Plant Virus Biodiversity and Ecology

Plant Virus Biodiversity and Ecology was one of two scientific theme areas in the State of Oklahoma's Research Infrastructure Improvement Award from the Experimental Program to Stimulate Competitive Research (EPSCoR) of the National Science Foundation (NSF) for 2005-2008 funding. The theme area began receive funding in May 2005.

Opportunity

"Viruses, parasitic organisms that rely on their host for “life sustaining" functions, have been found associated with almost every known organism, from eubacteria to archaebacteria to eukaryotes. They are as diverse in structure and molecular biology as the hosts they are associated with. We have not yet encountered the totality of virus biodiversity. ... Their biodiversity and abundance suggest an important role for viruses in our ecosystems. To explore this role, we need information beyond the mere discovery and cataloging of viral sequences. We need to know virus host associations, their geographic distributions, how these change with time, and the principles that govern these associations and distributions. A thorough understanding of virus biodiversity will have profound implications for our understanding of the evolution and ecology of higher organisms." The EPSCoR program funded the creation of infrastructure to address these needs.

Major Findings

Virus abundance

• About one-third of plant specimens yielded evidence of the presence of one or more viruses.
• The proportions of samples of individual species yielding such evidence varied widely for the frequently sampled species, but was always greater than zero.
• A considerable number of samples yielded evidence of the presence of multiple viruses.

Virus diversity

• Viral diversity was dependent of the family of viruses being considered.
• For several families (for example, tymovirus and tobamovirus) evidence of only a single species of virus was encountered.
• In other families (for example, Partitiviridae) evidence of a large diversity was found.
• Virus families frequently mentioned as agricultural pathogens (Geminiviridae, Potyviridae) were remarkably scarce in the data.
• Overall, signatures of hudreds of putative viruses were found.
• Only three of the putatively discovered viruses were viruses previously described by sequence.

Host distribution of viruses

• In the diverse kind of distribution apparent multiple viruses are found in multiple species of plants, in many cases (but not entirely) a one-on-one mapping of virus and plant species. Taxa exhibiting this distribution are: Chrysoviruses Endornaviruses, Totiviruses, Totivirids, Partitiviruses.
• In the limited kind of distribution, the virus is found in a single or very few plant species. Exemplifying this distribution are Ambrosia associated virus 1, TGP Allexivirus 1, Closteroviridae, Luteoviridae, Rhabdoviridae.
• In the cosmopolitan kind of distribution, the virus or apparent virus is found in high titer in one species but also in lower titer in many other species. Examples include TGP sobemovirus 1, Asclepias asymptomatic virus, TGP Comovirid 1, TGP Tobamovirus 1, TGP Panicovirus 1, TGP Carmovirus 1.
• Other kinds of virus-like sequences include one set similar to one oryzavirus segment, several (but not many) bacteriophage sequences, and pararetroviral sequences that may be from viruses or from chromosomal elements.

Novel features

• The RNA2 of TGP Comovirid 1 has an extra ORF beginning before the polyprotein ORF.
• RNA of TGP Tobamovirus 1 has an extra ORF beginning at the end of the RdRP ORF and continuing, out-of-frame, through the middle of the movement protein ORF.
• Sequences similar to one RNA segment of an oryzavirus have been found in several plants, but no evidence of other segments was uncovered.
• A 3' terminal ORF of the Ambrosia asymptomatic virus encodes a protein of similar length to that of a mandarivirus, overlapping the coar protein ORF, but is more similar in sequence to the 3' ORF of carlaviruses.
• A putative badnavirus has a fusion of the canonical ORFs 1 and 2.

Pathogenicity

• Obvious symptoms of infection were only noted on about 2% of the plant samples collected.
• The proportion of plant samples with evidence of virus presence was much greater than 2%
• Factors such as life-history traits and competitive ability were not evaluated.
• One virus, the tymovirus Asclepias asymptomatic virus, was reconstructed and infected both its original host species (A. viridis) and N. benthamiana, but only the latter showed symptoms of disease.

