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Dwivedi M, Singh P, Pandey AK. Botrytis fruit rot management: What have we achieved so far? Food Microbiol 2024; 122:104564. [PMID: 38839226 DOI: 10.1016/j.fm.2024.104564] [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: 12/18/2023] [Revised: 05/11/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
Botrytis cinerea is a destructive necrotrophic phytopathogen causing overwhelming diseases in more than 1400 plant species, especially fruit crops, resulting in significant economic losses worldwide. The pathogen causes rotting of fruits at both pre-harvest and postharvest stages. Aside from causing gray mold of the mature fruits, the fungus infects leaves, flowers, and seeds, which makes it a notorious phytopathogen. Worldwide, in the majority of fruit crops, B. cinerea causes gray mold. In order to effectively control this pathogen, extensive research has been conducted due to its wide host range and the huge economic losses it causes. It is advantageous to explore detection and diagnosis techniques of B. cinerea to provide the fundamental basis for mitigation strategies. Botrytis cinerea has been identified and quantified in fruit/plant samples at pre- and post-infection levels using various detection techniques including DNA markers, volatile organic compounds, qPCR, chip-digital PCR, and PCR-based nucleic acid sensors. In addition, cultural, physical, chemical, biological, and botanical methods have all been used to combat Botrytis fruit rot. This review discusses research progress made on estimating economic losses, detection and diagnosis, as well as management strategies, including cultural, physical, chemical, and biological studies on B. cinerea along with knowledge gaps and potential areas for future research.
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Affiliation(s)
- Mansi Dwivedi
- Department of Botany, DDU Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India
| | - Pooja Singh
- Department of Botany, DDU Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India.
| | - Abhay K Pandey
- Department of Botany, DDU Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India; Department of Mycology & Microbiology, Tea Research Association, North Bengal Regional R & D Center, Nagrakata, 735225, Jalpaiguri, West Bengal, India.
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Bawane P, Deshpande S, Yele S. Industrial and Pharmaceutical Applications of Microbial Diversity of Hypersaline Ecology from Lonar Soda Crater. Curr Pharm Biotechnol 2024; 25:1564-1584. [PMID: 38258768 DOI: 10.2174/0113892010265978231109085224] [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: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/04/2023] [Indexed: 01/24/2024]
Abstract
The unidentified geochemical and physiochemical characteristics of Soda Lakes across the globe make it a novel reservoir and bring attention to scientific civic for its conceivable industrial and pharmaceutical applications. In India, in the Maharashtra state, Lonar Lake is a naturally created Soda Lake by a meteorite impact. Phylogenetic data from this lake explored a diverse array of microorganisms like haloalkaliphilic bacteria and Archaea. Previously reported studies postulated the major microbial communities present in this lake ecosystem are Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria. Furthermore, it also contains Bacteroidetes, Nitrospirae, and Verrucomicrobia. This lake is also rich in phytoplankton, with the predominant presence of the Spirulina plantensis. Unique microbial strains from Lonar Lake ecosystems have fascinated consideration as a source of biological molecules with medicinal, industrial, and biotechnological potential. Recent literature revealed the isolation of antibioticproducing bacteria and alkaline proteases-producing alkaliphilic bacterium, as well as novel species of rare methylotrophs, other bacterial strains involved in producing vital enzymes, and unique actinomycetes are also reported. It indicates that the novel bacterial assemblage not reached hitherto may exist in this modified and unique ecology. This comprehensive review provides information about microbial diversity and its industrial and pharmaceutical interests that exist in Lonar Lake, which could be the future source of bioactive enzymes, biosurfactants, and biofuel and also useful in bioremediation. Furthermore, the novel species of microorganisms isolated from Lonar Lake have applications in the biosynthesis of medicines like antibiotics, antivirals, antifungals, anti-inflammatory agents, and precursors for synthesising valuable products. Data consolidated in the present review will cater to the needs of emerging industrial sectors for their commercial and therapeutic applications.
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Affiliation(s)
- Pradip Bawane
- Department of Pharmacognosy, SVKM's NMIMS, Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, Mumbai, 400056, India
- Department of Pharmacognosy, Shri Vile Parle Kelavani Mandal's Institute of Pharmacy, Dhule, Maharashtra, India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
| | - Santosh Yele
- Department of Pharmacognosy, SVKM's NMIMS, School of Pharmacy & Technology Management, Telangana Hyderabad, 509301, India
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Kharshandi F, Kayang H. Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric. Arch Microbiol 2023; 205:221. [PMID: 37149500 DOI: 10.1007/s00203-023-03565-1] [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: 01/03/2023] [Revised: 03/28/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.
