1
|
Wallner A, Antonielli L, Mesguida O, Rey P, Compant S. Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability. BMC Genomics 2024; 25:720. [PMID: 39054421 PMCID: PMC11271205 DOI: 10.1186/s12864-024-10610-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: 03/26/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Paenibacillus polymyxa is a bacterial species of high interest, as suggested by the increased number of publications on its functions in the past years. Accordingly, the number of described strains and sequenced genomes is also on the rise. While functional diversity of P. polymyxa has been suggested before, the available genomic data is now sufficient for robust comparative genomics analyses. RESULTS Using 157 genomes, we found significant disparities among strains currently affiliated to P. polymyxa. Multiple taxonomic groups were identified with conserved predicted functions putatively impacting their respective ecology. As strains of this species have been reported to exhibit considerable potential in agriculture, medicine, and bioremediation, it is preferable to clarify their taxonomic organization to facilitate reliable and durable approval as active ingredients. CONCLUSIONS Strains currently affiliated to P. polymyxa can be separated into two major species groups with differential potential in nitrogen fixation, plant interaction, secondary metabolism, and antimicrobial resistance, as inferred from genomic data.
Collapse
Affiliation(s)
- Adrian Wallner
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria.
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
| | - Ouiza Mesguida
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
- GreenCell, Biopôle Clermont-Limagne, Saint Beauzire, 63360, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, 64000, France
| | - Stéphane Compant
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology, Konrad Lorenz Str. 24, Tulln, 3430, Austria
| |
Collapse
|
2
|
Dini S, Oz F, Bekhit AEDA, Carne A, Agyei D. Production, characterization, and potential applications of lipopeptides in food systems: A comprehensive review. Compr Rev Food Sci Food Saf 2024; 23:e13394. [PMID: 38925624 DOI: 10.1111/1541-4337.13394] [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: 11/14/2023] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Lipopeptides are a class of lipid-peptide-conjugated compounds with differing structural features. This structural diversity is responsible for their diverse range of biological properties, including antimicrobial, antioxidant, and anti-inflammatory activities. Lipopeptides have been attracting the attention of food scientists due to their potential as food additives and preservatives. This review provides a comprehensive overview of lipopeptides, their production, structural characteristics, and functional properties. First, the classes, chemical features, structure-activity relationships, and sources of lipopeptides are summarized. Then, the gene expression and biosynthesis of lipopeptides in microbial cell factories and strategies to optimize lipopeptide production are discussed. In addition, the main methods of purification and characterization of lipopeptides have been described. Finally, some biological activities of the lipopeptides, especially those relevant to food systems along with their mechanism of action, are critically examined.
Collapse
Affiliation(s)
- Salome Dini
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Fatih Oz
- Department of Food Engineering, Agriculture Faculty, Atatürk University, Erzurum, Turkey
| | | | - Alan Carne
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Saadaoui M, Faize M, Rifai A, Tayeb K, Omri Ben Youssef N, Kharrat M, Roeckel-Drevet P, Chaar H, Venisse JS. Evaluation of Tunisian wheat endophytes as plant growth promoting bacteria and biological control agents against Fusarium culmorum. PLoS One 2024; 19:e0300791. [PMID: 38758965 PMCID: PMC11101125 DOI: 10.1371/journal.pone.0300791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/05/2024] [Indexed: 05/19/2024] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) applications have emerged as an ideal substitute for synthetic chemicals by their ability to improve plant nutrition and resistance against pathogens. In this study, we isolated fourteen root endophytes from healthy wheat roots cultivated in Tunisia. The isolates were identified based from their 16S rRNA gene sequences. They belonged to Bacillota and Pseudomonadota taxa. Fourteen strains were tested for their growth-promoting and defense-eliciting potentials on durum wheat under greenhouse conditions, and for their in vitro biocontrol power against Fusarium culmorum, an ascomycete responsible for seedling blight, foot and root rot, and head blight diseases of wheat. We found that all the strains improved shoot and/or root biomass accumulation, with Bacillus mojavensis, Paenibacillus peoriae and Variovorax paradoxus showing the strongest promoting effects. These physiological effects were correlated with the plant growth-promoting traits of the bacterial endophytes, which produced indole-related compounds, ammonia, and hydrogen cyanide (HCN), and solubilized phosphate and zinc. Likewise, plant defense accumulations were modulated lastingly and systematically in roots and leaves by all the strains. Testing in vitro antagonism against F. culmorum revealed an inhibition activity exceeding 40% for five strains: Bacillus cereus, Paenibacillus peoriae, Paenibacillus polymyxa, Pantoae agglomerans, and Pseudomonas aeruginosa. These strains exhibited significant inhibitory effects on F. culmorum mycelia growth, sporulation, and/or macroconidia germination. P. peoriae performed best, with total inhibition of sporulation and macroconidia germination. These finding highlight the effectiveness of root bacterial endophytes in promoting plant growth and resistance, and in controlling phytopathogens such as F. culmorum. This is the first report identifying 14 bacterial candidates as potential agents for the control of F. culmorum, of which Paenibacillus peoriae and/or its intracellular metabolites have potential for development as biopesticides.
