Summary/Description: This OCB activity is aimed at developing a focused marine microbial nucleic acid (na) 'omics intercomparison and intercalibration effort. Increasingly, field programs of relevance to the OCB community include major components that use high-throughput molecular barcoding, metagenomics, and transcriptomics (nucleic acid ‘omics or na'omics herein) to understand the functioning of prokaryotic and eukaryotic microbes in the ocean. Recent examples of these programs include integration of microbial sampling at ocean time-series sites, the EXPORTS field campaign, and the international BioGEOTRACES program, which couples these measurements with ocean chemistry in conjunction with GEOTRACES cruise sampling. A pressing challenge for both our community and the broader microbiome research community is the need for more standardization and intercalibration to facilitate comparison between na’omics data (Nayfach et al. Cell. 2016 Aug 25; 166(5): 1103–1116; Stulberg et al. Nature Microbiology 2016. Article number: 15015). These issues were highlighted as a critical need at a recent OCB-supported workshop held in November 2018 to discuss the next wave of potential international field programs (Biogeoscapes) that would tightly couple ocean chemistry sampling with na'omics measurements. To ensure the success of this and other such programs, we seek to bring together experts and stakeholders in a small workshop in order to identify a path towards na’omics standardization and intercalibration solutions.
We envision developing a series of recommendations around the following issues to be tested in future intercalibration activities.
- Sample biomass collection and nucleic acid preservation for downstream analysis
- Extraction protocols for nucleic acids
- Addition of standard reference material to nucleic acid isolation protocols
- Isolation methods unique to RNA
- Sequence library construction
- Considerations unique to barcoding methods
- Integration of bioinformatic considerations
Read or download the activity proposal (PDF)
Bethany Jenkins - University of Rhode Island
Andrew Allen - University of California, San Diego and UCSD and the J. Craig Venter Institute
Paul Berube - Massachusetts Institute of Technology
Scott Gifford - University of North Carolina, Chapel Hill
Adrian Marchetti - University of North Carolina, Chapel Hill
Alyson Santoro - University of California, Santa Barbara