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Affiliation(s)
- Ferry Kharshandi
- Microbial Ecology Laboratory, Centre for Advanced Studies in Botany, Department of Botany, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.
| | - Highland Kayang
- Microbial Ecology Laboratory, Centre for Advanced Studies in Botany, Department of Botany, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
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Lipid-rich endo-metabolites from a vertically transmitted fungal endophyte Penicillium sp. PM031 attenuate virulence factors of phytopathogenic Ralstonia solanacearum. Microbiol Res 2022; 261:127058. [DOI: 10.1016/j.micres.2022.127058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/15/2022] [Accepted: 05/01/2022] [Indexed: 11/19/2022]
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Shahzad GIR, Passera A, Maldera G, Casati P, Marcello I, Bianco PA. Biocontrol Potential of Endophytic Plant-Growth-Promoting Bacteria against Phytopathogenic Viruses: Molecular Interaction with the Host Plant and Comparison with Chitosan. Int J Mol Sci 2022; 23:6990. [PMID: 35805989 PMCID: PMC9266900 DOI: 10.3390/ijms23136990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Endophytic plant-growth-promoting bacteria (ePGPB) are interesting tools for pest management strategies. However, the molecular interactions underlying specific biocontrol effects, particularly against phytopathogenic viruses, remain unexplored. Herein, we investigated the antiviral effects and triggers of induced systemic resistance mediated by four ePGPB (Paraburkholderia fungorum strain R8, Paenibacillus pasadenensis strain R16, Pantoea agglomerans strain 255-7, and Pseudomonas syringae strain 260-02) against four viruses (Cymbidium Ring Spot Virus-CymRSV; Cucumber Mosaic Virus-CMV; Potato Virus X-PVX; and Potato Virus Y-PVY) on Nicotiana benthamiana plants under controlled conditions and compared them with a chitosan-based resistance inducer product. Our studies indicated that ePGPB- and chitosan-treated plants presented well-defined biocontrol efficacy against CymRSV and CMV, unlike PVX and PVY. They exhibited significant reductions in symptom severity while promoting plant height compared to nontreated, virus-infected controls. However, these phenotypic traits showed no association with relative virus quantification. Moreover, the tested defense-related genes (Enhanced Disease Susceptibility-1 (EDS1), Non-expressor of Pathogenesis-related genes-1 (NPR1), and Pathogenesis-related protein-2B (PR2B)) implied the involvement of a salicylic-acid-related defense pathway triggered by EDS1 gene upregulation.
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Affiliation(s)
| | | | | | | | - Iriti Marcello
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroecology, University of Milan, 20133 Milan, Italy; (G.-i.-R.S.); (A.P.); (G.M.); (P.C.); (P.A.B.)
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Passera A, Follador A, Morandi S, Miotti N, Ghidoli M, Venturini G, Quaglino F, Brasca M, Casati P, Pilu R, Bulgarelli D. Bacterial Communities in the Embryo of Maize Landraces: Relation with Susceptibility to Fusarium Ear Rot. Microorganisms 2021; 9:microorganisms9112388. [PMID: 34835513 PMCID: PMC8621305 DOI: 10.3390/microorganisms9112388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Locally adapted maize accessions (landraces) represent an untapped resource of nutritional and resistance traits for breeding, including the shaping of distinct microbiota. Our study focused on five different maize landraces and a reference commercial hybrid, showing different susceptibility to fusarium ear rot, and whether this trait could be related to particular compositions of the bacterial microbiota in the embryo, using different approaches. Our cultivation-independent approach utilized the metabarcoding of a portion of the 16S rRNA gene to study bacterial populations in these samples. Multivariate statistical analyses indicated that the microbiota of the embryos of the accessions grouped in two different clusters: one comprising three landraces and the hybrid, one including the remaining two landraces, which showed a lower susceptibility to fusarium ear rot in field. The main discriminant between these clusters was the frequency of Firmicutes, higher in the second cluster, and this abundance was confirmed by quantification through digital PCR. The cultivation-dependent approach allowed the isolation of 70 bacterial strains, mostly Firmicutes. In vivo assays allowed the identification of five candidate biocontrol strains against fusarium ear rot. Our data revealed novel insights into the role of the maize embryo microbiota and set the stage for further studies aimed at integrating this knowledge into plant breeding programs.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
- Correspondence:
| | - Alessia Follador
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Stefano Morandi
- Institute of Sciences of Food Production, Italian National Research Council, Via Celoria 2, 20133 Milan, Italy; (S.M.); (M.B.)
