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Cardoni M, Mercado-Blanco J. Confronting stresses affecting olive cultivation from the holobiont perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1261754. [PMID: 38023867 PMCID: PMC10661416 DOI: 10.3389/fpls.2023.1261754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
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Affiliation(s)
- Martina Cardoni
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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2
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Identification and complete genome sequencing of a divergent olive virus T isolate and an olive leaf yellowing-associated virus isolate naturally infecting olive trees in Greece. Virus Genes 2022; 58:560-569. [PMID: 36152231 PMCID: PMC9636108 DOI: 10.1007/s11262-022-01934-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Several new full genome sequences of olive viruses came to light recently via high-throughput sequencing (HTS) analysis. In this study, total RNA HTS analysis of two Greek olive trees revealed the presence of an olive virus T (OlVT) isolate and an olive leaf yellowing-associated virus (OLYaV) isolate. The full viral genome of OlVT isolate (50Ch) is composed of 6862 nucleotides encoding for three proteins (replicase, movement protein, and capsid protein) with typical betaflexiviruses' genomic features. However, both sequence and phylogenetic data analysis exhibited high levels of variability between 50Ch and the previously characterized OlVT isolates. In addition, the almost full genome of the Greek OLYaV isolate (OL2) was obtained, which is composed of 16,693 nucleotides encoding for 11 open reading frames (ORFs) and shares common genomic features with the recently characterized OLYaV isolates from Spain and Brazil. Sequence and phylogenetic analysis revealed high similarity between these three isolates. Due to problems encountered with the detection of both viruses, new nested RT-PCR assays were developed and applied. In addition, recombination events were observed in OlVT isolates (50Ch GR-168), thus highlighting the potential role of this mechanism in the evolution of the virus. This study is adding further knowledge to the limited information available about these recently characterized olive infecting viral pathogens and highlights their widespread distribution in Greece, one of the most important olive producing countries of the world.
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Ruiz-García AB, Canales C, Morán F, Ruiz-Torres M, Herrera-Mármol M, Olmos A. Characterization of Spanish Olive Virome by High Throughput Sequencing Opens New Insights and Uncertainties. Viruses 2021; 13:v13112233. [PMID: 34835039 PMCID: PMC8622421 DOI: 10.3390/v13112233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/04/2023] Open
Abstract
The use of high throughput sequencing (HTS) for the analysis of Spanish olive trees showing leaf yellowing discoloration, defoliation, and/or decline has provided new insights into the olive viruses present in Spain and has opened discussions about the pros and cons of these technologies for diagnostic purposes. In this study, we report for the first time in Spanish orchards the presence of olive leaf yellowing-associated virus (OLYaV), for which the second full coding sequence has been determined. This virus has also been detected in a putative vector, the psyllid Euphyllura olivina. In addition, the presence in Spain of Olea europaea geminivirus (OEGV), recently reported in Italy, has been confirmed, and the full-length sequence of two isolates was obtained by HTS and Sanger sequencing. These results, as well as the detection of other viral sequences related to olive latent virus 3 (OLV-3) and olive viral satellite RNA, raises questions on the biological significance of the findings, about the requirement of standardization on the interpretation of HTS results, and the necessity of additional tests to confirm the relevance of the HTS detection of viral sequences.
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Affiliation(s)
- Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Celia Canales
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Manuel Ruiz-Torres
- Laboratorio de Producción y Sanidad Vegetal de Jaén, Junta de Andalucía, Sierra Morena, 12b, 23620 Mengíbar, Spain; (M.R.-T.); (M.H.-M.)
| | - Magdalena Herrera-Mármol
- Laboratorio de Producción y Sanidad Vegetal de Jaén, Junta de Andalucía, Sierra Morena, 12b, 23620 Mengíbar, Spain; (M.R.-T.); (M.H.-M.)
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
- Correspondence:
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A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae. Viruses 2021; 13:v13102035. [PMID: 34696465 PMCID: PMC8540022 DOI: 10.3390/v13102035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/02/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA-A and DNA-B) of the OEGV-PT is similar to Old World begomoviruses in length, but it lacks a pre-coat protein (AV2), which is a typical feature of New World begomoviruses (NW). DNA-A genome organization is closer to NW, containing four ORFs; three in complementary-sense AC1/Rep, AC2/TrAP, AC3/REn and one in virion-sense AV1/CP, but no AC4, typical of begomoviruses. DNA-B comprises two ORFs; MP in virion sense with higher similarity to the tyrosine phosphorylation site of NW, but in opposite sense to begomoviruses; BC1, with no known conserved domains in the complementary sense and no NSP typical of bipartite begomoviruses. Our results show that OEGV presents the longest common region among the begomoviruses, and the TATA box and four replication-associated iterons in a completely new arrangement. We propose two new putative conserved regions for the geminiviruses CP. Lastly, we highlight unique features that may represent a new evolutionary direction for geminiviruses and suggest that OEGV-PT evolution may have occurred from an ancient OW monopartite Begomovirus that lost V2 and C4, gaining functions on cell-to-cell movement by acquiring a DNA-B component.
