1
|
Ji T, Salotti I, Altieri V, Li M, Rossi V. Seasonal Periodicity of the Airborne Spores of Fungi Causing Grapevine Trunk Diseases: An Analysis of 247 Studies Published Worldwide. PLANT DISEASE 2024:PDIS04230709RE. [PMID: 37874281 DOI: 10.1094/pdis-04-23-0709-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Grapevine trunk diseases (GTDs) are among the most devastating grapevine diseases globally. GTDs are caused by numerous fungi belonging to different taxa, which release spores into the vineyard and infect wood tissue, mainly through wounds caused by viticultural operations. The timing of operations to avoid infection is critical concerning the periodicity of GTD spores in vineyards, and many studies have been conducted in different grape-growing areas worldwide. However, these studies provide conflicting and fragmented information. To synthesize current knowledge, we conducted a systematic literature review, extracted quantitative data from published papers, and used these data to identify trends and knowledge gaps that need to be addressed in future studies. Our database included 26 papers covering 247 studies and 3,529 spore sampling records concerning a total of 29 fungal taxa responsible for Botryosphaeria dieback (BD), Esca complex (EC), and Eutypa dieback (ED). We found a clear seasonality in the presence and abundance of BD spores, with a peak from fall to spring, more in the northern hemisphere than in the southern hemisphere, but not for EC and ED. Spores of these fungi were present throughout the growing season in both hemispheres, possibly because of higher variability in spore types, sporulation conditions, and spore release mechanisms in EC and ED fungi than in BD. Our analysis has limitations because of knowledge gaps and data availability for some fungi (e.g., basidiomycetes, which cause EC). These limitations are discussed to facilitate further research.
Collapse
Affiliation(s)
- Tao Ji
- Department of Horticulture, Agricultural College of Shihezi University/Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi 832003, China
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza 29122, Italy
| | - Irene Salotti
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza 29122, Italy
| | - Valeria Altieri
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza 29122, Italy
| | - Ming Li
- National Engineering Research Center for Information Technology in Agriculture (NERCITA)/Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza 29122, Italy
| |
Collapse
|
2
|
Ji T, Altieri V, Salotti I, Li M, Rossi V. Role of Rain in the Spore Dispersal of Fungal Pathogens Associated with Grapevine Trunk Diseases. PLANT DISEASE 2024; 108:1041-1052. [PMID: 37822098 DOI: 10.1094/pdis-03-23-0403-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Grapevine trunk diseases are caused by a complex of fungi that belong to different taxa, which produce different spore types and have different spore dispersal mechanisms. It is commonly accepted that rainfall plays a key role in spore dispersal, but there is conflicting information in the literature on the relationship between rain and spore trapping in aerobiology studies. We conducted a systematic literature review, extracted quantitative data from published papers, and used the pooled data for Bayesian analysis of the effect of rain on spore trapping. We selected 17 papers covering 95 studies and 8,778 trapping periods, concerning a total of 26 fungal taxa causing Botryosphaeria dieback (BD), Esca complex (EC), and Eutypa dieback (ED). Results confirmed the role of rain in the spore dispersal of these fungi but revealed differences among the different fungi. Rain was a good predictor of spore trapping for ED (AUROC = 0.820) and BD (0.766) but not for the ascomycetes involved in EC (0.569) and not for the only basidiomycetes, Fomitiporella viticola, studied as for spore discharge (AUROC not significant). Prediction of spore trapping was more accurate for negative prognosis than for positive prognosis; a rain cutoff of ≥0.2 mm provided an overall accuracy of ≥0.61 for correct prognoses. Spores trapped in rainless periods accounted for only <10% of the total spores. Our analysis had some drawbacks, which were mainly caused by knowledge gaps and limited data availability; these drawbacks are discussed to facilitate further research.
