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Khan HA, Baig DI, Bhatti MF. An Overview of Mycoviral Curing Strategies Used in Evaluating Fungal Host Fitness. Mol Biotechnol 2023; 65:1547-1564. [PMID: 36841858 PMCID: PMC9963364 DOI: 10.1007/s12033-023-00695-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/11/2023] [Indexed: 02/27/2023]
Abstract
The number of novel mycoviruses is increasing at a high pace due to advancements in sequencing technologies. As a result, an uncountable number of mycoviral sequences are available in public sequence repositories. However, only genomic information is not sufficient to understand the impact of mycoviruses on their host biology. Biological characterization is required to determine the nature of mycoviruses (cryptic, hypervirulent, or hypovirulent) and to search for mycoviruses with biocontrol and therapeutic potential. Currently, no particular selective method is used as the gold standard against these mycoviral infections. Given the importance of curing, we present an overview of procedures used in preparation of isogenic lines, along with their benefits and drawbacks. We concluded that a combination of single-spore isolation and hyphal tipping is the best fit for preparation of isogenic lines. Furthermore, recent bioinformatic approaches should be introduced in the field of mycovirology to predict virus-specific antivirals to get robust results.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
- Department of Biotechnology, University of Mianwali, Punjab, 42200 Pakistan
| | - Danish Ilyas Baig
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000 Pakistan
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2
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Khan HA, Nerva L, Bhatti MF. The good, the bad and the cryptic: The multifaceted roles of mycoviruses and their potential applications for a sustainable agriculture. Virology 2023; 585:259-269. [PMID: 37453341 DOI: 10.1016/j.virol.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Mycoviruses are natural inhabitants of fungi and have been identified in almost all fungal taxonomic groups. Mycoviruses that infect phytopathogenic fungi are now becoming a hot research area due to their potential for the biocontrol of important plant pathogens. But, before considering a mycovirus for biocontrol, we should be fully aware of the effects it induces in a fungal host and its interactions with other viruses, fungal strains and even the host plants. Mycoviral infections are generally associated with different effects, ranging from hypovirulence to hypervirulence, but they can often be cryptic (latent infections). The cryptic lifestyle has been associated to many mycoviruses, but thanks to growing knowledge we are now aware that it is often associated to axenic conditions while the real effects can be observed only in nature. Other mycoviruses either promote (hypervirulence) or (hypovirulence) fungal pathogenicity by a strong impact on the fungal physiology or by blocking the production of toxins or effectors. Finally, indirect effects of mycoviral infections can also be provided to the plant that hosts the fungal isolate, highlighting not only their potential as direct biocontrol agents but also as priming agents for plant resilience to biotic and abiotic stresses. This review provides a broad overview of mycoviral interactions both with their hosts and with other mycoviruses, highlighting the most interesting examples. In contrast to what has been observed to date, we believe that the collective availability of these data will not only improve our understanding of mycoviruses, but also increase our confidence in considering them as alternative measures against fungal diseases to improve the sustainable production of food and feed commodities.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan; Department of Biotechnology, University of Mianwali, Punjab, 42200, Pakistan
| | - Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile, 31015, Conegliano, (TV), Italy.
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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3
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Jaccard A, Dubuis N, Kellenberger I, Brodard J, Schnee S, Gindro K, Schumpp O. New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus. J Gen Virol 2023; 104:001879. [PMID: 37549001 PMCID: PMC10539651 DOI: 10.1099/jgv.0.001879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5' and 3' end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.
