Autonomous Systems for the Collection, in situ Preservation and Return of Microbial Samples from Aquatic Ecosystems Grant uri icon


  • As the research community transitions away from descriptive studies of aquatic microbes to system-level investigations of, for example, community responses to changing geochemical conditions, toxic spills, ocean acidification, expanding Oxygen Minimum Zones, algal bloom dynamics and food web dynamics, it is essential that researchers have instrumentation that meets these new challenges. Studies of labile organic molecules such as messenger RNA, proteins, and metabolites are now routinely used to assess microbial community activities. Instrumentation for robotic time-series or adaptive user-controlled sampling must be capable of acquisition of samples onto the surface of a filter and chemically preserving collected cells at the site in the environment they reside (in situ) to minimize introduction of artifacts in the resulting data. Proposed fabrication and testing of technical sampling platforms will add much needed infrastructure for research in the form of flexible, multiple-application water column sampling that will enhance collaborative research and will make possible more comprehensive and accurate studies microbial community activity. Each development effort will provide training opportunities for high school through graduate students. Results will be contributed to a high-profile Scientific Committee on Oceanic Research (SCOR) Working Group White Paper on proposed standards of practice for studies of marine microbiology, and on Woods Hole Oceanographic Institution and Edgcomb laboratory websites. The principal investigators will produce a freely available E-lecture submitted to Limnology and Oceanography E-Lectures ( on the advances represented in these platforms, rationale for their use, and expected commercial availability. The capabilities of each platform will be unique to the field of microbial ecology. The objective will be to fabricate and field test two complementary sampling platforms that share recent new technology developments in our laboratories. The capabilities of the two platforms will enable application of these advances for a wide range of sampling objectives, and demonstration of their successes will make it possible to implement these new technologies into commercially-available instrumentation. One platform, the Helical Rotary Valve-Miniature Microbial Sampler (HRV-MMS) will permit collection of at least 200 samples (up to 4-times the numbers now possible with existing technology) within the footprint of a compact instrument that can be quite readily implemented in Autonomous Underwater Vehicles, Remote Operated Vehicles, Deep Submergence Vehicles, hydrocast, or mooring-based sampling platforms. Most of the engineering design work for this platform has been completed. The second proposed development involves an advancement of the Microbial Sampling-Submersible Incubation Device (MS-SID) platform, which can be deployed by hydrowire, on fixed moorings, or released on Global Positioning System-tracked surface float systems to collect up to 48 samples (user-defined volumes dependent on filter porosity and targeted filtration times), each consisting of up to 6 replicates collected simultaneously (total 288 samples) and/or conduct in situ incubation-style microbial metabolic rate measurements. The new helical rotary valve design that will be implemented on both platforms has significant advantages over existing valve technologies in terms of sampling flow rates and dramatically lower flow resistances.

date/time interval

  • September 1, 2017 - August 31, 2019

sponsor award ID

  • 1737173