Collapse
Affiliation(s)
- Tao Ji
- Department of Horticulture, Agricultural College of Shihezi University/Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction Corps, Shihezi 832003, Xinjiang, China
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Valeria Altieri
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Irene Salotti
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Ming Li
- National Engineering Research Center for Information Technology in Agriculture (NERCITA)/Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| |
Collapse
|
3
|
Ji T, Salotti I, Altieri V, Li M, Rossi V. Temperature-Dependent Growth and Spore Germination of Fungi Causing Grapevine Trunk Diseases: Quantitative Analysis of Literature Data. PLANT DISEASE 2023:PDIS09222249RE. [PMID: 36366834 DOI: 10.1094/pdis-09-22-2249-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Grapevine trunk diseases (GTDs) are serious threats in all viticultural areas of the world, and their management is always complex and usually inadequate. Fragmented and inconsistent information on the epidemiology and environmental requirements of the causal fungi is among the reasons for poor disease control. Therefore, we conducted a quantitative analysis of literature data to determine the effects of temperature on mycelial growth and the effects of temperature and moisture duration on spore germination. Using the collected information, we then developed mathematical equations describing the response of mycelial growth to temperature, and the response of spore germination to temperature and moisture for the different species and disease syndromes. We considered 27 articles (selected from a total of 207 articles found through a systematic literature search) and 116 cases; these involved 43 fungal species belonging to three disease syndromes. The mycelial growth of the fungi causing Botryosphaeria dieback (BD) and the esca complex (EC) responded similarly to temperature, and preferred higher temperatures than those causing Eutypa dieback (ED) (with optimal temperature of 25.3, 26.5, and 23.3°C, respectively). At any temperature, the minimal duration of the moist period required for 50% spore germination was shorter for BD (3.0 h) than for EC (17.2 h) or ED (15.5 h). Mathematical equations were developed accounting for temperature-moisture relationships of GTD fungi, which showed concordance correlation coefficients ≥0.888; such equations should be useful for reducing the risk of infection.
Collapse
Affiliation(s)
- Tao Ji
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Irene Salotti
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Valeria Altieri
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Ming Li
- National Engineering Research Center for Information Technology in Agriculture (NERCITA) and Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| |
Collapse
|
4
|
Pan M, Lin L, Tian C, Fan X. Identification and pathogenicity of six fungal species causing canker and dieback disease on golden rain tree in Beijing, China. Mycology 2023; 14:37-51. [PMID: 36816770 PMCID: PMC9930857 DOI: 10.1080/21501203.2022.2096144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Golden rain trees (Koelreuteria paniculata) are largely cultivated because of their important ornamental, medicinal, and economic value. However, they are affected by canker and dieback disease to a large extent. To determine the fungi associated with canker and dieback disease of golden rain trees, isolations were obtained from diseased branches and twigs during 2019 and 2020 in greenbelts and nurseries in Beijing, China. Isolates were identified as six species (Allocryptovalsa castaneicola, Botryosphaeria dothidea, Cytospora koelreutericola sp. nov., Dothiorella acericola, Eutypella citricola, and Peroneutypa scoparia) based on morphological features and phylogenetic analyses of ITS, act, rpb2, tef1-α, and tub2. The results of pathogenicity tests indicated that all fungi produced discoloration and Botryosphaeria dothidea was highly aggressive to golden rain tree. In conclusion, this study explored the taxonomy, phylogeny, and pathogenicity of different fungal species associated with canker and dieback disease on golden rain tree and provided fundamental knowledge to improve disease management.
Collapse
Affiliation(s)
- Meng Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Lu Lin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Xinlei Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China,CONTACT Xinlei Fan
| |
Collapse
|
5
|
Reveglia P, Billones-Baaijens R, Savocchia S. Phytotoxic Metabolites Produced by Fungi Involved in Grapevine Trunk Diseases: Progress, Challenges, and Opportunities. PLANTS (BASEL, SWITZERLAND) 2022; 11:3382. [PMID: 36501420 PMCID: PMC9736528 DOI: 10.3390/plants11233382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Grapevine trunk diseases (GTDs), caused by fungal pathogens, are a serious threat to vineyards worldwide, causing significant yield and economic loss. To date, curative methods are not available for GTDs, and the relationship between the pathogen and symptom expression is poorly understood. Several plant pathologists, molecular biologists, and chemists have been investigating different aspects of the pathogenicity, biochemistry, and chemical ecology of the fungal species involved in GTDs. Many studies have been conducted to investigate virulence factors, including the chemical characterization of phytotoxic metabolites (PMs) that assist fungi in invading and colonizing crops such as grapevines. Moreover, multidisciplinary studies on their role in pathogenicity, symptom development, and plant-pathogen interactions have also been carried out. The aim of the present review is to provide an illustrative overview of the biological and chemical characterization of PMs produced by fungi involved in Eutypa dieback, Esca complex, and Botryosphaeria dieback. Moreover, multidisciplinary investigations on host-pathogen interactions, including those using cutting-edge Omics techniques, will also be reviewed and discussed. Finally, challenges and opportunities in the role of PMs for reliable field diagnosis and control of GTDs in vineyards will also be explored.