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Affiliation(s)
| | - Nathalie Dubuis
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | | | - Justine Brodard
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Sylvain Schnee
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Katia Gindro
- Department of Plant Protection, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Department of Plant Protection, Agroscope, Nyon, Switzerland
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Villan Larios DC, Diaz Reyes BM, Pirovani CP, Loguercio LL, Santos VC, Góes-Neto A, Fonseca PLC, Aguiar ERGR. Exploring the Mycovirus Universe: Identification, Diversity, and Biotechnological Applications. J Fungi (Basel) 2023; 9:jof9030361. [PMID: 36983529 PMCID: PMC10052124 DOI: 10.3390/jof9030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
Viruses that infect fungi are known as mycoviruses and are characterized by the lack of an extracellular phase. In recent years, the advances on nucleic acids sequencing technologies have led to a considerable increase in the number of fungi-infecting viral species described in the literature, with a special interest in assessing potential applications as fungal biocontrol agents. In the present study, we performed a comprehensive review using Scopus, Web of Science, and PubMed databases to mine mycoviruses data to explore their molecular features and their use in biotechnology. Our results showed the existence of 267 mycovirus species, of which 189 are recognized by the International Committee on Taxonomy of Viruses (ICTV). The majority of the mycoviruses identified have a dsRNA genome (38.6%), whereas the Botourmiaviridae (ssRNA+) alone represents 14% of all mycoviruses diversity. Regarding fungal hosts, members from the Sclerotinicaeae appeared as the most common species described to be infected by mycoviruses, with 16 different viral families identified so far. It is noteworthy that such results are directly associated with the high number of studies and strategies used to investigate the presence of viruses in members of the Sclerotinicaeae family. The knowledge about replication strategy and possible impact on fungi biology is available for only a small fraction of the mycoviruses studied, which is the main limitation for considering these elements potential targets for biotechnological applications. Altogether, our investigation allowed us to summarize the general characteristics of mycoviruses and their hosts, the consequences, and the implications of this knowledge on mycovirus–fungi interactions, providing an important source of information for future studies.
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Affiliation(s)
- Diana Carolina Villan Larios
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Brayan Maudiel Diaz Reyes
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Leandro Lopes Loguercio
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
| | - Vinícius Castro Santos
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil;
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil;
| | - Paula Luize Camargos Fonseca
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
- Correspondence: (P.L.C.F.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biological Sciences, Center for Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (D.C.V.L.); (B.M.D.R.); (C.P.P.); (L.L.L.)
- Correspondence: (P.L.C.F.); (E.R.G.R.A.)
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5
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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Ikeda A, Chiba Y, Kuroki M, Urayama SI, Hagiwara D. Efficient elimination of RNA mycoviruses in aspergillus species using RdRp-inhibitors ribavirin and 2'-C-methylribonucleoside derivatives. Front Microbiol 2022; 13:1024933. [PMID: 36274709 PMCID: PMC9583132 DOI: 10.3389/fmicb.2022.1024933] [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: 08/22/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
RNA viruses in fungi (mycoviruses) are model systems for understanding the relationships between eukaryotic microorganisms and RNA viruses. To reveal the effects of mycoviruses on host fungi, it is essential to compare the phenotypes between isogenic fungal isolates with or without RNA virus infection. Since active entry machinery for RNA mycoviruses has never been identified, introducing mycoviruses to fungi is a difficult and time-consuming process. Therefore, most studies have tried to generate virus-free isolates from infected strains by eliminating the mycovirus. However, methods of elimination have not been evaluated in a quantitative and comparative manner. In this study, we established a method to remove mycoviruses from host cells using the antiviral drugs ribavirin, 2'-C-methylcytidine (2CMC), 2'-C-methyladenosine (2CMA), and 7d2CMA, and compared the efficiency of removal in virus-infected strains of Aspergillus fumigatus. The results indicated that treatment with the drugs removed RNA viruses of diverse proportions in the families Chrysoviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and an unclassified RNA virus group. Viruses belonging to Narnaviridae were hardly eliminated by these antiviral treatments when they were the sole infectious agents. We found that 2CMC showed activity against a wider range of RNA mycoviruses compared to ribavirin, 2CMA, and 7d2CMA, although 7d2CMA also efficiently removed dsRNA viruses from the families Chrysoviridae, Partitiviridae, and Polymycoviridae. These results indicated that removal of mycoviruses depends on the specific viral species and antiviral drug. This is the first report demonstrating a preferential antiviral effect against mycoviruses, which will enhance research on microbial RNA viruses and support their elimination from economically important fungi such as edible mushrooms.
