Mycoviruses of filamentous fungi and their relevance to plant pathology

Mycoviruses (fungal viruses) are reviewed with emphasis on plant pathogenic fungi. Based on the presence of virus-like particles and unencapsidated dsRNAs, mycoviruses are common in all major fungal groups. Over 80 mycovirus species have been officially recognized from ten virus families, but a paucity of nucleic acid sequence data makes assignment of many reported mycoviruses difficult. Although most of the particle types recognized to date are isometric, a variety of morphologies have been found and, additionally, many apparently unencapsidated dsRNAs have been reported. Until recently, most characterized mycoviruses have dsRNA genomes, but ssRNA mycoviruses now constitute about one-third of the total. Two hypotheses for the origin of mycoviruses of plant pathogens are discussed: the first that they are of unknown but ancient origin and have coevolved along with their hosts, the second that they have relatively recently moved from a fungal plant host into the fungus. Although mycoviruses are typically readily transmitted through asexual spores, transmission through sexual spores varies with the host fungus. Evidence for natural horizontal transmission has been found. Typically, mycoviruses are apparently symptomless (cryptic) but beneficial effects on the host fungus have been reported. Of more practical interest to plant pathologists are those viruses that confer a hypovirulent phenotype, and the scope for using such viruses as biocontrol agents is reviewed. New tools are being developed based on host genome studies that will help to address the intellectual challenge of understanding the fungal–virus interactions and the practical challenge of manipulating this relationship to develop novel biocontrol agents for important plant pathogens.     

Presence of Transposons and Mycoviruses in Botrytis cinerea Isolates Collected from a German Grapevine Growing Region

Transposons and infection of fungal strains with mycoviruses can have significant effects on distinctive phenotypic traits of phytopathogenic fungi such as mycelial growth and sporulation, pathogenicity or fungicide resistance. Two transposable elements (TE), Boty and Flipper, are known to be associated with the ubiquitous fungus Botrytis cinerea. In addition, the presence of two types of ssRNAsRNA viruses, BVX and BVF, has been reported in B. cinerea. In this study, we assessed the genetic diversity of B. cinerea isolates, all sampled within a small‐sized German viticultural area (‘Rheingau’) by examining and classifying them according to the presence of TEs and mycoviruses. A subset of the isolates was further analysed with microsatellite markers to determine the origin of particular isolates with or without one or both mycoviruses. Virtually all isolates (98%) sampled in two different years (2008 and 2010) were screened positive for the presence of a transposon. Presence of one or both B. cinerea mycoviruses was confirmed for 37% of the analysed isolates sampled in 2010, representing the first record of B. cinerea mycoviruses in German isolates. Assignment on individual B. cinerea isolates to different genetic groups was independent of the presence or absence of a mycovirus or a transposable element, respectively. Furthermore, we found no correlation between the presence of either a mycovirus or a transposable element and different viticultural management practices, soil properties or levels of nitrogen fertilization applied to the respective vineyards. However, mycelial growth of B. cinerea strains containing mycovirus BVF was significantly reduced at lower temperatures.     

Deep sequencing of mycovirus‐derived small RNAs from Botrytis species

RNA silencing is an ancient regulatory mechanism operating in all eukaryotic cells. In fungi, it was first discovered in Neurospora crassa, although its potential as a defence mechanism against mycoviruses was first reported in Cryphonectria parasitica and, later, in several fungal species. There is little evidence of the antiviral potential of RNA silencing in the phytopathogenic species of the fungal genus Botrytis. Moreover, little is known about the RNA silencing components in these fungi, although the analysis of public genome databases identified two Dicer‐like genes in B. cinerea, as in most of the ascomycetes sequenced to date. In this work, we used deep sequencing to study the virus‐derived small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species, and have different types of genome [double‐stranded RNA (dsRNA), (+)single‐stranded RNA (ssRNA) and (–)ssRNA]. In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation, either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5′ end, and are unevenly distributed along the viral genome, showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking similarities with vsiRNAs produced by plant viruses, suggesting similar pathways of viral targeting in plants and fungi. We have shown that the fungal RNA silencing machinery acts against the mycoviruses used in this work in a similar manner independent of their viral or fungal origin.     

