Coevolution of a Persistent Plant Virus and Its Pepper Hosts

Exploring the Global Trends of Bacillus, Trichoderma and Entomopathogenic Fungi for Pathogen and Pest Control in Chili Cultivation

Chili, renowned globally and deeply ingrained in various cultures. Regrettably, the onset of diseases instigated by pests and pathogens has inflicted substantial losses on chili crops, with some farms experiencing complete production decimation. Challenges confronting chili cultivation include threats from pathogenic microbes like Xanthomonas, Fusarium, Phytophthora, Verticillium, Rhizoctonia, Colletotrichium and Viruses, alongside pests such as whiteflies, mites, thrips, aphids, and fruit flies. While conventional farming practices often resort to chemical pesticides to combat these challenges, their utilization poses substantial risks to both human health and the environment. In response to this pressing issue, this review aims to evaluate the potential of microbe-based biological control as eco-friendly alternatives to chemical pesticides for chili cultivation. Biocontrol agents such as Bacillus spp., Trichoderma spp., and entomopathogenic fungi present safer and more environmentally sustainable alternatives to chemical pesticides. However, despite the recognised potential of biocontrol agents, research on their efficacy in controlling the array of pests and pathogens affecting chili farming remains limited. This review addresses this gap by evaluating the efficiency of biocontrol agents, drawing insights from existing studies conducted in other crop systems, regarding pest and pathogen management. Notably, an analysis of Scopus publications revealed fewer than 30 publications in 2023 focused on these three microbial agents. Intriguingly, India, as the world's largest chili producer, leads in the number of publications concerning Bacillus spp., Trichoderma spp., and entomopathogenic fungi in chili cultivation. Further research on microbial agents is imperative to mitigate infections and reduce reliance on chemical pesticides for sustainable chili production.

Identification and characterization of Phaseolus vulgaris endornavirus 1, 2 and 3 in common bean cultivars of East Africa

Persistent viruses include members of the family Endornavirus that cause no apparent disease and are transmitted exclusively via seed or pollen. It is speculated that these RNA viruses may be mutualists that enhance plant resilience to biotic and abiotic stresses. Using reverse transcription coupled polymerase chain reactions, we investigated if common bean (Phaseolus vulgaris L.) varieties popular in east Africa were hosts for Phaseolus vulgaris endornavirus (PvEV) 1, 2 or 3. Out of 26 bean varieties examined, four were infected with PvEV1, three were infected with both PvEV1 and PvEV2 and three had infections of all three (PvEV) 1, 2 and 3. Notably, this was the first identification of PvEV3 in common bean from Africa. Using high-throughput sequencing of two east African bean varieties (KK022 and KK072), we confirmed the presence of these viruses and generated their genomes. Intra- and inter-species sequence comparisons of these genomes with comparator sequences from GenBank revealed clear species demarcation. In addition, phylogenetic analyses based on sequences generated from the helicase domains showed that geographical distribution does not correlate to genetic relatedness or the occurrence of endornaviruses. These findings are an important first step towards future investigations to determine if these viruses engender positive effects in common bean, a vital crop in east Africa.

Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape

Viruses can affect coral health by infecting their symbiotic dinoflagellate partners (Symbiodiniaceae). Yet, viral dynamics in coral colonies exposed to environmental stress have not been studied at the reef scale, particularly within individual viral lineages. We sequenced the viral major capsid protein (mcp) gene of positive-sense single-stranded RNA viruses known to infect symbiotic dinoflagellates ('dinoRNAVs') to analyze their dynamics in the reef-building coral, Porites lobata. We repeatedly sampled 54 colonies harboring Cladocopium C15 dinoflagellates, across three environmentally distinct reef zones (fringing reef, back reef, and forereef) around the island of Moorea, French Polynesia over a 3-year period and spanning a reef-wide thermal stress event. By the end of the sampling period, 28% (5/18) of corals in the fringing reef experienced partial mortality versus 78% (14/18) of corals in the forereef. Over 90% (50/54) of colonies had detectable dinoRNAV infections. Reef zone influenced the composition and richness of viral mcp amino acid types ('aminotypes'), with the fringing reef containing the highest aminotype richness. The reef-wide thermal stress event significantly increased aminotype dispersion, and this pattern was strongest in the colonies that experienced partial mortality. These findings demonstrate that dinoRNAV infections respond to environmental fluctuations experienced in situ on reefs. Further, viral productivity will likely increase as ocean temperatures continue to rise, potentially impacting the foundational symbiosis underpinning coral reef ecosystems.

A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery

Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.