| | - Niccolò Miotti
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Martina Ghidoli
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Giovanni Venturini
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Via Celoria 2, 20133 Milan, Italy; (S.M.); (M.B.)
| | - Paola Casati
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Roberto Pilu
- Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy; (A.F.); (N.M.); (M.G.); (G.V.); (F.Q.); (P.C.); (R.P.)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Invergowrie DD2 5DA, UK;
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Singh P, Xie J, Qi Y, Qin Q, Jin C, Wang B, Fang W. A Thermotolerant Marine Bacillus amyloliquefaciens S185 Producing Iturin A5 for Antifungal Activity against Fusarium oxysporum f. sp. cubense. Mar Drugs 2021; 19:md19090516. [PMID: 34564178 PMCID: PMC8472358 DOI: 10.3390/md19090516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Fusarium wilt of banana (also known as Panama disease), is a severe fungal disease caused by soil-borne Fusarium oxysporum f. sp. cubense (Foc). In recent years, biocontrol strategies using antifungal microorganisms from various niches and their related bioactive compounds have been used to prevent and control Panama disease. Here, a thermotolerant marine strain S185 was identified as Bacillus amyloliquefaciens, displaying strong antifungal activity against Foc. The strain S185 possesses multiple plant growth-promoting (PGP) and biocontrol utility properties, such as producing indole acetic acid (IAA) and ammonia, assimilating various carbon sources, tolerating pH of 4 to 9, temperature of 20 to 50 °C, and salt stress of 1 to 5%. Inoculation of S185 colonized the banana plants effectively and was mainly located in leaf and root tissues. To further investigate the antifungal components, compounds were extracted, fractionated, and purified. One compound, inhibiting Foc with minimum inhibitory concentrations (MICs) of 25 μg/disk, was identified as iturin A5 by high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) and nuclear magnetic resonance (NMR). The isolated iturin, A5, resulted in severe morphological changes during spore germination and hyphae growth of Foc. These results specify that B. amyloliquefaciens S185 plays a key role in preventing the Foc pathogen by producing the antifungal compound iturin A5, and possesses potential as a cost-effective and sustainable biocontrol strain for Panama disease in the future. This is the first report of isolation of the antifungal compound iturin A5 from thermotolerant marine B. amyloliquefaciens S185.
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Affiliation(s)
- Pratiksha Singh
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
| | - Jin Xie
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
| | - Yanhua Qi
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
| | - Qijian Qin
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
| | - Cheng Jin
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Wang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (B.W.); (W.F.)
| | - Wenxia Fang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China; (P.S.); (J.X.); (Y.Q.); (Q.Q.); (C.J.)
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (B.W.); (W.F.)
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Passera A, Rossato M, Oliver JS, Battelli G, Shahzad GIR, Cosentino E, Sage JM, Toffolatti SL, Lopatriello G, Davis JR, Kaiser MD, Delledonne M, Casati P. Characterization of Lysinibacillus fusiformis strain S4C11: In vitro, in planta, and in silico analyses reveal a plant-beneficial microbe. Microbiol Res 2020; 244:126665. [PMID: 33340794 DOI: 10.1016/j.micres.2020.126665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/09/2020] [Accepted: 11/27/2020] [Indexed: 01/10/2023]
Abstract
Despite sharing many of the traits that have allowed the genus Bacillus to gain recognition for its agricultural relevance, the genus Lysinibacillus is not as well-known and studied. The present study employs in vitro, in vivo, in planta, and in silico approaches to characterize Lysinibacillus fusiformis strain S4C11, isolated from the roots of an apple tree in northern Italy. The in vitro and in vivo assays demonstrated that strain S4C11 possesses an antifungal activity against different fungal pathogens, and is capable of interfering with the germination of Botrytis cinerea conidia, as well as of inhibiting its growth through the production of volatile organic molecules. In planta assays showed that the strain possesses the ability to promote plant growth, that is not host-specific, both in controlled conditions and in a commercial nursery. Biocontrol assays carried out against phytopathogenic viruses gave contrasting results, suggesting that the strain does not activate the host's defense pathways. The in silico analyses were carried out by sequencing the genome of the strain through an innovative approach that combines Illumina and High-Definition Mapping methods, allowing the reconstruction of a main chromosome and two plasmids from strain S4C11. The analysis of the genes encoded by the genome contributed to the characterization of the strain, detecting genes related to the biocontrol effect detected in the experimental trials.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy.
