan Tsai
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung City, 804, Taiwan
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Lebano I, Fracchetti F, Vigni ML, Mejia JF, Felis G, Lampis S. MALDI-TOF as a powerful tool for identifying and differentiating closely related microorganisms: the strange case of three reference strains of Paenibacillus polymyxa. Sci Rep 2024; 14:2585. [PMID: 38297004 PMCID: PMC10831075 DOI: 10.1038/s41598-023-50010-w] [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: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 02/02/2024] Open
Abstract
Accurate identification and typing of microbes are crucial steps in gaining an awareness of the biological heterogeneity and reliability of microbial material within any proprietary or public collection. Paenibacillus polymyxa is a bacterial species of great agricultural and industrial importance due to its plant growth-promoting activities and production of several relevant secondary metabolites. In recent years, matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an alternative rapid tool for identifying, typing, and differentiating closely related strains. In this study, we investigated the diversity of three P. polymyxa strains. The mass spectra of ATCC 842T, DSM 292, and DSM 365 were obtained, analysed, and compared to select discriminant peaks using ClinProTools software and generate classification models. MALDI-TOF MS analysis showed inconsistent results in identifying DSM 292 and DSM 365 as belonging to P. polimixa species, and comparative analysis of mass spectra revealed the presence of highly discriminatory biomarkers among the three strains. 16S rRNA sequencing and Average Nucleotide Identity (ANI) confirmed the discrepancies found in the proteomic analysis. The case study presented here suggests the enormous potential of the proteomic-based approach, combined with statistical tools, to predict and explore differences between closely related strains in large microbial datasets.
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Affiliation(s)
- Ilaria Lebano
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy.
| | | | - Mario Li Vigni
- Syngenta Biologicals (Valagro SpA), 66041, Atessa, CH, Italy
| | | | - Giovanna Felis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy
| | - Silvia Lampis
- Department of Biotechnology and VUCC-DBT Verona University Culture Collection, University of Verona, 37154, Verona, VR, Italy.
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4
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Li Y, Chen S. Structure modification of an antibiotic: by engineering the fusaricidin bio-synthetase A in Paenibacillus polymyxa. Front Microbiol 2023; 14:1239958. [PMID: 37822742 PMCID: PMC10562733 DOI: 10.3389/fmicb.2023.1239958] [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: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
Fusaricidin, a lipopeptide antibiotic, is specifically produced by Paenibacillus polymyxa strains, which could strongly inhibit Fusarium species fungi. Fusaricidin bio-synthetase A (FusA) is composed of six modules and is essential for synthesizing the peptide moiety of fusaricidin. In this study, we confirmed the FusA of Paenibacillus polymyxa strain WLY78 involved in producing Fusaricidin LI-F07a. We constructed six engineered strains by deletion of each module within FusA from the genome of strain WLY78. One of the engineered strains is able to produce a novel compound that exhibits better antifungal activity than that of fusaricidin LI-F07a. This new compound, known as fusaricidin [ΔAla6] LI-F07a, has a molecular weight of 858. Our findings reveal that it exhibits a remarkable 1-fold increase in antifungal activity compared to previous fusaricidin, and the fermentation yield reaches ~55 mg/L. This research holds promising implications for plant protection against infections caused by Fusarium and Botrytis pathogen infection.
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Affiliation(s)
- Yunlong Li
- Chengdu NewSun Crop Science Co. Ltd., Chengdu, China
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Lin S, Chen X, Xie L, Zhang Y, Zeng F, Long Y, Ren L, Qi X, Wei J. Biocontrol potential of lipopeptides produced by Paenibacillus polymyxa AF01 against Neoscytalidium dimidiatum in pitaya. Front Microbiol 2023; 14:1188722. [PMID: 37266020 PMCID: PMC10231640 DOI: 10.3389/fmicb.2023.1188722] [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: 03/17/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Pitaya canker, caused by Neoscytalidium dimidiatum, is one of the most important fungal diseases that cause significant losses in production. To replace chemical pesticides, the use of biocontrol strains to manage plant diseases has been the focus of research. In this study, the bacterial strain AF01, identified as Paenibacillus polymyxa, exhibited significant antifungal effects against N. dimidiatum and four other pitaya fungal pathogens. The strain P. polymyxa AF01 produces 13 fusaricidins, which directly inhibit mycelial growth, spore germination and germ tube elongation by causing the membrane integrity and cell ultrastructure to incur irreversible damage. Pot experiment and yield test confirmed that AF01 provided preservative effects by reducing the disease index. In comparison to the untreated control groups, RNA-seq data showed that P. polymyxa AF01 selectively blocked some transcription and translation processes and inhibited RNA and DNA structural dynamics, energy production and conversion, and signal transduction, particularly cell wall biosynthesis, changes in membrane permeability, and impairment of protein biosynthesis. Thus, P. polymyxa AF01 could be potentially useful as a suitable biocontrol agent for pitaya canker.
