Modernizing Ecosystem Assessments & Improving ‘Omics Tools
The PMEL Ocean Molecular Ecology group continues to develop, advance, and adopt molecular methods to increase the efficacy of molecular ecology approaches. These efforts include the design and implementation of novel assays for key species, advancing quantitative metabarcoding approaches, developing novel approaches from difficult to process samples (e.g., archived samples), the adoption of advanced sequencing approaches and platforms, enhancement of reference barcode databases, and innovation and expansion of automated environmental DNA (eDNA) samplers. Together. we work collaboratively across NOAA Research to enhance NOAA ‘Omics capabilities by advancing molecular methods, bioinformatics, resources, and capabilities and achieve NOAA 'Omics Strategic Plan objectives.
We support the development of robust software resources for NOAA and broader marine 'omics community including reference database generating tools, visualization software, advanced taxonomic classifiers, and end-to-end sequence to interpretation pipelines. We are deeply engaged with ‘omics data management and bioinformatic efforts including maintaining the infrastructure needed to generate, analyze, and manage massive sequencing data sets. In addition, we enhance foundational genomic repositories through the creation and curation of reference databases of priority marine taxa. This includes the sequencing of whole and mitochondrial genomes to generate high-quality voucher reference specimens collaborating with key NOAA, federal, state, local, and academic partners. These efforts will improve our ability to characterize marine species through biomolecular approaches, furthering NOAA and academic monitoring efforts.
Key to the success of the NOAA ‘Omics program is the harmonization and standardization of molecular sampling efforts across ocean observing platforms. To achieve these objectives, we work with NOAA ‘Omics, local, state, and federal management agencies; industry representatives; and academics to 1) identify gaps among current monitoring efforts, 2) identify key management questions and relevant biodiversity targets, 3) coordinate the design and validation of molecular assays for priority targets, and 4) coordinate leveraged studies to compare current sampling practices and identify key areas of disagreement across platform-specific sampling methods. Together our goal is to create a central repository to share protocols, standards, and bioinformatics pipelines to support a community across laboratories and programs.