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Li B, Yang P, Feng Y, Du C, Qi G, Zhao X. Rhizospheric microbiota of suppressive soil protect plants against Fusarium solani infection. PEST MANAGEMENT SCIENCE 2024; 80:4186-4198. [PMID: 38578633 DOI: 10.1002/ps.8122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Fusarium infection has caused huge economic losses in many crops. The study aimed to compare the microbial community of suppressive and conducive soils and relate to the reduction of Fusarium wilt. RESULTS High-throughput sequencing and microbial network analysis were used to investigate the differences in the rhizosphere microbiota of the suppressive and conducive soils and to identify the beneficial keystone taxa. Plant pathogens were enriched in the conducive soil. Potential plant-beneficial microorganisms and antagonistic microorganisms were enriched in the suppressive soil. More positive interactions and keystone taxa existed in the suppressive soil network. Thirty-nine and 16 keystone taxa were identified in the suppressive and conducive soil networks, respectively. Sixteen fungal strains and 168 bacterial strains were isolated from suppressive soil, some of which exhibited plant growth-promotion traits. Thirty-nine bacterial strains and 10 fungal strains showed antagonistic activity against F. solani. Keystone taxa Bacillus and Trichoderma exhibited high antifungal activity. Lipopeptides produced by Bacillus sp. RB150 and chitinase from Trichoderma spp. inhibited the growth of F. solani. Microbial consortium I (Bacillus sp. RB150, Pseudomonas sp. RB70 and Trichoderma asperellum RF10) and II (Bacillus sp. RB196, Bacillus sp. RB150 and T. asperellum RF10) effectively controlled root rot disease, the spore number of F. solani was reduced by 94.2% and 83.3%. CONCLUSION Rhizospheric microbiota of suppressive soil protects plants against F. solani infection. Antagonistic microorganisms in suppressive soil inhibit pathogen growth and infection. Microbial consortia consisted of keystone taxa well control root rot disease. These findings help control Fusarium wilt. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Baolong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ping Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yali Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chenyang Du
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Li S, Wang Z, Gao M, Li T, Cui X, Zu J, Sang S, Fan W, Zhang H. Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype. BIOLOGY 2023; 12:biology12030476. [PMID: 36979167 PMCID: PMC10045276 DOI: 10.3390/biology12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Didymella arachidicola is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts (Arachis hypogaea L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of D. arachidicola remain to be revealed. In the present study, we collected 41 D. arachidicola isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in D. arachidicola. The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of D. arachidicola isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of D. arachidicola.
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Affiliation(s)
- Shaojian Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Tong Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Xiaowei Cui
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Junhuai Zu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Suling Sang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Wanwan Fan
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Haiyan Zhang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
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Hanafy RA, Wang Y, Stajich JE, Pratt CJ, Youssef NH, Elshahed MS. Phylogenomic analysis of the Neocallimastigomycota: proposal of Caecomycetaceae fam. nov., Piromycetaceae fam. nov., and emended description of the families Neocallimastigaceae and Anaeromycetaceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36827202 DOI: 10.1099/ijsem.0.005735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The anaerobic gut fungi (AGF) represent a coherent phylogenetic clade within the Mycota. Twenty genera have been described so far. Currently, the phylogenetic and evolutionary relationships between AGF genera remain poorly understood. Here, we utilized 52 transcriptomic datasets from 14 genera to resolve AGF inter-genus relationships using phylogenomics, and to provide a quantitative estimate (amino acid identity, AAI) for intermediate rank assignments. We identify four distinct supra-genus clades, encompassing all genera producing polyflagellated zoospores, bulbous rhizoids, the broadly circumscribed genus Piromyces, and the Anaeromyces and affiliated genera. We also identify the genus Khoyollomyces as the earliest evolving AGF genus. Concordance between phylogenomic outputs and RPB1 and D1/D2 LSU, but not RPB2, MCM7, EF1α or ITS1, phylogenies was observed. We combine phylogenomic analysis and AAI outputs with informative phenotypic traits to propose accommodating 14/20 AGF genera into four families: Caecomycetaceae fam. nov. (encompassing the genera Caecomyces and Cyllamyces), Piromycetaceae fam. nov. (encompassing the genus Piromyces), emend the description of the family Neocallimastigaceae to encompass the genera Neocallimastix, Orpinomyces, Pecoramyces, Feramyces, Ghazallomyces, Aestipascuomyces and Paucimyces, as well as the family Anaeromycetaceae to include the genera Oontomyces, Liebetanzomyces and Capellomyces in addition to Anaeromyces. We refrain from proposing families for the deeply branching genus Khoyollomyces and for genera with uncertain position (Buwchfawromyces, Joblinomyces, Tahromyces, Agriosomyces and Aklioshbomyces) pending availability of additional isolates and sequence data; and these genera are designated as 'genera incertae sedis' in the order Neocallimastigales. Our results establish an evolutionary-grounded Linnaean taxonomic framework for the AGF, provide quantitative estimates for rank assignments, and demonstrate the utility of RPB1 as an additional informative marker in Neocallimastigomycota taxonomy.