Collapse
Affiliation(s)
- Mouadh Saadaoui
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, France
- Université de Tunis El Manar, Campus Universitaire Farhat Hached, Tunis, Tunisia
- Field Crops Laboratory, National Institute for Agricultural Research of Tunisia, Tunisia, Tunisia
| | - Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization CNRST-URL10, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
| | - Aicha Rifai
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization CNRST-URL10, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
| | - Koussa Tayeb
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization CNRST-URL10, Faculty of Sciences, University Chouaib Doukkali, El Jadida, Morocco
| | - Noura Omri Ben Youssef
- Field Crops Laboratory, National Institute for Agricultural Research of Tunisia, Tunisia, Tunisia
- National Institute of Agronomy of Tunisia, Tunis, Tunisia
| | - Mohamed Kharrat
- Field Crops Laboratory, National Institute for Agricultural Research of Tunisia, Tunisia, Tunisia
| | | | - Hatem Chaar
- Field Crops Laboratory, National Institute for Agricultural Research of Tunisia, Tunisia, Tunisia
- National Institute of Agronomy of Tunisia, Tunis, Tunisia
| | | |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Yang F, Jiang H, Ma K, Hegazy A, Wang X, Liang S, Chang G, Yu L, Tian B, Shi X. Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt. Front Microbiol 2024; 15:1359263. [PMID: 38591040 PMCID: PMC11000672 DOI: 10.3389/fmicb.2024.1359263] [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: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.
Collapse
Affiliation(s)
- Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Huayan Jiang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Abeer Hegazy
- National Water Research Center, Shubra El Kheima, Egypt
| | - Xin Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shen Liang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Gaozheng Chang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Liqin Yu
- Henan Natural Products Biotechnology Co., Ltd., Zhengzhou, China
| | - Baoming Tian
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuanjie Shi
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
7
|
Yuan P, Chen Z, Xu M, Cai W, Liu Z, Sun D. Microbial cell factories using Paenibacillus: status and perspectives. Crit Rev Biotechnol 2023:1-17. [PMID: 38105503 DOI: 10.1080/07388551.2023.2289342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/22/2023] [Indexed: 12/19/2023]
Abstract
Considered a "Generally Recognized As Safe" (GRAS) bacterium, the plant growth-promoting rhizobacterium Paenibacillus has been widely applied in: agriculture, medicine, industry, and environmental remediation. Paenibacillus species not only accelerate plant growth and degrade toxic substances in wastewater and soil but also produce industrially-relevant enzymes and antimicrobial peptides. Due to a lack of genetic manipulation tools and methods, exploitation of the bioresources of naturally isolated Paenibacillus species has long been limited. Genetic manipulation tools and methods continue to improve in Paenibacillus, such as shuttle plasmids, promoters, and genetic tools of CRISPR. Furthermore, genetic transformation systems develop gradually, including: penicillin-mediated transformation, electroporation, and magnesium amino acid-mediated transformation. As genetic manipulation methods of homologous recombination and CRISPR-mediated editing system have developed gradually, Paenibacillus has come to be regarded as a promising microbial chassis for biomanufacturing, expanding its application scope, such as: industrial enzymes, bioremediation and bioadsorption, surfactants, and antibacterial agents. In this review, we describe the applications of Paenibacillus bioproducts, and then discuss recent advances and future challenges in the development of genetic manipulation systems in this genus. This work highlights the potential of Paenibacillus as a new microbial chassis for mining bioresources.
Collapse
Affiliation(s)
- Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Ziyan Chen
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Mengtao Xu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Wenfeng Cai
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Zhizhi Liu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| |
Collapse
|
8
|
Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D. Microbial diversity in soils suppressive to Fusarium diseases. FRONTIERS IN PLANT SCIENCE 2023; 14:1228749. [PMID: 38111879 PMCID: PMC10726057 DOI: 10.3389/fpls.2023.1228749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/10/2023] [Indexed: 12/20/2023]
Abstract
Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.
Collapse
Affiliation(s)
- Irena Todorović
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | | | - Daniel Muller
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Dobrzyński J, Jakubowska Z, Kulkova I, Kowalczyk P, Kramkowski K. Biocontrol of fungal phytopathogens by Bacillus pumilus. Front Microbiol 2023; 14:1194606. [PMID: 37560520 PMCID: PMC10407110 DOI: 10.3389/fmicb.2023.1194606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.
