1
|
Belete MT, Kim SE, Gudeta WF, Igori D, Kwon JA, Lee SH, Moon JS. Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis. Virol J 2024; 21:86. [PMID: 38622686 PMCID: PMC11017662 DOI: 10.1186/s12985-024-02361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.
Collapse
Affiliation(s)
- Mesele Tilahun Belete
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Amhara Agricultural Research Institute, Plant Biotechnology Research Division, Bahir Dar, Ethiopia
| | - Se Eun Kim
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Workitu Firmosa Gudeta
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jeong A Kwon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 98411, Republic of Korea.
| | - Jae Sun Moon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
2
|
Vergani L, Patania J, Riva V, Nerva L, Nuzzo F, Gambino G, Borin S, Mapelli F. Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants. Appl Environ Microbiol 2024; 90:e0207823. [PMID: 38289136 PMCID: PMC10880630 DOI: 10.1128/aem.02078-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/03/2024] [Indexed: 02/22/2024] Open
Abstract
Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.
Collapse
Affiliation(s)
- Lorenzo Vergani
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Milan, Italy
| | - Joa Patania
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Milan, Italy
| | - Valentina Riva
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Milan, Italy
| | - Luca Nerva
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
- Italy Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics, Conegliano, Italy
| | - Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Turin, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Milan, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Science (DeFENS), University of Milan, Milan, Italy
| |
Collapse
|
3
|
Vinogradova S, Porotikova E, Navrotskaya E, Galbacs ZN, Massart S, Varallyay E. The First Virome of a Russian Vineyard. PLANTS (BASEL, SWITZERLAND) 2023; 12:3292. [PMID: 37765456 PMCID: PMC10534617 DOI: 10.3390/plants12183292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.
Collapse
Affiliation(s)
- Svetlana Vinogradova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Elena Porotikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Emiliya Navrotskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, Liège University, 5030 Gembloux, Belgium
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, H-2100 Godollo, Hungary
| |
Collapse
|
4
|
Tarquini G, Dall'Ara M, Ermacora P, Ratti C. Traditional Approaches and Emerging Biotechnologies in Grapevine Virology. Viruses 2023; 15:v15040826. [PMID: 37112807 PMCID: PMC10142720 DOI: 10.3390/v15040826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Environmental changes and global warming may promote the emergence of unknown viruses, whose spread is favored by the trade in plant products. Viruses represent a major threat to viticulture and the wine industry. Their management is challenging and mostly relies on prophylactic measures that are intended to prevent the introduction of viruses into vineyards. Besides the use of virus-free planting material, the employment of agrochemicals is a major strategy to prevent the spread of insect vectors in vineyards. According to the goal of the European Green Deal, a 50% decrease in the use of agrochemicals is expected before 2030. Thus, the development of alternative strategies that allow the sustainable control of viral diseases in vineyards is strongly needed. Here, we present a set of innovative biotechnological tools that have been developed to induce virus resistance in plants. From transgenesis to the still-debated genome editing technologies and RNAi-based strategies, this review discusses numerous illustrative studies that highlight the effectiveness of these promising tools for the management of viral infections in grapevine. Finally, the development of viral vectors from grapevine viruses is described, revealing their positive and unconventional roles, from targets to tools, in emerging biotechnologies.
Collapse
Affiliation(s)
- Giulia Tarquini
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Mattia Dall'Ara
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Paolo Ermacora
- Department of Agricultural, Environmental, Food and Animal Sciences (Di4A), University of Udine, 33100 Udine, Italy
| | - Claudio Ratti
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| |
Collapse
|
5
|
Genetic Diversity of Viral Populations Associated with Ananas Germplasm and Improvement of Virus Diagnostic Protocols. Pathogens 2022; 11:pathogens11121470. [PMID: 36558805 PMCID: PMC9787488 DOI: 10.3390/pathogens11121470] [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: 10/26/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Pineapple (Ananas comosus L. [Merr.]) accessions from the U.S. Tropical Plant Genetic Resources and Disease Research (TPGRDR) in Hilo, Hawaii were subjected to RNA-sequencing to study the occurrence of viral populations associated with this vegetatively propagated crop. Analysis of high-throughput sequencing data obtained from 24 germplasm accessions and public domain transcriptome shotgun assembly (TSA) data identified two novel sadwaviruses, putatively named "pineapple secovirus C" (PSV-C) and "pineapple secovirus D" (PSV-D). They shared low amino acid sequence identity (from 34.8 to 41.3%) compared with their homologs in the Pro-pol region of the previously reported PSV-A and PSV-B. The complete genome (7485 bp) corresponding to a previously reported partial sequence of the badnavirus, pineapple bacilliform ER virus (PBERV), was retrieved from one of the datasets. Overall, we discovered a total of 69 viral sequences representing ten members within the Ampelovirus, Sadwavirus, and Badnavirus genera. Genetic diversity and recombination events were found in members of the pineapple mealybug wilt-associated virus (PMWaV) complex as well as PSVs. PMWaV-1, -3, and -6 presented recombination events across the quintuple gene block, while no recombination events were found for PMWaV-2. High recombination frequency of the RNA1 and RNA2 molecules from PSV-A and PSV-B were congruent with the diversity found by phylogenetic analyses. Here, we also report the development and improvement of RT-PCR diagnostic protocols for the specific identification and detection of viruses infecting pineapple based on the diverse viral populations characterized in this study. Given the high occurrence of recombination events, diversity, and discovery of viruses found in Ananas germplasm, the reported and validated RT-PCR assays represent an important advance for surveillance of viral infections of pineapple.
Collapse
|
6
|
Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia). Viruses 2022; 14:v14061314. [PMID: 35746784 PMCID: PMC9230720 DOI: 10.3390/v14061314] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.
Collapse
|