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Khan A, Singh AV, Gautam SS, Agarwal A, Punetha A, Upadhayay VK, Kukreti B, Bundela V, Jugran AK, Goel R. Microbial bioformulation: a microbial assisted biostimulating fertilization technique for sustainable agriculture. FRONTIERS IN PLANT SCIENCE 2023; 14:1270039. [PMID: 38148858 PMCID: PMC10749938 DOI: 10.3389/fpls.2023.1270039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/03/2023] [Indexed: 12/28/2023]
Abstract
Addressing the pressing issues of increased food demand, declining crop productivity under varying agroclimatic conditions, and the deteriorating soil health resulting from the overuse of agricultural chemicals, requires innovative and effective strategies for the present era. Microbial bioformulation technology is a revolutionary, and eco-friendly alternative to agrochemicals that paves the way for sustainable agriculture. This technology harnesses the power of potential microbial strains and their cell-free filtrate possessing specific properties, such as phosphorus, potassium, and zinc solubilization, nitrogen fixation, siderophore production, and pathogen protection. The application of microbial bioformulations offers several remarkable advantages, including its sustainable nature, plant probiotic properties, and long-term viability, positioning it as a promising technology for the future of agriculture. To maintain the survival and viability of microbial strains, diverse carrier materials are employed to provide essential nourishment and support. Various carrier materials with their unique pros and cons are available, and choosing the most appropriate one is a key consideration, as it substantially extends the shelf life of microbial cells and maintains the overall quality of the bioinoculants. An exemplary modern bioformulation technology involves immobilizing microbial cells and utilizing cell-free filters to preserve the efficacy of bioinoculants, showcasing cutting-edge progress in this field. Moreover, the effective delivery of bioformulations in agricultural fields is another critical aspect to improve their overall efficiency. Proper and suitable application of microbial formulations is essential to boost soil fertility, preserve the soil's microbial ecology, enhance soil nutrition, and support crop physiological and biochemical processes, leading to increased yields in a sustainable manner while reducing reliance on expensive and toxic agrochemicals. This manuscript centers on exploring microbial bioformulations and their carrier materials, providing insights into the selection criteria, the development process of bioformulations, precautions, and best practices for various agricultural lands. The potential of bioformulations in promoting plant growth and defense against pathogens and diseases, while addressing biosafety concerns, is also a focal point of this study.
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Affiliation(s)
- Amir Khan
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Ajay Veer Singh
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Shiv Shanker Gautam
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Aparna Agarwal
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Arjita Punetha
- School of Environmental Science and Natural Resource, Dehradun, Uttarakhand, India
| | - Viabhav Kumar Upadhayay
- Department of Microbiology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agriculture University, Samastipur, India
| | - Bharti Kukreti
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Vindhya Bundela
- Biofortification Lab, Department of Microbiology, College of Basic Sciences and Humanities, Govind Ballabh Pant University of Agriculture and Technology, U.S. Nagar, Uttarakhand, India
| | - Arun Kumar Jugran
- G. B. Pant National Institute of Himalayan Environment (GBPNIHE), Garhwal Regional Centre, Srinager, Uttarakhand, India
| | - Reeta Goel
- Department of Biotechnology, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
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Schnyder A, Eberl L, Agnoli K. Investigating the Biocontrol Potential of the Natural Microbiota of the Apple Blossom. Microorganisms 2022; 10:microorganisms10122480. [PMID: 36557734 PMCID: PMC9784478 DOI: 10.3390/microorganisms10122480] [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: 11/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Erwinia amylovora, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident microbiota of the apple blossom in combatting plant disease-causing organisms, with a focus on controlling fire blight. We obtained 538 isolates from sites around Canton Zurich, which we tested for activity against Pectobacterium carotovorum and E. amylovora. We also evaluated the isolates' activity against oomycete and fungal pathogens. Nine isolates showed activity against P. carotovorum, and eight of these against E. amylovora. Furthermore, 117 showed antifungal, and 161 anti-oomycete, activity. We assigned genera and in some cases species to 238 of the isolates by sequencing their 16S RNA-encoding gene. Five strains showed activity against all pathogens and were tested in a detached apple model for anti-E. amylovora activity. Of these five strains, two were able to antagonize E. amylovora, namely Bacillus velezensis #124 and Pantoea agglomerans #378. We sequenced the P. agglomerans #378 genome and analyzed it for secondary metabolite clusters using antiSMASH, revealing the presence of a putative bacteriocin cluster. We also showed that B. velezensis #124 exhibits strong activity against three different fungi and two oomycetes in vitro, suggesting a broader capacity for biocontrol. Our results showcase the protective potential of the natural apple blossom microbiota. We isolated two candidate biocontrol strains from apple blossoms, suggesting that they might persist at the most common entry point for the causative agent of fire blight. Furthermore, they are probably already part of the human diet, suggesting they might be safe for consumption, and thus are promising candidates for biocontrol applications.