Collapse
Affiliation(s)
- Jakub Dobrzyński
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Zuzanna Jakubowska
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Iryna Kulkova
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jabłonna, Poland
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Białystok, Białystok, Poland
| |
Collapse
|
11
|
Al-Mutar DMK, Noman M, Abduljaleel Alzawar NS, Li D, Song F. Cyclic Lipopeptides of Bacillus amyloliquefaciens DHA6 Are the Determinants to Suppress Watermelon Fusarium Wilt by Direct Antifungal Activity and Host Defense Modulation. J Fungi (Basel) 2023; 9:687. [PMID: 37367623 DOI: 10.3390/jof9060687] [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: 05/23/2023] [Revised: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 06/28/2023] Open
Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (Fon), poses a serious threat to watermelon productivity. We previously characterized six antagonistic bacterial strains, including DHA6, capable of suppressing watermelon Fusarium wilt under greenhouse conditions. This study investigates the role of extracellular cyclic lipopeptides (CLPs) produced by strain DHA6 in Fusarium wilt suppression. Taxonomic analysis based on the 16S rRNA gene sequence categorized strain DHA6 as Bacillus amyloliquefaciens. MALDI-TOF mass spectrometry identified five families of CLPs, i.e., iturin, surfactin, bacillomycin, syringfactin, and pumilacidin, in the culture filtrate of B. amyloliquefaciens DHA6. These CLPs exhibited significant antifungal activity against Fon by inducing oxidative stress and disrupting structural integrity, inhibiting mycelial growth and spore germination. Furthermore, pretreatment with CLPs promoted plant growth and suppressed watermelon Fusarium wilt by activating antioxidant enzymes (e.g., catalase, superoxide dismutase, and peroxidase) and triggering genes involved in salicylic acid and jasmonic acid/ethylene signaling in watermelon plants. These results highlight the critical roles of CLPs as determinants for B. amyloliquefaciens DHA6 in suppressing Fusarium wilt through direct antifungal activity and modulation of plant defense responses. This study provides a foundation for developing B. amyloliquefaciens DHA6-based biopesticides, serving as both antimicrobial agents and resistance inducers, to effectively control Fusarium wilt in watermelon and other crops.
Collapse
Affiliation(s)
- Dhabyan Mutar Kareem Al-Mutar
- Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Basra Agriculture Directorate, Almudaina 61008, Iraq
| | - Muhammad Noman
- Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Dayong Li
- Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fengming Song
- Key Laboratory of Crop Diseases and Insect Pests of Ministry of Agriculture, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
12
|
Tian B, Qu Z, Mehmood MA, Xie J, Cheng J, Fu Y, Jiang D. Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat. Microbiol Spectr 2023; 11:e0098123. [PMID: 37212718 PMCID: PMC10269679 DOI: 10.1128/spectrum.00981-23] [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: 03/08/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.
Collapse
Affiliation(s)
- Binnian Tian
- College of Plant Protection, Southwest University, Chongqing, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing, China
| | - Zheng Qu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Mirza Abid Mehmood
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
13
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
14
|
Liu L, Xie Y, Zhong X, Deng Q, Shao Q, Cai Z, Huang X. Facilitating effects of the reductive soil disinfestation process combined with Paenibacillus sp. amendment on soil health and physiological properties of Momordica charantia. FRONTIERS IN PLANT SCIENCE 2023; 13:1095656. [PMID: 36733598 PMCID: PMC9888761 DOI: 10.3389/fpls.2022.1095656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Reductive soil disinfestation (RSD) is an anaerobic and facultative anaerobic microbial-mediated soil management process. The extent of improvement of diseased soil properties by RSD relative to comparable healthy soil is, however, not well characterized. Importantly, how to promote the colonization efficiency of these facultative anaerobic functional species to ensure soil and plant health remain unknown. Here, Fusarium wilt-diseased soil of Momordica charantia grown under a plastic-shed field (PS-CK) was used to conduct molasses-RSD (MO-RSD) along with Paenibacillus sp. (a model of facultative anaerobic species) (MOPA-RSD) treatment, and the soil from a nearby open-air paddy field was considered comparable healthy soil (OA-CK). Both RSD treatments significantly improved the properties of PS-CK soil, and the extent of improvement of soil pH, Fusarium oxysporum reduction efficiency (98.36%~99.56%), and microbial community and functional composition were higher than that achieved for OA-CK soil, which indicated that RSD-regulated most soil properties outperformed those of the comparable healthy soil. The disease incidence and ascorbic acid content of M. charantia in MO-RSD- and MOPA-RSD-treated soils were considerably decreased, while the weight and soluble protein contents were correspondingly increased, as compared to those of M. charantia in PS-CK soil. Specifically, the changes in these physiological properties of M. charantia in MOPA-RSD soil performed well than that in MO-RSD soil. The relative abundances of Cohnella, Effusibacillus, Rummeliibacillus, Oxobacter, Thermicanus, and Penicillium enriched in both RSD-treated soils were positively correlated with Paenibacillus and negatively correlated with F. oxysporum population and disease incidence (P < 0.05). Notably, the relative abundances of these potential probiotics were considerably higher in MOPA-RSD-treated soil than in MO-RSD alone-treated soil. These results show that the RSD process with inoculation of Paenibacillus sp. could promote the colonization of this species and simultaneously stimulate the proliferation of other probiotic consortia to further enhance soil health and plant disease resistance.