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Affiliation(s)
- Shanyu Lin
- College of Agriculture, Guangxi University, Nanning, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Xiaohang Chen
- Baise Agricultural Scientific Research Institute, Baise, China
| | - Ling Xie
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Yan Zhang
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Fenghua Zeng
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Yanyan Long
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Plant Protection Research Institute, Guangxi Academy of Agricultural Science, Nanning, Guangxi, China
| | - Liyun Ren
- College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning, China
| | - Xiuling Qi
- College of Agricultural Engineering, Guangxi Vocational University of Agriculture, Nanning, China
| | - Jiguang Wei
- College of Agriculture, Guangxi University, Nanning, China
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Hossain A, Ali MA, Lin L, Luo J, You Y, Masum MMI, Jiang Y, Wang Y, Li B, An Q. Biocontrol of Soft Rot Dickeya and Pectobacterium Pathogens by Broad-Spectrum Antagonistic Bacteria within Paenibacillus polymyxa Complex. Microorganisms 2023; 11:microorganisms11040817. [PMID: 37110240 PMCID: PMC10142376 DOI: 10.3390/microorganisms11040817] [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: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Polymyxin-producing bacteria within the Paenibacillus polymyxa complex have broad-spectrum activities against fungi and bacteria. Their antibacterial activities against soft rot Dickeya and Pectobacterium phytopathogens containing multiple polymyxin-resistant genes were not clear. Here, we selected nine strains within the P. polymyxa complex having broad-spectrum antagonistic activities against phytopathogenic fungi and a polymyxin-resistant D. dadantii strain causing stem and root rot disease of sweet potato and did antagonistic assays on nutrient agar and sweet potato tuber slices. These strains within the P. polymyxa complex showed clear antagonistic activities against D. dadantii in vitro and in vivo. The most effective antagonistic strain P. polymyxa ShX301 showed broad-spectrum antagonistic activities against all the test Dickeya and Pectobacterium strains, completely eliminated D. dadantii from sweet potato seed tubers, and promoted the growth of sweet potato seedlings. Cell-free culture filtrate of P. polymyxa ShX301 inhibited D. dadantii growth, swimming motility, and biofilm formation and disrupted D. dadantii plasma membranes, releasing nucleic acids and proteins. Multiple lipopeptides produced by P. polymyxa ShX301 may play a major role in the bactericidal and bacteriostatic actions. This study clarifies that the antimicrobial spectrum of polymyxin-producing bacteria within the P. polymyxa complex includes the polymyxin-resistant Dickeya and Pectobacterium phytopathogens and strengthens the fact that bacteria within the P. polymyxa complex have high probability of being effective biocontrol agents and plant growth promoters.
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Affiliation(s)
- Afsana Hossain
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Arshad Ali
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Li Lin
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Yuxin You
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Md Mahidul Islam Masum
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou 311400, China
| | - Yanli Wang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianli An
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Tsai SH, Chen YT, Yang YL, Lee BY, Huang CJ, Chen CY. The Potential Biocontrol Agent Paenibacillus polymyxa TP3 Produces Fusaricidin-Type Compounds Involved in the Antagonism Against Gray Mold Pathogen Botrytis cinerea. PHYTOPATHOLOGY 2022; 112:775-783. [PMID: 34587815 DOI: 10.1094/phyto-04-21-0178-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Paenibacillus polymyxa is a beneficial bacterium for plant health. P. polymyxa TP3 exhibits antagonistic activity toward Botrytis cinerea and alleviates gray mold symptoms on the leaves of strawberry plants. Moreover, suppression of gray mold on the flowers and fruits of strawberry plants in field trials, including vegetative cells and endospores, was demonstrated, indicating the potential of strain TP3 as a biological control agent. To examine the anti-B. cinerea compounds produced by P. polymyxa TP3, we performed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and fusaricidin-corresponding mass spectra were detected. Moreover, fusaricidin-related signals appeared in imaging mass spectrometry of TP3 when confronted with B. cinerea. By using liquid chromatography mass spectrometry-based molecular networking approach, we identified several fusaricidins including a new variant of mass/charge ratio 917.5455 with serine in the first position of the hexapeptide. Via advanced mass spectrometry and network analysis, fusaricidin-type compounds produced by P. polymyxa TP3 were efficiently disclosed and were presumed to play roles in the antagonism against gray mold pathogen B. cinerea.
