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By Erin Loury
Nothing spoils the day for a would-be sunbather like a health advisory and beach closure due to polluted waters. But even more distressing than a cancelled vacation is the fact that a beach’s “open” or “closed” status may not actually reflect the water contamination of that given day. Closing beach waters to human contact is an important decision, with consequences for public health and the local tourism economy. However, the amount of time usually required to monitor beach water quality creates a critical flaw in the system. “You’re opening and closing beaches based on the water that was there yesterday,” explains Chris Scholin, president and chief executive officer of the Monterey Bay Aquarium Research Institute (MBARI). Scholin’s device makes it possible to analyze water quality in a few hours rather than overnight.
Traditionally, scientists must collect beach water samples, bring them to a laboratory, and culture and count the fecal bacteria that come from human or other animal waste. While not typically disease-causing themselves, these bacteria are often associated with human illnesses, and scientists must determine if they exceed regulatory thresholds set by the Environmental Protection Agency (EPA). This process takes 24 hours at best, and in the ephemeral world of microbe concentrations that constantly shift with the currents such a lag time renders the regulatory process of beach closures inefficient, and sometimes ineffective.
Automated science in real-time
To achieve a real-time solution to monitor beaches, water quality scientists need rapid-fire instruments to record biological data, similar to the probes oceanographers have used for years to collect temperature, salinity and nutrient data. Enter Scholin’s brainchild of 20 years in the making: a robot called the Environmental Sample Processor, or ESP. Described by Scholin as “a laboratory in a can,” the ESP is a robotic underwater molecular biology lab built by MBARI engineers that is about the size of a kitchen garbage can. Scientists can program the ESP to automatically perform a range of tasks, from collecting water samples and extracting genetic material, to using that material to identify the microbe species and toxin abundance in the sample. The ESP transmits the results to a laboratory via radio signals in a matter of hours and archives the samples for scientists to examine later.
Center for Ocean Solutions (COS) early career fellow Kevan Yamahara said that the ESP’s ability to collect and analyze water samples on site makes the technology cutting-edge. “The ESP is ‘state of the art’ because it executes high-level tasks that usually require a researcher several different steps to perform, such as running molecular probe analysis,” he said. “It’s been interesting to go from doing everything myself, like collecting samples and pipetting, to having the instrument do everything for me.” Yamahara remarked that a challenge that goes hand in hand with harnessing the power of automated technology is learning to control the instrument’s various functions through computer coding.
Human health where the land meets the sea
In a partnership facilitated by COS, Yamahara is currently working with Scholin and Alexandria Boehm of Stanford University to fine-tune the ESP to monitor beach water quality. Poor water quality is a central challenge to ocean and human health that surfaces at the land-sea interface. “Most of the human population lives within a few miles of the coastlines and our waste has to go somewhere. Most of it goes right into the ocean,” Scholin said. “By the very nature of where we live, humans have an impact on the coastal environment.”
Boehm explains that people who swim in sewage-polluted waters are subject to a slew of pathogens that can cause everything from gastrointestinal and respiratory illnesses to ear, nose and throat infections and skin rashes. However, measuring these pathogens directly in seawater is very difficult and time consuming. “They are present in such low concentrations, and detecting a rare target in a sea of microorganisms is very challenging,” said Boehm, although she hopes to develop such detection methods in the future.
Instead, the EPA has created water quality standards based on levels of fecal indicator bacteria, such as Enterococcus, which are normal intestinal inhabitants in warm-blooded animals. While not typically the causes of disease themselves, the presence of these bacteria is linked to increased likelihood of health risks. To circumvent growing the bacteria in a lab, Boehm, Scholin and Yamahara are using molecular methods called quantitative polymerase chain reaction, or qPCR. This “photocopying” process amplifies the amount of microbe DNA in a sample, and allows the researchers to indentify their bacteria of interest in a watery lineup based on the species’ unique genetic markers.