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Virus Surveys in Olive Orchards in Greece Identify Olive Virus T, a Novel Member of the Genus Tepovirus. Pathogens 2021; 10:pathogens10050574. [PMID: 34066889 PMCID: PMC8150953 DOI: 10.3390/pathogens10050574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022] Open
Abstract
Field surveys were conducted in Greek olive orchards from 2017 to 2020 to collect information on the sanitary status of the trees. Using a high-throughput sequencing approach, viral sequences were identified in total RNA extracts from several trees and assembled to reconstruct the complete genomes of two isolates of a new viral species of the genus Tepovirus (Betaflexiviridae), for which the name olive virus T (OlVT) is proposed. A reverse transcription–polymerase chain reaction assay was developed which detected OlVT in samples collected in olive growing regions in Central and Northern Greece, showing a virus prevalence of 4.4% in the olive trees screened. Sequences of amplified fragments from the movement–coat protein region of OlVT isolates varied from 75.64% to 99.35%. Three olive varieties (Koroneiki, Arbequina and Frantoio) were infected with OlVT via grafting to confirm a graft-transmissible agent, but virus infections remained latent. In addition, cucumber mosaic virus, olive leaf yellowing-associated virus and cherry leaf roll virus were identified.
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Ruiz-García AB, Candresse T, Canales C, Morán F, Machado de Oliveira C, Bertolini E, Olmos A. Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus. PLANTS 2020; 9:plants9101272. [PMID: 32992518 PMCID: PMC7599613 DOI: 10.3390/plants9101272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/27/2022]
Abstract
Genome organization and phylogenetic relationships of olive leaf yellowing-associated virus (OLYaV) with other members of the Closteroviridae family were determined. The complete coding sequence of OLYaV was obtained by high throughput sequencing of total RNA from a 35-year-old olive tree (cv. Zarzaleña) from Brazil, showing olive leaf yellowing disease and deformations in the wood. This represents the first report of OLYaV in this country. A genomic sequence of 16,700 nt containing 11 open reading frames (ORFs) was recovered, representing the complete virus coding capacity. The knowledge of the nucleotide sequence of the genome including the gene that codes the coat protein will facilitate the development of diagnostic tests, which are limited so far to PCR-based methods targeting the HSP70h gene. Interestingly, a thaumatin-like protein (ORF2), previously reported in other unassigned viruses in the Closteroviridae family, persimmon virus B and actidinia virus 1, was identified in the OLYaV genome. Phylogenetic analysis of shared proteins (ORF1a, ORF1b, HSP70h, HSP90h and CP) with all members of the Closteroviridae family provides new insight into the taxonomic position of these three closteroviruses and suggests they could represent a new genus in the family.
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Affiliation(s)
- Ana Belén Ruiz-García
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Thierry Candresse
- University Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, 33882 Villenave d’Ornon, France;
| | - Celia Canales
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Félix Morán
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
| | - Carlos Machado de Oliveira
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (C.M.d.O.); (E.B.)
| | - Edson Bertolini
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91540-000, Brazil; (C.M.d.O.); (E.B.)
| | - Antonio Olmos
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Spain; (A.B.R.-G.); (C.C.); (F.M.)
