This proposal is directed toward research theme 4, the development of technology for improved response, mitigation, detection, characterization and remediation associated with oil spills and accompanying release of gas.
Within the GoM, the benthic environment 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, the characterization of these communities has been impractical for large- scale deployment due to the tedious and time-consuming nature of the taxonomy required to accurately describe these communities. This project leverages recent and dramatic advances in DNA sequencing technology that have transformed the process of rapid, accurate, and cheap assays of community biodiversity. To achieve these goals, the project team brings together the interdisciplinary expertise in marine biology, taxonomy, genomics and bioinformatics necessary for the development of a meaningful and robust technology and has formulated three objectives.
Objective 1: 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.
Objective 2: 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.
Objective 3: 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.
Specific products of this research will be SOPs and associated infrastructure necessary for implementation of this technology. This will include large datasets (genomic, taxonomic, and environmental metadata) that will be made freely available. All data analyses associated with this project will be published in open-access journals. All genomic samples will be deposited in and distributed by the Global Genome Initiative and Ocean Genome Legacy.
One of the most important goals of this project is training the next generation of environmental biologists with interdisciplinary tools. Toward that goal, there will be 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.
Beyond the specific goals of this project, the methods and infrastructure being developed here will be applicable to virtually all geographic regions and ultimately beyond the marine environment. In addition, the large number of new genomes from key species in the benthic ecosystem, the archived DNA samples, as well as the metagenomic datasets of diverse environmental samples, will contribute to fundamental knowledge about the workings of these ecosystems that are so critical to the health of our environment.
Project Research Overview (2016):
An overview of the proposed research activities from the GoMRI 2016 Meeting in Tampa.
Direct link to the Research Overview presentation.