Project Overview

Summary:

In January 2016, Dr. W. Kelley Thomas at the University of New Hampshire, was awarded an RFP-V grant of $2,572,666 to lead the GoMRI project entitled Genomic Responses to the Deepwater Horizon event and development of high-throughput biological assays for oil spillswhich consisted of 4 collaborative institutions and approximately 21 research team members (including students). This project leveraged 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 brought together the interdisciplinary expertise in marine biology, taxonomy, genomics and bioinformatics necessary for the development of a meaningful and robust technology and worked towards three primary 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. 

Research Highlights

            As of December 31, 2019, this project’s research included 2 research cruises/expeditions, resulted in 5 peer-reviewed publications, 19 scientific presentations, and 6 datasets being submitted to the GoMRI Information and Data Cooperative (GRIIDC), which are/will be made available to the public. The project also engaged 3 Masters and PhD students over its award period. Significant outcomes of this project’s research are highlighted below. 

Workshops: Two workshops were hosted (Year 2 and Year 3) which brought together taxonomic experts, molecular biology experts, and bioinformatics experts with students at the undergraduate and graduate levels and interested faculty/investigators to work together to learn the methodological and analytical protocols involved in biodiversity survey and assessment as it relates to meiofaunal samples.  The attendees in these workshops included US-based and international participants.  There were 59 participants in year 2 and 64 participants in year 3. 

Specimen info and analysis:  In years 1-3, a total of 302 individual meiofaunal specimens went through the genome sequencing pipeline.  Of these, 216 were successfully sequenced representing 76 families and 127 unique species. 

In year 4, a supplement enabled further assessment of the impacts of the Deepwater Horizon event on benthic communities.  An additional 58 archived stations have been analyzed to enhance resolution of that assessment and determine if impacts occurred further afield. A principal component analysis (PCA) was used to summarize oil spill impacts, and the benthic footprint of the oil spill was estimated using Empirical Bayesian Kriging (EBK) interpolation. The spill caused very high levels of total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAH), and Barium in the sediment, and the benthic response was low diversity, low evenness, and low taxonomic richness of the infauna communities, and high nematode to copepod ratios. Based on the larger sample set, we now know the area of impact was approximately 263 km² around the wellhead, which is 78% higher than the original estimate. Particularly severe damages to benthic communities were found in an area of 58 km², which is 142% higher than the original estimate. The addition of the new stations extended the area of the benthic footprint map to about twice as large as originally thought and improved the resolution of the spatial interpolation.  This demonstrates that limiting sampling and analysis to save time and money will result in missing impacts that have actually occurred. Also, the new data proves that optimizing spatial extent is the true form of replication for environmental impact assessment study design. 

From the molecular data gathered, two sets of hybrid capture probes were developed and are being tested and used for metagenomic samples. The first set of probes are based on the mitochondrial genomes, and the second set of probes are based on single-copy orthologous nuclear genes.  These probes will be useful for the assessment of populations and communities of meiofauna, as well as temporal and spatial comparisons. 

An extension of meiofaunal characterization included the analysis of their microbiomes (Bacteria and Archaea) that are critical to ecosystem function and survival of the meiofaunal organisms.  This data revealed species-specific core microbiomes for meiofaunal taxa as well as accessory microbiomes that are geographically distinct (Gulf of Mexico, Atlantic, or Pacific samplings).

 Proposal Abstract - RFP-V PI W. Kelly Thomas