| | - Marzia Rossato
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Giovanna Battelli
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Gul-I-Rayna Shahzad
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Emanuela Cosentino
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Silvia L Toffolatti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Giulia Lopatriello
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | | | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
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Wang X, Xiao C, Ji C, Liu Z, Song X, Liu Y, Li C, Yan D, Li H, Qin Y, Liu X. Isolation and characterization of endophytic bacteria for controlling root rot disease of Chinese jujube. J Appl Microbiol 2020; 130:926-936. [PMID: 32777121 DOI: 10.1111/jam.14818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 11/29/2022]
Abstract
AIM Fusarium oxysporum is the primary pathogen causing root rot disease that severely affects cultivation of jujube fruit in the Xinjiang province of China. The aim of this study was to identify endophytic bacteria in healthy jujube organs that could effectively suppress F. oxysporum growth. METHODS AND RESULTS Different plant organs (leaves, twigs and roots) were collected from healthy Chinese jujube cultivated in southern Xinjiang province of China. The endophytic bacterium Brevibacterium halotolerans JZ7 was selected for its strong antagonistic activity and growth-promoting characteristics. Gas-chromatography mass-spectrometry analysis showed that acetoin, 2,3-butanediol and fenretinide were the three dominant volatile organic compounds produced by strain JZ7. Fenretinide strongly suppressed spore germination of F. oxysporum in vitro. Pot experiments showed that strain JZ7 colonized both the roots and rhizosphere soil of Chinese jujube and significantly reduced F. oxysporum level in jujube rhizosphere soil. CONCLUSION We demonstrated that B. halotolerans JZ7 can be developed into a biological control agent to combat root rot disease of Chinese jujube in the Xinjiang province of China. SIGNIFICANCE AND IMPACT OF THE STUDY The suggested strategy for biological control of jujube root rot disease is fully in accordance with the current principles of sustainability.
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Affiliation(s)
- X Wang
- College of Horticulture, Shandong Agricultural Universities, Taian, Shandong, China.,Ministry of Agriculture Key Laboratory of Seaweed Fertilizers, Qingdao, China
| | - C Xiao
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - C Ji
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - Z Liu
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - X Song
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - Y Liu
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - C Li
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - D Yan
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - H Li
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
| | - Y Qin
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Brightmoon Seaweed Group Co Ltd, Qingdao, China
| | - X Liu
- College of Forestry, Shandong Agricultural Universities, Taian, Shandong, China
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De Simone N, Pace B, Grieco F, Chimienti M, Tyibilika V, Santoro V, Capozzi V, Colelli G, Spano G, Russo P. Botrytis cinerea and Table Grapes: A Review of the Main Physical, Chemical, and Bio-Based Control Treatments in Post-Harvest. Foods 2020; 9:E1138. [PMID: 32824971 PMCID: PMC7555317 DOI: 10.3390/foods9091138] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/26/2022] Open
Abstract
Consumers highly appreciate table grapes for their pleasant sensory attributes and as good sources of nutritional and functional compounds. This explains the rising market and global interest in this product. Along with other fruits and vegetables, table grapes are considerably perishable post-harvest due to the growth of undesired microorganisms. Among the microbial spoilers, Botrytis cinerea represents a model organism because of its degrading potential and the huge economic losses caused by its infection. The present review provides an overview of the recent primary physical, chemical, and biological control treatments adopted against the development of B. cinerea in table grapes to extend shelf life. These treatments preserve product quality and safety. This article also focuses on the compliance of different approaches with organic and sustainable production processes. Tailored approaches include those that rely on controlled atmosphere and the application of edible coating and packaging, as well as microbial-based activities. These strategies, applied alone or in combination, are among the most promising solutions in order to prolong table grape quality during cold storage. In general, the innovative design of applications dealing with hurdle technologies holds great promise for future improvements.
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Affiliation(s)
- Nicola De Simone
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (N.D.S.); (G.C.); (G.S.); (P.R.)
| | - Bernardo Pace
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy;
| | - Francesco Grieco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), Via Prov.le Lecce-Monteroni, 73100 Lecce, Italy;
| | | | | | - Vincenzo Santoro
- A.B.A. Mediterranea s.c.a.r.l., Via Parini, 1, 74013 Ginosa, Italy;
| | - Vittorio Capozzi
- Institute of Sciences of Food Production, National Research Council of Italy (CNR), c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy;
| | - Giancarlo Colelli
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (N.D.S.); (G.C.); (G.S.); (P.R.)
| | - Giuseppe Spano
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (N.D.S.); (G.C.); (G.S.); (P.R.)
| | - Pasquale Russo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (N.D.S.); (G.C.); (G.S.); (P.R.)