Collapse
Affiliation(s)
- Liangliang Liu
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Yi Xie
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
- School of Geography, Nanjing Normal University, Nanjing, China
| | - Xin Zhong
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
| | - Quanquan Deng
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
| | - Qin Shao
- Engineering Technology Research Center of Jiangxi Universities and Colleges for Selenium Agriculture, College of Life Science and Environmental Resources, Yichun University, Yichun, China
| | - Zucong Cai
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing, China
| | - Xinqi Huang
- School of Geography, Nanjing Normal University, Nanjing, China
- Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Nanjing Normal University, Nanjing, China
| |
Collapse
|
15
|
Yang S, Jin D, Li H, Jiang L, Cui J, Huang W, Rang J, Li Y, Xia L. Screening of new Paenibacillus polymyxa S3 and its disease resistance of grass carp (Ctenopharyngodon idellus). JOURNAL OF FISH DISEASES 2023; 46:17-29. [PMID: 36097971 DOI: 10.1111/jfd.13714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
A new strain of Paenibacillus polymyxa S3 with antagonistic effects on 11 major fish pathogens (especially Aeromonas hydrophila), but had no toxicity to grass carp, was screened from the sediment of fishponds. In vivo colonization studies showed that strain S3 could be colonized and distributed in the gill and abdomen of the grass carp. Bioassay results showed that the weight growth rate of grass carp in the strain S3 oral group (16.01%) and strain S3 immersion group (16.44%) was significantly higher than those of the control group (8.61%). At the same time, the activities of ACP, AKP, CAT and GSH-Px in the serum of grass carp in oral and immersion groups were significantly higher than those of the control group. In addition, the treatment with strain S3 could significantly upregulate the expression of the antioxidant-related genes and immune-related genes Keap1, Nrf2, C3, LZM, IgM, TLR-4 and MyD-88 in grass carp tissues. The challenge test showed that strain S3 treatment significantly increased the survival rate of grass carp infected with Aeromonas hydrophila. Whole genome sequencing analysis showed that strain S3 had 16 active metabolite gene clusters, indicating that it had abundant gene resources, which provided important support for its development for fish microecological preparations. In summary, a new strain of Paenibacillus polymyxa S3 with antibacterial activity against a variety of fish pathogens was screened in this study and its probiotic function was evaluated, proving its potential value in fisheries.
Collapse
Affiliation(s)
- Shijia Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Duo Jin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Hui Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Lingzhi Jiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Jun Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Weitao Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Jie Rang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - YunLong Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, Changsha, China
| |
Collapse
|
16
|
Lu Z, Chen M, Long X, Yang H, Zhu D. Biological potential of Bacillus subtilis BS45 to inhibit the growth of Fusarium graminearum through oxidative damage and perturbing related protein synthesis. Front Microbiol 2023; 14:1064838. [PMID: 36891382 PMCID: PMC9987035 DOI: 10.3389/fmicb.2023.1064838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/31/2023] [Indexed: 02/22/2023] Open
Abstract
Fusarium root rot (FRR) caused by Fusarium graminearum poses a threat to global food security. Biological control is a promising control strategy for FRR. In this study, antagonistic bacteria were obtained using an in-vitro dual culture bioassay with F. graminearum. Molecular identification of the bacteria based on the 16S rDNA gene and whole genome revealed that the species belonged to the genus Bacillus. We evaluated the strain BS45 for its mechanism against phytopathogenic fungi and its biocontrol potential against FRR caused by F. graminearum. A methanol extract of BS45 caused swelling of the hyphal cells and the inhibition of conidial germination. The cell membrane was damaged and the macromolecular material leaked out of cells. In addition, the mycelial reactive oxygen species level increased, mitochondrial membrane potential decreased, oxidative stress-related gene expression level increased and oxygen-scavenging enzyme activity changed. In conclusion, the methanol extract of BS45 induced hyphal cell death through oxidative damage. A transcriptome analysis showed that differentially expressed genes were significantly enriched in ribosome function and various amino acid transport pathways, and the protein contents in cells were affected by the methanol extract of BS45, indicating that it interfered with mycelial protein synthesis. In terms of biocontrol capacity, the biomass of wheat seedlings treated with the bacteria increased, and the BS45 strain significantly inhibited the incidence of FRR disease in greenhouse tests. Therefore, strain BS45 and its metabolites are promising candidates for the biological control of F. graminearum and its related root rot diseases.