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Affiliation(s)
- Anya Schnyder
- Institut für Veterinärbakteriologie, Universität Bern, 3001 Bern, Switzerland
| | - Leo Eberl
- Department of Microbiology, Institute of Plant and Microbial Biology, University of Zürich, 8008 Zurich, Switzerland
| | - Kirsty Agnoli
- Department of Microbiology, Institute of Plant and Microbial Biology, University of Zürich, 8008 Zurich, Switzerland
- Correspondence:
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Kim SG, Lee SB, Jo SJ, Cho K, Park JK, Kwon J, Giri SS, Kim SW, Kang JW, Jung WJ, Lee YM, Roh E, Park SC. Phage Cocktail in Combination with Kasugamycin as a Potential Treatment for Fire Blight Caused by Erwinia amylovora. Antibiotics (Basel) 2022; 11:1566. [PMID: 36358221 PMCID: PMC9686651 DOI: 10.3390/antibiotics11111566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 08/27/2023] Open
Abstract
Recently, there has been an increasing number of blight disease reports associated with Erwinia amylovora and Erwinia pyrifoliae in South Korea. Current management protocols that have been conducted with antibiotics have faced resistance problems and the outbreak has not decreased. Because of this concern, the present study aimed to provide an alternative method to control the invasive fire blight outbreak in the nation using bacteriophages (phages) in combination with an antibiotic agent (kasugamycin). Among 54 phage isolates, we selected five phages, pEa_SNUABM_27, 31, 32, 47, and 48, based on their bacteriolytic efficacy. Although only phage pEa_SNUABM_27 showed host specificity for E. amylovora, all five phages presented complementary lytic potential that improved the host infectivity coverage of each phage All the phages in the cocktail solution could lyse phage-resistant strains. These strains had a decreased tolerance to the antibiotic kasugamycin, and a synergistic effect of phages and antibiotics was demonstrated both in vitro and on immature wound-infected apples. It is noteworthy that the antibacterial effect of the phage cocktail or phage cocktail-sub-minimal inhibitory concentration (MIC) of kasugamycin was significantly higher than the kasugamycin at the MIC. The selected phages were experimentally stable under environmental factors such as thermal or pH stress. Genomic analysis revealed these are novel Erwinia-infecting phages, and did not encode antibiotic-, virulence-, or lysogenic phage-related genes. In conclusion, we suggest the potential of the phage cocktail and kasugamycin combination as an effective strategy that would minimize the use of antibiotics, which are being excessively used in order to control fire blight pathogens.