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Affiliation(s)
- Radwa A Hanafy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.,Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Carrie J Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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Yabaneri C, Sevim A. Endophytic fungi from the common walnut and their in vitro antagonistic activity against Ophiognomonia leptostyla. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01218-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Jing M, Xu X, Peng J, Li C, Zhang H, Lian C, Chen Y, Shen Z, Chen C. Comparative Genomics of Three Aspergillus Strains Reveals Insights into Endophytic Lifestyle and Endophyte-Induced Plant Growth Promotion. J Fungi (Basel) 2022; 8:jof8070690. [PMID: 35887447 PMCID: PMC9323082 DOI: 10.3390/jof8070690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Aspergillus includes both plant pathogenic and beneficial fungi. Although endophytes beneficial to plants have high potential for plant growth promotion and improving stress tolerance, studies on endophytic lifestyles and endophyte-plant interactions are still limited. Here, three endophytes belonging to Aspergillus, AS31, AS33, and AS42, were isolated. They could successfully colonize rice roots and significantly improved rice growth. The genomes of strains AS31, AS33, and AS42 were sequenced and compared with other Aspergillus species covering both pathogens and endophytes. The genomes of AS31, AS33, and AS42 were 36.8, 34.8, and 35.3 Mb, respectively. The endophytic genomes had more genes encoding carbohydrate-active enzymes (CAZymes) and small secreted proteins (SSPs) and secondary metabolism gene clusters involved in indole metabolism than the pathogens. In addition, these endophytes were able to improve Pi (phosphorus) accumulation and transport in rice by inducing the expression of Pi transport genes in rice. Specifically, inoculation with endophytes significantly increased Pi contents in roots at the early stage, while the Pi contents in inoculated shoots were significantly increased at the late stage. Our results not only provide important insights into endophyte-plant interactions but also provide strain and genome resources, paving the way for the agricultural application of Aspergillus endophytes.
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Affiliation(s)
- Minyu Jing
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
| | - Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
| | - Jing Peng
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
| | - Can Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Tokyo 188-0002, Japan;
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.S.); (C.C.); Tel.: +86-2584396391 (C.C.)
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (M.J.); (X.X.); (J.P.); (C.L.); (H.Z.); (Y.C.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.S.); (C.C.); Tel.: +86-2584396391 (C.C.)
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Liu X, Zhou ZY, Cui JL, Wang ML, Wang JH. Biotransformation ability of endophytic fungi: from species evolution to industrial applications. Appl Microbiol Biotechnol 2021; 105:7095-7113. [PMID: 34499202 PMCID: PMC8426592 DOI: 10.1007/s00253-021-11554-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022]
Abstract
Abstract Increased understanding of the interactions between endophytic fungi and plants has led to the discovery of a new generation of chemical compounds and processes between endophytic fungi and plants. Due to the long-term co-evolution between fungal endophytes and host plants, endophytes have evolved special biotransformation abilities, which can have critical consequences on plant metabolic processes and their composition. Biotransformation or bioconversion can impact the synthesis and decomposition of hormones, sugars, amino acids, vitamins, lipids, proteins, and various secondary metabolites, including flavonoids, polysaccharides, and terpenes. Endophytic fungi produce enzymes and various bioactive secondary metabolites with industrial value and can degrade or sequester inorganic and organic small molecules and macromolecules (e.g., toxins, pollutants, heavy metals). These fungi also have the ability to cause highly selective catalytic conversion of high-value compounds in an environmentally friendly manner, which can be important for the production/innovation of bioactive molecules, food and nutrition, agriculture, and environment. This work mainly summarized recent research progress in this field, providing a reference for further research and application of fungal endophytes. Key points •The industrial value of degradation of endophytes was summarized. • The commercial value for the pharmaceutical industry is reviewed. Graphical abstract ![]()
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Affiliation(s)
- Xi Liu
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China.,Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Zhong-Ya Zhou
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China.,Modern Research Center for Traditional Chinese Medicine, The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Jin-Long Cui
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Meng-Liang Wang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Jun-Hong Wang
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006, Shanxi, China
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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Del Pilar Martínez-Diz M, Andrés-Sodupe M, Berbegal M, Bujanda R, Díaz-Losada E, Gramaje D. Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples. PLANT DISEASE 2020; 104:1144-1150. [PMID: 32053059 DOI: 10.1094/pdis-03-19-0529-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Black-foot disease is one of the most important soilborne diseases affecting planting material in grapevine nurseries and young vineyards. Accurate, early, and specific detection and quantification of black-foot disease causing fungi are essential to alert growers and nurseries to the presence of the pathogens in soil, and to prevent the spread of these pathogens through grapevines using certified pathogen-free planting material and development of resistance. We comparatively assessed the accuracy, efficiency, and specificity of droplet digital PCR (ddPCR) and real-time PCR (qPCR) techniques for the detection and quantification of Ilyonectria liriodendri in bulk and rhizosphere soils, as well as grapevine endorhizosphere. Fungal abundance was not affected by soil-plant fractions. Both techniques showed a high degree of correlation across the samples assessed (R2 = 0.95) with ddPCR being more sensitive to lower target concentrations. Roots of asymptomatic vines were found to be a microbial niche that is inhabited by black-foot disease fungi.
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Affiliation(s)
- María Del Pilar Martínez-Diz
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
- Universidade da Coruña, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Marcos Andrés-Sodupe
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Mónica Berbegal
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Rebeca Bujanda
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
| | - Emilia Díaz-Losada
- Estación de Viticultura y Enología de Galicia (AGACAL-EVEGA), Ponte San Clodio s/n 32428-Leiro-Ourense, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. de Burgos Km. 6, 26007 Logroño, Spain
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