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Affiliation(s)
- Ayano Ikeda
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Misa Kuroki
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Syun-ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Ibaraki, Japan,*Correspondence: Syun-ichi Urayama,
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Ibaraki, Japan,Daisuke Hagiwara,
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7
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Li B, Cao Y, Ji Z, Zhang J, Meng X, Dai P, Hu T, Wang S, Cao K, Wang Y. Coinfection of Two Mycoviruses Confers Hypovirulence and Reduces the Production of Mycotoxin Alternariol in Alternaria alternata f. sp. mali. Front Microbiol 2022; 13:910712. [PMID: 35756001 PMCID: PMC9218907 DOI: 10.3389/fmicb.2022.910712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/22/2022] Open
Abstract
Alternaria leaf blotch caused by Alternaria alternata apple pathotype (Alternaria mali) is an important fungal disease that affects the production of apples worldwide. Mycoviruses harbored in plant pathogenic fungi can confer hypovirulence in their hosts and have attracted widespread attention as potential biocontrol tools. In this study, the coinfection of two mycoviruses, named A. alternata chrysovirus 1 strain QY2 (AaCV1-QY2) and A. alternata magoulivirus 1 (AaMV1), respectively, were isolated from A. alternata f. sp. mali strain QY21. Sequence analyses revealed that AaCV1-QY2 virus belonged to the genus Betachrysovirus and AaMV1 virus belonged to the genus Magoulvirus. These two mycoviruses were found to be associated with hypovirulence in A. alternata, among which AaCV1-QY2 might play a relatively leading role. Because the elimination of AaMV1 from the strain QY21 does not affect the hypovirulence trait, which indicates that the virus AaCV1-QY2 can independently induce slow growth and reduce host virulence. Moreover, the presence of viruses decreased the accumulation of the mycotoxin alternariol (AOH) in A. alternata strains. Intriguingly, AaCV1-QY2/AaMV1 mycoviruses can be horizontally transmitted to other A. alternata strains, and this coinfection can promote the interspecific transmission efficiency of AaCV1-QY2. To our knowledge, this study reports the first description of the member of Chrysovirus is related to hypovirulence in Alternaria spp. that facilitates the development of biocontrol measures of A. mali Roberts.
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Affiliation(s)
- Bo Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Yuhan Cao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Zixuan Ji
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jingyi Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xianglong Meng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Pengbo Dai
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Tongle Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shutong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Keqiang Cao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Yanan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
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Kashif M, Jurvansuu J, Hyder R, Vainio EJ, Hantula J. Phenotypic Recovery of a Heterobasidion Isolate Infected by a Debilitation-Associated Virus Is Related to Altered Host Gene Expression and Reduced Virus Titer. Front Microbiol 2022; 12:661554. [PMID: 35310390 PMCID: PMC8930199 DOI: 10.3389/fmicb.2021.661554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
The fungal genus Heterobasidion includes forest pathogenic species hosting a diverse group of partitiviruses. They include the host debilitating Heterobasidion partitivirus 13 strain an1 (HetPV13-an1), which was originally observed in a slowly growing H. annosum strain 94233. In this study, a relatively fast-growing sector strain 94233-RC3 was isolated from a highly debilitated mycelial culture of 94233, and its gene expression and virus transcript quantities as well as the genomic sequence of HetPV13-an1 were examined. The sequence of HetPV13-an1 genome in 94233-RC3 was identical to that in the original 94233, and thus not the reason for the partial phenotypic recovery. According to RNA-seq analysis, the HetPV13-an1 infected 94233-RC3 transcribed eight genes differently from the partitivirus-free 94233-32D. Three of these genes were downregulated and five upregulated. The number of differentially expressed genes was considerably lower and the changes in their expression were small compared to those of the highly debilitated original strain 94233 with the exception of the most highly upregulated ones, and therefore viral effects on the host transcriptome correlated with the degree of the virus-caused debilitation. The amounts of RdRp and CP transcripts of HetPV13-an1 were considerably lower in 94233-RC3 and also in 94233 strain infected by a closely related mildly debilitating virus HetPV13-an2, suggesting that the virus titer would have a role in determining the effect of HetPV13 viruses on their hosts.