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Affiliation(s)
- Sang-Guen Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sung-Bin Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Su-Jin Jo
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kevin Cho
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jung-Kum Park
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Sang-Wha Kim
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Jeong-Woo Kang
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Won-Joon Jung
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Young-Min Lee
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Eunjung Roh
- Crop Protection Division, National Institute of Agriculture Sciences, Rural Development Administration, Wanju 55365, Korea
| | - Se-Chang Park
- Laboratory of Aquatic Biomedicine, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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Agbavor C, Mirza BS, Wait A. The Effects of Phyllosphere Bacteria on Plant Physiology and Growth of Soybean Infected with Pseudomonas syringae. PLANTS (BASEL, SWITZERLAND) 2022; 11:2634. [PMID: 36235499 PMCID: PMC9571934 DOI: 10.3390/plants11192634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Phyllosphere bacteria are an important determinant of plant growth and resistance to pathogens. However, the efficacy of phyllosphere bacteria in regulating infection of Pseudomonas syringae pv. glycinea (Psg) and its influence on soybean growth and physiology is unknown. In a greenhouse study, we assessed the influence of a phyllosphere bacterial consortium (BC) of 13 species isolated from field-grown soybean leaves on uninfected and deliberately Psg infected soybean plants. We measured Psg density on infected leaves with and without the application of the BC. The BC application resulted in a significant reduction in Psg cells. We also measured plant biomass, nodule mass and number, gas exchange, and leaf chlorophyll and nitrogen in four treatment groups: control plants, plants with a BC and no infection (BC), plants with BC and infected with Psg (BC + Psg), and plants infected with Psg alone. For all variables, plants infected with Psg alone showed significant reduction in measured variables compared to both BC treatments. Therefore, the bacterial consortium was effective in controlling the negative effects of Psg on growth and physiology. The BC treatment sometimes resulted in increases in measured variables such as plant biomass, nodule numbers, and leaf chlorophyll as compared to control and BC + Psg treatments. Overall, the positive influence of BC treatment on plant growth and physiology highlights its potential applications to increase crop yield and control bacterial pathogens.
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Affiliation(s)
| | - Babur S. Mirza
- Correspondence: ; Tel.: +1-417-836-5062; Fax: +1-417-836-4204
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Shen Z, Thomashow LS, Ou Y, Tao C, Wang J, Xiong W, Liu H, Li R, Shen Q, Kowalchuk GA. Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt. Research (Wash D C) 2022; 2022:9818073. [PMID: 36204250 PMCID: PMC9513836 DOI: 10.34133/2022/9818073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/22/2022] [Indexed: 11/08/2022] Open
Abstract
Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.
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Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
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6
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Barbé S, Figàs-Segura À, Benada M, Navarro-Herrero I, Sampaio TM, Biosca EG, Marco-Noales E. Plant-associated microbiota as a source of antagonistic bacteria against the phytopathogen Erwinia amylovora. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:559-569. [PMID: 35403335 DOI: 10.1111/1758-2229.13064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Control of bacterial plant diseases is a major concern, as they affect economically important species and spread easily, such as the case of fire blight of rosaceous caused by Erwinia amylovora. In the search for alternatives to the use of agrochemicals and antibiotics, this work presents a screening of natural bacterial antagonists of this relevant and devastating phytopathogen. We recovered bacterial isolates from different plant tissues and geographical origins and then selected those with the strongest ability to reduce fire blight symptoms ex vivo and remarkable in vitro antagonistic activity against E. amylovora. None of them elicited a hypersensitivity reaction in tobacco leaves, most produced several hydrolytic enzymes and presented other biocontrol and/or plant growth-promoting activities, such as siderophore production and phosphate solubilization. These isolates, considered as biocontrol candidates, were identified by 16S rRNA sequencing as Pseudomonas rhizosphaerae, Curtobacterium flaccumfaciens, Enterobacter cancerogenus, Pseudomonas azotoformans, Rosenbergiella epipactidis and Serratia plymuthica. This is the first time that the last five bacterial species are reported to have biocontrol potential against E. amylovora.