- Correspondence: ; Tel.: +34-963424073
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Campos MD, Zellama MS, Varanda C, Materatski P, Peixe A, Chaouachi M, Félix MDR. Establishment of a Sensitive qPCR Methodology for Detection of the Olive-Infecting Viruses in Portuguese and Tunisian Orchards. FRONTIERS IN PLANT SCIENCE 2019; 10:694. [PMID: 31191591 PMCID: PMC6549245 DOI: 10.3389/fpls.2019.00694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
Sensitive detection of viruses in olive orchards is actually of main importance since these pathogenic agents cannot be treated, their dissemination is quite easy, and they can have eventual negative effects on olive oil quality. The work presented here describes the development and application of a new SYBR® Green-based real-time quantitative PCR (qPCR) analysis for specific and reliable quantification of highly spread olive tree viruses: Olive latent virus 1 (OLV-1), Tobacco necrosis virus D (TNV-D), Olive mild mosaic virus (OMMV), and Olive leaf yellowing-associated virus (OLYaV). qPCR methodology revealed high specificity and sensitivity, estimated in the range of 0.8-8 copies of the virus genome, for the studied viruses. For validation of the method, total RNA and double strand RNA (dsRNA) from naturally infected trees were used. In a first trial, dsRNAs from trees of cv. "Galega vulgar" from a Portuguese orchard, were subjected to qPCR and from the 30 samples tested, 26 were TNV-D and/or OMMV-positive and 25 were OLV-1 positive. In a second trial, total RNA from trees of different cultivars from Tunisian orchards, were here tested by qPCR and all viruses were detected. From the 33 samples studied, the most prevalent virus detected in Tunisia orchards was OLV-1 (31 samples diagnosed), followed by OLYaV (20 samples diagnosed), and finally the combination in last TNV-D and/or OMMV (12 samples diagnosed). In both trials, qPCR demonstrated to be effective and sensitive, even when using total RNA as template. qPCR through the use of a SYBR® Green methodology enabled, for the first time, a reliable, sensitive, and reproducible estimation of virus accumulation in infected olive trees, in which viruses are usually in low titres, that will allow gaining new insights in virus biology essential for disease control and give an important contribution for establishment of sanitary certification of olive propagative material.
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Affiliation(s)
- Maria Doroteia Campos
- ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Mohamed Salem Zellama
- Laboratoire de Recherche “Bioressources: Biologie Intégrative & Valorisation," Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Carla Varanda
- ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Patrick Materatski
- ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Instituto de Investigação e Formação Avançada, Universidade de Évora, Évora, Portugal
| | - Augusto Peixe
- Departamento de Fitotecnia, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Escola de Ciências e Tecnologia, Universidade de Évora, Évora, Portugal
| | - Maher Chaouachi
- Laboratoire de Recherche “Bioressources: Biologie Intégrative & Valorisation," Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Maria do Rosário Félix
- Departamento de Fitotecnia, ICAAM – Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Escola de Ciências e Tecnologia, Universidade de Évora, Évora, Portugal
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Fontana A, Piscopo A, De Bruno A, Tiberini A, Muzzalupo I, Albanese G. Impact of Olive Leaf Yellowing Associated Virus on Olive (
Olea europaea
L.) Oil. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201800472] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Fontana
- Università degli Studi Mediterranea di Reggio CalabriaDipartimento di AGRARIAReggio CalabriaItaly
| | - Amalia Piscopo
- Università degli Studi Mediterranea di Reggio CalabriaDipartimento di AGRARIAReggio CalabriaItaly
| | - Alessandra De Bruno
- Università degli Studi Mediterranea di Reggio CalabriaDipartimento di AGRARIAReggio CalabriaItaly
| | - Antonio Tiberini
- Università degli Studi Mediterranea di Reggio CalabriaDipartimento di AGRARIAReggio CalabriaItaly
| | - Innocenzo Muzzalupo
- Consiglio per la Ricerca in agricoltura e l'analisi dell'Economia Agrariacentro di ricerca per OlivicolturaFrutticoltura e Agrumicoltura (CREA‐OFA)Rende (CS)Italy
| | - Giuliana Albanese
- Università degli Studi Mediterranea di Reggio CalabriaDipartimento di AGRARIAReggio CalabriaItaly
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Varanda CMR, Nolasco G, Clara MI, Félix MR. Genetic diversity of the coat protein of olive latent virus 1 isolates. Arch Virol 2013; 159:1351-7. [DOI: 10.1007/s00705-013-1953-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/16/2013] [Indexed: 11/28/2022]
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10
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Godena S, Bendini A, Giambanelli E, Cerretani L, Ðermić D, Ðermić E. Cherry leafroll virus: Impact on olive fruit and virgin olive oil quality. EUR J LIPID SCI TECH 2012. [DOI: 10.1002/ejlt.201100277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sara Godena
- Institute of Agriculture and Tourism, Poreč, Croatia
| | - Alessandra Bendini
- Department of Food Science, University of Bologna, Alma Mater Studiorum, Cesena (FC), Italy
| | - Elisa Giambanelli
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, Alma Mater Studiorum, Cesena (FC), Italy
| | - Lorenzo Cerretani
- Department of Agricultural Economics and Agricultural Engineering, University of Bologna, Alma Mater Studiorum, Cesena (FC), Italy
| | - Damir Ðermić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Edyta Ðermić
- Faculty of Agriculture, Department of Plant Pathology, University of Zagreb, Zagreb, Croatia
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