The expanding field of plant virus ecology: Historical foundations, knowledge gaps, and research directions

Comparative Performance Evaluation of Double-Stranded RNA High-Throughput Sequencing for the Detection of Viral Infection in Temperate Fruit Crops

There is limited information on the compared performances of biological, serological. and molecular assays with high-throughput sequencing (HTS) for viral indexing in temperate fruit crops. Here, using a range of samples of predetermined virological status, we compared two performance criteria (inclusivity and analytical sensitivity) of enzyme-linked immunosorbent assay (ELISA), molecular hybridization, reverse transcription (RT)-PCR, and double-stranded RNA (dsRNA) HTS for the detection of a total of 14 viruses (10 genera) and four viroids (three genera). When undiluted samples from individual plants were used, ELISA had the lowest performance, with an overall detection rate of 68.7%, followed by RT-PCR (82.5%) and HTS (90.7%; 100% if considering only viruses). The lower performance of RT-PCR reflected the inability to amplify some isolates as a consequence of point mutations affecting primer-binding sites. In addition, HTS identified viruses that had not been identified by other assays in nearly two-thirds of the samples. Analysis of serial dilutions of fruit tree samples allowed comparison of analytical sensitivities for various viruses. ELISA showed the lowest analytical sensitivity, but RT-PCR showed higher analytical sensitivity than HTS for most of the samples. Overall, these results confirm the superiority of HTS over biological indexing in terms of speed and inclusivity and show that while the absolute analytical sensitivity of RT-PCR tends to be higher than that of HTS, PCR inclusivity is affected by viral genetic diversity. Taken together, these results make a strong case for the implementation of HTS-based approaches in fruit tree viral testing protocols supporting quarantine and certification programs.

Helper Component-Proteinase of Triticum Mosaic Virus Is a Viral Determinant of Wheat Curl Mite Transmission

Triticum mosaic virus (TriMV; genus Poacevirus; family Potyviridae) is an economically important virus in the Great Plains region of the United States. TriMV is transmitted by the wheat curl mite (Aceria tosichella) Type 2 genotype but not by Type 1. Helper component-proteinase (HC-Pro) is a vector transmission determinant for several potyvirids, but the role of HC-Pro in TriMV transmission is unknown. In this study, we examined the requirement of the HC-Pro cistron of TriMV for wheat curl mite (Type 2) transmission through deletion and point mutations and constructing TriMV chimeras with heterologous HC-Pros from other potyvirids. TriMV with complete deletion of HC-Pro failed to be transmitted by wheat curl mites at detectable levels. Furthermore, TriMV chimeras with heterologous HC-Pros from aphid-transmitted turnip mosaic virus and tobacco etch virus, or wheat curl mite-transmitted wheat streak mosaic virus, failed to be transmitted by wheat curl mites. These data suggest that heterologous HC-Pros did not complement TriMV for wheat curl mite transmission. A decreasing series of progressive nested in-frame deletions at the N-terminal region of HC-Pro comprising amino acids 3 to 125, 3 to 50, 3 to 25, 3 to 15, 3 to 8, and 3 and 4 abolished TriMV transmission by wheat curl mites. Additionally, mutation of conserved His20, Cys49, or Cys52 to Ala in HC-Pro abolished TriMV transmissibility by wheat curl mites. These data suggest that the N-terminal region of HC-Pro is crucial for TriMV transmission by wheat curl mites. Collectively, these data demonstrate that the HC-Pro cistron of TriMV is a viral determinant for wheat curl mite transmission.

Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses

Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

Rice volatile compound (E)-β-caryophyllene induced by rice dwarf virus (RDV) attracts the natural enemy Cyrtorhinus lividipennis to prey on RDV insect vectors

BACKGROUND

Rice dwarf virus (RDV)-induced rice plant volatiles (E)-β-caryophyllene and 2-heptanol modulate the olfactory behavior of RDV insect vectors that promote viral acquisition and transmission. However, it remains elusive whether these two volatiles could influence the behaviors of the natural enemies of RDV insect vectors. Herein, we determined the effects of these two volatiles on the olfactory and predatory behaviors of Cyrtorhinus lividipennis (Hemiptera: Miridae), an important predator of RDV insect vectors in rice paddies.

RESULTS

The results showed that C. lividipennis preferred RDV-infected rice plant odors over RDV-free rice plant odors. C. lividipennis was attracted by (E)-β-caryophyllene, but showed no behavioral responses to 2-heptanol. The attraction of (E)-β-caryophyllene towards C. lividipennis was further confirmed using oscas1 rice plants, which do not release (E)-β-caryophyllene in response to RDV infection, through a series of complementary assays. The oviposition preference of the RDV vector insect Nephotettix cincticeps (Hemiptera: Cicadellidae) showed no significant difference between RDV-infected and RDV-free wild-type plants, nor between oscas1-RDV and oscas1 plants. However, the predation rate of C. lividipennis for N. cincticeps eggs on RDV-infected plants was higher than that on RDV-free plants, whereas there was no significant difference between oscas1-RDV and oscas1 plants.

CONCLUSION

(E)-β-caryophyllene induced by RDV attracted more C. lividipennis to prey on N. cincticeps eggs and played a crucial role in plant-virus-vector-enemy interactions. These novel findings will promote the design of new strategies for disease control by controlling the populations of insect vectors, for example recruiting more natural enemies by virus-induced plant volatiles. © 2023 Society of Chemical Industry.

Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community

IMPORTANCE

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.

Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem

As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.

Integrating Community Ecology into Models of Vector-Borne Virus Transmission

Vector-borne plant viruses are a diverse and dynamic threat to agriculture with hundreds of economically damaging viruses and insect vector species. Mathematical models have greatly increased our understanding of how alterations of vector life history and host-vector-pathogen interactions can affect virus transmission. However, insect vectors also interact with species such as predators and competitors in food webs, and these interactions affect vector population size and behaviors in ways that mediate virus transmission. Studies assessing how species' interactions affect vector-borne pathogen transmission are limited in both number and scale, hampering the development of models that appropriately capture community-level effects on virus prevalence. Here, we review vector traits and community factors that affect virus transmission, explore the existing models of vector-borne virus transmission and areas where the principles of community ecology could improve the models and management, and finally evaluate virus transmission in agricultural systems. We conclude that models have expanded our understanding of disease dynamics through simulations of transmission but are limited in their ability to reflect the complexity of ecological interactions in real systems. We also document a need for experiments in agroecosystems, where the high availability of historical and remote-sensing data could serve to validate and improve vector-borne virus transmission models.

Direct and indirect viral associations predict coexistence in wild plant virus communities

Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.

Heat-Killed Tobacco Mosaic Virus Mitigates Plant Abiotic Stress Symptoms

Since the discovery of the tobacco mosaic virus in the 1890s, awareness has grown in regard to how viruses affect the environment. Viral infections are now known to cause various effects besides pathogenicity, with some viruses in fact having a beneficial impact on plants. Although research has focused on disease-causing viruses that can infect plants, many wild plants are also infected with non-pathogenic viral agents. Traditionally, abiotic, and biotic stresses have been studied as isolated stimuli that trigger signaling pathways within the plant. However, both biotic and abiotic stress can trigger complex molecular interactions within plants, which in turn drive interconnected response pathways. Here, we demonstrate that heat-killed tobacco mosaic virus (TMV) can increase abiotic stress tolerance in plants, an effect that could potentially be implemented in challenging growth environments. To our knowledge, this is the first report of plant abiotic stress tolerance following treatment with heat-killed viral particles.

Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae

Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.

Cucumber Mosaic Virus Infection in Arabidopsis: A Conditional Mutualistic Symbiont?

A cucumber mosaic virus isolate, named Ho [CMV(Ho)], was isolated from a symptomless Arabidopsis halleri field sample containing low virus titers. An analysis of CMV(Ho) RNA molecules indicated that the virus isolate, besides the usual cucumovirus tripartite RNA genome, additionally contained defective RNA3 molecules and a satellite RNA. To study the underlying mechanism of the persistent CMV(Ho) infection in perennial A. halleri, infectious cDNA clones were generated for all its genetic elements. CMV, which consists of synthetic transcripts from the infectious tripartite RNA genomes, and designated CMV(Ho)tr, multiplied in A. halleri and annual Arabidopsis thaliana Col-0 to a similar level as the virulent strain CMV(Y), but did not induce any symptoms in them. The response of Col-0 to a series of reassortant CMVs between CMV(Ho)tr and CMV(Y) suggested that the establishment of an asymptomatic phenotype of CMV(Ho) infection was due to the 2b gene of CMV RNA2, but not due to the presence of the defective RNA3 and satellite RNA. The accumulation of CMV(Ho) 2b protein tagged with the FLAG epitope (2b.Ho-FLAG) in 2b.Ho-FLAG-transformed Col-0 did not induce any symptoms, suggesting a 2b-dependent persistency of CMV(Ho)tr infection in Arabidopsis. The 2b protein interacted with Argonaute 4, which is known to regulate the cytosine methylation levels of host genomic DNA. Whole genomic bisulfite sequencing analysis of CMV(Ho)tr- and mock-inoculated Col-0 revealed that cytosine hypomethylation in the promoter regions of 82 genes, including two genes encoding transcriptional regulators (DOF1.7 and CBP1), was induced in response to CMV(Ho)tr infection. Moreover, the increased levels of hypomethylation in the promoter region of both genes, during CMV(Ho)tr infection, were correlated with the up- or down-regulation of their expression. Taken altogether, the results indicate that during persistent CMV(Ho) infection in Arabidopsis, host gene expression may be epigenetically modulated resulting from a 2b-mediated cytosine hypomethylation of host genomic DNA.

Tomato Yellow Leaf Curl Virus (TYLCV) Promotes Plant Tolerance to Drought

A growing body of research points to a positive interplay between viruses and plants. Tomato yellow curl virus (TYLCV) is able to protect tomato host plants against extreme drought. To envisage the use of virus protective capacity in agriculture, TYLCV-resistant tomato lines have to be infected first with the virus before planting. Such virus-resistant tomato plants contain virus amounts that do not cause disease symptoms, growth inhibition, or yield loss, but are sufficient to modify the metabolism of the plant, resulting in improved tolerance to drought. This phenomenon is based on the TYLCV-dependent stabilization of amounts of key osmoprotectants induced by drought (soluble sugars, amino acids, and proteins). Although in infected TYLCV-susceptible tomatoes, stress markers also show an enhanced stability, in infected TYLCV-resistant plants, water balance and osmolyte homeostasis reach particularly high levels. These tomato plants survive long periods of time during water withholding. However, after recovery to normal irrigation, they produce fruits which are not exposed to drought, similarly to the control plants. Using these features, it might be possible to cultivate TYLCV-resistant plants during seasons characterized by water scarcity.