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Affiliation(s)
- Silvia Barbé
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Àngela Figàs-Segura
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - M'hamed Benada
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
- Faculty of Natural Sciences, Earth and the Universe, 8 Mai 1945 University, Guelma, Algeria
| | - Inmaculada Navarro-Herrero
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Telma Maria Sampaio
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
| | - Elena G Biosca
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Valencia, Spain
| | - Ester Marco-Noales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), CV-315 km 10.7, 46113 Moncada, Valencia, Spain
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Priority Effects in the Apple Flower Determine If the Siderophore Desferrioxamine Is a Virulence Factor for Erwinia amylovora CFBP1430. Appl Environ Microbiol 2022; 88:e0243321. [PMID: 35285239 PMCID: PMC9004392 DOI: 10.1128/aem.02433-21] [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] [Indexed: 11/20/2022] Open
Abstract
Iron is crucial for bacterial growth and virulence. Under iron-deficiency bacteria produce siderophores, iron chelators that facilitate the iron uptake into the cell via specific receptors. Erwinia amylovora, the causative agent of fire blight, produces hydroxamate-type desferrioxamine siderophores (DFO). The presented study reassesses the impact of DFO as a virulence factor of E. amylovora during its epiphytic phase on the apple flower. When inoculated in semisterile Golden Delicious flowers no difference in replication and induction of calyx necrosis could be observed between E. amylovora CFBP1430 siderophore synthesis (DfoA) or uptake (FoxR receptor) mutants and the parental strain. In addition, mutant strains only weakly induced a foxR promoter-gfpmut2 reporter construct in the flowers. When analyzing the replication of the receptor mutant in apple flowers harboring an established microbiome, either naturally, in case of orchard flowers, or by pre-inoculation of semisterile greenhouse flowers, it became evident that the mutant strain had a significantly reduced replication compared to the parental strain. The results suggest that apple flowers per se are not an iron-limiting environment for E. amylovora and that DFO is an important competition factor for the pathogen in precolonized flowers. IMPORTANCE Desferrioxamine is a siderophore produced by the fire blight pathogen E. amylovora under iron-limited conditions. In the present study, no or only weak induction of an iron-regulated promoter-GFP reporter was observed on semisterile apple flowers, and siderophore synthesis or uptake (receptor) mutants exhibited colonization of the flower and necrosis induction at parental levels. Reduced replication of the receptor mutant was observed when the flowers were precolonized by microorganisms. The results indicate that apple flowers are an iron-limited environment for E. amylovora only if precolonization with microorganisms leads to iron competition. This is an important insight for the timing of biocontrol treatments.
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Bozorov TA, Toshmatov ZO, Kahar G, Zhang D, Shao H, Gafforov Y. Wild Apple-Associated Fungi and Bacteria Compete to Colonize the Larval Gut of an Invasive Wood-Borer Agrilus mali in Tianshan Forests. Front Microbiol 2021; 12:743831. [PMID: 34721341 PMCID: PMC8554297 DOI: 10.3389/fmicb.2021.743831] [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: 07/19/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
The gut microflora of insects plays important roles throughout their lives. Different foods and geographic locations change gut bacterial communities. The invasive wood-borer Agrilus mali causes extensive mortality of wild apple, Malus sieversii, which is considered a progenitor of all cultivated apples, in Tianshan forests. Recent analysis showed that the gut microbiota of larvae collected from Tianshan forests showed rich bacterial diversity but the absence of fungal species. In this study, we explored the antagonistic ability of the gut bacteria to address this absence of fungi in the larval gut. The results demonstrated that the gut bacteria were able to selectively inhibit wild apple tree-associated fungi. Among them, Pseudomonas synxantha showed strong antagonistic ability, producing antifungal compounds. Using different analytical methods, such as column chromatography, mass spectrometry, HPLC, and NMR, an antifungal compound, phenazine-1-carboxylic acid (PCA), was identified. Activity of the compound was determined by the minimum inhibitory concentration method and electron microscopy. Moreover, our study showed that the gut bacteria could originate from noninfested apple microflora during infestation. Overall, the results showed that in newly invaded locations, A. mali larvae changed their gut microbiota and adopted new gut bacteria that prevented fungal colonization in the gut.