Mycoviruses mediate mycotoxin regulation in Aspergillus ochraceus

To date, no demonstration of a direct correlation between the presence of mycoviruses and the quantitative or qualitative modulation of mycotoxins has been shown. In our study, we transfected a virus-free ochratoxin A (OTA)-producing isolate of Aspergillus ochraceus with purified mycoviruses from a different A. ochraceus isolate and from Penicillium aurantiogriseum. Among the mycoviruses tested, only Aspergillus ochraceus virus (AoV), a partitivirus widespread in A. ochraceus, caused a specific interaction that led to an overproduction of OTA, which is regulated by the European Commission and is the second most important contaminant of food and feed commodities. Gene expression analysis failed to reveal a specific viral upregulation of the mRNA of genes considered to play a role in the OTA biosynthetic pathway. Furthermore, AoOTApks1, a polyketide synthase gene considered essential for OTA production, is surprisingly absent in the genome of our OTA-producing isolate. The possible biological and evolutionary implications of the mycoviral regulation of mycotoxin production are discussed.     

Biology and mycovirus-assisted biological control of Sclerotinia sclerotiorum infecting vegetable and oilseed crops

Abstract

Plant disease caused by pathogenic fungal infection causes maximum crop damage. Among different fungal diseases, rot caused by Sclerotinia spp.; is a primary concern for vegetables and oilseed industry. Disease management using Chemical fungicides is a potential hazard and leads to the development of many fungicide-resistant strains. Hypovirulence associated mycoviruses is a possible environment-friendly solution, and current studies are aiming to exploit their potential as biocontrol agents. The use of the mycovirus mediated hypovirulent approach has emerged as a new technique to identify successful biocontrol agents. Most mycoviruses are known to have RNA genomes, double-stranded RNA (dsRNA) or single-stranded RNA (ssRNA). A total of six dsRNA mycoviruses and a one ssDNA mycovirus have been reported from Sclerotinia sclerotiorum till date which includes the most recent entry as published by Hamid and his group in 2018. In contrast to dsRNA mycovirus, ssDNA mycovirus reported from Sclerotinia sclerotiorum has significant potential to be used as a biocontrol agent in the fields. Despite several reports on mycoviruses of Sclerotinia, not much could be done to explore its commercial importance. The present review describes the recent developments in the area of mycoviruses of Sclerotinia sclerotiorum and associated biocontrol potential.     

Natural Occurrence ofChondrostereum purpureumin Relation to Its Use as a Biological Control Agent in Canadian Forests

The incidence of natural fructification ofChondrostereum purpureumwas estimated quantitatively on southern Vancouver Island during two winter seasons in randomly located 1000-m²plots and compared with potential added fructification that might occur as a result of using the fungus to control stump-sprouting of hardwood weeds in young forest stands. Fructification was surveyed in forests as well as in urban or agricultural areas by estimating the surface areas of woody substrates covered with basidiocarps. In addition to random plots, estimates were made also in locations where the fungus would be expected to occur (woodpiles, silvicultural thinnings, and killed trees). Basidiocarps were found throughout the area in various types of forest cover as well as in urban or agricultural situations. The amount of added fructification through the use of the fungus as a biological control agent was determined from inoculated plots as well as from calculated stump-surface areas developed from published stand-density data. Added fructification was multiplied by a factor representing the maximum biological control frequency in order to compare added fructification with natural fructification values. From the various calculations, it was determined that the added fructification ofC. purpureumis of the same order of magnitude as naturally occurring levels or even lower. In addition, there is a distinct geographical separation between predominantly forestry and predominantly settled areas where fruit and ornamental trees are cultivated. Accordingly, it was concluded that using the fungus as a biological control agent in forestry is not likely to pose a significant threat to fruit growing and commercial forests.     