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Affiliation(s)
- Shuen-Huang Tsai
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Yu-Ting Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| | - Bo-Yi Lee
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi 60004, Taiwan, Republic of China
| | - Chao-Ying Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
- Master Program for Plant Medicine, National Taiwan University, Taipei 10617, Taiwan, Republic of China
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Li Y, Zhang H, Li Y, Chen S. Fusaricidin Biosynthesis Is Controlled via a KinB-Spo0A-AbrB Signal Pathway in Paenibacillus polymyxa WLY78. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1378-1389. [PMID: 34890249 DOI: 10.1094/mpmi-05-21-0117-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusaricidins produced by Paenibacillus polymyxa are important lipopeptide antibiotics against fungi. The fusGFEDCBA (fusaricidin biosynthesis) operon is responsible for synthesis of fusaricidins. However, the regulation mechanisms of fusaricidin biosynthesis remain to be fully clarified. In this study, we revealed that fusaricidin production is controlled by a complex regulatory network including KinB-Spo0A-AbrB. Evidence suggested that the regulator AbrB represses the transcription of the fus gene cluster by direct binding to the fus promoter, in which the sequences (5'-AATTTTAAAATAAATTTTGTGATTT-3') located from -136 to -112 bp relative to the transcription start site is required for this repression. Spo0A binds to the abrB promoter that contains the Spo0A-binding sequences (5'-TGTCGAA-3', 0A box) and in turn prevents the further transcription of abrB. The decreasing concentration of AbrB allows for the derepression of the fus promoter repressed by AbrB. The genome of P. polymyxa WLY78 contains two orthologs (named Kin1508 and Kin4833) of Bacillus subtilis KinB, but only Kin4833 activates sporulation and fusaricidin production, indicating that this kinase may be involved in phosphorylating Spo0A to initiate sporulation and regulate the abrB transcription. Our results reveal that Kin4833 (KinB), Spo0A, and AbrB are involved in regulation of fusaricidin production and a signaling mechanism that links fusaricidin production and sporulation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yunlong Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Haowei Zhang
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yongbin Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing, China
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Mülner P, Schwarz E, Dietel K, Herfort S, Jähne J, Lasch P, Cernava T, Berg G, Vater J. Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1. Pathogens 2021; 10:pathogens10111485. [PMID: 34832640 PMCID: PMC8621861 DOI: 10.3390/pathogens10111485] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/18/2023] Open
Abstract
Paenibacilli are efficient producers of potent agents against bacterial and fungal pathogens, which are of great interest both for therapeutic applications in medicine as well as in agrobiotechnology. Lipopeptides produced by such organisms play a major role in their potential to inactivate pathogens. In this work we investigated two lipopeptide complexes, the fusaricidins and the polymyxins, produced by Paenibacillus polymyxa strains DSM 32871 and M1 by MALDI-TOF mass spectrometry. The fusaricidins show potent antifungal activities and are distinguished by an unusual variability. For strain DSM 32871 we identified numerous yet unknown variants mass spectrometrically. DSM 32871 produces polymyxins of type E (colistins), while M1 forms polymyxins P. For both strains, novel but not yet completely characterized polymyxin species were detected, which possibly are glycosylated. These compounds may be of interest therapeutically, because polymyxins have gained increasing attention as last-resort antibiotics against multiresistant pathogenic Gram-negative bacteria. In addition, the volatilomes of DSM 32781 and M1 were investigated with a GC–MS approach using different cultivation media. Production of volatile organic compounds (VOCs) was strain and medium dependent. In particular, strain M1 manifested as an efficient VOC-producer that exhibited formation of 25 volatiles in total. A characteristic feature of Paenibacilli is the formation of volatile pyrazine derivatives.