The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind

My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A Survey of Main Pepper Crop Viruses in Different Cultivation Systems for the Selection of the Most Appropriate Resistance Genes in Sensitive Local Cultivars in Northern Spain

Viral diseases have become one of the main phytosanitary problems for pepper growers in the Basque Country (northern Spain). In 2014, a survey was carried out to determine the prevalence of the most common viruses found in Gernika pepper and Ibarra chili pepper landraces. A total of 97 plots were surveyed and classified according to the crop system. Within these plots, 1107 plants were sampled and tested for tobacco mosaic virus (TMV), tomato mosaic virus (ToMV), tobacco mild green mosaic virus (TMGMV), pepper mild mottle virus (PMMoV), paprika mild mottle virus (PaMMV), potato virus Y (PVY) and tomato spotted wilt virus (TSWV) applying a DAS-ELISA test. PaMMV was verified by the non-radioactive molecular hybridization technique and it was found to be negative. All viruses were detected, but the most prevalent viruses were PVY and TMGMV (19.8% and 10.6% of tested plants, respectively). Differences among cultivation systems were found for most of the tested viruses. PVY had a higher level of infection under open field conditions (27.3%) than under greenhouse conditions (12.3%). Inversely, the viruses belonging to the Tobamovirus genus and TSWV prevailed under greenhouse conditions (28.9% and 5.2%) when compared to open field (11.2% and 1.1%), respectively. Single (28%) and multiple infections (8.9%) were found. All PMMoV isolates were classified as pathotype P1.2. Survey results indicated that tobamovirus and PVY resistance genes would be the most appropriate to be included in breeding programs with these sensitive pepper landraces.

RdRp or RT, That is the Question

The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.

Detection of Persistent Viruses by High-Throughput Sequencing in Tomato and Pepper from Panama: Phylogenetic and Evolutionary Studies

High-throughput sequencing from symptomatic tomato and pepper plants collected in Panama rendered the complete genome of the southern tomato virus (isolate STV_Panama) and bell pepper endornavirus (isolate BPEV_Panama), and almost-complete genomes of three other BPEV isolates. Tomato chlorosis virus, tomato mosaic virus, and impatiens necrotic spot virus were also detected. Analysis of the complete genome of STV and BPEV worldwide isolates revealed nucleotide diversities of 0.004246 and 0.070523, respectively. Bayesian phylogenetic analysis showed two main groups for each virus (I and II), and several subgroups for BPEV (IA, IB, IC, IIA and IIB). Isolate STV_Panama clustered with NC_12-03-08 from USA and Tom3-T from France (99.97% nucleotide identity) in Group I and BPEV_Panama was close to the Canadian isolate BPEV_Ontario (99.66% nucleotide identity) in Subgroup IB. No correlation was observed between geographic and genetic distances for both viruses. Panamanian BPEV isolates were divergent, belonging to Groups I and II (nucleotide identities > 87.33%). Evolutionary analysis showed purifying selection in all encoding regions of both viruses, being stronger in the overlapping region of both STV genes. Finally, recombination was detected in BPEV but not in STV. This is the first report of STV and BPEV in Panama.

Genetic plasticity in RNA2 is associated with pathogenic diversification of broad bean wilt virus 2

Broad bean wilt virus 2 (BBWV2) is an evolutionarily successful RNA virus with an extensive host range and worldwide distribution that causes severe damage to crops. While numerous BBWV2 isolates from various plant species have been identified and their genome sequences determined, little information is available on the virulence and symptomatic characteristics corresponding to the genomic sequences. In this study, we provide integrated information on the molecular and pathogenic characteristics of three genetically distant BBWV2 isolates: BBWV2-PC, -LS2, and P3 obtained from Gentiana scabra, Leonurus sibiricus, and Pisum sativum, respectively. Phylogenetic and diversity analyses of the BBWV2 population included 42 isolates from various host species and revealed that RNA2 has higher genetic plasticity than RNA1 and may have evolved under host-imposed constraints. In addition, we generated an infectious cDNA clone of BBWV2-PC RNA2 (pBBWV2-PC-R2). Pseudo-recombination analysis of pBBWV2-PC-R2 further demonstrated that RNA2 determines the pathogenic characteristics of the PC isolate.