Virus-induced plant volatiles mediate the olfactory behaviour of its insect vectors

Plant viruses can manipulate their hosts to release odours that are attractive or repellent to their insect vectors. However, the volatile organic compounds (VOCs), either individually or as mixtures, which play a key role in the olfactory behaviour of insect vectors remains largely unknown. Our study focused on green rice leafhoppers (GRLHs) vectoring rice dwarf virus (RDV) revealed that RDV infection significantly induced the emission of (E)-β-caryophyllene and 2-heptanol by rice plants, which influenced the olfactory behaviour of both non-viruliferous and viruliferous GRLHs. (E)-β-caryophyllene attracted non-viruliferous GRLHs to settle on RDV-infected plants, but neither attracted nor repelled viruliferous GRLHs. In contrast, 2-heptanol repelled viruliferous GRLHs to settle on RDV-infected plants, but neither repelled nor attracted non-viruliferous GRLHs. Suppression of (E)-β-caryophyllene synthase OsCAS via CRISPR-Cas9 to generate oscas-1 plants enabled us to confirm the important role played by (E)-β-caryophyllene in modulating the virus-vector-host plant interaction. These novel results reveal the role of these virus-induced VOCs in modulating the behaviour of its GRLH insect vector and may facilitate the design of new strategies for disease control through manipulation of plant volatile emissions.

Grapevine vein clearing virus Is Prevalent and Genetically Variable in Grape Aphid (Aphis illinoisensis Shimer) Populations

Grapevine vein clearing virus (GVCV) causes severe stunting and death of cultivated grapevines and is prevalent in native Vitis spp. and Ampelopsis cordata in the Midwest region of the United States. GVCV can be transmitted from wild A. cordata to Vitis spp. by grape aphid (Aphis illinoisensis) under greenhouse conditions, but its prevalence, genetic composition, and genome number in native grape aphids are unknown. In this study, we collected grape aphids from native Vitaceae across the state of Missouri in 2018 and 2019, and conducted diagnostic, genetic, and quantitative analyses. GVCV was detected in 91 of the 105 randomly sampled communities on 71 Vitaceae plants (87%). It was present in 211 of 525 single grape aphids (40%). Diverse GVCV variants from aphids were present on both GVCV-negative and GVCV-positive plants. Identical GVCV variants were found in grape aphids sampled from wild and cultivated Vitaceae, indicating that viruliferous aphids likely migrate and disperse GVCV variants among wild and cultivated Vitaceae. In addition, we found that the number of GVCV genomes varies largely in the stylet and body of individual aphids. Our study provides a snapshot of GVCV epidemics and genetic structure in its mobile vector and sessile hosts. This presents a good model for studying the epidemiology, ecology, and evolution of a plant virus.

Low virus diversity and spread in wild Capsicum spp. accessions from Ecuador under natural inoculum pressure

Challenging wild plant accessions with pathogens is an initial approach for finding resistance genes for breeding programs. Viruses can be transmitted artificially by mechanical or arthropod-borne inoculation, but these experimental assays do not always reproduce natural conditions in the field. In this study, 56 wild Capsicum spp. accessions from Ecuador that were under natural inoculum pressure for six months were screened for virus infections by RNA sequencing. These plants exhibited low virus diversity in comparison to a commercial pepper cultivar that was used as a susceptible host. Subjecting numerous plants to natural infection prior to artificial assays may indicate promising accessions to track within virus/vector resistance breeding programs.

Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

The Epidemiology of Plant Virus Disease: Towards a New Synthesis

Epidemiology is the science of how disease develops in populations, with applications in human, animal and plant diseases. For plant diseases, epidemiology has developed as a quantitative science with the aims of describing, understanding and predicting epidemics, and intervening to mitigate their consequences in plant populations. Although the central focus of epidemiology is at the population level, it is often necessary to recognise the system hierarchies present by scaling down to the individual plant/cellular level and scaling up to the community/landscape level. This is particularly important for diseases caused by plant viruses, which in most cases are transmitted by arthropod vectors. This leads to range of virus-plant, virus-vector and vector-plant interactions giving a distinctive character to plant virus epidemiology (whilst recognising that some fungal, oomycete and bacterial pathogens are also vector-borne). These interactions have epidemiological, ecological and evolutionary consequences with implications for agronomic practices, pest and disease management, host resistance deployment, and the health of wild plant communities. Over the last two decades, there have been attempts to bring together these differing standpoints into a new synthesis, although this is more apparent for evolutionary and ecological approaches, perhaps reflecting the greater emphasis on shorter often annual time scales in epidemiological studies. It is argued here that incorporating an epidemiological perspective, specifically quantitative, into this developing synthesis will lead to new directions in plant virus research and disease management. This synthesis can serve to further consolidate and transform epidemiology as a key element in plant virus research.

