Plant Virus Biodiversity and Ecology

Plant Virus Biodiversity and Ecology is 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. Preliminary experiments reveal that 65% of plants surveyed contain double-stranded (ds) RNA, a characteristic of virus infection, suggesting an easily accessible wealth of information. 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. With RII funding we will create the infrastructure to address these needs, essentially creating the field of plant virus ecology."

Resources

Oklahoma is an ideal site to initiate this exciting endeavor. Through previous EPSCoR support, Oklahoma has 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. Ayoubi & Melcher, 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. Bioinformatics expertise at OU (J. Wren) promises to support enhanced VirOligo data entry.
• Plant Biotechnology Network ties 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.
• Tools to run BLAST against the PVBE sequences.

Plan of Work

The plan of work is divided into several phases, some overlapping

• Sampling
  • In this phase, we will sample as many plant species as possible, each with limited replicates.
    • In the first part of this phase, abundant and easy to collect species, totaling about 100 will be sampled. These will be used to test methods and adjust further protocols.
    • In the second part, we will sample the remaining accessible species.
  • In the second phase, we will, based on the results of phase one, select ecological hypotheses that appear testable with the material we have. These include questions of changes in virus species populations in particular plant species with distance, changes with time or with weather conditions, or age of perennial plants.
• Overlapping with the above phases, we will characterize novel viruses for:
  • nucleotide sequence
  • protein and nucleic acid structures
  • biological properties.
• The figure outlines the flow of work.
  

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 March 12, 2007