Genome structure and diversity of novel endornaviruses from wheat sharp eyespot pathogen Rhizoctonia cerealis

Rhizoctonia cerealis (teleomorph Ceratobasidium cereale) is a soil-borne plant pathogenic fungus that can cause sharp eyespot in wheat or yellow patch in grasses. In this study, 21 new endornavirus genomes were obtained from five R. cerealis strains through the high-throughput sequencing of viral double-stranded RNA. Eighteen viruses were identified as Alphaendornavirus, and three viruses were identified as new species of Betaendornavirus on the basis of the phylogenetic analysis of the deduced amino acid sequences of RNA-dependent RNA polymerase. Notably, 12 of the new alphaendornaviruses could encode two open reading frames (ORFs), which were a rare feature of Endornaviridae. The amino acid sequences encoded by ORF2 from different endornaviruses had very low identity, and their functions and evolution origins remained unclear. Different endornavirus species with remarkably different genome structures could be found in the same R. cerealis strain. This study indicated that endornaviruses are common in R. cerealis and display wide diversity. Betaendornaviruses were found in R. cerealis, and a new species was proposed. This study is the first to report that the endornaviruses from R. cerealis can encode two ORFs and enhances our understanding of the viruses in the Endornaviridae family.

Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus

Understanding the evolutionary history of a virus and the mechanisms influencing the direction of its evolution is essential for the development of more durable strategies to control the virus in crop fields. While the deployment of host resistance in crops is the most efficient means to control various viruses, host resistance itself can act as strong selective pressure and thus play a critical role in the evolution of virus virulence. Cucumber mosaic virus (CMV), a plant RNA virus with high evolutionary capacity, has caused endemic disease in various crops worldwide, including pepper (Capsicum annuum L.), because of frequent emergence of resistance-breaking variants. In this study, we examined the molecular and evolutionary characteristics of recently emerged, resistance-breaking CMV variants infecting pepper. Our population genetics analysis revealed that the high divergence capacity of CMV RNA1 might have played an essential role in the host-interactive evolution of CMV and in shaping the CMV population structure in pepper. We also demonstrated that nonsynonymous mutations in RNA1 encoding the 1a protein enabled CMV to overcome the deployed resistance in pepper. Our findings suggest that resistance-driven selective pressures on RNA1 might have contributed in shaping the unique evolutionary pattern of CMV in pepper. Therefore, deployment of a single resistance gene may reduce resistance durability against CMV and more integrated approaches are warranted for successful control of CMV in pepper.

Brachypodium and plant viruses: entwined tools for discovery

In just a decade, Brachypodium distachyon (Brachypodium) has fulfilled its initial promise as a key tool for realizing new strategies for understanding host and pathogen biology during virus infections of the Poaceae. For this Tansley Insight, I have identified four areas - from the laboratory to the field - that may be particularly fruitful to explore, with a particular focus on Brachypodium-virus infections. These focus areas include: mechanisms of RNA modification of host plants and viruses; coevolution of virus-host interactions; viruses as tools of discovery; and how to explicate the complex outcomes during multivirus infections. Here, I broadly frame our current knowledge of Brachypodium-virus interactions and how these findings may inform virus studies of grasses in the laboratory, field and natural settings.

Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems

A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.

Ultrastructural Analysis of Cells From Bell Pepper (Capsicum annuum) Infected With Bell Pepper Endornavirus

Endornaviruses include viruses that infect fungi, oomycetes, and plants. The genome of plant endornaviruses consists of linear ssRNA ranging in size from approximately 13-18 kb and lacking capsid protein and cell-to-cell movement capability. Although, plant endornaviruses have not been shown to cause detectable changes in the plant phenotype, they have been associated with alterations of the host physiology. Except for the association of cytoplasmic vesicles with infections by Vicia faba endornavirus, effects on the plant cell ultrastructure caused by endornaviruses have not been reported. Bell pepper endornavirus (BPEV) has been identified in several pepper (Capsicum spp.) species. We conducted ultrastructural analyses of cells from two near-isogenic lines of the bell pepper (C. annuum) cv. Marengo, one infected with BPEV and the other BPEV-free, and found cellular alterations associated with BPEV-infections. Some cells of plants infected with BPEV exhibited alterations of organelles and other cell components. Affected cells were located mainly in the mesophyll and phloem tissues. Altered organelles included mitochondrion, chloroplast, and nucleus. The mitochondria from BPEV-infected plants exhibited low number of cristae and electron-lucent regions. Chloroplasts contained plastoglobules and small vesicles in the surrounding cytoplasm. Translucent regions in thylakoids were observed, as well as hypertrophy of the chloroplast structure. Many membranous vesicles were observed in the stroma along the envelope. The nuclei revealed a dilation of the nuclear envelope with vesicles and perinuclear areas. The organelle changes were accompanied by membranous structure rearrangements, such as paramural bodies and multivesicular bodies. These alterations were not observed in cells from plants of the BPEV-free line. Overall, the observed ultrastructural cell alterations associated with BPEV are similar to those caused by plant viruses and viroids and suggest some degree of parasitic interaction between BPEV and the plant host.

