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Martins V, Teixeira A, Gerós H. A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry. Food Microbiol 2024; 118:104408. [PMID: 38049270 DOI: 10.1016/j.fm.2023.104408] [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: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 12/06/2023]
Abstract
The methodologies for profiling the grape berry microbiota have exponentially evolved in the past 25 years. Recently, concerns arose regarding the homogeneity in the protocols of grape harvesting, sequencing and bioinformatic analyses, but the bias introduced by the microbiota isolation method is still unexplored. This study followed a simple approach of comparing two most used methods of microbiota collection from grape berries (washing vs crushing), hypothesizing a significant impact in the outcome of the microbiota profiles analyzed by NGS metabarcoding. Experiments conducted in fruits of three cultivars of the Douro wine region showed that only 52 % of OTUs were common to both surface and juice microbiota, suggesting specific microbial niches. Thirteen fungal genera were abundantly detected in the fruit surface, including Alternaria, Aureobasidium, Cladosporium, Didymella and Bipolaris. Fermentative yeasts including Meyerozyma and Saccharomyces cerevisiae were exclusively detected in the juice, together with several Penicillium species. Distinct habitat preferences of species within the genera Alternaria, Sporobolomyces and Rhodotorula were also revealed. The study showed that the microbiota isolation method is crucial in the detection of certain plant pathogenic/saprophytic fungi and yeasts with biotechnological and oenological interest, adding novelty to the globally accepted assumption that S. cerevisiae in musts originates primarily from the cellar.
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Affiliation(s)
- Viviana Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - António Teixeira
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Theologidis I, Karamitros T, Vichou AE, Kizis D. Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive ( Olea europaea) Twigs. J Fungi (Basel) 2023; 9:1119. [PMID: 37998924 PMCID: PMC10672464 DOI: 10.3390/jof9111119] [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: 10/26/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.
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Affiliation(s)
- Ioannis Theologidis
- Laboratory of Toxicological Control of Pesticides, Scientific Directorate of Pesticides' Control & Phytopharmacy, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Attica, Greece
| | - Aikaterini-Eleni Vichou
- Laboratory of Mycology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
| | - Dimosthenis Kizis
- Laboratory of Mycology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, 8 St. Delta Street, 14561 Athens, Attica, Greece
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Hamie N, Nacouzi D, Choker M, Salameh M, Darwiche L, El Kayal W. Maturity Assessment of Different Table Grape Cultivars Grown at Six Different Altitudes in Lebanon. PLANTS (BASEL, SWITZERLAND) 2023; 12:3237. [PMID: 37765401 PMCID: PMC10536932 DOI: 10.3390/plants12183237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Table grapes are harvested based on well-known maturity indices that must be monitored after fruit veraison. The aim of this study was to assess these indices across multiple locations and environmental conditions, encompassing different table grape cultivars such as Black Pearl, Crimson Seedless, Superior Seedless, and Red Globe. For this reason, grape sampling was conducted across six distinct locations characterized by varying altitudes above sea level (m asl) and environmental conditions over the ripening season. The main maturity indices, including pH, sugar content, titratable acidity, berry firmness, and other parameters were monitored over the growing season. Moreover, the quantification of total polyphenols, total anthocyanins, and antioxidant activity was determined using spectrophotometric assays at harvesting. The study has examined the effect of the vineyard's location on grape quality and its interaction with the cultivar and environment. Crimson Seedless maintained a relatively high level of acidity with altitude near harvesting. Black Pearl exhibited a notable decline in both sugar content and berry firmness as elevation increased, whereas Red Globe demonstrated contrasting outcomes. The optimal maturity of Superior Seedless was observed at an elevation of 1000 m asl. Black Pearl and Crimson Seedless exhibited better adaptability to intermediate elevations (650 and 950 m asl), while Red Globe and Superior Seedless showed better adaptability to higher elevations (1000-1150 m asl). Among the studied cultivars, Black Pearl exhibited significantly higher levels of total polyphenols and anthocyanins, while close values were noticed between red and green cultivars.
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Affiliation(s)
- Najwane Hamie
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
| | - Diana Nacouzi
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
| | - Mariam Choker
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
| | - Maya Salameh
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
| | - Linda Darwiche
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
| | - Walid El Kayal
- Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), P.O. Box 11-0236, Beirut 1107, Lebanon
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Del Frari G, Aggerbeck MR, Gobbi A, Ingrà C, Volpi L, Nascimento T, Ferrandino A, Hansen LH, Ferreira RB. Pruning Wound Protection Products Induce Alterations in the Wood Mycobiome Profile of Grapevines. J Fungi (Basel) 2023; 9:jof9040488. [PMID: 37108942 PMCID: PMC10141712 DOI: 10.3390/jof9040488] [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: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Fungal pathogens involved in grapevine trunk diseases (GTDs) may infect grapevines throughout their lifetime, from nursery to vineyard, via open wounds in stems, canes or roots. In vineyards, pruning wound protection products (PWPPs) offer the best means to reduce the chance of infection by GTD fungi. However, PWPPs may affect non-target microorganisms that comprise the natural endophytic mycobiome residing in treated canes, disrupting microbial homeostasis and indirectly influencing grapevine health. Using DNA metabarcoding, we characterized the endophytic mycobiome of one-year-old canes of cultivars Cabernet Sauvignon and Syrah in two vineyards in Portugal and Italy and assessed the impact of established and novel PWPPs on the fungal communities of treated canes. Our results reveal a large fungal diversity (176 taxa), and we report multiple genera never detected before in grapevine wood (e.g., Symmetrospora and Akenomyces). We found differences in mycobiome beta diversity when comparing vineyards (p = 0.01) but not cultivars (p > 0.05). When examining PWPP-treated canes, we detected cultivar- and vineyard-dependent alterations in both alpha and beta diversity. In addition, numerous fungal taxa were over- or under-represented when compared to control canes. Among them, Epicoccum sp., a beneficial genus with biological control potential, was negatively affected by selected PWPPs. This study demonstrates that PWPPs induce alterations in the fungal communities of grapevines, requiring an urgent evaluation of their direct and indirect effects on plants health with consideration of factors such as climatic conditions and yearly variations, in order to better advise viticulturists and policy makers.