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11
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Passera A, Vacchini V, Cocetta G, Shahzad GIR, Arpanahi AA, Casati P, Ferrante A, Piazza L. Towards Nutrition-Sensitive Agriculture: An evaluation of biocontrol effects, nutritional value, and ecological impact of bacterial inoculants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138127. [PMID: 32272400 DOI: 10.1016/j.scitotenv.2020.138127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
Nutrition-Sensitive Agriculture (NSA) is a novel concept in agriculture that considers not only yield, but also nutritional value of produce, sustainability of production, and ecological impact of agriculture. In accordance with its goals, NSA would benefit from applying microbial-based products as they are deemed more sustainable than their synthetic counterparts. This study characterized 3 plant-beneficial bacterial strains (Paenibacillus pasadenensis strain R16, Pseudomonas syringae strain 260-02, Bacillus amyloliquefaciens strain CC2) on their biocontrol activity and effect on nutritional and texture quality of romaine lettuce plants (Lactuca sativa) in greenhouse. The pathogens used in the trials are Rhizoctonia solani and Pythium ultimum. The obtained results indicate that strain R16 had a significant ability to cause a statistically significant reduction in the symptoms caused by both P. ultimum (reduction of 32%) and R. solani (reduction of 42%), while the other two strains showed a less efficient biocontrol ability. Indices of the nutritional quality (content in phenols, carotenoids and chlorophyll) were unaffected by the treatments, indicating that the product was equivalent to that obtained without using the bacteria, while the texture of the leaves benefits from the biocontrol treatments. In particular, the mechanical resistance of the leaves was significantly higher in non-treated plants affected by R. solani but was restored to the values of healthy plants when the bacterial inoculants were present as well. The ecological impact was evaluated by characterizing the bacterial microbiota in bulk soil, rhizosphere, and root in the presence or absence of the inoculants. The composition of the microbiota, analyzed with a Unifrac model to describe beta-diversity, was radically different in the rhizosphere and the root endosphere among treatments, while the bulk soil formed a single cluster regardless of treatment, indicating that the use of these treatments did not have an ecological impact outside of the plant.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Violetta Vacchini
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Giacomo Cocetta
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Gul-I-Rayna Shahzad
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Ali Abdohllai Arpanahi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Laura Piazza
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy.
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12
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Asaturova A, Gyrnets E, Allakhverdian V, Astakhov M, Saenko K. The study of the antifungal activity of the Bacillus subtilis BZR 336g strain under the conditions of periodic cultivation with the addition of citric acid, corn extract and some microelements. BIO WEB OF CONFERENCES 2020. [DOI: 10.1051/bioconf/20202100015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We studied the antifungal activity of the Bacillus subtilis BZR 336g strain against the test culture of the fungus Fusarium oxysporum var. orthoceras App. et Wr. BZR 6, depending on the addition of citric acid crystalline hydrate, a microelements solution and corn extract to the liquid nutrient medium. It was found that citric acid at a concentration of 15 g/l improves the bioavailability of microelements and increases antifungal activity. Corn extract and microelements without the formation of a chelate form with citric acid do not affect the fungicidal properties of B. subtilis BZR 336g. However, the corn extract at a concentration of 3 g / l increases the titer of bacteria in the liquid culture from 2 ± 0.1 × 108 to 1 ± 0.08 × 108 CFU/ml. The combined use of the studied components allowed us to achieve a significant increase in the antifungal activity of B. subtilis BZR 336g by 3.1 times. At the same time, the effect of synergism in their complex interaction was noted, which is probably due to a qualitative and quantitative change in the composition of B. subtilis BZR 336g antifungal metabolites.