High-Throughput Sequencing Reveals Bell Pepper Endornavirus Infection in Pepper (Capsicum annum) in Slovakia and Enables Its Further Molecular Characterization

Ribosomal RNA-depleted total RNAs from a sweet pepper plant (Capsicum annuum, labelled as N65) grown in western Slovakia and showing severe virus-like symptoms (chlorosis, mottling and deformation of leaf lamina) were subjected to high-throughput sequencing (HTS) on an Illumina MiSeq platform. The de novo assembly of ca. 5.5 million reads, followed by mapping to the reference sequences, revealed the coinfection of pepper by several viruses; i.e., cucumber mosaic virus (CMV), watermelon mosaic virus (WMV), pepper cryptic virus 2 (PCV2) and bell pepper endornavirus (BPEV). A complete polyprotein-coding genomic sequence (14.6 kb) of BPEV isolate N65 was determined. A comparison of BPEV-N65 sequences with BPEV genomes available in GenBank showed 86.1% to 98.6% identity at the nucleotide level. The close phylogenetic relationship with isolates from India and China resulted in their distinct grouping compared to the other BPEV isolates. Further analysis has revealed the presence of BPEV in sweet or chili peppers obtained from various sources and locations in Slovakia (plants grown in gardens, greenhouse or retail shop). Additionally, the partial sequencing of two genomic portions from 15 BPEV isolates revealed that the Slovak isolates segregated into two molecular clusters, indicating a genetically distinct population (mean inter-group nucleotide divergence reaching 12.7% and 14.5%, respectively, based on the genomic region targeted). Due to the mix infections of BPEV-positive peppers by potato virus Y (PVY) and/or CMV, the potential role of individual viruses in the observed symptomatology could not be determined. This is the first evidence and characterization of BPEV from the central European region.

Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses

Indirect evidence of mitochondrial viruses in plants comes from discovery of genomic fragments integrated into the nuclear and mitochondrial DNA of a number of plant species. Here, we report the existence of replicating mitochondrial virus in plants: from transcriptome sequencing (RNA-seq) data of infected Chenopodium quinoa, a plant species commonly used as a test plant in virus host range experiments, among other virus contigs, we could assemble a 2.7-kb contig that had highest similarity to mitoviruses found in plant genomes. Northern blot analyses confirmed the existence of plus- and minus-strand RNA corresponding to the mitovirus genome. No DNA corresponding to the genomic RNA was detected, excluding the endogenization of such virus. We have tested a number of C. quinoa accessions, and the virus was present in a number of commercial varieties but absent from a large collection of Bolivian and Peruvian accessions. The virus could not be transmitted mechanically or by grafting, but it is transmitted vertically through seeds at a 100% rate. Small RNA analysis of a C. quinoa line carrying the mitovirus and infected by alfalfa mosaic virus showed that the typical antiviral silencing response active against cytoplasmic viruses (21- to 22-nucleotide [nt] vsRNA peaks) is not active against CqMV1, since in this specific case the longest accumulating vsRNA length is 16 nt, which is the same as that corresponding to RNA from mitochondrial genes. This is evidence of a distinct viral RNA degradation mechanism active inside mitochondria that also may have an antiviral effect.IMPORTANCE This paper reports the first biological characterization of a bona fide plant mitovirus in an important crop, Chenopodium quinoa, providing data supporting that mitoviruses have the typical features of cryptic (persistent) plant viruses. We, for the first time, demonstrate that plant mitoviruses are associated with mitochondria in plants. In contrast to fungal mitoviruses, plant mitoviruses are not substantially affected by the antiviral silencing pathway, and the most abundant mitovirus small RNA length is 16 nt.

Evolutionary and ecological links between plant and fungal viruses

Contents Summary 86 I. Introduction 86 II. Lineages shared by plant and fungal viruses 87 III. Virus transmission between plants and fungi 90 IV. Additional plant virus families identified in fungi by metagenomics 91 Acknowledgements 91 References 91 SUMMARY: Plants and microorganisms have been interacting in both positive and negative ways for millions of years. They are also frequently infected with viruses that can have positive or negative impacts. A majority of virus families with members that infect fungi have counterparts that infect plants, and in some cases the phylogenetic analyses of these virus families indicate transmission between the plant and fungal kingdoms. These similarities reflect the host relationships; fungi are evolutionarily more closely related to animals than to plants but share very few viral signatures with animal viruses. The details of several of these interactions are described, and the evolutionary implications of viral cross-kingdom interactions and horizontal gene transfer are proposed.

Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya

Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.