Collapse
Affiliation(s)
| | | | - Sandra Savocchia
- Gulbali Institute, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| |
Collapse
|
6
|
Yang EF, Karunarathna SC, Dai DQ, Stephenson SL, Elgorban AM, Al-Rejaie S, Xiong YR, Promputtha I, Samarakoon MC, Tibpromma S. Taxonomy and Phylogeny of Fungi Associated with Mangifera indica from Yunnan, China. J Fungi (Basel) 2022; 8:1249. [PMID: 36547582 PMCID: PMC9780836 DOI: 10.3390/jof8121249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
During investigations of saprobic fungi associated with mango (Mangifera indica) in Baoshan and Honghe of Yunnan Province (China), fungal taxa belonging to the orders Botryosphaeriales, Calosphaeriales, Chaetothyriales, Diaporthales, and Xylariales were recorded. Morphological examinations coupled with phylogenetic analyses of multigene sequences (ITS, LSU, SSU, tef1-α, rpb1, rpb2, β-tubulin and CAL) were used to identify the fungal taxa. A new genus viz. Mangifericola, four new species viz. Cyphellophora hongheensis, Diaporthe hongheensis, Hypoxylon hongheensis, and Mangifericola hongheensis, four new host and geographical records viz. Aplosporella artocarpi, Hypomontagnella monticulosa, Paraeutypella citricola and Pleurostoma ootheca, and two new collections of Lasiodiplodia are reported.
Collapse
Affiliation(s)
- Er-Fu Yang
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Master of Science Program in Applied Microbiology (International Program), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Samantha C. Karunarathna
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Dong-Qin Dai
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 12211, Saudi Arabia
| | - Salim Al-Rejaie
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh 12211, Saudi Arabia
| | - Yin-Ru Xiong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Milan C. Samarakoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saowaluck Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| |
Collapse
|
7
|
Fungal Grapevine Trunk Diseases in Romanian Vineyards in the Context of the International Situation. Pathogens 2022; 11:pathogens11091006. [PMID: 36145437 PMCID: PMC9503734 DOI: 10.3390/pathogens11091006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Vitis vinifera, known as the common grape vine, represents one of the most important fruit crops in the world. Romania is a wine-producing country with a rich and long tradition in viticulture. In the last decade, increasing reports of damage caused by grapevine trunk diseases (GTDs) have raised concerns in all wine producing countries. Up to now, no study was performed regarding the GTDs situation in Romania, an important grapevine grower in Europe. In this study, we aim, after a comprehensive presentation of the fungal GTDs worldwide, to review the scientific information related to these diseases in Romania in order to open a national platform in an international framework. In order to achieve this, we consulted over 500 references from different scientific databases and cited 309 of them. Our review concludes that, in Romania, there is little amount of available literature on this matter. Three out of six fungal GTDs are reported and well documented in all of the Romanian viticultural zones (except for viticultural zone 4). These are Eutypa dieback, Phomopsis dieback, and Esca disease. Of the fungal pathogens considered responsible Eutypa lata, Phomopsis viticola and Stereum hirsutum are the most studied and well documented in Romania. Management measures are quite limited, and they mostly include preventive measures to stop the GTDs spread and the removal of affected grapevines.
Collapse
|
8
|
Azevedo-Nogueira F, Rego C, Gonçalves HMR, Fortes AM, Gramaje D, Martins-Lopes P. The road to molecular identification and detection of fungal grapevine trunk diseases. FRONTIERS IN PLANT SCIENCE 2022; 13:960289. [PMID: 36092443 PMCID: PMC9459133 DOI: 10.3389/fpls.2022.960289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.
Collapse
Affiliation(s)
- Filipe Azevedo-Nogueira
- DNA & RNA Sensing Lab, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Cecília Rego
- LEAF - Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | | | - Ana Margarida Fortes
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - David Gramaje
- Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC), University of La Rioja and Government of La Rioja, Logroño, Spain
| | - Paula Martins-Lopes
- DNA & RNA Sensing Lab, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
9
|
Onetto CA, Sosnowski MR, Van Den Heuvel S, Borneman AR. Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters. PLoS Genet 2022; 18:e1010153. [PMID: 35363788 PMCID: PMC9007359 DOI: 10.1371/journal.pgen.1010153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/13/2022] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata. Despite the relevance of this species to the global wine industry, its genomic diversity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E. lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic diversity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations. Eutypa dieback of grapevine, caused by the Ascomycete fungus Eutypa lata, is responsible for significant economic losses to the wine industry. Despite the worldwide prevalence of this pathogen, its genomic diversity remains unknown, with only a single publicly available genome assembly. This knowledge gap was addressed by performing whole-genome sequencing of 40 E. lata isolates sourced from different hosts and geographical locations around Australia. Investigation of the genetic diversity of this population showed a high degree of gene-flow and sexual recombination as well as demographic expansion. Through the inspection of signatures of selective sweeps, repeat-mediated chromosomal rearrangements, and pan-genomic elements, it was shown that this species has a highly dynamic secondary metabolite production potential that could have important implications for its pathogenicity and lifestyle. In addition, application of a k-mer based GWAS methodology, identified a potential locus associated with the growth of this species within canes of Vitis vinifera.