Virus Accumulation and Whitefly Performance Modulate the Role of Alternate Host Species as Inoculum Sources of Tomato Yellow Leaf Curl Virus

Evaluating alternate hosts that facilitate the persistence of a virus in the landscape is key to understanding virus epidemics. In this study, we explored the role of several plant species (eggplant, pepper, and Palmer amaranth) as inoculum sources of tomato yellow leaf curl virus (TYLCV) and as reservoirs for its insect vector, Bemisia tabaci (Gennadius). All inoculated species were infected with TYLCV, but whiteflies acquired fewer viral copies via feeding from pepper and eggplant than from tomato and Palmer amaranth. Further, back-transmission assays to recipient tomato resulted in TYLCV infection only when TYLCV was acquired from Palmer amaranth or tomato. Analysis suggested that the role of plant species as TYLCV inoculum sources may be determined by the accumulation of viral copies in the plant, and consequently in the insect vector. In addition, results showed that all three alternate species could sustain populations of B. tabaci, while differentially influencing fitness of whiteflies. Eggplant was a superior host for whiteflies, whereas whitefly survival was compromised on pepper. Together, we demonstrate that both plant-virus and plant-vector interactions could influence the role of an alternate host in TYLCV epidemics, and in our region of study we highlight the potential risk of hosts such as Palmer amaranth in the spread of TYLCV.

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

Enhanced heat tolerance of viral-infected aphids leads to niche expansion and reduced interspecific competition

Vector-borne pathogens are known to alter the phenotypes of their primary hosts and vectors, with implications for disease transmission as well as ecology. Here we show that a plant virus, barley yellow dwarf virus, increases the surface temperature of infected host plants (by an average of 2 °C), while also significantly enhancing the thermal tolerance of its aphid vector Rhopalosiphum padi (by 8 °C). This enhanced thermal tolerance, which was associated with differential upregulation of three heat-shock protein genes, allowed aphids to occupy higher and warmer regions of infected host plants when displaced from cooler regions by competition with a larger aphid species, R. maidis. Infection thereby led to an expansion of the fundamental niche of the vector. These findings show that virus effects on the thermal biology of hosts and vectors can influence their interactions with one another and with other, non-vector organisms.

Plant-insect vector-virus interactions under environmental change

Insects play an important role in the spread of viruses from infected plants to healthy hosts through a variety of transmission strategies. Environmental factors continuously influence virus transmission and result in the establishment of infection or disease. Plant virus diseases become epidemic when viruses successfully dominate the surrounding ecosystem. Plant-insect vector-virus interactions influence each other; pushing each other for their benefit and survival. These interactions are modulated through environmental factors, though environmental influences are not readily predictable. This review focuses on exploiting the diverse relationships, embedded in the plant-insect vector-virus triangle by highlighting recent research findings. We examined the interactions between viruses, insect vectors, and host plants, and explored how these interactions affect their behavior.

Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches

Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at the family level but also by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. A large viral diversity dominated by novel dsRNA viruses was detected in all sites, while a large between-site variability limited the ability to draw a clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 versus 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow us to reason methodological choices in phytovirome studies and likely in other virome studies where RNA viruses are the focal taxa.IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them but also on the comparative performance-methodological approaches for their study. We used and compared two viral sequence enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA), for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing us to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is recommended because it consistently provided a more comprehensive description of the analyzed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.

Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach

Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.

Global Dimensions of Plant Virus Diseases: Current Status and Future Perspectives

Viral diseases provide a major challenge to twenty-first century agriculture worldwide. Climate change and human population pressures are driving rapid alterations in agricultural practices and cropping systems that favor destructive viral disease outbreaks. Such outbreaks are strikingly apparent in subsistence agriculture in food-insecure regions. Agricultural globalization and international trade are spreading viruses and their vectors to new geographical regions with unexpected consequences for food production and natural ecosystems. Due to the varying epidemiological characteristics of diverent viral pathosystems, there is no one-size-fits-all approach toward mitigating negative viral disease impacts on diverse agroecological production systems. Advances in scientific understanding of virus pathosystems, rapid technological innovation, innovative communication strategies, and global scientific networks provide opportunities to build epidemiologic intelligence of virus threats to crop production and global food security. A paradigm shift toward deploying integrated, smart, and eco-friendly strategies is required to advance virus disease management in diverse agricultural cropping systems.

High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico

Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.

Diverse and variable virus communities in wild plant populations revealed by metagenomic tools

Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.

Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems

Viruses are ubiquitous within all habitats that support cellular life and represent the most important emerging infectious diseases of plants. Despite this, it is only recently that we have begun to describe the ecological roles of plant viruses in unmanaged systems and the influence of ecosystem properties on virus evolution. We now know that wild plants frequently harbor infections by diverse virus species, but much remains to be learned about how viruses influence host traits and how hosts influence virus evolution and vector interactions. To identify knowledge gaps and suggest avenues for alleviating research deficits, we performed a quantitative synthesis of a representative sample of virus ecology literature, developed criteria for expanding the suite of pathosystems serving as models, and applied these criteria through a case study. We found significant gaps in the types of ecological systems studied, which merit more attention. In particular, there is a strong need for a greater diversity of logistically tractable, wild dicot perennial study systems suitable for experimental manipulations of infection status. Based on criteria developed from our quantitative synthesis, we evaluated three California native dicot perennials typically found in Mediterranean-climate plant communities as candidate models: Cucurbita foetidissima (buffalo gourd), Cucurbita palmata (coyote gourd), and Datura wrightii (sacred thorn-apple). We used Illumina sequencing and network analyses to characterize viromes and viral links among species, using samples taken from multiple individuals at two different reserves. We also compared our Illumina workflow with targeted RT-PCR detection assays of varying costs. To make this process accessible to ecologists looking to incorporate virology into existing studies, we describe our approach in detail and discuss advantages and challenges of different protocols. We also provide a bioinformatics workflow based on open-access tools with graphical user interfaces. Our study provides evidence that dicot perennials in xeric habitats support multiple, asymptomatic infections by viruses known to be pathogenic in related crop hosts. Quantifying the impacts of these interactions on plant performance and virus epidemiology in our logistically tractable host systems will provide fundamental information about plant virus ecology outside of crop environments.

