Our lab takes advantage of the revolution in DNA sequencing technology to develop bioinformatics tools for precise and fast detection, classification, and identification of plant pathogens and biocontrol agents. A second area of research focuses on environmental microbes that may play a role in the formation of precipitation.
Many bacterial species of significant scientific and economic interest display a high level of phenotypic variation. For example, different strains of the same bacterial species may cause a range of different diseases in humans or may not cause any disease at all. Also, different strains of the same plant-pathogenic species may cause different diseases on different crops or may not cause any disease at all. The Vinatzer lab in collaboration with Dr. Lenwood S. Heath (Computer Science) developed a web server that allows users to precisely circumscribe, name, and describe any group of bacteria, be it a species, an intra-specific group, or even a single pathogenic strain that caused a disease outbreak. Unknown bacteria can be identified as members of these groups based on their genome sequences alone. The platform is based on the concept of Life Identification Numbers (LINs) and leverages a combination of algorithms to calculate, or infer, Average Nucleotide Identity (ANI). While the platform does not rely on named species, it is compatible with rigorous description of named species as well. The platform can be found at http://genomerxiv.cs.vt.edu/. We are currently getting ready to develop a second platform for fungal identification, in collaboration wit Dr. Nik Grunwald and Dr. Uehling at Oregon State University, and expect the platform to go online in late 2024.
Fast and accurate plant disease diagnosis and pathogen identification before plants are distributed by nurseries and sold to farmers and home owners could make the difference between successfully preventing a disease outbreak or losing billions of dollars because of crops that are damaged or destroyed by emerging diseases, such as citrus greening. Shotgun metagenomic sequencing in combination with efficient algorithms and comprehensive pathogen genome databases offer the possibility to revolutionize plant disease diagnostics and pathogen identification. We thus perform research on how to improve protocols for pathogen DNA extraction directly from plants and bioinformatic analysis of metagenomic sequences.
Ice nucleation is a fundamental process in the earth’s atmosphere. While pure water melts at 0°C, pure water only freezes at approximately -38°C. At higher temperatures, water only freezes in the presence of particles that facilitate the transition from the liquid to the solid state. The most efficient particles that can do this are called ice nucleation particles (INPs) because they provide a nucleus from which ice crystals grow. In other words, they have ice nucleation activity (INA). The most effective INPs are produced by a small number of bacterial and fungal species. These species are hypothesized to contribute to the freezing of cloud droplets in the atmosphere leading to the formation of precipitation and to a change of the ratio of liquid to frozen water in mixed phase clouds, which in turn affects earth's radiation balance, and consequently, earth’s temperature. Moreover, INPs can increase the damage of spring frost to fruit tree blossoms, sometimes leading to the total loss of a crop in a geographic region. But INPs can also have positive impacts. Some bacterial INPs are used for snow production in ski resorts and bacterial and fungal INPs have the potential to be employed in cloud seeding to increase precipitation. Finally, INPs could be used in the food industry to concentrate fruit juices and change the properties of ice cream and other frozen products, as long as they are found harmless to human health. Identifying the molecular basis of ice nucleation in the fungal genus Fusarium can be expected to have long term positive impacts because of the fundamental role of INPs in weather and climate, their negative impact on fruit production, their potential for improving food products, and their ability to lengthen the ski season in ski resorts. The approach used in this project to identify the molecular basis of ice nucleation is three-pronged combining a computational approach, a biochemical approach, and a genetic approach. The results from these computational and biochemical approaches will be combined to make a short list of putative genes coding for fungal INPs. These genes will then be expressed in organisms that on their own do not have ice nucleation activity to determine which genes are sufficient to confer ice nucleation activity to these organisms. The genes that do that can then be considered to encode fungal INPs.