Collapse
Affiliation(s)
- Ziyun Lu
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Meiling Chen
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Xinyi Long
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Huilin Yang
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China
| | - Du Zhu
- Key Laboratory of Protection and Utilization of Subtropic Plant Resources of Jiangxi Province, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Bioprocess Engineering of Jiangxi Province, Jiangxi Science and Technology Normal University, Nanchang, China
| |
Collapse
|
17
|
Singh RR, Wesemael WML. Endophytic Paenibacillus polymyxa LMG27872 inhibits Meloidogyne incognita parasitism, promoting tomato growth through a dose-dependent effect. FRONTIERS IN PLANT SCIENCE 2022; 13:961085. [PMID: 36186028 PMCID: PMC9516289 DOI: 10.3389/fpls.2022.961085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
The root-knot nematode, Meloidogyne incognita, is a major pest in tomato production. Paenibacillus polymyxa, which is primarily found in soil and colonizing roots, is considered a successful biocontrol organism against many pathogens. To evaluate the biocontrol capacity of P. polymyxa LMG27872 against M. incognita in tomato, experiments were conducted both in vitro and in vivo. A dose-response effect [30, 50, and 100% (108 CFU/mL)] of bacterial suspensions (BSs) on growth and tomato susceptibility to M. incognita with soil drenching as a mode of application was first evaluated. The results show that the biological efficacy of P. polymyxa LMG27872 against M. incognita parasitism in tomato was dose-dependent. A significantly reduced number of galls, egg-laying females (ELF), and second-stage juveniles (J2) were observed in BS-treated plants, in a dose-dependent manner. The effect of P. polymyxa on tomato growth was also dose-dependent. A high dose of BSs had a negative effect on growth; however, this negative effect was not observed when the BS-treated plants were challenged with M. incognita, indicating tolerance or a defense priming mechanism. In subsequent in vivo experiments, the direct effect of BSs was evaluated on J2 mortality and egg hatching of M. incognita. The effect of BS on J2 mortality was observed from 12 to 24 h, whereby M. incognita J2 was significantly inhibited by the BS treatment. The effect of P. polymyxa on M. incognita egg hatching was also dependent on the BS dose. The results show a potential of P. polymyxa LMG27872 to protect plants from nematode parasitism and its implementation in integrated nematode management suitable for organic productions.
Collapse
Affiliation(s)
- Richard Raj Singh
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim M. L. Wesemael
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Plant Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| |
Collapse
|
18
|
Jia R, Chen J, Hu L, Liu X, Xiao K, Wang Y. Alcaligenes faecalis Juj3 alleviates Plasmodiophora brassicae stress to cabbage via promoting growth and inducing resistance. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.942409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clubroot is a devastating disease threatening global cruciferous vegetable production caused by Plasmodiophora brassicae (Pb). We have evaluated the positive effects of the Alcaligenes faecalis Juj3 on cabbage growth promotion and Pb stress alleviation through pot and field experiments. The Juj3 strain was isolated from a healthy cabbage rhizosphere with growth-promoting characteristics and was identified as A. faecalis based on morphological traits and phylogeny. Seed germination assays revealed that Juj3 inoculation enhances cabbage bud shoot and root growth. In pot experiments, inoculation with Juj3 fermentation powder at cabbage sowing dates significantly improved the seedling biomass. Combining seed treatments with root irrigation after transplanting considerably reduced the clubroot disease index and resulted in appreciable biocontrol efficacy (83.7%). Gene expression analyses of cabbage after Juj3 inoculation showed that PR2 and EIN3 expression were significantly up-regulated. Physiologically, Juj3 inoculation enhanced cabbage chlorophyll content and root activity in a normal environment. Irrespective of whether plants were under normal environment or Pb stresses, Juj3 improved photosynthesis. Field trial analyses revealed that Juj3 exhibits satisfactory biocontrol efficacy in cabbage (51.4%) and Chinese cabbage (37.7%). Moreover, Juj3 could also enhance cabbage and Chinese cabbage biomass to improve the yield quality. These findings pave the way for future use of A. faecalis as biocontrol agents for clubroot and reveal the great potential of the rhizobacterium for plant growth-promoting applications in agriculture and horticulture.
Collapse
|
19
|
Xu W, Yang Q, Xie X, Goodwin PH, Deng X, Zhang J, Sun R, Wang Q, Xia M, Wu C, Yang L. Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat. BIOLOGY 2022; 11:778. [PMID: 35625506 PMCID: PMC9138608 DOI: 10.3390/biology11050778] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/08/2022] [Accepted: 05/18/2022] [Indexed: 12/02/2022]
Abstract
Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion.
Collapse
Affiliation(s)
- Wen Xu
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Qian Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xia Xie
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Paul H. Goodwin
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G2W1, Canada;
| | - Xiaoxu Deng
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Jie Zhang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Runhong Sun
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Qi Wang
- College of Plant Protection, China Agricultural University, Beijing 100083, China;
| | - Mingcong Xia
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Chao Wu
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| | - Lirong Yang
- Henan International Joint Laboratory of Crop Protection, Henan Biopesticide Engineering Research Center, Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (W.X.); (Q.Y.); (X.X.); (X.D.); (J.Z.); (R.S.); (M.X.); (C.W.)