Vector population growth and condition-dependent movement drive the spread of plant pathogens

Plant viruses, often spread by arthropod vectors, impact natural and agricultural ecosystems worldwide. Intuitively, the movement behavior and life history of vectors influence pathogen spread, but the relative contribution of each factor has not been examined. Recent research has highlighted the influence of host infection status on vector behavior and life history. Here, we developed a model to explore how vector traits influence the spread of vector-borne plant viruses. We allowed vector life history (growth rate, carrying capacity) and movement behavior (departure and settlement rates) parameters to be conditional on whether the plant host is infected or healthy and whether the vector is viruliferous (carrying the virus) or not. We ran simulations under a wide range of parameter combinations and quantified the fraction of hosts infected over time. We also ran case studies of the model for Barley yellow dwarf virus, a persistently transmitted virus, and for Potato virus Y, a non-persistently transmitted virus. We quantified the relative importance of each parameter on pathogen spread using Latin hypercube sampling with the statistical partial rank correlation coefficient technique. We found two general types of mechanisms in our model that increased the rate of pathogen spread. First, increasing factors such as vector intrinsic growth rate, carrying capacity, and departure rate from hosts (independent of whether these factors were condition-dependent) led to more vectors moving between hosts, which increased pathogen spread. Second, changing condition-dependent factors such as a vector's preference for settling on a host with a different infection status than itself, and vector tendency to leave a host of the same infection status, led to increased contact between hosts and vectors with different infection statuses, which also increased pathogen spread. Overall, our findings suggest that vector population growth rates had the greatest influence on rates of virus spread, but rates of vector dispersal from infected hosts and from hosts of the same infection status were also very important. Our model highlights the importance of simultaneously considering vector life history and behavior to better understand pathogen spread. Although developed for plant viruses, our model could readily be utilized with other vector-borne pathogen systems.

Spatiotemporal Distribution and Environmental Drivers of Barley yellow dwarf virus and Vector Abundance in Kansas

Several aphid species transmit barley yellow dwarf, a globally destructive disease caused by viruses that infect cereal grain crops. Data from >400 samples collected across Kansas wheat fields in 2014 and 2015 were used to develop spatiotemporal models predicting the extent to which landcover, temperature and precipitation affect spring aphid vector abundance and presence of individuals carrying Barley yellow dwarf virus (BYDV). The distribution of Rhopalosiphum padi abundance was not correlated with climate or landcover, but Sitobion avenae abundance was positively correlated with fall temperature and negatively correlated to spring temperature and precipitation. The abundance of Schizaphis graminum was negatively correlated with fall precipitation and winter temperature. The incidence of viruliferous (+BYDV) R. padi was positively correlated with fall precipitation but negatively correlated with winter precipitation. In contrast, the probability of +BYDV S. avenae was unaffected by precipitation but was positively correlated with fall temperatures and distance to forest or shrubland. R. padi and S. avenae were more prevalent at eastern sample sites where ground cover is more grassland than cropland, suggesting that grassland may provide over-summering sites for vectors and pose a risk as potential BYDV reservoirs. Nevertheless, land cover patterns were not strongly associated with differences in abundance or the probability that viruliferous aphids were present.

Rice dwarf virus infection alters green rice leafhopper host preference and feeding behavior

Host plants, pathogens and their herbivore vectors systems have complex relationships via direct and indirect interactions. Although there are substantial gaps in understanding these systems, the dynamics of the relationships may influence the processes of virus transmission and plant disease epidemics. Rice dwarf virus (RDV) is mainly vectored by green rice leafhoppers (GRLHs), Nephotettix cincticeps (Uhler) (Hemiptera: Cicadellidae) in a persistently circulative manner. In this study, host plant selection preferences of non-viruliferous and viruliferous (carrying RDV) GRLHs between RDV-free and RDV-infected plants were tested. Non-viruliferous GRLHs preferred RDV-infected rice plants over RDV-free rice plants, and viruliferous GRLHs preferred RDV-free rice plants over RDV-infected rice plants. In odor selection preference bioassay using a four-field olfactometer, non-viruliferous GRLHs preferred odors of RDV-infected rice plants over healthy rice and viruliferous GRLHs preferred odors of RDV-free rice plants over RDV-infected ones. In 6 h plant penetration behavior bioassay using electrical penetration graphs, non-viruliferous GRLHs spent shorter time in non-penetration and much longer time in xylem feeding on RDV-infected, compared to RDV-free rice plants. Viruliferous GRLHs exhibited more salivation and stylet movement on RDV-free rice plants than on RDV-infected rice plants. We infer from these findings that RDV influences these vector behaviors by altering host plant physiology to promote viral transmission.