Grapevine virome and production of healthy plants by somatic embryogenesis

Grapevine (Vitis spp.) is a widespread fruit tree hosting many viral entities that interact with the plant modifying its responses to the environment. The production of virus-free plants is becoming increasingly crucial for the use of grapevine as a model species in different studies. Using high-throughput RNA sequencing, the viromes of seven mother plants grown in a germplasm collection vineyard were sequenced. In addition to the viruses and viroids already detected in grapevine, we identified 13 putative new mycoviruses. The different spread among grapevine tissues collected in vineyard, greenhouse and in vitro conditions suggested a clear distinction between viruses/viroids and mycoviruses that can successfully be exploited for their identification. Mycoviruses were absent in in vitro cultures, while plant viruses and viroids were particularly accumulated in these plantlets. Somatic embryogenesis applied to the seven mother plants was effective in the elimination of the complete virome, including mycoviruses. However, different sanitization efficiencies for viroids and grapevine pinot gris virus were observed among genotypes. The absence of mycoviruses in in vitro plantlets, associated with the absence of all viral entities in somaclones, suggested that this regeneration technique is also effective to eradicate endophytic/epiphytic fungi, resulting in gnotobiotic or pseudo-gnotobiotic plants.     

Molecular characterization of vegetative incompatibility genes that restrict hypovirus transmission in the chestnut blight fungus Cryphonectria parasitica

Genetic nonself recognition systems such as vegetative incompatibility operate in many filamentous fungi to regulate hyphal fusion between genetically dissimilar individuals and to restrict the spread of virulence-attenuating mycoviruses that have potential for biological control of pathogenic fungi. We report here the use of a comparative genomics approach to identify seven candidate polymorphic genes associated with four vegetative incompatibility (vic) loci of the chestnut blight fungus Cryphonectria parasitica. Disruption of candidate alleles in one of two strains that were heteroallelic at vic2, vic6, or vic7 resulted in enhanced virus transmission, but did not prevent barrage formation associated with mycelial incompatibility. Detailed characterization of the vic6 locus revealed the involvement of nonallelic interactions between two tightly linked genes in barrage formation, heterokaryon formation, and asymmetric, gene-specific influences on virus transmission. The combined results establish molecular identities of genes associated with four C. parasitica vic loci and provide insights into how these recognition factors interact to trigger incompatibility and restrict virus transmission.     

The effects of dsRNA mycoviruses on growth and murine virulence of Aspergillus fumigatus

Some isolates of the opportunistic human pathogenic fungus Aspergillus fumigatus are known to be infected with mycoviruses. The dsRNA genomes of two of these mycoviruses, which include a chrysovirus and a partitivirus, have been completely sequenced and an RT-PCR assay for the viruses has been developed. Through curing virus-infected A. fumigatus isolates by cycloheximide treatment and transfecting virus-free isolates with purified virus, as checked by RT-PCR, isogenic virus-free and virus-infected lines of the fungus were generated whose phenotypes and growth have been directly compared. Mycovirus infection of A. fumigatus with either the chrysovirus or the partitivirus resulted in significant aberrant phenotypic alterations and attenuation of growth of the fungus but had no effect on susceptibility to common antifungals. Chrysovirus infection of A. fumigatus caused no significant alterations to murine pathogenicity.     

Revisitation of sites surveyed 19 years ago reveals impoverishment of longhorned beetles in natural and planted forests

As planted forests expand in area, they are beginning to dominate landscapes as a matrix and cause the fragmentation of remaining natural forests. To understand and predict the responses of biological assemblages to maturing planted landscapes, examining the effects of forest type (natural vs planted) and forest age on such assemblages is particularly important. Therefore, to document the effects of forest type and age on longhorned beetle assemblages, in 2008 we collected beetles in broad‐leaved natural and cedar planted forests where beetles had also been collected in 1989. Beetle species composition differed greatly between the two forest types in 1989, whereas this difference was less pronounced in 2008. Species richness and total abundance were higher in natural forests than in planted forests in 1989. In 2008, species richness had decreased in both forest types, but the difference between the two forest types had been maintained. Total abundance was also markedly lower in 2008, and the difference between forest types was much smaller. Although larval host plants were not associated with the responses of species to year (forest age or maturation), beetle species whose larvae fed on either broad‐leaved or coniferous trees (or both) exhibited slight preferences for natural forests. These results suggest that longhorned beetle assemblages become impoverished in planted landscapes as the planted matrix matures. Changes in species composition with forest maturation may be difficult to predict based on larval host plants. However, consideration of larval host plants may enable the prediction of changes in species composition caused by the replacement of natural forests by planted forests.     