Collapse
Affiliation(s)
| | - Mark R. Sosnowski
- South Australian Research and Development Institute, Adelaide, Australia
- School of Wine, Food and Agriculture, The University of Adelaide, Adelaide, Australia
| | | | - Anthony R. Borneman
- The Australian Wine Research Institute, Adelaide, Australia
- School of Wine, Food and Agriculture, The University of Adelaide, Adelaide, Australia
- * E-mail:
| |
Collapse
|
10
|
Kirkman ER, Hilton S, Sethuraman G, Elias DMO, Taylor A, Clarkson J, Soh AC, Bass D, Ooi GT, McNamara NP, Bending GD. Diversity and Ecological Guild Analysis of the Oil Palm Fungal Microbiome Across Root, Rhizosphere, and Soil Compartments. Front Microbiol 2022; 13:792928. [PMID: 35222328 PMCID: PMC8874247 DOI: 10.3389/fmicb.2022.792928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere microbiome is a major determinant of plant health, which can interact with the host directly and indirectly to promote or suppress productivity. Oil palm is one of the world’s most important crops, constituting over a third of global vegetable oil production. Currently there is little understanding of the oil palm microbiome and its contribution to plant health and productivity, with existing knowledge based almost entirely on culture dependent studies. We investigated the diversity and composition of the oil palm fungal microbiome in the bulk soil, rhizosphere soil, and roots of 2-, 18-, and 35-year old plantations in Selangor, Malaysia. The fungal community showed substantial variation between the plantations, accounting for 19.7% of community composition, with compartment (root, rhizosphere soil, and bulk soil), and soil properties (pH, C, N, and P) contributing 6.5 and 7.2% of community variation, respectively. Rhizosphere soil and roots supported distinct communities compared to the bulk soil, with significant enrichment of Agaricomycetes, Glomeromycetes, and Lecanoromycetes in roots. Several putative plant pathogens were abundant in roots in all the plantations, including taxa related to Prospodicola mexicana and Pleurostoma sp. The mycorrhizal status and dependency of oil palm has yet to be established, and using 18S rRNA primers we found considerable between-site variation in Glomeromycotinian community composition, accounting for 31.2% of variation. There was evidence for the selection of Glomeromycotinian communities in oil palm roots in the older plantations but compartment had a weak effect on community composition, accounting for 3.9% of variation, while soil variables accounted for 9% of community variation. While diverse Mucoromycotinian fungi were detected, they showed very low abundance and diversity within roots compared to bulk soil, and were not closely related to taxa which have been linked to fine root endophyte mycorrhizal morphology. Many of the fungal sequences showed low similarity to established genera, indicating the presence of substantial novel diversity with significance for plant health within the oil palm microbiome.