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13
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Abaidullah M, Peng S, Kamran M, Song X, Yin Z. Current Findings on Gut Microbiota Mediated Immune Modulation against Viral Diseases in Chicken. Viruses 2019; 11:v11080681. [PMID: 31349568 PMCID: PMC6722953 DOI: 10.3390/v11080681] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
Chicken gastrointestinal tract is an important site of immune cell development that not only regulates gut microbiota but also maintains extra-intestinal immunity. Recent studies have emphasized the important roles of gut microbiota in shaping immunity against viral diseases in chicken. Microbial diversity and its integrity are the key elements for deriving immunity against invading viral pathogens. Commensal bacteria provide protection against pathogens through direct competition and by the production of antibodies and activation of different cytokines to modulate innate and adaptive immune responses. There are few economically important viral diseases of chicken that perturb the intestinal microbiota diversity. Disruption of microbial homeostasis (dysbiosis) associates with a variety of pathological states, which facilitate the establishment of acute viral infections in chickens. In this review, we summarize the calibrated interactions among the microbiota mediated immune modulation through the production of different interferons (IFNs) ILs, and virus-specific IgA and IgG, and their impact on the severity of viral infections in chickens. Here, it also shows that acute viral infection diminishes commensal bacteria such as Lactobacillus, Bifidobacterium, Firmicutes, and Blautia spp. populations and enhances the colonization of pathobionts, including E. coli, Shigella, and Clostridial spp., in infected chickens.
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Affiliation(s)
- Muhammad Abaidullah
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuwei Peng
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Kamran
- Queensland Alliance for Agriculture and food Innovation, The University of Queensland, Brisbane 4072, Australia
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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14
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Passera A, Compant S, Casati P, Maturo MG, Battelli G, Quaglino F, Antonielli L, Salerno D, Brasca M, Toffolatti SL, Mantegazza F, Delledonne M, Mitter B. Not Just a Pathogen? Description of a Plant-Beneficial Pseudomonas syringae Strain. Front Microbiol 2019; 10:1409. [PMID: 31293547 PMCID: PMC6598456 DOI: 10.3389/fmicb.2019.01409] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Plants develop in a microbe-rich environment and must interact with a plethora of microorganisms, both pathogenic and beneficial. Indeed, such is the case of Pseudomonas, and its model organisms P. fluorescens and P. syringae, a bacterial genus that has received particular attention because of its beneficial effect on plants and its pathogenic strains. The present study aims to compare plant-beneficial and pathogenic strains belonging to the P. syringae species to get new insights into the distinction between the two types of plant–microbe interactions. In assays carried out under greenhouse conditions, P. syringae pv. syringae strain 260-02 was shown to promote plant-growth and to exert biocontrol of P. syringae pv. tomato strain DC3000, against the Botrytis cinerea fungus and the Cymbidium Ringspot Virus. This P. syringae strain also had a distinct volatile emission profile, as well as a different plant-colonization pattern, visualized by confocal microscopy and gfp labeled strains, compared to strain DC3000. Despite the different behavior, the P. syringae strain 260-02 showed great similarity to pathogenic strains at a genomic level. However, genome analyses highlighted a few differences that form the basis for the following hypotheses regarding strain 260-02. P. syringae strain 260-02: (i) possesses non-functional virulence genes, like the mangotoxin-producing operon Mbo; (ii) has different regulation pathways, suggested by the difference in the autoinducer system and the lack of a virulence activator gene; (iii) has genes encoding DNA methylases different from those found in other P. syringae strains, suggested by the presence of horizontal-gene-transfer-obtained methylases that could affect gene expression.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Stéphane Compant
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Maria Giovanna Maturo
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Giovanna Battelli
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Livio Antonielli
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Domenico Salerno
- Department Medicina e Chirurgia, Università degli Studi di Milano-Bicocca, Vedano al Lambro, Italy
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Silvia Laura Toffolatti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Francesco Mantegazza
- Department Medicina e Chirurgia, Università degli Studi di Milano-Bicocca, Vedano al Lambro, Italy
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Birgit Mitter
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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15
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Isolation and Characterization of Antagonistic Bacteria Paenibacillus jamilae HS-26 and Their Effects on Plant Growth. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3638926. [PMID: 31032343 PMCID: PMC6457365 DOI: 10.1155/2019/3638926] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/22/2019] [Accepted: 03/03/2019] [Indexed: 11/17/2022]
Abstract
Soilborne pathogens affect plant growth and food production worldwide. The application of chemical fertilizers and pesticides to control plant diseases has harmful effects; fortunately, plant growth-promoting rhizobacteria can be used as a potential alternative strategy. Here, Paenibacillus jamilae HS-26 was selected for its highly antagonistic activity against several soilborne pathogens. The bacterium synthesized hydrolytic enzymes and released extracellular antifungal metabolites and volatile organic compounds—primarily, N, N-diethyl-1, 4-phenylenediamine, which was detected by gas chromatography-mass spectrometry and shown to inhibit fungal mycelial growth. Furthermore, HS-26 was useful for nitrogen fixation, phosphate and potassium solubilization, and siderophore and indoleacetic acid production. In vitro tests and pot experiments revealed that HS-26 considerably increased plant biometric parameters. Illumina MiSeq sequencing data showed a significant reduction in soilborne pathogens and increase in beneficial bacteria in the wheat rhizosphere after treatment with strain HS-26.