The Role of Viruses in the Phytobiome

Viruses are an important but sequence-diverse and often understudied component of the phytobiome. We succinctly review current information on how plant viruses directly affect plant health and physiology and consequently have the capacity to modulate plant interactions with their biotic and abiotic environments. Virus interactions with other biota in the phytobiome, including arthropods, fungi, and nematodes, may also impact plant health. For example, viruses interact with and modulate the interface between plants and insects. This has been extensively studied for insect-vectored plant viruses, some of which also infect their vectors. Other viruses have been shown to alter the impacts of plant-interacting phytopathogenic and nonpathogenic fungi and bacteria. Viruses that infect nematodes have also recently been discovered, but the impact of these and phage infecting soil bacteria on plant health remain largely unexplored.

The next generation of natural history collections

The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preserving, analyzing, and integrating biological samples—a generation devoted to interdisciplinary research into complex biological interactions and processes. Next-generation collections may be essential for breakthrough research on the spread of infectious diseases, feeding Earth's growing population, adapting to climate change, and other grand research challenges. A decade-long investment in research collection infrastructure will be needed.

From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study

The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel georeferenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these "geometagenomics" approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations, and environmental conditions on plant virus diversity and prevalence. To exemplify how such top-down approaches can provide a far deeper understanding of host-virus associations, we provide a case-study focusing on geminiviruses within two complex ecosystems containing both cultivated and uncultivated areas. Geminiviruses are a highly relevant model for studying the evolutionary and ecological aspects of viral emergence because the family Geminiviridae includes many of the most important crop pathogens that have emerged over the past century. In addition to revealing unprecedented degrees of geminivirus diversity within the analyzed ecosystems, the geometagenomics-based approach enabled the focused in-depth analysis of the complex evolutionary dynamics of some of the highly divergent geminivirus species that were discovered.

Ecological Complexity in Plant Virus Host Range Evolution

The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.

Plant and Insect Viruses in Managed and Natural Environments: Novel and Neglected Transmission Pathways

The capacity to spread by diverse transmission pathways enhances a virus' ability to spread effectively and survive when circumstances change. This review aims to improve understanding of how plant and insect viruses spread through natural and managed environments by drawing attention to 12 novel or neglected virus transmission pathways whose contribution is underestimated. For plant viruses, the pathways reviewed are vertical and horizontal transmission via pollen, and horizontal transmission by parasitic plants, natural root grafts, wind-mediated contact, chewing insects, and contaminated water or soil. For insect viruses, they are transmission by plants serving as passive "vectors," arthropod vectors, and contamination of pollen and nectar. Based on current understanding of the spatiotemporal dynamics of virus spread, the likely roles of each pathway in creating new primary infection foci, enlarging previously existing infection foci, and promoting generalized virus spread are estimated. All pathways except transmission via parasitic plants, root grafts, and wind-mediated contact transmission are likely to produce new primary infection foci. All 12 pathways have the capability to enlarge existing infection foci, but only to a limited extent when spread occurs via virus-contaminated soil or vertical pollen transmission. All pathways except those via parasitic plant, root graft, contaminated soil, and vertical pollen transmission likely contribute to generalized virus spread, but to different extents. For worst-case scenarios, where mixed populations of host species occur under optimal virus spread conditions, the risk that host species jumps or virus emergence events will arise is estimated to be "high" for all four insect virus pathways considered, and, "very high" or "moderate" for plant viruses transmitted by parasitic plant and root graft pathways, respectively. To establish full understanding of virus spread and thereby optimize effective virus disease management, it is important to examine all transmission pathways potentially involved, regardless of whether the virus' ecology is already presumed to be well understood or otherwise.

Method-centered digital communities on protocols.io for fast-paced scientific innovation

The Internet has enabled online social interaction for scientists beyond physical meetings and conferences. Yet despite these innovations in communication, dissemination of methods is often relegated to just academic publishing. Further, these methods remain static, with subsequent advances published elsewhere and unlinked. For communities undergoing fast-paced innovation, researchers need new capabilities to share, obtain feedback, and publish methods at the forefront of scientific development. For example, a renaissance in virology is now underway given the new metagenomic methods to sequence viral DNA directly from an environment. Metagenomics makes it possible to “see” natural viral communities that could not be previously studied through culturing methods. Yet, the knowledge of specialized techniques for the production and analysis of viral metagenomes remains in a subset of labs.  This problem is common to any community using and developing emerging technologies and techniques. We developed new capabilities to create virtual communities in protocols.io, an open access platform, for disseminating protocols and knowledge at the forefront of scientific development. To demonstrate these capabilities, we present a virology community forum called VERVENet. These new features allow virology researchers to share protocols and their annotations and optimizations, connect with the broader virtual community to share knowledge, job postings, conference announcements through a common online forum, and discover the current literature through personalized recommendations to promote discussion of cutting edge research. Virtual communities in protocols.io enhance a researcher’s ability to: discuss and share protocols, connect with fellow community members, and learn about new and innovative research in the field.  The web-based software for developing virtual communities is free to use on protocols.io. Data are available through public APIs at protocols.io.