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Affiliation(s)
- Giovanni Del Frari
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | | | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Chiara Ingrà
- Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy
| | - Lorenzo Volpi
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Teresa Nascimento
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Alessandra Ferrandino
- Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Ricardo Boavida Ferreira
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
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Jia Y, Liu Y, Hu W, Cai W, Zheng Z, Luo C, Li D. Development of Candida autochthonous starter for cigar fermentation via dissecting the microbiome. Front Microbiol 2023; 14:1138877. [PMID: 36910204 PMCID: PMC9998997 DOI: 10.3389/fmicb.2023.1138877] [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: 01/06/2023] [Accepted: 02/08/2023] [Indexed: 03/14/2023] Open
Abstract
Introduction The main goal of tobacco fermentation technology is to minimize the alkaloid content while improving flavor substance content. Methods This study revealed the microbial community structure and their metabolic functions during cigar leaf fermentation by high-throughput sequencing and correlation analysis, and evaluated the fermentation performance of functional microbes based on in vitro isolation and bioaugmentation fermentation. Results The relative abundance of Staphylococcus and Aspergillus increased first but then decreased during the fermentation, and would occupy the dominant position of bacterial and fungal communities, respectively, on the 21st day. Correlation analysis predicted that Aspergillus, Staphylococcus and Filobasidium could contribute to the formation of saccharide compounds, Bacillus might have degradation effects on nitrogenous substances. In particular, Candida, as a co-occurring taxa and biomarker in the later stage of fermentation, could not only degrade nitrogenous substrates and synthesize flavor substances, but also contribute to maintaining the stability of microbial community. Moreover, based on in vitro isolation and bioaugmentation inoculation, it was found that Candida parapsilosis and Candida metapsilosis could significantly reduce the alkaloids content and increase the content of flavor components in tobacco leaves. Discussion This study found and validated the critical role of Candida in the fermentation of cigar tobacco leaves through high-throughput sequencing and bioaugmentation inoculation, which would help guide the development of microbial starters and directional regulation of cigar tobacco quality.
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Affiliation(s)
- Yun Jia
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Industrial Co., Ltd., Chengdu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yuanfa Liu
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanrong Hu
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Industrial Co., Ltd., Chengdu, China
| | - Wen Cai
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Industrial Co., Ltd., Chengdu, China
| | - Zhaojun Zheng
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cheng Luo
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Industrial Co., Ltd., Chengdu, China
| | - Dongliang Li
- Cigar Fermentation Technology Key Laboratory of China Tobacco, China Tobacco Industrial Co., Ltd., Chengdu, China
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Gökdemir FŞ, İşeri ÖD, Sharma A, Achar PN, Eyidoğan F. Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnostic of Fungal Pathogens in Plants. J Fungi (Basel) 2022; 8:1195. [PMID: 36422016 PMCID: PMC9699264 DOI: 10.3390/jof8111195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 09/19/2023] Open
Abstract
Crop output is directly impacted by infections, with fungi as the major plant pathogens, making accurate diagnosis of these threats crucial. Developing technology and multidisciplinary approaches are turning to genomic analyses in addition to traditional culture methods in diagnostics of fungal plant pathogens. The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping identification of organisms, identification at the species level, illumination of metabolic pathways, and determination of microbiota. Moreover, the data obtained so far show that this new approach is promising as an emerging new trend in fungal disease detection. Another approach covered by mNGS technologies, known as metabarcoding, enables use of specific markers specific to a genetic region and allows for genotypic identification by facilitating the sequencing of certain regions. Although the core concept of mNGS remains constant across applications, the specific sequencing methods and bioinformatics tools used to analyze the data differ. In this review, we focus on how mNGS technology, including metabarcoding, is applied for detecting fungal pathogens and its promising developments for the future.
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Affiliation(s)
- Fatma Şeyma Gökdemir
- Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
| | - Özlem Darcansoy İşeri
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
- Institute of Food, Agriculture and Livestock Development, Başkent University, Ankara 06790, Turkey
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
| | - Premila N. Achar
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Füsun Eyidoğan
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Başkent University, Ankara 06790, Turkey
- Institute of Food, Agriculture and Livestock Development, Başkent University, Ankara 06790, Turkey
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New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True? J Fungi (Basel) 2022; 8:jof8070737. [PMID: 35887492 PMCID: PMC9320658 DOI: 10.3390/jof8070737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 02/01/2023] Open
Abstract
The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.
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Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome. J Fungi (Basel) 2021; 7:jof7090686. [PMID: 34575724 PMCID: PMC8468433 DOI: 10.3390/jof7090686] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO4 when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.
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Affiliation(s)
- Franck Carbonero
- Department of Nutrition and Exercise Physiology, Elson Floyd School of Medicine, Washington State University-Spokane, Spokane, WA, 99202, USA.
| | - Gary Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA
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