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Affiliation(s)
- Tohir A Bozorov
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.,Laboratory of Molecular Biochemistry and Genetics, Institute of Genetics and Plants Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Zokir O Toshmatov
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.,Laboratory of Molecular Biochemistry and Genetics, Institute of Genetics and Plants Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Gulnaz Kahar
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Hua Shao
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Yusufjon Gafforov
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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Li Z, Li A, Hoyt JR, Dai W, Leng H, Li Y, Li W, Liu S, Jin L, Sun K, Feng J. Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China. Microb Biotechnol 2021; 15:469-481. [PMID: 33559264 PMCID: PMC8867990 DOI: 10.1111/1751-7915.13765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/20/2021] [Indexed: 11/28/2022] Open
Abstract
White‐nose syndrome, a disease that is caused by the psychrophilic fungus Pseudogymnoascus destructans, has threatened several North America bat species with extinction. Recent studies have shown that East Asian bats are infected with P. destructans but show greatly reduced infections. While several factors have been found to contribute to these reduced infections, the role of specific microbes in limiting P. destructans growth remains unexplored. We isolated three bacterial strains with the ability to inhibit P. destructans, namely, Pseudomonas yamanorum GZD14026, Pseudomonas brenneri XRD11711 and Pseudomonas fragi GZD14479, from bats in China. Pseudomonas yamanorum, with the highest inhibition score, was selected to extract antifungal active substance. Combining mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy analyses, we identified the active compound inhibiting P. destructans as phenazine‐1‐carboxylic acid (PCA), and the minimal inhibitory concentration (MIC) was 50.12 μg ml−1. Whole genome sequencing also revealed the existence of PCA biosynthesis gene clusters. Gas chromatography‐mass spectrometry (GC‐MS) analysis identified volatile organic compounds. The results indicated that 10 ppm octanoic acid, 100 ppm 3‐tert‐butyl‐4‐hydroxyanisole (isoprenol) and 100 ppm 3‐methyl‐3‐buten‐1‐ol (BHA) inhibited the growth of P. destructans. These results support that bacteria may play a role in limiting the growth of P. destructans on bats.
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Affiliation(s)
- Zhongle Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, 24060, USA
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Yanfei Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Wei Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Sen Liu
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Jiang Feng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
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Moffat AD, Elliston A, Patron NJ, Truman AW, Carrasco Lopez JA. A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition. Synth Biol (Oxf) 2021; 6:ysab004. [PMID: 33623825 PMCID: PMC7889406 DOI: 10.1093/synbio/ysab004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 11/20/2022] Open
Abstract
Biofoundries integrate high-throughput software and hardware platforms with synthetic biology approaches to enable the design, execution and analyses of large-scale experiments. The unique and powerful combination of laboratory infrastructure and expertise in molecular biology and automation programming, provide flexible resources for a wide range of workflows and research areas. Here, we demonstrate the applicability of biofoundries to molecular microbiology, describing the development and application of automated workflows to identify the genetic basis of growth inhibition of the plant pathogen Streptomyces scabies by a Pseudomonas strain isolated from a potato field. Combining transposon mutagenesis with automated high-throughput antagonistic assays, the workflow accelerated the screening of 2880 mutants to correlate growth inhibition with a biosynthetic gene cluster within 2 weeks.