Collapse
Affiliation(s)
- Eleanor R. Kirkman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gomathy Sethuraman
- Crops for the Future Research Centre, Semenyih, Malaysia
- Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Dafydd M. O. Elias
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - John Clarkson
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Aik Chin Soh
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - David Bass
- Department of Life Sciences, Natural History Museum, London, United Kingdom
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom
| | - Gin Teng Ooi
- Crops for the Future Research Centre, Semenyih, Malaysia
| | - Niall P. McNamara
- UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, United Kingdom
| | - Gary D. Bending
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Gary D. Bending,
| |
Collapse
|
11
|
Reis P, Gaspar A, Alves A, Fontaine F, Rego C. Combining an HA + Cu (II) Site-Targeted Copper-Based Product with a Pruning Wound Protection Program to Prevent Infection with Lasiodiplodia spp. in Grapevine. PLANTS (BASEL, SWITZERLAND) 2021; 10:2376. [PMID: 34834739 PMCID: PMC8625631 DOI: 10.3390/plants10112376] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 05/06/2023]
Abstract
The genus Lasiodiplodia has been reported from several grape growing regions and is considered as one of the fastest wood colonizers, causing Botryosphaeria dieback. The aim of this study was to (i) evaluate the efficacy of Esquive®, a biocontrol agent, on vineyard pruning wound protection, applied single or, in a combined protection strategy with a new site-targeted copper-based treatment (LC2017), and (ii) compare their efficacy with chemical protection provided by the commercially available product, Tessior®. For two seasons, protectants were applied onto pruning wounds, while LC2017 was applied throughout the season according to the manufacturer's instructions. Pruning wounds of two different cultivars were inoculated with three isolates of Lasiodiplodia spp. Efficacy of the wound protectants, varied between both years of the assay and according to the cultivar studied but were able to control the pathogen to some extent. The application of LC2017 did not show clear evidence of improving the control obtained by the sole application of the other products tested. Nevertheless, LC2017 showed a fungistatic effect against Lasiodiplodia spp., in vitro, and has previously shown an elicitor effect against grapevine trunk diseases. Therefore, this combination of two protection strategies may constitute a promising long-term approach to mitigate the impact of Botryosphaeria dieback.
Collapse
Affiliation(s)
- Pedro Reis
- 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; (A.G.); (C.R.)
| | - Ana Gaspar
- 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; (A.G.); (C.R.)
| | - Artur Alves
- CESAM—Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Florence Fontaine
- SFR Condorcet FR CNRS 3417, Université de Reims Champagne-Ardenne, Résistance Induite et Bioprotection des Plantes EA 4707, BP 1039, CEDEX 2, 51687 Reims, France;
| | - Cecília Rego
- 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; (A.G.); (C.R.)
| |
Collapse
|
12
|
Mehrabi M, Asgari B, Hemmati R. Two new species of Eutypella and a new combination in the genus Peroneutypa (Diatrypaceae). Mycol Prog 2019. [DOI: 10.1007/s11557-019-01503-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
13
|
|
14
|
Massonnet M, Morales-Cruz A, Minio A, Figueroa-Balderas R, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum. Front Microbiol 2018; 9:1784. [PMID: 30150972 PMCID: PMC6099105 DOI: 10.3389/fmicb.2018.01784] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022] Open
Abstract
The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.
Collapse
Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| |
Collapse
|
15
|
Gramaje D, Úrbez-Torres JR, Sosnowski MR. Managing Grapevine Trunk Diseases With Respect to Etiology and Epidemiology: Current Strategies and Future Prospects. PLANT DISEASE 2018; 102:12-39. [PMID: 30673457 DOI: 10.1094/pdis-04-17-0512-fe] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fungal trunk diseases are some of the most destructive diseases of grapevine in all grape growing areas of the world. Management of GTDs has been intensively studied for decades with some great advances made in our understanding of the causal pathogens, their epidemiology, impact, and control. However, due to the breadth and complexity of the problem, no single effective control measure has been developed. Management of GTD must be holistic and integrated, with an interdisciplinary approach conducted in both nurseries and vineyards that integrates plant pathology, agronomy, viticulture, microbiology, epidemiology, biochemistry, physiology, and genetics. In this review, we identify a number of areas of future prospect for effective management of GTDs worldwide, which, if addressed, will provide a positive outlook on the longevity of vineyards in the future.
