Post-collection activities
This section discusses the steps scientists take at sea through the time scientists publish the results and upload data in public databases.
Step 1. When the expedition sails, the chief scientist directs the scientific operations.
In some cases, the cruise is solely for the benefit of the chief scientists’ lab. In other cases, the funding agencies will send two or more research teams out, each of whom has been provided support by the agency. The leads of each team designate a single chief scientist to coordinate the expedition. However, it is quite common for each team to pursue its own line of research. In such cases, the chief scientist will not have direct influence on the scientific activities of the other team; they are merely working to coordinate the activities on board ship. It is important to bear this in mind because, with some exceptions, each science team is responsible for its own activities and outcomes on board ship.
Step 2. Collection of samples and storage on-board
During most biological expeditions, samples are collected for shoreside analyses. There are some examples where all the necessary equipment to complete the analyses, e.g., autonomous imaging systems, are brought onboard so that no physical samples are taken home. However, this is exceedingly rare and scientists are encouraged to bring back some number of samples to “ground-truth” their data. As such, scientists must consider the best way to preserve their samples for later analyses. Typical methods of preservation include the use of a preservative (e.g., ethanol or formaldehyde), desiccation, refrigeration, or freezing. For most biomolecular analyses such as gene sequencing, mRNA sequencing (so-called transcriptomics), protein sequencing (proteomics), and metabolite analyses (metabolomics), the preferred method is cryo-preservation at -80°C temperatures. As such, many research vessels have ultracold freezers and/or liquid nitrogen onboard for use by the scientists while they are on board ship. It is common for scientists to use these for the duration of the cruise.
Step 3. Shipment of collected samples for analysis (e.g., sequencing facility, home institution, etc.)
Scientists will ship the samples back to the home institution while they are still frozen. Maintaining the cold chain is one of the biggest challenges, and the costs associated with doing so can be extraordinary. Dry ice and to a lesser extent liquid nitrogen are used to keep samples cold, and ensuring that samples arrive before they thaw requires the services of a specialized courier service that maintains the cold chain. Shipping samples from ABNJ, e.g., from the Central Pacific Ocean, to a sequencing facility in Asia, Europe, or the U.S., can cost several thousand U.S. dollars or more for a small package. There are ways to preserve genomic or environmental DNA and other biomolecules in ethanol, in a manner that does not require ultra-cold storage, but the analysis that can be done with such samples is more limited. In some cases, samples are sent to a facility where they are destructively sampled to recover the DNA or other molecules. The resulting data can, of course, be widely shared. However, if replicate tissues are desired for further analyses, it is up to the science party to collect and freeze additional samples in advance for dissemination or archiving.
Step 4. Submission of a post-collection report.
Nearly all grants are subject to terms that are specified by the funding agency. Today, the majority of U.S., Asian, and European agencies require that the data and information collected during an expedition be made publicly available after an embargo period. The funding agencies typically require annual progress reports as well as disclosures of any commercialization. As previously mentioned, these requirements are presented by the home institution as the recipient of funding; usually institutional staff sign the grant agreement on behalf of the home institution. This is a subtle but an important distinction because it is the home institution, not the Expedition Leader, that enters into an agreement with the grant-providing organization.