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Calvo-Garrido C, Roudet J, Aveline N, Davidou L, Dupin S, Fermaud M. Microbial Antagonism Toward Botrytis Bunch Rot of Grapes in Multiple Field Tests Using One Bacillus ginsengihumi Strain and Formulated Biological Control Products. FRONTIERS IN PLANT SCIENCE 2019; 10:105. [PMID: 30804972 PMCID: PMC6378282 DOI: 10.3389/fpls.2019.00105] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/23/2019] [Indexed: 05/09/2023]
Abstract
Botrytis bunch rot (BBR), caused by the necrotrophic fungus Botrytis cinerea, is a major disease of wine and table grapes worldwide. Due to negative effects of pesticides on the environment and human health, alternative control strategies against BBR, such as biological control agents (BCAs), are required to produce high-quality grapes and wines with high standards of food safety. However, few biological control products against BBR are available, and their efficacy is sometimes variable. This study aimed to evaluate and compare (1) the efficacy of new bacterial BCA strains developed at INRA Bordeaux and (2) the BBR reductions achieved by commercial biocontrol products that are already registered or close to being registered. During three consecutive seasons, 10 field experiments were established in six different experimental vineyards in southwestern France. Spray applications were performed at key phenological stages (five or six during the season), or at high BBR-risk periods late in the season according to a Disease Risk Index model. At harvest, BBR incidence and severity (% of symptomatic berries per bunch) were visually determined. The experiments included four bacterial strains at an early experimental stage, particularly Bacillus ginsengihumi (S38). Nine commercial BCA products were also tested, including Bacillus subtilis, Bacillus amyloliquefaciens, Aureobasidium pullulans, Ulocladium oudemansii, and Candida sake. Among the four experimental bacterial strains, only B. ginsengihumi S38 significantly controlled the BBR, presenting reductions in the average severity ranging from 35 to 60%, compared to untreated control, throughout the three seasons. Several commercial BCAs achieved significant reductions in BBR severity ranging from 21 to 58%, although not in every trial. The treatments that achieved higher reductions in severity rates were based on C. sake (45%), B. subtilis (54%), and B. amyloliquefaciens (58%). The efficacy of those BCAs was consistent throughout the studied seasons. The results confirmed the suitability of several biological control products under the conditions in vineyards in southwestern France, while also highlighting the good performance of the novel experimental BCA B. ginsengihumi S38 strain, which achieved similar control rates to the products registered for commercial use. The major factors involved in the variability in the results are also discussed.
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Affiliation(s)
- Carlos Calvo-Garrido
- SAVE, INRA, Institut National de la Recherche Agronomique, Bordeaux Science Agro, ISVV 33882, Villenave d'Ornon, France
| | - Jean Roudet
- SAVE, INRA, Institut National de la Recherche Agronomique, Bordeaux Science Agro, ISVV 33882, Villenave d'Ornon, France
| | - Nicolas Aveline
- Institut Français de la Vigne et du Vin–Vinopôle Bordeaux-Aquitaine, Blanquefort, France
| | - Ludivine Davidou
- Chambre d'Agriculture de la Gironde (CA33)–Service Vigne et Vin. CS 20115, Blanquefort, France
| | - Sévérine Dupin
- Chambre d'Agriculture de la Gironde (CA33)–Service Vigne et Vin. CS 20115, Blanquefort, France
| | - Marc Fermaud
- SAVE, INRA, Institut National de la Recherche Agronomique, Bordeaux Science Agro, ISVV 33882, Villenave d'Ornon, France
- *Correspondence: Marc Fermaud
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17
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Cui N, Huang X, Kong Z, Huang Y, Huang Q, Yang S, Zhang L, Xu C, Zhang X, Cui Y. Newcastle Disease Virus Infection Interferes With the Formation of Intestinal Microflora in Newly Hatched Specific-Pathogen-Free Chicks. Front Microbiol 2018; 9:900. [PMID: 29867811 PMCID: PMC5949361 DOI: 10.3389/fmicb.2018.00900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 04/18/2018] [Indexed: 01/25/2023] Open
Abstract
Newcastle disease virus (NDV) infection leads to disproportion of intestinal tract microbiol population in chickens. Whether vertical infection of NDV affects the formation of a healthy and diverse intestinal community in newly hatched chicks, which might further perturb the establishment of a normal intestinal mucosal immunity, is unclear. This study examined the effects of NDV infection of chick embryos on the formation of the intestinal microbiome of chicks at hatch using 16S rRNA genes pyrosequencing. Eleven-day-old specific-pathogen-free chicken eggs were inoculated via intra-allantoic way with Class I NDV strain. At hatch, chicks were randomly selected and their duodenal and cecal contents were extracted and examined for the composition of gut microflora by Illumina sequencing of the V3+V4 region of the 16S rRNA genes. The results showed that the duodenal flora possesses a greater sample richness and higher microbial diversity as compared with the ceca flora in newly hatched chicks. In addition, there is a clear association with loss of important bacterial population in concert with an enrichment of potentially pathogenic population and NDV infections, both in the duodenum and ceca. It is also increasingly observed that the NDV infection may be associated with the dysbiosis of gut flora. This study presented a profile of the early intestinal microbiota in specific-pathogen-free chicks at hatch and strongly indicates that NDV infection interferes with the formation of intestinal microbiome in newly hatched chicks.