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Affiliation(s)
| | | | - Rafiqul Hyder
- Natural Resources Institute Finland, Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland, Helsinki, Finland
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9
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Sutela S, Piri T, Vainio EJ. Discovery and Community Dynamics of Novel ssRNA Mycoviruses in the Conifer Pathogen Heterobasidion parviporum. Front Microbiol 2021; 12:770787. [PMID: 34899655 PMCID: PMC8652122 DOI: 10.3389/fmicb.2021.770787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Heterobasidion species are highly destructive basidiomycetous conifer pathogens of the Boreal forest region. Earlier studies have revealed dsRNA virus infections of families Curvulaviridae and Partitiviridae in Heterobasidion strains, and small RNA deep sequencing has also identified infections of Mitoviridae members in these fungi. In this study, the virome of Heterobasidion parviporum was examined for the first time by RNA-Seq using total RNA depleted of rRNA. This method successfully revealed new viruses representing two established (+)ssRNA virus families not found earlier in Heterobasidion: Narnaviridae and Botourmiaviridae. In addition, we identified the presence of a recently described virus group tentatively named “ambiviruses” in H. parviporum. The H. parviporum isolates included in the study originated from experimental forest sites located within 0.7 km range from each other, and a population analysis including 43 isolates was conducted at one of the experimental plots to establish the prevalence of the newly identified viruses in clonally spreading H. parviporum individuals. Our results indicate that viral infections are considerably more diverse and common among Heterobasidion isolates than known earlier and include ssRNA viruses with high prevalence and interspecies variation.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tuula Piri
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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10
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Abstract
This study provides new information on the infection biology and pathogenicity of an important root-rot fungus, Heterobasidion annosum sensu stricto (Fr.) Bref., through a detailed examination of the vegetative spread of clonal individuals and their capacity to produce fruiting bodies on young pine seedlings. The seedlings were planted in a clear-cutting area (c. 1.2 ha in size) after a pine generation that showed slight external symptoms of Heterobasidion root rot. The first dead seedlings were found five years after planting and during a nine-year monitoring period; nearly 600 seedlings were killed by H. annosum s.s. in 48 individual disease centers. Based on pairing tests of 482 isolates, 117 different H. annosum s.s. genotypes were identified. On average, 2.9 genotypes occurred in a single disease center. The extensive secondary spread of genotypes within root systems (up to 48 pine seedlings infected by the same genotype) resulted in annually expanding disease centers. In addition, more than half of the seedlings killed by H. annosum s.s. produced perennial fruiting bodies thus providing air-borne inoculum. The risk of spore infection should be taken into account in any type of cutting operation in young pine stands. Moreover, new control measures directed towards the secondary spread of H. annosum s.s. in pine regeneration are urgently needed in order to maintain the productivity of the pine forest on infested sites.