| |
Collapse
|
20
|
Xiaofang L, Wenhuan H, Xingfu T, Yanhong Z. Identification of the roselle root rot pathogen and its sensitivity to different fungicides. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Didak Ljubas B, Novak M, Trontel A, Rajković A, Kelemen Z, Marđetko N, Grubišić M, Pavlečić M, Tominac VP, Šantek B. Production of Different Biochemicals by Paenibacillus polymyxa DSM 742 From Pretreated Brewers' Spent Grains. Front Microbiol 2022; 13:812457. [PMID: 35308344 PMCID: PMC8931609 DOI: 10.3389/fmicb.2022.812457] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Brewers' spent grains (BSG) are a by-product of the brewing industry that is mainly used as feedstock; otherwise, it has to be disposed according to regulations. Due to the high content of glucose and xylose, after pretreatment and hydrolysis, it can be used as a main carbohydrate source for cultivation of microorganisms for production of biofuels or biochemicals like 2,3-butanediol or lactate. 2,3-Butanediol has applications in the pharmaceutical or chemical industry as a precursor for varnishes and paints or in the food industry as an aroma compound. So far, Klebsiella pneumoniae, Serratia marcescens, Clostridium sp., and Enterobacter aerogenes are being used and investigated in different bioprocesses aimed at the production of 2,3-butanediol. The main drawback is bacterial pathogenicity which complicates all production steps in laboratory, pilot, and industrial scales. In our study, a gram-positive GRAS bacterium Paenibacillus polymyxa DSM 742 was used for the production of 2,3-butanediol. Since this strain is very poorly described in literature, bacterium cultivation was performed in media with different glucose and/or xylose concentration ranges. The highest 2,3-butanediol concentration of 18.61 g l-1 was achieved in medium with 70 g l-1 of glucose during 40 h of fermentation. In contrast, during bacterium cultivation in xylose containing medium there was no significant 2,3-butanediol production. In the next stage, BSG hydrolysates were used for bacterial cultivation. P. polymyxa DSM 742 cultivated in the liquid phase of pretreated BSG produced very low 2,3-butanediol and ethanol concentrations. Therefore, this BSG hydrolysate has to be detoxified in order to remove bacterial growth inhibitors. After detoxification, bacterium cultivation resulted in 30 g l-1 of lactate, while production of 2,3-butanediol was negligible. The solid phase of pretreated BSG was also used for bacterium cultivation after its hydrolysis by commercial enzymes. In these cultivations, P. polymyxa DSM 742 produced 9.8 g l-1 of 2,3-butanediol and 3.93 g l-1 of ethanol. On the basis of the obtained results, it can be concluded that different experimental setups give the possibility of directing the metabolism of P. polymyxa DSM 742 toward the production of either 2,3-butanediol and ethanol or lactate.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Božidar Šantek
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
23
|
Costa A, Corallo B, Amarelle V, Stewart S, Pan D, Tiscornia S, Fabiano E. Paenibacillus sp. Strain UY79, Isolated from a Root Nodule of Arachis villosa, Displays a Broad Spectrum of Antifungal Activity. Appl Environ Microbiol 2022; 88:e0164521. [PMID: 34757818 PMCID: PMC8788682 DOI: 10.1128/aem.01645-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
A nodule-inhabiting Paenibacillus sp. strain (UY79) isolated from wild peanut (Arachis villosa) was screened for its antagonistic activity against diverse fungi and oomycetes (Botrytis cinerea, Fusarium verticillioides, Fusarium oxysporum, Fusarium graminearum, Fusarium semitectum, Macrophomina phaseolina, Phomopsis longicolla, Pythium ultimum, Phytophthora sojae, Rhizoctonia solani, Sclerotium rolfsii, and Trichoderma atroviride). The results obtained show that Paenibacillus sp. UY79 was able to antagonize these fungi/oomycetes and that agar-diffusible compounds and volatile compounds (different from HCN) participate in the antagonism exerted. Acetoin, 2,3-butanediol, and 2-methyl-1-butanol were identified among the volatile compounds produced by strain UY79 with possible antagonistic activity against fungi/oomycetes. Paenibacillus sp. strain UY79 did not affect symbiotic association or growth promotion of alfalfa plants when coinoculated with rhizobia. By whole-genome sequence analysis, we determined that strain UY79 is a new species of Paenibacillus within the Paenibacillus polymyxa complex. Diverse genes putatively involved in biocontrol activity were identified in the UY79 genome. Furthermore, according to genome mining and antibiosis assays, strain UY79 would have the capability to modulate the growth of bacteria commonly found in soil/plant communities. IMPORTANCE Phytopathogenic fungi and oomycetes are responsible for causing devastating losses in agricultural crops. Therefore, there is enormous interest in the development of effective and complementary strategies that allow the control of the phytopathogens, reducing the input of agrochemicals in croplands. The discovery of new strains with expanded antifungal activities and with a broad spectrum of action is challenging and of great future impact. Diverse strains belonging to the P. polymyxa complex have been reported to be effective biocontrol agents. Results presented here show that the novel discovered strain of Paenibacillus sp. presents diverse traits involved in antagonistic activity against a broad spectrum of pathogens and is a potential and valuable strain to be further assessed for the development of biofungicides.
