Genomic responses to the Deepwater Horizon event and development of high-throughput biological assays for oil spills
This is a collaborative project led by Kelley Thomas at the University of New Hampshire; Co-PIs include the Bik Lab, Paul Montagna the Harte Research Institute for Gulf of Mexico Studies (Texas A&M), and Jon Norenburg at the Smithsonian National Museum of Natural History. Our grant is funded through the Gulf of Mexico Research Initiative, and a detailed overview of the award can be found on the GOMRI website.
The overall aim of this project is to improve the response, mitigation, detection, characterization and remediation associated with oil spills and accompanying release of gas.
The benthic environment in the Gulf of Mexico (GoM) is biologically hyper-diverse, performing critical ecosystem functions that have consequences for the ecology of the entire GoM region. Benthic communities are strongly impacted by oil spills, which render them a valuable tool for assaying and monitoring the impacts of contamination. However, detailed and extensive characterization of these communities has been impractical for due to the tedious and time-consuming nature of the taxonomic efforts required to accurately describe small benthic fauna. Our project leverages high-throughput sequencing technologies that now enable rapid, accurate, and cheap assays of community biodiversity. To achieve these goals, our GOMRI project team brings together the interdisciplinary expertise in marine biology, taxonomy, genomics and bioinformatics necessary for the development of a meaningful and robust technology. Project goals include three main objectives:
- Use targeted sequencing of individual benthic eukaryotes to generate a representative sample of diverse genomes from which to select an expanded set of nuclear and mitochondrial loci for targeted mining of shotgun metagenomic data.
- Assess eukaryotic community structure across space and time via high-throughput sequencing of environmental metagenomes using a new and expanded array of nuclear and mitochondrial marker genes.
- Establish Standard Operating Procedures (SOPs) and reproducible bioinformatic workflows for environmental monitoring of oil spills. This will include establishing a database for integration of taxonomic and molecular datasets, and dissemination of tools and educational resources.
One of the most important goals of this project is training the next generation of environmental biologists with interdisciplinary tools. Toward that goal, we will organize two formal workshops each year. These workshops will expose students to the full spectrum of this technology from sample preparation, through taxonomy, to metagenomics and bioinformatics. These workshops are also opportunities to attract underrepresented groups and to link the research team with GoM stakeholders. All workshops will be held at the Harte Research Institute for Gulf of Mexico Studies at Texas A&M University, Corpus Christi.
The proposal leverages a set of pre- and post-spill samples from diverse, impacted benthic habitats, some of which have already received significant analysis. The group also brings significant cyberinfrastructure (databases) and advanced bioinformatics tools (PhyloSift, iPython workflows, data visualization software) that will be modified to support the specific goals of this proposal.