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11
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O'Connor E, Doyle S, Amini A, Grogan H, Fitzpatrick DA. Transmission of mushroom virus X and the impact of virus infection on the transcriptomes and proteomes of different strains of Agaricus bisporus. Fungal Biol 2021; 125:704-717. [PMID: 34420697 DOI: 10.1016/j.funbio.2021.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 11/19/2022]
Abstract
Cultivation of Agaricus bisporus is a large horticultural industry for many countries worldwide, where a single variety is almost grown exclusively. Mushroom virus X (MVX), a complex of multiple positive-sense single stranded RNA (ss(+)RNA) viruses, is a major pathogen of typical A. bisporus crops. MVX can manifest a variety of symptoms in crops and is highly infective and difficult to eradicate once established in host mycelium. Currently our knowledge regarding the molecular response of A. bisporus fruit bodies to MVX infection is limited. In order to study the response of different A. bisporus strains with different susceptibilities to MVX, we designed a model system to evaluate the in-vitro transmission of viruses in A. bisporus hyphae over a time-course, at two crucial phases in the crop cycle. The symptom expression of MVX in these varieties and the transcriptomic and proteomic response of fruit bodies to MVX-infection were examined. Transmission studies revealed the high potential of MVX to spread to uninfected mycelium yet not into the fruit bodies of certain strains in a crop. MVX affected colour and quality of multiple fruit bodies. Gene expression is significantly altered in all strains and between times of inoculation in the crop. Genes related to stress responses displayed differential expression. Proteomic responses revealed restriction of cellular signalling and vesicle transport in infected fruit bodies. This in-depth analysis examining many factors relevant to MVX infection in different A. bisporus strains, will provide key insights into host responses for this commercially important food crop.
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Affiliation(s)
- Eoin O'Connor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland; Horticulture Development Department, Teagasc Food Research Centre, Ashtown, Dublin 15, D15 KN3K, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Aniça Amini
- Sylvan-Somycel (ESSC - Unité 2), ZI SUD, Rue Lavoisier, BP 25, 37130 Langeais, France
| | - Helen Grogan
- Horticulture Development Department, Teagasc Food Research Centre, Ashtown, Dublin 15, D15 KN3K, Ireland
| | - David A Fitzpatrick
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland.
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12
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Rumbou A, Vainio EJ, Büttner C. Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems. Microorganisms 2021; 9:microorganisms9081730. [PMID: 34442809 PMCID: PMC8399312 DOI: 10.3390/microorganisms9081730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.
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Affiliation(s)
- Artemis Rumbou
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
- Correspondence:
| | - Eeva J. Vainio
- Natural Resources Institute Finland, Forest Health and Biodiversity, Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Carmen Büttner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
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13
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Poimala A, Parikka P, Hantula J, Vainio EJ. Viral diversity in Phytophthora cactorum population infecting strawberry. Environ Microbiol 2021; 23:5200-5221. [PMID: 33848054 DOI: 10.1111/1462-2920.15519] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/18/2021] [Accepted: 04/08/2021] [Indexed: 01/31/2023]
Abstract
Eighty-eight Phytophthora cactorum strains isolated from crown or leather rot of strawberry in 1971-2019 were screened for viruses using RNA-seq and RT-PCR. Remarkably, all but one isolate were virus-infected, most of them harbouring more than one virus of different genera or species. The most common virus occurring in 94% of the isolates was the Phytophthora cactorum RNA virus 1 (PcRV1) resembling members of Totiviridae. Novel viruses related to members of Endornaviridae, named Phytophthora cactorum alphaendornaviruses 1-3 (PcAEV1-3), were found in 57% of the isolates. Four isolates hosted viruses with affinities to Bunyaviridae, named Phytophthora cactorum bunyaviruses 1-3 (PcBV1-3), and a virus resembling members of the proposed genus 'Ustivirus', named Phytophthora cactorum usti-like virus (PcUV1), was found in a single isolate. Most of the virus species were represented by several distinct strains sharing ≥81.4% aa sequence identity. We found no evidence of spatial differentiation but some temporal changes in the P. cactorum virus community were observed. Some isolates harboured two or more closely related strains of the same virus (PcAEV1 or PcRV1) sharing 86.6%-96.4% nt identity in their polymerase sequence. This was surprising as viruses with such a high similarity are typically mutually exclusive.
