Autonomous Long-Term High-Frequency Sampling of Marine Microbes

Marine and coastal ecosystems are facing an unprecedented set of challenges, highlighting the need for integrated assessment approaches. Microbes respond to environmental perturbations on relatively short time-scales, therefore information about the microbial food web has the power to become a useful ecological indicator for ecosystem status. However, a major difficulty in studying interactions within food webs is the ability to acquire samples frequently enough to see changes throughout an oceanic ‘event’. The Environmental Sample Processor (ESP) is an in situ sampling device that can collect, process and store microbial DNA and RNA from seawater, enabling fine-scale temporal resolution. Two ESP deployments during the summers of 2015 and 2016 were designed to determine potential biases and study microbial interactions at a temporal scale that is unprecedented using standard pelagic microbial sampling methods, respectively. From May to October 2015 a comparative experiment using the ESP while simultaneously collecting samples using a traditional approach was conducted to test the archiving capabilities of the ESP. Thirty-nine timepoints were collected in duplicate for each sampling method. Initial results indicate differences in microbial richness between ESP and standard samples using 16S and 18S rDNA amplicon data, however these differences may be due, in part, to as yet unknown conditions and we conclude that the ESP technology is a viable and crucial tool that can be used for the archiving microbial samples over significant periods of time. From May to October 2016 an ESP was deployed next to the Del Mar Southern California Coastal Ocean Observing System (SCCOOS) mooring at 15 meters below the sea surface. Daily samples were collected for the entire deployment with additional higher frequency sampling occurring during a detected phytoplankton bloom. In total 128 time-points were collected using serial filtration resulting in 384 samples. The temporal resolution from using these technologies has greatly enhanced the study of microbial food web dynamics and prove useful as tools for ocean observing.