Collapse
Affiliation(s)
- David Gramaje
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de la Rioja, Logroño 26007, Spain
| | - José Ramón Úrbez-Torres
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Science and Technology Branch, Summerland, British Columbia V0H1Z0, Canada
| | - Mark R Sosnowski
- South Australian Research and Development Institute, GPO Box 397, Adelaide SA 5001, Australia; and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, SA 5005, Australia
| |
Collapse
|
16
|
Moyo P, Mostert L, Spies CFJ, Damm U, Halleen F. Diversity of Diatrypaceae Species Associated with Dieback of Grapevines in South Africa, with the Description of Eutypa cremea sp. nov. PLANT DISEASE 2018; 102:220-230. [PMID: 30673471 DOI: 10.1094/pdis-05-17-0738-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent studies in grape-growing areas including Australia, California, and Spain have revealed an extensive diversity of Diatrypaceae species on grapevines showing dieback symptoms and cankers. However, in South Africa, little is known regarding the diversity of these species in vineyards. The aim of this study was, therefore, to identify and characterize Diatrypaceae species associated with dieback symptoms of grapevine in South Africa. Isolates were collected from dying spurs of grapevines aged 4 to 8 years old, grapevine wood showing wedge-shaped necrosis when cut in cross section as well as from perithecia on dead grapevine wood. The collected isolates were identified based on morphological characters and phylogenetic analyses of the internal transcribed spacer region (ITS) and β-tubulin gene. Seven Diatrypaceae species were identified on grapevine, namely Cryptovalsa ampelina, C. rabenhorstii, Eutypa consobrina, E. lata, E. cremea sp. nov., Eutypella citricola, and E. microtheca. The dying spurs yielded the highest diversity of species when compared with the wedge-shaped necrosis and/or perithecia. C. ampelina was the dominant species in the dying spurs, followed by E. citricola, whereas E. lata was the dominant species isolated from the wedge-shaped necroses and perithecia. These results confirm E. lata as an important grapevine canker pathogen in South Africa, but the frequent association of C. ampelina with spur dieback suggests that this pathogen plays a more prominent role in dieback than previously assumed. In some cases, more than one species were isolated from a single symptom, which suggests that interactions may be occurring leading to decline of grapevines. C. rabenhorstii, E. consobrina, E. citricola, E. microtheca, and E. cremea are reported for the first time on grapevine in South Africa.
Collapse
Affiliation(s)
- Providence Moyo
- Department of Plant Pathology, University of Stellenbosch, Matieland, 7602, South Africa
| | - Lizel Mostert
- Department of Plant Pathology, University of Stellenbosch, Matieland, 7602, South Africa
| | - Christoffel F J Spies
- Plant Protection Division, ARC Infruitec-Nietvoorbji, Stellenbosch, 7599, South Africa
| | - Ulrike Damm
- Senckenberg Museum of Natural History Görlitz, 02806 Görlitz, Germany
| | - Francois Halleen
- Plant Protection Division, ARC Infruitec-Nietvoorbji, Stellenbosch, 7599, South Africa
| |
Collapse
|
17
|
Mayorquin JS, Wang DH, Twizeyimana M, Eskalen A. Identification, Distribution, and Pathogenicity of Diatrypaceae and Botryosphaeriaceae Associated with Citrus Branch Canker in the Southern California Desert. PLANT DISEASE 2016; 100:2402-2413. [PMID: 30686172 DOI: 10.1094/pdis-03-16-0362-re] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Several members of the families Botryosphaeriaceae and Diatrypaceae are known as canker and dieback pathogens of a number of woody hosts. Because desert citrus production in California can occur in proximity to table grape production, it was suspected that fungi associated with grapevine cankers might also be associated with citrus branch canker and dieback decline. To determine the fungi associated with branch canker and dieback disease of citrus in the southern California desert regions, surveys were conducted from 2011 to 2013 in the major citrus-growing regions of Riverside, Imperial, and San Diego Counties. Cankered tissues were collected from branches showing symptoms typical of branch canker and dieback. Various fungal species were recovered from necrotic tissues and species were identified morphologically and by phylogenetic comparison of partial sequences of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), β-tubulin gene, and elongation factor 1-α genes with those of other species in GenBank. Four fungi, including Neoscytalidium hyalinum, Eutypella citricola, E. microtheca, and an unnamed Eutypella sp., were associated with branch canker. N. hyalinum was the most frequently recovered fungus from symptomatic tissues (31%) followed by E. citricola (10%), E. microtheca (4%), and the Eutypella sp. (2%). In pathogenicity tests, all fungi caused lesions when inoculated on 'Lisbon' lemon (citrus) branches. Lesions caused by the Eutypella sp. were significantly longer than those of the other Eutypella spp.; however, they did not differ significantly from those produced by N. hyalinum. The most-parsimonious unrooted trees based on the combined data of ITS and partial β-tubulin gene region sequences showed three distinct clades of Eutypella spp. (E. citricola, E. microtheca, and an unidentified Eutypella sp.). Similarly, ITS and partial translation elongation factor 1-α gene region sequences differentiated two species of Neoscytalidium, N. hyalinum and N. novaehollandiae. Identifying the diversity, distribution, and occurrence of these fungal pathogens is useful for the management of citrus branch canker and dieback disease in the desert citrus-growing regions of California.
Collapse
Affiliation(s)
- Joey S Mayorquin
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| | - Danny H Wang
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| | - Mathias Twizeyimana
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| | - Akif Eskalen
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521
| |
Collapse
|
18
|
|