Collapse
Affiliation(s)
- Andrés Costa
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Belén Corallo
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Vanesa Amarelle
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| | - Silvina Stewart
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa Cultivos de Secano. Estación Experimental La Estanzuela, Colonia, Uruguay
| | - Dinorah Pan
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Susana Tiscornia
- Sección Micología, Facultad de Ciencias-Universidad de la República, Montevideo, Uruguay
| | - Elena Fabiano
- Biochemistry and Microbial Genomics Department, Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura, Montevideo, Uruguay
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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; 10:1485. [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.
Collapse
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.)
| |
Collapse
|
26
|
Ha J, Gao Y, Zhang R, Li K, Zhang Y, Niu X, Chen X, Luo K, Chen Y. Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava ( Manihot esculenta Crantz) Genotypes. Front Microbiol 2021; 12:729022. [PMID: 34659156 PMCID: PMC8515189 DOI: 10.3389/fmicb.2021.729022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.
Collapse
Affiliation(s)
- Jingwen Ha
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yu Gao
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Rui Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Ke Li
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yijie Zhang
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xiaolei Niu
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kai Luo
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| | - Yinhua Chen
- Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou, China
| |
Collapse
|
27
|
Yu J, Yang M, Han J, Pang X. Fungal and mycotoxin occurrence, affecting factors, and prevention in herbal medicines: a review. TOXIN REV 2021. [DOI: 10.1080/15569543.2021.1925696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jingsheng Yu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| | - Meihua Yang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianping Han
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| | - Xiaohui Pang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| |
Collapse
|
28
|
Liu M, Zhao X, Li X, Wu X, Zhou H, Gao Y, Zhang X, Zhou F. Antagonistic Effects of Delia antiqua (Diptera: Anthomyiidae)-Associated Bacteria Against Four Phytopathogens. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:597-610. [PMID: 33547790 DOI: 10.1093/jee/toab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Indexed: 06/12/2023]
Abstract
Recent studies have revealed multiple roles of insect-associated microbes such as lignin degradation, entomopathogen inhibition, and antibiotic production. These functions improve insect host fitness, and provide a novel source of discovering beneficial microbes for industrial and agricultural production. Previously published research found that in the symbiosis formed by the dipteran pest Delia antiqua (Meigen) (Diptera: Anthomyiidae) and its associated bacteria, the bacteria showed effective inhibition of one fungal entomopathogen, Beauveria bassiana. The antifungal activity of those associated bacteria indicates their potential to be used as biocontrol agents for fungal phytopathogens. In this study, we first isolated and identified bacteria associated with D. antiqua using a culture-dependent method. Second, we tested the antifungal activity of these bacteria against four phytopathogens including Fusarium moniliforme, Botryosphaeria dothidea, and two Fusarium oxysporum strains using the dual-culture method. In total, 74 species belonging to 30 genera, 23 families, eight classes, and four phyla were isolated and identified. Among those bacteria, Ochrobactrum anthropi, Morganella morganii, Arthrobacter sp. 3, and Acinetobacter guillouiae showed significant volatile inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum, respectively. Moreover, bacteria including Rhodococcus equi, Leucobacter aridicollis, Paenibacillus sp. 3, and Lampropedia sp. showed significant contact inhibition activity against F. moniliforme, B. dothidea, and both F. oxysporum. Our work provides a new source for discovering biocontrol agents against phytopathogens.
Collapse
Affiliation(s)
- Mei Liu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | - Xiaoyan Zhao
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | | | - Xiaoqing Wu
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | - Hongzi Zhou
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | - Yunxiao Gao
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | - Xinjian Zhang
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| | - Fangyuan Zhou
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan, China
| |
Collapse
|
29
|
Langendries S, Goormachtig S. Paenibacillus polymyxa, a Jack of all trades. Environ Microbiol 2021; 23:5659-5669. [PMID: 33684235 DOI: 10.1111/1462-2920.15450] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 02/05/2023]
Abstract
The bacterium Paenibacillus polymyxa is found naturally in diverse niches. Microbiome analyses have revealed enrichment in the genus Paenibacillus in soils under different adverse conditions, which is often accompanied by improved growth conditions for residing plants. Furthermore, Paenibacillus is a member of the core microbiome of several agriculturally important crops, making its close association with plants an interesting research topic. This review covers the versatile interaction possibilities of P. polymyxa with plants and its applicability in industry and agriculture. Thanks to its array of produced compounds and traits, P. polymyxa is likely an efficient plant growth-promoting bacterium, with the potential of biofertilization, biocontrol and protection against abiotic stresses. By contrast, cases of phytotoxicity of P. polymyxa have been described as well, in which growth conditions seem to play a key role. Because of its adjustable character, we propose this bacterial species as an outstanding model for future studies on host-microbe communications and on the manner how the environment can influence these interactions.