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Affiliation(s)
- Pascal Mülner
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Elisa Schwarz
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
| | - Kristin Dietel
- ABITEP GmbH, Glienicker Weg 185, 12489 Berlin, Germany; (P.M.); (E.S.); (K.D.)
| | - Stefanie Herfort
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Jennifer Jähne
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Peter Lasch
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petergasse 12, 8010 Graz, Austria; (T.C.); (G.B.)
| | - Joachim Vater
- Robert Koch-Institut, ZBS6, Proteomics and Spectroscopy, Seestr 10, 13353 Berlin, Germany; (S.H.); (J.J.); (P.L.)
- Correspondence:
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10
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Soni R, Rawal K, Keharia H. Genomics assisted functional characterization of Paenibacillus polymyxa HK4 as a biocontrol and plant growth promoting bacterium. Microbiol Res 2021; 248:126734. [PMID: 33690069 DOI: 10.1016/j.micres.2021.126734] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/22/2021] [Accepted: 02/21/2021] [Indexed: 10/22/2022]
Abstract
The diseases caused by phytopathogens account for huge economic losses in the agricultural sector. Paenibacillus polymyxa is one of the agriculturally important biocontrol agents and plant growth promoting bacterium. This study describes the antifungal potential of P. polymyxa HK4 against an array of fungal phytopathogens and its ability to stimulate seed germination of cumin and groundnut under in vitro conditions. The cumin and groundnut seeds bacterized with HK4 exhibited enhanced germination efficiency in comparison to controls. The use of HK4 as a soil inoculant significantly promoted the shoot length and fresh weight of groundnut plants in pot studies. The draft genome analysis of HK4 revealed the genetic attributes for motility, root colonization, antagonism, phosphate solubilization, siderophore production and production of volatile organic compounds. The bacterium HK4 harnessed several hydrolytic enzymes that may assist its competence in the rhizosphere. The PCR amplification and sequence analysis of the conserved region of the fusA gene amplicon revealed the ability of HK4 to produce fusaricidin. Furthermore, the LC-ESI-MS/MS of crude cell pellet extract of HK4 confirmed the presence of fusaricidin as a major antifungal metabolite. This study demonstrated the potential of HK4 as a biocontrol agent and a plant growth promoter.
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Affiliation(s)
- Riteshri Soni
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India
| | - Khushboo Rawal
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India
| | - Hareshkumar Keharia
- Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, 388 315, Anand, Gujarat, India.
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Ali MA, Lou Y, Hafeez R, Li X, Hossain A, Xie T, Lin L, Li B, Yin Y, Yan J, An Q. Functional Analysis and Genome Mining Reveal High Potential of Biocontrol and Plant Growth Promotion in Nodule-Inhabiting Bacteria Within Paenibacillus polymyxa Complex. Front Microbiol 2021; 11:618601. [PMID: 33537018 PMCID: PMC7848036 DOI: 10.3389/fmicb.2020.618601] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteria belonging to the genus Paenibacillus were frequently isolated from legume nodules. The nodule-inhabiting Paenibacillus as a resource of biocontrol and plant growth-promoting endophytes has rarely been explored. This study explored the nodule-inhabiting Paenibacillus' antifungal activities and biocontrol potentials against broad-spectrum important phytopathogenic fungi. We collected strains which were isolated from nodules of Robinia pseudoacacia, Dendrolobium triangulare, Ormosia semicastrata, Cicer arietinum, Acacia crassicarpa, or Acacia implexa and belong to P. peoriae, P. kribbensis, P. endophyticus, P. enshidis, P. puldeungensis, P. taichungensis, or closely related to P. kribbensis, or P. anseongense. These nodule-inhabiting Paenibacillus showed diverse antagonistic activities against five phytopathogenic fungi (Fusarium graminearum, Magnaporthe oryzae, Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea). Six strains within the P. polymyxa complex showed broad-spectrum and potent activities against all the five pathogens, and produced multiple hydrolytic enzymes, siderophores, and lipopeptide fusaricidins. Fusaricidins are likely the key antimicrobials responsible for the broad-spectrum antifungal activities. The nodule-inhabiting strains within the P. polymyxa complex were able to epiphytically and endophytically colonize the non-host wheat plants, produce indole acetic acids (IAA), and dissolve calcium phosphate and calcium phytate. P. peoriae strains RP20, RP51, and RP62 could fix N2. P. peoriae RP51 and Paenibacillus sp. RP31, which showed potent plant colonization and plant growth-promotion competence, effectively control fungal infection in planta. Genome mining revealed that all strains (n = 76) within the P. polymyxa complex contain ipdC gene encoding indole-3-pyruvate decarboxylase for biosynthesis of IAA, 96% (n = 73) contain the fus cluster for biosynthesis of fusaricidins, and 43% (n = 33) contain the nif cluster for nitrogen fixation. Together, our study highlights that endophytic strains within the P. polymyxa complex have a high probability to be effective biocontrol agents and biofertilizers and we propose an effective approach to screen strains within the P. polymyxa complex.
