The MBARI Environmental Sample Processor—the ESP—provides on-site (in situ) collection and analysis of water samples from the ocean, identifying the presence of organisms and/or biological toxins.

The instrument uses an electromechanical fluidic system designed to autonomously collect and filter water samples. Then it either preserves and archives the sample for use after the ESP is recovered or directly applies molecular detection technology to investigate the biology of the sample in near real-time.

CEO/President Chris Scholin works on the second-generation ESP. Photo: Kim Fulton-Bennett © MBARI 2006

Why build an ESP?

Whether trying to identify microorganisms or understand why certain algae produce toxins, analysis typically requires collecting water samples at sea and returning them to a fully equipped laboratory. This can introduce a significant time lag between sample collection and informative results. Additionally, water collection can become very expensive if boats or ships are needed on a regular basis.

Thus in the early 2000s, MBARI initiated the development of the ESP and new techniques to allow the remote application of molecular probe technology. The hope was to provide a “persistent presence” in the ocean, bringing the laboratory to the sea, and thus reaping cost savings in the most expensive part of microbial oceanography—sample collection.

Data from these tests can be sent to shore in near real-time, allowing scientists and policy makers to make rapid decisions related to beach safety or shellfish harvesting. Additionally, the persistent presence of the ESP allows for the capture of episodic or very short-lived eve

Additional Information

The current second-generation (2G) ESP uses small chambers called “pucks” to house the filter material. Water is pulled through the puck until one liter has been filtered or the filter is so loaded with biomass that no more water will pass, whichever comes first. Once filtering is complete, two things can happen, depending on the wishes of the researcher.

The ESP uses small chambers called “pucks” to house the filter material. Photo: Todd Walsh © MBARI 2006.

First, the sample can be “archived”. This means preservative is added to the filter, and the puck is put away for processing once the instrument is recovered. We use RNALater™, which locks all gene expression at the moment it’s applied, without need for freezing. We have had remarkable results using this preservative, obtaining high quality DNA and RNA from the sample even with deployments over eight months long!

Second, the sample can be processed. Here we add a lytic agent and heat to the puck, which breaks open cells, releasing proteins and nucleic acids from every microbe captured on the filter. This new liquid, called a homogenate, is a slurry of molecules that will be very useful in downstream analysis.

The homogenate can be used in a number of ways, depending on how the ESP is configured. Normally, we perform a sandwich-hybridization assay (SHA), introducing some homogenate to a puck containing a pre-printed set of nucleic acid probes. If any of the nucleic acids within the homogenate are complementary to the printed array they will bind and, after addition of a few more chemicals, the printed spot will glow. SHA is particularly useful when biomass is overly abundant; no purification is required and there is no inhibition when arrays are presented with concentrated homogenate. The glowing spots on the array image are then captured with an on-board camera, saved as a .TIFF file, and sent via radio or cell phone back to shore for analysis.

Left, early printing (2000–2013); right, current printing (2014–present). © MBARI

If the ESP has a module attached called the micro-fluidic block (MFB), we can perform quantitative PCR unattended, under the surface of the ocean. The MFB was designed for the manipulation of not milliliters but microliters of fluid, a requirement for qPCR analysis. A small qPCR module was developed in collaboration with Lawrence Livermore National Laboratory, and we have performed in situ qPCR from surface waters (depths of 10 meters) to hydrothermal vents at underwater volcanos (1,800 meters). qPCR is quite sensitive at finding rare targets, but is easily inhibited by large amounts of biomass. Thus SHA and qPCR represent two ends of a continuum depending on the targets of interest and the biomass one expects to encounter.

The third generation (3G) ESP improves on the 2G in a number of ways and is currently under development (2017). The initial goal of the 3G ESP has always been to mount it on an autonomous underwater vehicle (AUV); giving this ecogenomic sensor mobility will be a transformative event in oceanography, as sampling events are no longer locked in one location, sampling water that happens to drift past.

The inside of the latest model of the third generation ESP. Photo: Todd Walsh © MBARI 2015.

To recast everything the 2G ESP does such that it will fit within a 12-inch-by-24-inch cylinder introduces some enormous engineering challenges, in particular how to shrink the entire instrument into something the size of two basketballs!  Obviously we would not have room for bags of communal reagents, and large waste containers; we had to think of a way to shrink the liquid requirements to perform the biology.

Rather than communal bags of reagents, the 3G ESP transitioned to use single cartridges. Photo: Todd Walsh © MBARI 2015.

While we stayed with the idea of filtering water within a puck, we developed the idea of a “cartridge” where all reagents were carried on each cartridge creating a self-contained, use-once entity arranged around a toroid ring. This resulted in a 60-cartridge “turbine” with each cartridge individually accessed and processed at a shared processing station. Cartridges are of two types:  archival and lyse-n-go and follow the functionality of the pucks in the 2G ESP.

Archival cartridges filter water, apply preservative, and await recovery once the vehicle’s mission is complete.

Lyse-n-go cartridges are more complex, requiring heater circuitry and slightly more convoluted fluid pathways through the cartridge. The goal of these cartridges is to create homogenate and then pass that homogenate off the cartridge to a downstream analytical processing module. Currently we are working with collaborators to develop a Surface Plasmon Resonance (SPR) module, a digital droplet PCR (ddPCR) module, and a Total Internal Reflection Fluorescence (TIRF) module. The future is very exciting given the various modalities we will be able to use to explore the world’s oceans.

The Environmental Sample Processor (ESP) provides on-site (in situ) collection and analysis of water samples from the subsurface ocean. The instrument is an electromechanical/fluidic system designed to collect discrete water samples, concentrate microorganisms or particles, and automate application of molecular probes which identify microorganisms and their gene products. The ESP also archives samples so that further analyses may be done after the instrument is recovered. The data is telemetered back to shore and is available in the portal below.  To start exploring data from the ESP, select the mission you are interested in from the “Select Deployment” drop down below, then click on the ESP you are interested in and then select the parameters you are interested in visualizing.  To make the portal full screen, you can click here to open in a new window.

A second generation ESP is deployed off the Santa Cruz pier. Photo © MBARI

The Environmental Sample Processor (ESP) pumps water through a filter and retains all particles/organisms larger than 0.2 micrometers. Using molecular biology techniques on the filtered material, the ESP can:

  • Identify the type and quantity of microorganisms and animals present in the water,
  • Monitor the appearance of toxins and other biological compounds, and
  • Investigate how marine microbes respond to seasonal variation and a changing climate

Data from these tests can be sent to shore in near real-time, allowing scientists and policy makers to make rapid decisions related to beach safety or shellfish harvesting. Additionally, the persistent presence of the ESP allows for the capture of episodic or very short-lived events.