Technical

• Isolation of dsRNA followed by its conversion to dsDNA and sequencing was an effective way of screening samples for evidence of virus presence. DNA viruses would be ignored by this process.
• Isolation of nucleic acids from a virus-like particle preparation from plant specimens used less material and gave comparable results to the dsRNA method except that it did not reveal viruses suspected of not existing in encapsidated forms.
• Microarray analysis has been developed to the point that it can be used to detect the presence of virus sequences from within a genus and distinguish among members of that genus. Its development may be useful in future biodiversity inventory surveys.

Resources

Oklahoma is an ideal site for this exciting endeavor. Through previous EPSCoR support, Oklahoma had built strength in molecular technologies associated with genomics (sequencing, microarray hybridization, bioinformatics) at its major graduate educational institutions (OU, TU, OSU and OUHSC). Oklahoma’s substantial infrastructure in ecology and biodiversity includes not only its diverse natural areas and plant species, but also its facilities and personnel for analysis of this diversity.

• Its Advanced Center for Genome Technology (ACGT, Roe, OU) is one of the world’s most efficient nucleotide sequencing facilities.
• The OSU Microarray Core Facility (OMCF, P. Hoyt, OSU) has state-of-the-art microarrayers and scanners, and the bioinformatics support for analysis of microarray data. Pioneering work in the use of microarrays for virus detection (Sengupta et al. 2003) was done at the OMCF. It also is a leader in microarray education and training.
• VirOligo, the database of virus-specific oligonucleotides (Melcher), resides at OSU.
• Plant Biotechnology Network tied together molecular plant biologists, including team members, from OU, OSU and SRN into a group with shared interests and collaborations. "The mission of this group is to enhance research and training activities in molecular plant biology ... throughout the state and to make such activities more visible to the international scientific community.”
• TU spearheaded the creation of a new research station (dedication, May 2004), at the Nature Conservancy's Tallgrass Prairie Preserve, including laboratories and classrooms. The vascular flora of the preserve consists of more than 740 species, and is vouchered with specimens in a reference herbarium at the preserve.
• The Flora of Oklahoma project is nearing completion and a digital specimen-based atlas of Oklahoma plants is available. Two major (OSU and OU) and several minor research herbaria document the flora. The effort is part of the Oklahoma Biological Survey.
• The Palmer Lab hosts the ordination web page which has been ranked (by Nedstat) as the most visited website in mathematics and computer science.
• Oklahoma Mesonet keeps track of weather conditions at over 110 stations throughout the state.

Terms

• Biodiversity: "Biodiversity, or biological diversity, may be defined as the variety of living organisms inhabiting a region. Because this definition only implies the existence of a very complex phenomenon, biologists further divide 'biodiversity' into three levels: genetic, species and community. " (Oklahoma Biological Survey). We have interest in all three levels of biological diversity defined in this manner.
• Biodiversity has also been defined as "species richness and relative species abundance in space and time. Species richness is simply the total number of species in a defined space at a given time, and relative species abundance refers to their commonness or rarity." (Stephen P. Hubbell, 2001 , The Unified Neutral Theory of Biodiversity and Biogeography, Princeton U. Press, p.3)
• The species diversity can be viewed as a subset of the genetic diversity.
• Biogeography: is the study of the geographic distribution of species.
• Species: for viruses, this term is not universally accepted. For our purposes, we will adopt a nucleotide sequence based definition. Two viruses belong to different species if their sequences, overall are less than 90% identical.
• Virus: we use this term as a collective noun. A virus particle is part of a larger entity, the virus, that has infected the organism.
• Virion: a virus particle.
• Thus, virus relative species abundance does not include the concept of virion titer, but rather measures the frequency or fraction of plant individuals (of one or several plant species) that harbor the virus.

Contact U. Melcher

Page posted June 14, 2004
Last updated November 13, 2009