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Affiliation(s)
- Ning Cui
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaoying Huang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.,Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Zhengjie Kong
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
| | - Yanyan Huang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qinghua Huang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shaohua Yang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lin Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chuantian Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiumei Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanshun Cui
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, China
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18
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Passera A, Marcolungo L, Casati P, Brasca M, Quaglino F, Cantaloni C, Delledonne M. Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity. PLoS One 2018; 13:e0189993. [PMID: 29351296 PMCID: PMC5774705 DOI: 10.1371/journal.pone.0189993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/06/2017] [Indexed: 01/27/2023] Open
Abstract
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Luca Marcolungo
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
- * E-mail:
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Cantaloni
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
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Leyva Salas M, Mounier J, Valence F, Coton M, Thierry A, Coton E. Antifungal Microbial Agents for Food Biopreservation-A Review. Microorganisms 2017; 5:microorganisms5030037. [PMID: 28698479 PMCID: PMC5620628 DOI: 10.3390/microorganisms5030037] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 11/16/2022] Open
Abstract
Food spoilage is a major issue for the food industry, leading to food waste, substantial economic losses for manufacturers and consumers, and a negative impact on brand names. Among causes, fungal contamination can be encountered at various stages of the food chain (e.g., post-harvest, during processing or storage). Fungal development leads to food sensory defects varying from visual deterioration to noticeable odor, flavor, or texture changes but can also have negative health impacts via mycotoxin production by some molds. In order to avoid microbial spoilage and thus extend product shelf life, different treatments—including fungicides and chemical preservatives—are used. In parallel, public authorities encourage the food industry to limit the use of these chemical compounds and develop natural methods for food preservation. This is accompanied by a strong societal demand for ‘clean label’ food products, as consumers are looking for more natural, less severely processed and safer products. In this context, microbial agents corresponding to bioprotective cultures, fermentates, culture-free supernatant or purified molecules, exhibiting antifungal activities represent a growing interest as an alternative to chemical preservation. This review presents the main fungal spoilers encountered in food products, the antifungal microorganisms tested for food bioprotection, and their mechanisms of action. A focus is made in particular on the recent in situ studies and the constraints associated with the use of antifungal microbial agents for food biopreservation.
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Affiliation(s)
- Marcia Leyva Salas
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM EA3882), Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
- UMR1253 Science et Technologie du Lait et de l'Œuf, INRA, Agrocampus Ouest, 65 rue de Saint Brieuc, 35000 Rennes, France.
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM EA3882), Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Florence Valence
- UMR1253 Science et Technologie du Lait et de l'Œuf, INRA, Agrocampus Ouest, 65 rue de Saint Brieuc, 35000 Rennes, France.
| | - Monika Coton
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM EA3882), Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
| | - Anne Thierry
- UMR1253 Science et Technologie du Lait et de l'Œuf, INRA, Agrocampus Ouest, 65 rue de Saint Brieuc, 35000 Rennes, France.
| | - Emmanuel Coton
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM EA3882), Université de Brest, Technopole Brest-Iroise, 29280 Plouzané, France.
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