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Affiliation(s)
- Alaster D Moffat
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Adam Elliston
- Department of Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, UK
| | - Nicola J Patron
- Department of Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Jose A Carrasco Lopez
- Department of Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, UK
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11
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Álvarez-García S, Mayo-Prieto S, Gutiérrez S, Casquero PA. Self-Inhibitory Activity of Trichoderma Soluble Metabolites and Their Antifungal Effects on Fusarium oxysporum. J Fungi (Basel) 2020; 6:E176. [PMID: 32957718 PMCID: PMC7559637 DOI: 10.3390/jof6030176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/24/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Self-inhibitory processes are a common feature shared by different organisms. One of the main mechanisms involved in these interactions regarding microorganisms is the release of toxic diffusible substances into the environment. These metabolites can exert both antimicrobial effects against other organisms as well as self-inhibitory ones. The in vitro evaluation of these effects against other organisms has been widely used to identify potential biocontrol agents against phytopathogenic microorganisms. In the present study, we performed membrane assays to compare the self-inhibitory effects of soluble metabolites produced by several Trichoderma isolates and their antifungal activity against a phytopathogenic strain of Fusarium oxysporum. The results demonstrated that Trichoderma spp. present a high self-inhibitory activity in vitro, being affected in both their growth rate and the macroscopic structure of their colonies. These effects were highly similar to those exerted against F. oxysporum in the same conditions, showing no significant differences in most cases. Consequently, membrane assays may not be very informative by themselves to assess putative biocontrol capabilities. Therefore, different methods, or a combination of antifungal and self-inhibitory experiments, could be a better approach to evaluate the potential biocontrol activity of microbial strains in order to pre-select them for further in vivo trials.
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Affiliation(s)
- Samuel Álvarez-García
- Grupo Universitario de Investigación en Ingeniería y Agricultura Sostenible (GUIIAS), Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, Avenida Portugal 41, 24071 León, Spain; (S.M.-P.); (P.A.C.)
| | - Sara Mayo-Prieto
- Grupo Universitario de Investigación en Ingeniería y Agricultura Sostenible (GUIIAS), Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, Avenida Portugal 41, 24071 León, Spain; (S.M.-P.); (P.A.C.)
| | - Santiago Gutiérrez
- Grupo Universitario de Investigación en Ingeniería y Agricultura Sostenible (GUIIAS), Área de Microbiología, Escuela de Ingeniería Agraria y Forestal, Universidad de León, Campus de Ponferrada, Avenida Astorga s/n, 24401 Ponferrada, Spain;
| | - Pedro Antonio Casquero
- Grupo Universitario de Investigación en Ingeniería y Agricultura Sostenible (GUIIAS), Instituto de Medio Ambiente, Recursos Naturales y Biodiversidad, Universidad de León, Avenida Portugal 41, 24071 León, Spain; (S.M.-P.); (P.A.C.)
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12
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Legein M, Smets W, Vandenheuvel D, Eilers T, Muyshondt B, Prinsen E, Samson R, Lebeer S. Modes of Action of Microbial Biocontrol in the Phyllosphere. Front Microbiol 2020; 11:1619. [PMID: 32760378 PMCID: PMC7372246 DOI: 10.3389/fmicb.2020.01619] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
A fast-growing field of research focuses on microbial biocontrol in the phyllosphere. Phyllosphere microorganisms possess a wide range of adaptation and biocontrol factors, which allow them to adapt to the phyllosphere environment and inhibit the growth of microbial pathogens, thus sustaining plant health. These biocontrol factors can be categorized in direct, microbe-microbe, and indirect, host-microbe, interactions. This review gives an overview of the modes of action of microbial adaptation and biocontrol in the phyllosphere, the genetic basis of the mechanisms, and examples of experiments that can detect these mechanisms in laboratory and field experiments. Detailed insights in such mechanisms are key for the rational design of novel microbial biocontrol strategies and increase crop protection and production. Such novel biocontrol strategies are much needed, as ensuring sufficient and consistent food production for a growing world population, while protecting our environment, is one of the biggest challenges of our time.
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Affiliation(s)
- Marie Legein
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Dieter Vandenheuvel
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Tom Eilers
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Babette Muyshondt
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Els Prinsen
- Laboratory for Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
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