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Affiliation(s)
- Md. Arshad Ali
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Lou
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Rahila Hafeez
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xuqing Li
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Afsana Hossain
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Ting Xie
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Li Lin
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jianli Yan
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou, China
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Martínez-Núñez MA, Rodríguez-Escamilla Z. Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes. Toxins (Basel) 2020; 12:E349. [PMID: 32466531 PMCID: PMC7354552 DOI: 10.3390/toxins12060349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico
| | - Zuemy Rodríguez-Escamilla
- UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico
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Abd Alamer IS, Tomah AA, Li B, Zhang JZ. Isolation, Identification and Characterization of Rhizobacteria Strains for Biological Control of Bacterial Wilt (Ralstonia solanacearum) of Eggplant in China. AGRICULTURE 2020; 10:37. [DOI: 10.3390/agriculture10020037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Bacterial wilt of eggplant is the most destructive disease caused by Ralstonia solanacearum throughout the world. Eleven bacterial strains with high antagonistic activity were obtained from 245 rhizobacteria. Based on analysis of morphology, 16S rRNA sequences, fatty acid profiles, gyrA and rpoB genes, they were identified as Pseudomonas putida (IMA3), Paenibacillus polymyxa (IMA5), Bacillus cereus (IMA4, IMA7 and IMA11) and the “operational group Bacillus amyloliquefaciens” (IMA1, IMA2, IMA6, IMA8, IMA9 and IMA10). The lipopeptide compounds produced by each strain also were determined. The biocontrol tests demonstrated that co-inoculation by strain IMA5 and the pathogen gave the greatest biocontrol efficiency of 87.0% and 69.2% 30 and 40 days after co-inoculation, respectively. Plant growth promotion tests revealed that IMA5 markedly promoted eggplant growth, enhancing aboveground seedling length and biomass by 60.8% and by 107.6% and underground root length and biomass by 33.0% and 69.2%, respectively. Hence, strain IMA5 could be considered for developing potential biocontrol agents and for promoting plant growth characteristics, to aid the management of the pathogen R. solanacearum in eggplants.
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Li Y, Chen S. Fusaricidin Produced by Paenibacillus polymyxa WLY78 Induces Systemic Resistance against Fusarium Wilt of Cucumber. Int J Mol Sci 2019; 20:E5240. [PMID: 31652608 PMCID: PMC6829208 DOI: 10.3390/ijms20205240] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/29/2022] Open
Abstract
Cucumber is an important vegetable crop in China. Fusarium wilt is a soil-borne disease that can significantly reduce cucumber yields. Paenibacillus polymyxa WLY78 can strongly inhibit Fusarium oxysporum f. sp. Cucumerium, which causes Fusarium wilt disease. In this study, we screened the genome of WLY78 and found eight potential antibiotic biosynthesis gene clusters. Mutation analysis showed that among the eight clusters, the fusaricidin synthesis (fus) gene cluster is involved in inhibiting the Fusarium genus, Verticillium albo-atrum, Monilia persoon, Alternaria mali, Botrytis cinereal, and Aspergillus niger. Further mutation analysis revealed that with the exception of fusTE, the seven genes fusG, fusF, fusE, fusD, fusC, fusB, and fusA within the fus cluster were all involved in inhibiting fungi. This is the first time that demonstrated that fusTE was not essential. We first report the inhibitory mode of fusaricidin to inhibit spore germination and disrupt hyphal membranes. A biocontrol assay demonstrated that fusaricidin played a major role in controlling Fusarium wilt disease. Additionally, qRT-PCR demonstrated that fusaricidin could induce systemic resistance via salicylic acid (SA) signal against Fusarium wilt of cucumber. WLY78 is the first reported strain to both produce fusaricidin and fix nitrogen. Therefore, our results demonstrate that WLY78 will have great potential as a biocontrol agent in agriculture.