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Affiliation(s)
- Anna Poimala
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Päivi Parikka
- Natural Resources Institute Finland (Luke), Plant Health, Humppilantie 18, Jokioinen, 31600, Finland
| | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity, Latokartanonkaari 9, Helsinki, FI-00790, Finland
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14
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Liu Y, Zhang L, Esmael A, Duan J, Bian X, Jia J, Xie J, Cheng J, Fu Y, Jiang D, Lin Y. Four Novel Botourmiaviruses Co-Infecting an Isolate of the Rice Blast Fungus Magnaporthe oryzae. Viruses 2020; 12:E1383. [PMID: 33287110 PMCID: PMC7761653 DOI: 10.3390/v12121383] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
Via virome sequencing, six viruses were detected from Magnaporthe oryzae strains YC81-2, including one virus in the family Tombusviridae, one virus in the family Narnaviridae and four viruses in the family Botourmiaviridae. Since the RNA-dependent RNA polymerase (RdRp) of one botourmiavirus show the highest identity (79%) with Magnaporthe oryzae ourmia-like virus 1 (MOLV1), the virus that was grouped into the genus Magoulivirus was designated as Magnaporthe oryzae botourmiavirus 2 (MOBV2). The three other novel botourmiaviruses were selected for further study. The complete nucleotide sequences of the three botourmiaviruses were determined. Sequence analysis showed that virus 1, virus 2, and virus 3 were 2598, 2385, and 2326 nts in length, respectively. The variable 3' untranslated region (3'-UTR) and 5'-UTR of each virus could be folded into a stable stem-loop secondary structure. Each virus consisted of a unique ORF encoding a putative RdRp. The putative proteins with a conserved GDD motif of RdRp showed the highest sequence similarity to RdRps of viruses in the family Botourmiaviridae. Phylogenetic analysis demonstrated that these viruses were three distinct novel botourmiaviruses, clustered into the Botourmiaviridae family but not belonging to any known genera of this family. Thus, virus 1, virus 2, and virus 3 were designated as Magnaporthe oryzae botourmiavirus 5, 6, and 7 (MOBV5, MOBV6, and MOBV7), respectively. Our results suggest that four distinct botourmiaviruses, MOBV2, MOBV5, MOBV6, and MOBV7, co-infect a single strain of Magnaporthe oryzae, and MOBV5, MOBV6, and MOBV7 are members of three unclassified genera in the family Botourmiaviridae.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
| | - Liyan Zhang
- Institute of Biotechnology, Heilongjiang Academy of Agricultural Sciences, Harbin 150001, China;
| | - Ahmed Esmael
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
- Botany and Microbiology Department, Faculty of Science, Benha University, Qalubiya Governorate, Benha 13511, Egypt
| | - Jie Duan
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Xuefeng Bian
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.L.); (A.E.); (J.J.); (J.X.); (D.J.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (X.B.); (J.C.); (Y.F.)
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15
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Velasco L, López-Herrera C, Cretazzo E. Two novel partitiviruses that accumulate differentially in Rosellinia necatrix and Entoleuca sp. infecting avocado. Virus Res 2020; 285:198020. [PMID: 32416260 DOI: 10.1016/j.virusres.2020.198020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/09/2020] [Accepted: 05/09/2020] [Indexed: 01/26/2023]
Abstract
Rosellinia necatrix is responsible for the white rot root disease of avocado in Southern Spain. Entoleuca sp. is a fungus isolated from roots of these same trees, but it is not pathogenic in avocado. Here, we describe two new species of partitiviruses detected in isolates of the avocado sympatric fungi Entoleuca sp. and R. necatrix, termed Entoleuca partitivirus 1 (EnPV1), genus Alphapartitivirus, and Entoleuca partitivirus 2 (EnPV2), genus Betapartitivirus. For both R. necatrix and Entoleuca sp., the dsRNA of the RdRp genomic segment of EnPV1 accumulates at a higher rate than the CP dsRNA, except for a set of Entoleuca sp. isolates where titers of the CP dsRNA are 35-50 times higher than those of the RdRp dsRNA and between 250-380 times higher than the CP dsRNA titers found in the rest of Entoleuca sp. and R. necatrix isolates. For EnPV2, the accumulation rates of the RdRp dsRNA in Entoleuca sp., is in most of the cases, higher than the CP dsRNA. In contrast, in R. necatrix isolates, EnPV2 dsRNA2 generally accumulates at a higher rate. Genetic analysis of the partitiviruses revealed that there is no apparent variation in the nucleotide sequences among the strains. RNA silencing of the partitiviruses appears to be limited in Entoleuca sp., as shown by small RNA sequencing. Finally, the investigation of the presence of these partitiviruses in a fungal collection revealed that they have no role in the pathogenicity of R. necatrix in avocado or in the avirulence of Entoleuca sp. in this host.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz De Investigación y Formación Agraria (IFAPA), 29130, Málaga, Spain.