Transmission of Fusarium boothii mycovirus via protoplast fusion causes hypovirulence in other phytopathogenic fungi

There is increasing concern regarding the use of fungicides to control plant diseases, whereby interest has increased in the biological control of phytopathogenic fungi by the application of hypovirulent mycoviruses as a possible alternative to fungicides. Transmission of hypovirulence-associated double-stranded RNA (dsRNA) viruses between mycelia, however, is prevented by the vegetative incompatibility barrier that often exists between different species or strains of filamentous fungi. We determined whether protoplast fusion could be used to transmit FgV1-DK21 virus, which is associated with hypovirulence on F. boothii (formerly F. graminearum strain DK21), to F. graminearum, F. asiaticum, F. oxysporum f. sp. lycopersici, and Cryphonectria parasitica. Relative to virus-free strains, the FgV1-DK21 recipient strains had reduced growth rates, altered pigmentation, and reduced virulence. These results indicate that protoplast fusion can be used to introduce FgV1-DK21 dsRNA into other Fusarium species and into C. parasitica and that FgV1-DK21 can be used as a hypovirulence factor and thus as a biological control agent.     

Community structure of land flatworms (Platyhelminthes, Terricola): comparisons between Araucaria and Atlantic forest in Southern Brazil

Abstract. Land flatworms (Platyhelminthes: Terricola) are sensitive to environmental changes and might be used as biological indicators of the degree of disturbance of their habitats. Nevertheless, studies on the structure of land flatworm communities are rare. In the present study, we investigated the terrestrial flatworm communities in two types of ombrophilous forest, Atlantic forest and Araucaria forest, aiming to answer the following questions: (1) Is the community structure of the two types of ombrophilous forest different? (2) Are there differences, regarding community structure, among distinct fragments of Araucaria forest? (3) Are there indicators of edge effects in these communities? The study site, the National Park of Aparados da Serra, is mainly covered, at high altitudes, by fragments of Araucaria forest immersed in a matrix of open areas (grasslands) and, in low altitudes, by a continuous Atlantic forest. We conducted monthly surveys in the two types of forest with three replications per forest type over a period of 2 years. Results indicated that: (1) community structure is clearly distinct between the two types of forest, as well as among fragments of the Araucaria forest; (2) there are no apparent edge effects; (3) the diversity indices of the two types of ombrophilous forest are not significantly different (Atlantic forest—H′=2.87, Araucaria forest—H′=2.55; p>0.05); and (4) there are significant differences in diversity indices between two fragments of Araucaria forest (H′=2.92 and 2.47; p<0.001). The following factors could affect community structure: type of vegetation, degree of human disturbance, and abiotic factors, such as pH and temperature.     

Double-Stranded RNA Mycovirus Infection of Aspergillus fumigatus Is Not Dependent on the Genetic Make-Up of the Host

Aspergillus fumigatus is a fungus that causes opportunistic infections in immunocompromised patients, with high morbidity and mortality. In its turn, A. fumigatus can become infected with mycoviruses. Most mycoviruses have a dsRNA genome and can cause fungal hypovirulence. For that reason, mycoviruses could theoretically be used as therapeutic tools to combat fungal infections. We determined if a certain genetic make-up of A. fumigatus was associated with the presence of mycoviruses in 86 clinical A. fumigatus isolates. Mycovirus screening was performed by isolating dsRNA from mycelial cultures using a Trizol/Chloroform method. The genetic relatedness of dsRNA infected A. fumigatus was determined by cell surface protein (CSP) typing and determination of the mating type. Sixteen (18.6%) of the 86 clinical A. fumigatus isolates contained dsRNA. The A. fumigatus collection could be divided into 11 different CSP types. DsRNA infected A. fumigatus isolates had similar CSP types as non-infected isolates. In both cases, the CSP types t01, t02, t03 and t04 were the most prevalent and the distribution comparable to the CSP types observed in other Dutch collections. Mating types MAT1-1 and MAT1-2 were evenly distributed among all A. fumigatus strains, regardless of CSP type. No difference was observed in mycovirus infections between MAT1-1 and MAT1-2 isolates. DsRNA mycovirus infections in A. fumigatus are not related to either CSP or mating type and therefore represent an interesting future therapeutic tool to combat fungal infections.     