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Affiliation(s)
- Yunlong Li
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100094, China.
| | - Sanfeng Chen
- State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100094, China.
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15
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Paenibacillus polymyxa bioactive compounds for agricultural and biotechnological applications. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101092] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Abdallah Y, Yang M, Zhang M, Masum MMI, Ogunyemi SO, Hossain A, An Q, Yan C, Li B. Plant growth promotion and suppression of bacterial leaf blight in rice by Paenibacillus polymyxa Sx3. Lett Appl Microbiol 2019; 68:423-429. [PMID: 30659625 DOI: 10.1111/lam.13117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 02/03/2023]
Abstract
The effects and mechanisms of Paenibacillus polymyxa Sx3 on growth promotion and the suppression of bacterial leaf blight in rice were evaluated in this study. The results from a plate assay indicated that Sx3 inhibited the growth of 20 strains of Xanthomonas oryzae pv. oryzae (Xoo). Rice seedling experiments indicated that Sx3 promoted plant growth and suppressed bacterial leaf blight. In addition, bacteriological tests showed that Sx3 was able to fix nitrogen, solubilize phosphate and produce indole acetic acid, indicating that various mechanisms may be involved in the growth promotion by Sx3. The culture filtrate of P. polymyxa Sx3 reduced bacterial growth, biofilm formation and disrupted the cell morphology of Xoo strain GZ 0005, as indicated by the transmission and scanning electron microscopic observations. In addition, MALDI-TOF MS analysis revealed that Sx3 could biosynthesize two types of secondary metabolites fusaricidins and polymyxin P. In summary, this study clearly indicated that P. polymyxa Sx3 has strong in vitro and in vivo antagonistic activity against Xoo, which may be at least partially attributed to its production of secondary metabolites. SIGNIFICANCE AND IMPACT OF THE STUDY: Antagonistic bacteria can grow well in their originating environment. However, it is unclear whether antagonistic bacteria were able to survive in different ecological environments. This study revealed that Paenibacillus polymyxa Sx3 isolated from rhizosphere soil of cotton significantly promoted the plant growth and suppressed bacterial leaf blight in rice. Therefore, it could be inferred that P. polymyxa Sx3 has the potential to be used as biocontrol agents in plants grown in different ecological environments.
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Affiliation(s)
- Y Abdallah
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Department of Plant Pathology, Minia University, El-Minya, Egypt
| | - M Yang
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - M Zhang
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Md M I Masum
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - S O Ogunyemi
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - A Hossain
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Q An
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - C Yan
- Institute of Plant Virology, Ningbo University, Ningbo, China.,Institute of Biotechnology, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - B Li
- State Key laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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17
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Olishevska S, Nickzad A, Déziel E. Bacillus and Paenibacillus secreted polyketides and peptides involved in controlling human and plant pathogens. Appl Microbiol Biotechnol 2019; 103:1189-1215. [DOI: 10.1007/s00253-018-9541-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/25/2022]
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18
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Identification of fusaricidins from the antifungal microbial strain Paenibacillus sp. MS2379 using ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. J Chromatogr A 2018; 1586:91-100. [PMID: 30558848 DOI: 10.1016/j.chroma.2018.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/20/2018] [Accepted: 12/04/2018] [Indexed: 11/21/2022]
Abstract
Paenibacillus sp. MS2379 is a highly efficient microbial strain producing fusaricidins, a class of lipopeptides that have demonstrated strong antifungal activities against a broad array of fungal pathogens. An integrated approach combining chromatographic fractionation, UHPLC-QTOF-MS analysis, and NMR spectroscopic interpretation was employed to characterize antifungal metabolites produced by this microbial strain, resulting in the identification of 48 fusaricidins including 30 cyclic and 18 open-chain species. In this regard, UHPLC-QTOF-MS played a vital role in determining structures of 28 new fusaricidins through peptide fragment analysis. The structural determination of the new fusaricidins by the high-resolution mass spectrometry was validated by follow-up isolation and NMR spectroscopic analysis of representative compounds. It is worth noting that novel fusaricidins with amino acid residues of serine and γ-aminobutyric acid were identified, which is of great biosynthetic significance for this biologically important class of compounds. The present study again illustrates the power of UHPLC-QTOF-MS for structural identification of lipopeptides, and the structural diversity of the identified fusaricidins makes this microbial strain unique as a potential biocontrol agent.