Synergies and antagonisms in virus interactions

Metagenomic surveys and data from next generation sequencing revealed that mixed infections among plant viruses are probably a rule rather than an exception in natural pathosystems. The documented cases may range from synergism to antagonism, which may depend from the spatiotemporal order of arrival of the viruses on the host and upon the host itself. In synergistic interactions, the measurable differences in replication, phenotypic and cytopathological changes, cellular tropism, within host movement, and transmission rate of one of the two viruses or both are increased. Conversely, a decrease in replication, or inhibition of one or more of the above functions by one virus against the other, leads to an antagonistic interaction. Viruses may interact directly and by transcomplementation of defective functions or indirectly, through responses mediated by the host like the defense mechanism based on RNA silencing. Outcomes of these interactions can be applied to the risk assessment of transgenic crops expressing viral proteins, or cross-protected crops for the identification of potential hazards. Prior to experimental evidence, mathematical models may help in forecasting challenges deriving from the great variety of pathways of synergistic and antagonistic interactions. Actually, it seems that such predictions do not receive sufficient credit in the framework of agriculture.

Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

BACKGROUND

Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands.

RESULTS

The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar.

CONCLUSIONS

Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.

Vector-Borne Bacterial Plant Pathogens: Interactions with Hemipteran Insects and Plants

Hemipteran insects are devastating pests of crops due to their wide host range, rapid reproduction, and ability to transmit numerous plant-infecting pathogens as vectors. While the field of plant-virus-vector interactions has flourished in recent years, plant-bacteria-vector interactions remain poorly understood. Leafhoppers and psyllids are by far the most important vectors of bacterial pathogens, yet there are still significant gaps in our understanding of their feeding behavior, salivary secretions, and plant responses as compared to important viral vectors, such as whiteflies and aphids. Even with an incomplete understanding of plant-bacteria-vector interactions, some common themes have emerged: (1) all known vector-borne bacteria share the ability to propagate in the plant and insect host; (2) particular hemipteran families appear to be incapable of transmitting vector-borne bacteria; (3) all known vector-borne bacteria have highly reduced genomes and coding capacity, resulting in host-dependence; and (4) vector-borne bacteria encode proteins that are essential for colonization of specific hosts, though only a few types of proteins have been investigated. Here, we review the current knowledge on important vector-borne bacterial pathogens, including Xylella fastidiosa, Spiroplasma spp., Liberibacter spp., and 'Candidatus Phytoplasma spp.'. We then highlight recent approaches used in the study of vector-borne bacteria. Finally, we discuss the application of this knowledge for control and future directions that will need to be addressed in the field of vector-plant-bacteria interactions.

Manipulation of hosts and vectors by plant viruses and impact of the environment

The effect of environmental factors on the efficiency of plant virus transmission is extremely difficult to predict, because they obviously impact concomitantly multiple steps of the complex three-way plant-virus-vector interaction. This review summarizes the diversity of the relationship between plants, viruses and insect vectors, and highlights the numerous phases of this process that can be altered by the virus in ways that can potentially enhance its transmission success. Many of the reported cases are often considered to be possible viral manipulations acting through modifications of the physiology of the host plant, indirectly reaching to the insect vector. Plants are extremely responsive to environmental fluctuations and so interferences with these putative viral manipulations are highly expected. The role of environmental factors in plant virus transmission can thus be envisaged solely in the context of this complexity. It is only briefly evoked here because this field of research is in its infancy and currently suffers from an impressive lack of experimental data.

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control

The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species

Ecological understanding of disease risk, emergence, and dynamics and of the efficacy of control strategies relies heavily on efficient tools for microorganism identification and characterization. Misdetection, such as the misclassification of infected hosts as healthy, can strongly bias estimates of disease prevalence and lead to inaccurate conclusions. In natural plant ecosystems, interest in assessing microbial dynamics is increasing exponentially, but guidelines for detection of microorganisms in wild plants remain limited, particularly so for plant viruses. To address this gap, we explored issues and solutions associated with virus detection by serological and molecular methods in noncrop plant species as applied to the globally important Barley yellow dwarf virus PAV (Luteoviridae), which infects wild native plants as well as crops. With enzyme-linked immunosorbent assays (ELISA), we demonstrate how virus detection in a perennial wild plant species may be much greater in stems than in leaves, although leaves are most commonly sampled, and may also vary among tillers within an individual, thereby highlighting the importance of designing effective sampling strategies. With reverse transcription-PCR (RT-PCR), we demonstrate how inhibitors in tissues of perennial wild hosts can suppress virus detection but can be overcome with methods and products that improve isolation and amplification of nucleic acids. These examples demonstrate the paramount importance of testing and validating survey designs and virus detection methods for noncrop plant communities to ensure accurate ecological surveys and reliable assumptions about virus dynamics in wild hosts.