Collapse
Affiliation(s)
- Sarah Langendries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium.,Center for Plant Systems Biology, VIB, Ghent, 9052, Belgium
| |
Collapse
|
30
|
Zhai Y, Zhu JX, Tan TM, Xu JP, Shen AR, Yang XB, Li JL, Zeng LB, Wei L. Isolation and characterization of antagonistic Paenibacillus polymyxa HX-140 and its biocontrol potential against Fusarium wilt of cucumber seedlings. BMC Microbiol 2021; 21:75. [PMID: 33676418 PMCID: PMC7936408 DOI: 10.1186/s12866-021-02131-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/09/2021] [Indexed: 11/18/2022] Open
Abstract
Objective The aim of this study is to evaluate the efficacy of the strain Paenibacillus polymyxa HX-140, isolated from the rhizosphere soil of rape, to control Fusarium wilt of cucumber seedlings caused by Fusarium oxysporum f. sp. cucumerinum. Results Strain HX-140 was able to produce protease, cellulase, β-1,3-glucanase and antifungal volatile organic compounds. An in vitro dual culture test showed that strain HX-140 exhibited broad spectrum antifungal activity against soil-borne plant pathogenic fungi. Strain HX-140 also reduced the infection of Fusarium wilt of cucumber seedlings by 55.6% in a greenhouse pot experiment. A field plot experiment confirmed the biocontrol effects and further revealed that antifungal activity was positively correlated with inoculum size by the root-irrigation method. Here, inoculums at 106 107 and 108 cfu/mL of HX-140 bacterial suspension reduced the incidence of Fusarium wilt of cucumber seedling by 19.5, 41.1, and 50.9%, respectively. Conclusions Taken together, our results suggest that P. polymyxa HX-140 has significant potential in the control of Fusarium wilt and possibly other fungal diseases of cucumber. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02131-3.
Collapse
Affiliation(s)
- Yang Zhai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China
| | - Jiu-Xiang Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China.,Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Tai-Meng Tan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China.,Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Jian-Ping Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China
| | - Ai-Rong Shen
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China.,Hunan Academy of Forestry, Changsha, 410004, China
| | - Xie-Bin Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China.,Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Ji-Lie Li
- Hunan Provincial Key Laboratory of Forestry Biotechnology, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Liang-Bin Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No.348 Xianjiahu West Road, Changsha, 410205, Hunan, China.
| | - Lin Wei
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, No.726 Yuanda 2nd Road, Changsha, 410125, Hunan, China.
| |
Collapse
|
31
|
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: 24] [Impact Index Per Article: 8.0] [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.
Collapse
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
| |
Collapse
|
32
|
Soni R, Nanjani S, Keharia H. Genome analysis reveals probiotic propensities of Paenibacillus polymyxa HK4. Genomics 2020; 113:861-873. [PMID: 33096257 DOI: 10.1016/j.ygeno.2020.10.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/24/2020] [Accepted: 10/16/2020] [Indexed: 12/14/2022]
Abstract
The legislations on the usage of antibiotics as growth promoters and prophylactic agents have compelled to develop alternative tools to upsurge the animal protection and contain antibiotic usage. Probiotics have emerged as an effective antibiotic substitute in animal farming. The present study explores the probiotic perspective of Paenibacillus polymyxa HK4 interlinking the genotypic and phenotypic characteristics. The draft genome of HK4 revealed the presence of ORFs encoding the functions associated with tolerance to gastrointestinal stress and adhesion. The biosynthetic gene clusters encoding non-ribosomally synthesized peptides, polyketides and lanthipeptides such as fusaricidin, tridecaptin, polymyxin, paenilan and paenibacillin were annotated in HK4 genome. The strain harbored the chromosomal gene conferring the resistance to lincosamides. No functional gene encoding virulence or toxins could be identified in the genome of HK4. The genome analysis data was complemented by the in vitro experiments confirming its survival during gastrointestinal transit, antimicrobial potential and antibiotic sensitivity. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The draft-genome sequence of Paenibacillus polymyxa HK4 has been deposited as whole-genome shotgun project at GenBank under the accession number PRJNA603023.
Collapse
Affiliation(s)
- Riteshri Soni
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India
| | - Sandhya Nanjani
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India
| | - Hareshkumar Keharia
- Post Graduate Department of Biosciences, UGC Center of Advanced Study, Sardar Patel University, Vadtal road, Bakrol 388315, Gujarat, India.
| |
Collapse
|
33
|
Zhou L, Zhang T, Tang S, Fu X, Yu S. Pan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol. Antonie van Leeuwenhoek 2020; 113:1539-1558. [PMID: 32816227 DOI: 10.1007/s10482-020-01461-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.
Collapse
Affiliation(s)
- Liangliang Zhou
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Ting Zhang
- College of Bioscience and Engineering, Jiangxi Agricultural university, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Shan Tang
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China
| | - Xueqin Fu
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, Jiangxi, People's Republic of China
| | - Shuijing Yu
- Faculty of Resource and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, Jiangxi, People's Republic of China.
| |
Collapse
|