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Menegatti C, Da Paixão Melo WG, Carrão DB, De Oliveira ARM, Do Nascimento FS, Lopes NP, Pupo MT. Paenibacillus polymyxa Associated with the Stingless Bee Melipona scutellaris Produces Antimicrobial Compounds against Entomopathogens. J Chem Ecol 2018; 44:1158-1169. [DOI: 10.1007/s10886-018-1028-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 01/19/2023]
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20
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Alkhalili RN, Canbäck B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. Int J Mol Sci 2018; 19:E2650. [PMID: 30200662 PMCID: PMC6165006 DOI: 10.3390/ijms19092650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 09/04/2018] [Indexed: 01/03/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified polycyclic peptides. Lanthipeptides that have antimicrobial activity are known as lantibiotics. Accordingly, the discovery of novel lantibiotics constitutes a possible solution for the problem of antibiotic resistance. We utilized the publicly available genome sequences and the bioinformatic tools tailored for the detection of lanthipeptides. We designed our strategy for screening of 252 firmicute genomes and detecting class-I lanthipeptide-coding gene clusters. The designed strategy resulted in identifying 69 class-I lanthipeptide sequences, of which more than 10% were putative novel. The identified putative novel lanthipeptides have not been annotated on the original or the RefSeq genomes, or have been annotated merely as coding for hypothetical proteins. Additionally, we identified bacterial strains that have not been previously recognized as lanthipeptide-producers. Moreover, we suggest corrections for certain firmicute genome annotations, and recommend lanthipeptide records for enriching the bacteriocin genome mining tool (BAGEL) databases. Furthermore, we propose Z-geobacillin, a putative class-I lanthipeptide coded on the genome of the thermophilic strain Geobacillus sp. ZGt-1. We provide lists of putative novel lanthipeptide sequences and of the previously unrecognized lanthipeptide-producing bacterial strains, so they can be prioritized for experimental investigation. Our results are expected to benefit researchers interested in the in vitro production of lanthipeptides.
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Affiliation(s)
- Rawana N Alkhalili
- Biotechnology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
| | - Björn Canbäck
- Department of Biology, Lund University, SE-221 00 Lund, Sweden.
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21
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Guo C, Guo XF, Zhao L, Chen DD, Wang J, Sun J. A Study on Immonium Ions and Immonium-Related Ions Depending on Different Collision Energies as Assessed by Q-TOF MS. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162018040088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Yang A, Zeng S, Yu L, He M, Yang Y, Zhao X, Jiang C, Hu D, Song B. Characterization and antifungal activity against Pestalotiopsis of a fusaricidin-type compound produced by Paenibacillus polymyxa Y-1. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 147:67-74. [PMID: 29933995 DOI: 10.1016/j.pestbp.2017.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/11/2017] [Accepted: 08/13/2017] [Indexed: 06/08/2023]
Abstract
Dendrobium nobile (D. nobile) is a valuable Chinese herbal medicine. The discovery of microbial resources from has provided a wealth of raw materials. Stalk rot, which is caused by Pestalotiopsis, is one of the most serious diseases of D nobile and has resulted in serious losses in production. However, an effective method for the prevention and control of stalk rot remains lacking. In this study, we aimed to identify a biocontrol strain against Pestalotiopsis. We isolated Paenibacillus polymyxa Y-1, an endophytic bacterium, from the stem of D. nobile. Three pairs of active metabolites isolated from this bacterium were identified as fusaricidin compounds. We then investigated the mechanism of fusaricidin compounds on Pestalotiopsis via proteomics. Proteomics data showed that the compounds mainly inhibit energy generation in the respiratory chain and amino acid biosynthesis of Pestalotiopsis.
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Affiliation(s)
- Anming Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Song Zeng
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Lu Yu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Ming He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Yuanyou Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Xiaozhen Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Chaolin Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Deyu Hu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China.