Virus disease in wheat predicted to increase with a changing climate

Current atmospheric CO2 levels are about 400 μmol mol(-1) and are predicted to rise to 650 μmol mol(-1) later this century. Although the positive and negative impacts of CO2 on plants are well documented, little is known about interactions with pests and diseases. If disease severity increases under future environmental conditions, then it becomes imperative to understand the impacts of pathogens on crop production in order to minimize crop losses and maximize food production. Barley yellow dwarf virus (BYDV) adversely affects the yield and quality of economically important crops including wheat, barley and oats. It is transmitted by numerous aphid species and causes a serious disease of cereal crops worldwide. This study examined the effects of ambient (aCO2 ; 400 μmol mol(-1) ) and elevated CO2 (eCO2 ; 650 μmol mol(-1) ) on noninfected and BYDV-infected wheat. Using a RT-qPCR technique, we measured virus titre from aCO2 and eCO2 treatments. BYDV titre increased significantly by 36.8% in leaves of wheat grown under eCO2 conditions compared to aCO2 . Plant growth parameters including height, tiller number, leaf area and biomass were generally higher in plants exposed to higher CO2 levels but increased growth did not explain the increase in BYDV titre in these plants. High virus titre in plants has been shown to have a significant negative effect on plant yield and causes earlier and more pronounced symptom expression increasing the probability of virus spread by insects. The combination of these factors could negatively impact food production in Australia and worldwide under future climate conditions. This is the first quantitative evidence that BYDV titre increases in plants grown under elevated CO2 levels.

Determinants of taxonomic composition of plant viruses at the Nature Conservancy's Tallgrass Prairie Preserve, Oklahoma

The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test the effects of host identity, location, and sampling year on the taxonomic composition of plant viruses in six native plant species [Ambrosia psilostachya (Asteraceae), Vernonia baldwinii (Asteraceae), Asclepias viridis (Asclepiadaceae), Ruellia humilis (Acanthaceae), Panicum virgatum (Poaceae) and Sorghastrum nutans (Poaceae)] from the Nature Conservancy's Tallgrass Prairie Preserve in northeastern Oklahoma. We sampled over 400 specimens of the target host plants from twenty sites (plots) in the Tallgrass Prairie Preserve over 4 years and tested them for the presence of plant viruses applying virus-like particle and double-stranded RNA enrichment methods. Many of the viral sequences identified could not be readily assigned to species, either due to their novelty or the shortness of the sequence. We thus grouped our putative viruses into operational viral taxonomic units for further analysis. Partial canonical correspondence analysis revealed that the taxonomic composition of plant viruses in the target species had a significant relationship with host species (P value: 0.001) but no clear relation with sampling site or year. Variation partitioning further showed that host identity explained about 2-5 per cent of the variation in plant virus composition. We could not interpret the significant relationship between virus composition and host plants with respect to host taxonomy or ecology. Only six operational viral taxonomic units had over 5 per cent incidence over a 4-year period, while the remainder exhibited sporadic infection of the target hosts. This study is the first of its kind to document the dynamics of the entire range of viruses in multiple plant species in a natural setting.

Viral pathogen production in a wild grass host driven by host growth and soil nitrogen

Nutrient limitation is a basic ecological constraint that has received little attention in studies on virus production and disease dynamics. Nutrient availability could directly limit the production of viral nucleic acids and proteins, or alternatively limit host growth and thus indirectly limit metabolic pathways necessary for viral replication. In order to compare direct and indirect effects of nutrient limitation on virus production within hosts, we manipulated soil nitrogen (N) and phosphorus (P) availability in a glasshouse for the wild grass host Bromus hordeaceus and the viral pathogen Barley yellow dwarf virus-PAV. We found that soil N additions increased viral concentrations within host tissues, and the effect was mediated by host growth. Specifically, in statistical models evaluating the roles of host biomass production, leaf N and leaf P, viral production depended most strongly on host biomass, rather than the concentration of either nutrient. Furthermore, at low soil N, larger plants supported greater viral concentrations than smaller ones, whereas at high N, smaller plants supported greater viral concentrations. Our results suggest that enhanced viral productivity under N enrichment is an indirect consequence of nutrient stimulation to host growth rate. Heightened pathogen production in plants has important implications for a world facing increasing rates of nutrient deposition.

Indirect Effects of One Plant Pathogen on the Transmission of a Second Pathogen and the Behavior of its Potato Psyllid Vector

Plant pathogens can influence the behavior and performance of insect herbivores. Studies of these associations typically focus on tripartite interactions between a plant host, a plant pathogen, and its insect vector. An unrelated herbivore or pathogen might influence such interactions. This study used a model system consisting of Tobacco mosaic virus (TMV), the psyllid Bactericera cockerelli Sulc, and tomatoes to investigate multipartite interactions among a pathogen, a nonvector, and a plant host, and determine whether shifts in host physiology were behind potential interactions. Additionally, the ability of TMV to affect the success of another pathogen, 'Candidatus Liberibacter solanacearum,' which is transmitted by the psyllid, was studied. In choice trials, psyllids preferred nearly fourfold noninfected plants to TMV-infected plants. No-choice bioassays demonstrated that there was no difference in psyllid development between TMV-infected and control plants; oviposition was twice as high on control plants. Following inoculation by psyllids, 'Candidatus Liberibacter solanacearum' titers were lower in TMV-infected plants than control plants. TMV-infected plants had lower levels of amino acids and sugars but little differences in phenolics and terpenoids, relative to control plants. Possibly, these changes in sugars are associated with a reduction in psyllid attractiveness in TMV-infected tomatoes resulting in decreased infection of 'Candidatus Liberibacter solanacearum.'