Resource availability at three presumed stages of a heathland succession on the Lüneburger Heide,Germany

Abstract. The availability of maj or plant resources was investigated in three vegetation types that were assumed to represent different stages of a secondary succession on heathland on the Lüneburger Heide, northwestern Germany. Canopy transmission and absorption of photosynthetically active radiation (PAR), soil-water availability, and nutrient (Ca, K, Mg, N, P) availability were monitored with high spatial and temporal resolution in (1) a Calluna vulgaris heathland, (2) a pioneer birch-pine forest and (3) a late-successional oak-beech forest, situated close to each other on comparable geological substrate (diluvial). Mean fractional transmission of PAR during summer decreased from 0.48 in the heathland to 0.04 in the oak-beech forest while the fractional canopy absorption increased from 0.49 to 0.92. Soil-water availability as indicated by the soil-water potential, was significantly influenced by differential canopy interception loss and characteristic rooting patterns in the three vegetation types. Annual mean nutrient concentrations in the equilibrium soil solution were similar or, for some elements, increased from the heathland to the birch-pine and the oak-beech forest despite a growing demand. A marked increase was found for the total nutrient pools in the soil-organic layer between early and late successional vegetation types. On the poor glacial parent material, nutrient pools seem to be strongly dependent on stand productivity and litter production which increased with succession. Thus, for nutrients, facilitation seems to be important in this type of succession.     

Mycoviruses of Botrytis cinerea isolates from different hosts

Botrytis cinerea (teleomorph Botryotinia fuckeliana) is a necrotrophic plant pathogenic fungus that causes grey mould and enormous economic losses worldwide in different crops. Control of B. cinerea is difficult due to the appearance of fungicide‐resistant isolates, and the diversity in virulence due to genetic variability and, perhaps, the infection with mycoviruses or fungal viruses. The discovery of mycoviruses and their possible application as biocontrol agents, as well as their use as tools to study the plant–pathogen interaction, has encouraged their study in B. cinerea. Herein, we have analysed the occurrence of mycoviruses in Spanish B. cinerea isolates to approach a better understanding of the interactions among viruses, fungi and plants in this pathosystem. Fifty‐five percent of the B. cinerea isolates analysed contained double‐stranded RNA (dsRNA) elements, and the number of dsRNA elements, their relative concentration and size were variable among isolates. Some of these dsRNAs were related to the presence of virus like rod or isometric particles, and to cellular degeneration and malformed mitochondria. We have also demonstrated that a 3 kb dsRNA present in 55% of the isolates having dsRNA elements was a mycovirus genome. Partial sequence of that mycovirus presented high identity in nucleotide and amino acid sequence with Botrytis cinerea mitovirus 1 (BcMV1). Analysis of the genetic distance within Spanish BcMV1 sequences showed the existence of different isolates of this mitovirus inside the Spanish B. cinerea population analysed. This is the first report of the variability of dsRNA elements and the partial genome sequence of a mitovirus associated with Spanish B. cinerea isolates and the genetic diversity within Spanish isolates of BcMV1.     

Non-detection of mycoviruses in amphibian chytrid fungus (Batrachochytrium dendrobatidis) from Australia

Mycoviruses may influence the pathogenicity of disease-causing fungi. Although mycoviruses have been found in some chytrid fungi, limited testing has not detected them in Batrachochytrium dendrobatidis (Bd), the cause of the devastating amphibian disease, chytridiomycosis. Here we conducted a survey for mycovirus presence in 38 Bd isolates from Australia (n = 31), Brazil (n = 5) and South Korea (n = 2) with a combination of modern high-throughput sequencing and conventional dsRNA cellulose chromatography. Mycoviruses were not detected in any isolates. This result was unexpected, given the long evolutionary history of Bd, as well as the high prevalence of mycoviruses in related fungal species. Given our widespread sampling in Australia and the limited number of Bd introductions, we suggest that mycoviruses are uncommon or absent from Australian Bd. Testing more isolates from regions where Bd originated, as well as regions with high diversity or low fungal virulence may identify mycoviruses that could aid in disease control.     

