Plant virus ecology

Viruses have generally been studied either as disease-causing infectious agents that have a negative impact on the host (most eukaryote-infecting viruses), or as tools for molecular biology (especially bacteria-infecting viruses, or phage). Virus ecology looks at the more complex issues of virus-host-environment interactions. For plant viruses this includes studies of plant virus biodiversity, including viruses sampled directly from plants and from a variety of other environments; how plant viruses impact species invasion; interactions between plants, viruses and insects; the large number of persistent viruses in plants that may have epigenetic effects; and viruses that provide a clear benefit to their plant hosts (mutualists). Plants in a non-agricultural setting interact with many other living entities such as animals, insects, and other plants, as well as their physical environment. Wild plants are almost always colonized by a number of microbes, including fungi, bacteria and viruses. Viruses may impact any of these interactions [1]

Plant virus metagenomics: Biodiversity and ecology

Viral metagenomics is the study of viruses in environmental samples, using next generation sequencing that produces very large data sets. For plant viruses, these studies are still relatively new, but are already indicating that our current knowledge grossly underestimates the diversity of these viruses. Some plant virus studies are using thousands of individual plants so that each sequence can be traced back to its precise host. These studies should allow for deeper ecological and evolutionary analyses. The finding of so many new plant viruses that do not cause any obvious symptoms in wild plant hosts certainly changes our perception of viruses and how they interact with their hosts. The major difficulty in these (as in all) metagenomic studies continues to be the need for better bioinformatics tools to decipher the large data sets. The implications of this new information on plant viruses for international agriculture remain to be addressed

Persistent plant viruses: Molecular hitchhikers or epigenetic elements?

Many plants harbor persistent cytoplasmic viruses that are not transmitted horizontally and do not move from cell to cell. These viruses have extensive longevity within individual plant cultivars. Based on phylogenetic evidence they appear to undergo rare transmission events between plants and fungi. Very few functions have been attributed to persistent viruses in plants, but their longevity and protection from the plant's immune system suggest that they provide a selective advantage for their hosts, at least under some conditions. In addition, some persistent plant virus sequences have been found in plant genomes and are expressed as functional genes. Hence, rather than simply molecular hitchhikers, they may be cytoplasmic epigenetic elements that could provide genetic information to their plant hosts

How does the genome structure and lifestyle of a virus affect its population variation?

Viruses use diverse strategies for their replication, related in part to the genome structure (double-stranded or single-stranded; positive sense or negative sense; RNA or DNA). During each round of replication, mutations are introduced in the viral genome and the mode of replication (stamping machine and geometric replication) may affect the population dynamics of the progeny virus. Our understanding of the relationships among genome strandedness, mode of replication and the population variation is still limited. Here we will review what is known about virus replication by stamping machine or geometric modes, and how that relates to the biology of single stranded versus double stranded RNA genomes. We will present how this may affect the mutation frequency and population dynamics. Finally the potential importance of the population dynamics in acute viruses and persistent viruses will be discussed

Plant virus metagenomics: what we know and why we need to know more

In the past decade the concept of plant viruses as strictly disease-causing entities has been challenged. While the most well-studied and obvious interactions between plants and viruses are related to disease, there are several examples of mutualistic relationships between plants and viruses, both indirect and direct. These mutualistic interactions have not been fully explored, and many questions remain unanswered. One problem is the lack of knowledge of plant viruses in nature. Metagenomic surveys have estimated that only a small fraction of virus species are known. Additionally, globalization has led to the increased movement of plant material and virus movement. As viruses move from one area to another, new potential hosts offer the possibility of new interactions, both negative and positive

Ecosystem simplification, biodiversity loss and plant virus emergence

Plant viruses can emerge into crops from wild plant hosts, or conversely from domestic (crop) plants into wild hosts. Changes in ecosystems, including loss of biodiversity and increases in managed croplands, can impact the emergence of plant virus disease. Although data are limited, in general the loss of biodiversity is thought to contribute to disease emergence. More in-depth studies have been done for human viruses, but studies with plant viruses suggest similar patterns, and indicate that simplification of ecosystems through increased human management may increase the emergence of viral diseases in crops

Differential responses to virus challenge of laboratory and wild accessions of Australian species of Nicotiana, and comparative analysis of RDR1 gene sequences

Nicotiana benthamiana is a model plant utilised internationally in plant virology because of its apparent hyper-susceptibility to virus infection. Previously, others showed that all laboratory accessions of N. benthamiana have a very narrow genetic basis, probably originating from a single source. It is unknown if responses to virus infection exhibited by the laboratory accession are typical of the species as a whole. To test this, 23 accessions of N. benthamiana were collected from wild populations and challenged with one to four viruses. Additionally, accessions of 21 other Nicotiana species and subspecies from Australia, one from Peru and one from Namibia were tested for susceptibility to the viruses, and for the presence of a mutated RNA-dependent RNA polymerase I allele (Nb-RDR1m) described previously from a laboratory accession of N. benthamiana. All Australian Nicotiana accessions tested were susceptible to virus infections, although there was symptom variability within and between species. The most striking difference was that plants of a laboratory accession of N. benthamiana (RA-4) exhibited hypersensitivity to Yellow tailflower mild mottle tobamovirus infection and died, whereas plants of wild N. benthamiana accessions responded with non-necrotic symptoms. Plants of certain N. occidentalis accessions also exhibited initial hypersensitivity to Yellow tailflower mild mottle virus resembling that of N. benthamiana RA-4 plants, but later recovered. The mutant Nb-RDR1m allele was identified from N. benthamiana RA-4 but not from any of 51 other Nicotiana accessions, including wild accessions of N. benthamiana, demonstrating that the accession of N. benthamiana used widely in laboratories is unusual