| | | | - Enrico Cretazzo
- Instituto Andaluz De Investigación y Formación Agraria (IFAPA), 29130, Málaga, Spain
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16
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Proteomic investigation of interhyphal interactions between strains of Agaricus bisporus. Fungal Biol 2020; 124:579-591. [PMID: 32448449 DOI: 10.1016/j.funbio.2020.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 11/23/2022]
Abstract
Hyphae of filamentous fungi undergo polar extension, bifurcation and hyphal fusion to form reticulating networks of mycelia. Hyphal fusion or anastomosis, a ubiquitous process among filamentous fungi, is a vital strategy for how fungi expand over their substrate and interact with or recognise self- and non-self hyphae of neighbouring mycelia in their environment. Morphological and genetic characterisation of anastomosis has been studied in many model fungal species, but little is known of the direct proteomic response of two interacting fungal isolates. Agaricus bisporus, the most widely cultivated edible mushroom crop worldwide, was used as an in vitro model to profile the proteomes of interacting cultures. The globally cultivated strain (A15) was paired with two distinct strains; a commercial hybrid strain and a wild isolate strain. Each co-culture presented a different interaction ranging from complete vegetative compatibility (self), lack of interactions, and antagonistic interactions. These incompatible strains are the focus of research into disease-resistance in commercial crops as the spread of intracellular pathogens, namely mycoviruses, is limited by the lack of interhyphal anastomosis. Unique proteomic responses were detected between all co-cultures. An array of cell wall modifying enzymes, plus fungal growth and morphogenesis proteins were found in significantly (P < 0.05) altered abundances. Nitrogen metabolism dominated in the intracellular proteome, with evidence of nitrogen starvation between competing, non-compatible cultures. Changes in key enzymes of A. bisporus morphogenesis were observed, particularly via increased abundance of glucanosyltransferase in competing interactions and certain chitinases in vegetative compatible interactions only. Carbohydrate-active enzyme arsenals are expanded in antagonistic interactions in A. bisporus. Pathways involved in carbohydrate metabolism and genetic information processing were higher in interacting cultures, most notably during self-recognition. New insights into the differential response of interacting strains of A. bisporus will enhance our understanding of potential barriers to viral transmission through vegetative incompatibility. Our results suggest that a differential proteomic response occurs between A. bisporus at strain-level and findings from this work may guide future proteomic investigation of fungal anastomosis.
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17
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Hantula J, Mäkelä S, Xu P, Brusila V, Nuorteva H, Kashif M, Hyder R, Vainio EJ. Multiple virus infections on Heterobasidion sp. Fungal Biol 2020; 124:102-109. [DOI: 10.1016/j.funbio.2019.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 11/27/2022]
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18
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Sutela S, Poimala A, Vainio EJ. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol Ecol 2019; 95:5542194. [DOI: 10.1093/femsec/fiz119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACTSoils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
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Affiliation(s)
- Suvi Sutela
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Anna Poimala
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
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19
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Thapa V, Roossinck MJ. Determinants of Coinfection in the Mycoviruses. Front Cell Infect Microbiol 2019; 9:169. [PMID: 31179246 PMCID: PMC6542947 DOI: 10.3389/fcimb.2019.00169] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Vaskar Thapa
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
| | - Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
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