Subtropical montane tree litter decomposition: Links with secondary forest types and species' shade tolerance

Abstract Litter decomposition plays an important role in secondary forest recovery in the tropics. In this study we assessed the decomposition rates of tree litter in species from different secondary forest types and with different shade tolerances. The three secondary forest types analysed are related to the effects of different previous land use intensities. The typical forest type (TYP) is related to low land use intensity, Alnus acuminata‐dominated forest (ALN) type is related to medium land‐use intensity and Amomyrtella güili‐dominated forest type (AMO) is related to high land use intensity. The effect of shade tolerance was assessed using maximum height of each species as an indicator of its light requirements. Associations with leaf functional traits such as specific leaf area (SLA), and tensile strength (LTS) were also assessed. We found that leaves of species from the TYP forest type decompose faster than those of the ALN and AMO forest types. These changes were consistent with differences in the SLA of the species, which was higher in the TYP forest type than in the ALN and AMO forest types. SLA, LTS and decomposition were not significantly correlated with tree maximum height. Our results show that the secondary forest types, which are related to land use intensities prior to abandonment have an important influence on litter decomposition. This implies potential long‐term effects on soil properties and species composition.     

林火干扰对森林生态系统土壤有机碳的影响研究进展

林火干扰是森林生态系统特殊而重要的生态因子,可改变生态系统的养分循环与能量传递。研究林火干扰对森林生态系统土壤有机碳的影响,有助于理解森林生态系统中土壤碳固持和碳循环过程,为制定科学合理的旨在减缓全球变化的林火管理策略具有重要意义。从4个方面阐述了林火干扰对森林生态系统土壤有机碳的影响及内在机制:分别从大尺度和小尺度两个方面阐述了林火干扰对土壤有机碳的影响及对森林生态系统碳循环与碳平衡的作用机制;探讨了不同林火干扰类型和林火干扰强度下,土壤活性有机碳对林火干扰的响应机制;阐明了林火干扰对土壤惰性有机碳的影响及作用机制;论述了林火干扰主要通过改变土壤有机碳的输入和输出过程进而影响土壤有机碳的稳定性及内在机制。最后提出了提高林火干扰对森林生态系统土壤有机碳影响定量化研究的4种路径选择:(1)全面比较研究不同林火干扰类型对土壤有机碳循环及其碳素再分配过程的功能特征;(2)进一步阐明林火干扰通过改变植被结构进而影响土壤生物群落结构,剖析土壤碳库循环的内在机制;(3)完善不同时空尺度下林火干扰对森林生态系统土壤碳库周转过程的定量化研究;(4)加强不同林火干扰类型土壤碳库稳定性差异的研究。     

Antennal sensory organs and glands of the harlequin ladybird,Harmonia axyridis

Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae) is a sub‐cosmopolitan species. Native to Asia, it has been released during the 20th century for classical and augmentative biological control of several herbivorous insects, mostly aphids and coccids. Despite its recognized positive impact on biological control, H. axyridis is now considered among the most dangerous invasive species in Europe and in most places where it has established. This is mostly due to its ability to reduce the populations of native predatory species of the same trophic guild. When exploring a new area, H. axyridis adults use semiochemical cues to acquire information about the habitat. Presumably, these cues are perceived by the sensilla located on the antennae. Surprisingly, in spite of the huge literature existing on H. axyridis, the antennal sensory organs have been poorly characterized. Here, we used scanning and transmission electron microscopy (SEM, TEM) techniques to study H. axyridis antennae, with focus on the various types of sensilla and their distribution in male and female individuals. The presence of various classes of antennal sensilla belonging to the main types described in insects (chemoreceptors, mechanoreceptors, and thermo‐hygroreceptors) was highlighted, as well as the widespread presence of antennal glands. The investigations showed some peculiar characteristics not known in Coccinellidae, such as the concentration of sensory structures at the level of the distal part of the apical antennomere and the discovery of antennal glands associated with it. No sexual dimorphism was revealed, neither for the general structure of the antenna (similar number of antennomeres and presence of modifications), nor for the total length and width of the antenna, the relative size of the antennomeres, the types of antennal sensilla, of their distribution and abundance. The potential relevance of these sensory structures and antennal glands, reported for the first time in Coccinellidae, is discussed in the context of intra‐ and interspecific communication.