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Vater J, Herfort S, Doellinger J, Weydmann M, Borriss R, Lasch P. Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa
E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin. Chembiochem 2018; 19:744-753. [DOI: 10.1002/cbic.201700615] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Joachim Vater
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Stefanie Herfort
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Joerg Doellinger
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Max Weydmann
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
| | - Rainer Borriss
- Humboldt Universität Berlin; Fachgebiet Phytomedizin; Lentzeallee 55-57 14195 Berlin Germany
- NordReet UG; Marienstrasse 27a 17489 Greifswald Germany
| | - Peter Lasch
- Robert Koch-Institut Berlin; ZBS6 Proteomics and Spectroscopy; Seestrasse 10 13353 Berlin Germany
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24
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Dunlap CA, Lueschow S, Carrillo D, Rooney AP. Screening of bacteria for antagonistic activity against phytopathogens of avocados. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Reimann M, Sandjo LP, Antelo L, Thines E, Siepe I, Opatz T. A new member of the fusaricidin family - structure elucidation and synthesis of fusaricidin E. Beilstein J Org Chem 2017; 13:1430-1438. [PMID: 28781709 PMCID: PMC5530608 DOI: 10.3762/bjoc.13.140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022] Open
Abstract
Two hitherto unknown fusaricidins were obtained from fermentation broths of three Paenibacillus strains. After structure elucidation based on tandem mass spectrometry and NMR spectroscopy, fusaricidin E was synthesized to confirm the structure and the suggested stereochemistry. The synthesis was based on a new strategy which includes an efficient access to the 15-guanidino-3-hydroxypentadecanoyl (GHPD) side chain from erucamide.
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Affiliation(s)
- Marcel Reimann
- Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany
| | - Louis P Sandjo
- Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany
- Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Bloco J/K, Universidade Federal de Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Luis Antelo
- Institute of Biotechnology and Drug Research, Erwin Schrödinger-Str. 56, 66776 Kaiserslautern, Germany
| | - Eckhard Thines
- Institute of Biotechnology and Drug Research, Erwin Schrödinger-Str. 56, 66776 Kaiserslautern, Germany
- Institute of Molecular Physiology, Microbiology and Wine Research, Johannes Gutenberg University Mainz, Johann-Joachim-Becher-Weg 15, 55128 Mainz, Germany
| | | | - Till Opatz
- Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10–14, 55128 Mainz, Germany
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Ryu J, Kim JM, Lee CW, Kim SW. Structural analysis and enhanced production of fusaricidin fromPaenibacillus kribbensisCU01 isolated from yellow loess. J Basic Microbiol 2017; 57:525-535. [DOI: 10.1002/jobm.201600692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Jaewon Ryu
- Department of Energy Convergence; Chosun University; Gwangju Republic of Korea
| | - Jong M. Kim
- Department of Energy Convergence; Chosun University; Gwangju Republic of Korea
| | - Chul W. Lee
- Department of Chemistry; Chonnam National University; Gwangju Republic of Korea
| | - Si W. Kim
- Department of Energy Convergence; Chosun University; Gwangju Republic of Korea
- Department of Environmental Engineering; Chosun University; Gwangju Republic of Korea
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27
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Vater J, Herfort S, Doellinger J, Weydmann M, Dietel K, Faetke S, Lasch P. Fusaricidins from Paenibacillus polymyxa M-1, a family of lipohexapeptides of unusual complexity-a mass spectrometric study. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:7-15. [PMID: 27714901 DOI: 10.1002/jms.3891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/17/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
Paenibacillus polymyxa are rhizobacteria with a high potential to produce natural compounds of biotechnological and medical interest. Main products of P. polymyxa are fusaricidins, a large family of antifungal lipopeptides with a 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid side chain. We use the P. polymyxa strain M-1 as a model organism for the exploration of the biosynthetic potential of these rhizobacteria. Using matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) about 40 new fusaricidins were detected which were fractionated by reversed-phase (rp) HPLC. Their structure was determined by MALDI-LIFT-TOF/TOF fragment analysis. The dominant fragment in the product ion spectra of fusaricidins appeared at m/z 256.3, 284.3 and 312.4, respectively, indicating variations in their fatty acid part. Two new subfamilies of fusaricidins were introduced which contain guanidino-3-hydroxyhepta- and nonadecanoic acid as fatty acid constituents. Apparently, the end-standing guanidine group is not modified as shown by direct infusion nano-electrospray ionization mass spectrometry (nano-ESI MS). The results of this study suggest that advanced mass spectrometry is the method of choice for investigating natural compounds of unusual diversity, like fusaricidins. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Joachim Vater
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Stefanie Herfort
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Joerg Doellinger
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Max Weydmann
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
| | - Kristin Dietel
- Abitep GmbH Berlin, Glienicker Weg 185, 12489, Berlin, Germany
| | | | - Peter Lasch
- Robert-Koch-Institut Berlin, ZB6 'Proteomics and Spectroscopy', Seestraße 10, 13353, Berlin, Germany
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