The team is also using genetic markers to identify the sources of fecal bacteria in seawater, distinguishing whether they are from humans or other animals, like various livestock. Boehm explained that knowing the sources of contamination is important to determine the clean-up approach of impaired water, and such work is currently a major focus of her lab’s research. The team is also working closely with the Southern California Coastal Water Research Project (SCCWRP) to improve beach water quality monitoring in California. Boehm’s work with colleagues estimates that the health costs of gastrointestinal illnesses caused by contaminated beach waters total $21 million to $51 million annually in southern California alone.
A “quiet revolution” and the need for speed
The rapid turnaround time of the ESP can help researchers get a handle on the moving target of bacterial concentrations in seawater. As Yamahara explained, “There’s minute by minute variation in the samples that you take, so over the course of the day you could see really high concentrations in the morning and low in the afternoon, and it can be different the next day.” The time sensitivity of the ESP could also provide an early warning system for events like harmful algal blooms that can poison shellfish or outbreaks of disease in offshore fish farms.
Scholin said that creating a network of autonomous data collectors in the environment could move monitoring the ocean’s microscopic biological community in the direction of weather forecasting. Rather than sending an army of water collectors scrambling around to sample the ocean, “You could ultimately have a lot of low-cost instrument stations that take measurements and beam it all back to a ‘clearing house’ that incorporates data into ocean forecast models,” Scholin explained. He describes the ESP as part of a “quiet revolution” moving towards in-situ science, freeing researchers from the constraints of bringing samples back to the lab. “It’s opened a whole new perspective of trying to look at the environment, and provides the ability of getting results in real-time that you can download to your laptop or iPhone,” he said. “People are just shocked that you could actually do that.”
Building Scholin’s dream machine
Scholin can trace the genesis of the ESP back to his graduate student days at the Woods Hole Oceanographic Institution. “We would go out and take water samples to collect harmful algae and spend weeks counting them under a microscope,” he said. His thesis pioneered molecular biology as a tool to detect and discriminate among tiny algal species based on their DNA, but his idea to automatically assess them in the field seemed like little more than a pipe dream. When Scholin joined MBARI as a postdoctorate fellow in 1992, “They were about the only people that thought I wasn’t crazy,” he said. His development of the ESP evolved into a full-time staff position, and Scholin now serves as MBARI’s president and CEO.
The ESP has also evolved over time from a first generation prototype, deployed in 2002, to its current form, the second-generation model launched in 2006. “It really pushes the limits of what we can do in a laboratory,” Scholin said of the ESP. The team has to prepackage all the chemical reagents needed to equip the robot for its one-month deployment and secure the fragile instruments to withstand the harsh ocean environment. “We have to try to make it ‘bomb proof’ so to speak, and make it work all by itself on essentially a stack of flashlight batteries. That’s a real challenge from an engineering perspective,” Scholin said.
Towards a future of commercial distribution
As one sign of the team’s engineering success, the company Spyglass Biosecurity recently picked up the commercial development and marketing of the ESP. In June of 2010 the first commercially-made ESP was delivered to Woods Hole to monitor phytoplankton blooms for the EPA. Although a single, fully-equipped research model of the ESP costs over $100,000 to produce, MBARI technicians have recently started work with support from the National Science Foundation to build cheaper, stripped-down models that perform specific tasks.
Three ESP units are also currently hard at work in Monterey Bay. One unit offshore from Moss Landing near the Monterey Submarine Canyon is helping to conduct research on microbe sulfur cycling, while two units deployed near New Brighton State Beach and the Santa Cruz pier are monitoring for harmful algal blooms and the neurotoxin domoic acid. Last spring, Scholin fully realized the communication power of this new technology while on an RV trip with his family: “I was sitting in the middle of Death Valley with my laptop and could monitor a harmful algal bloom off of southern California because we had sensors out there.” His graduate student dream had become reality.
After years of development and an ongoing refinement process, Scholin can offer proof of the ESP’s many capabilities to counter the naysayers. “Being able to run DNA probe arrays and see the comings and goings of these species was something we always believed we could do, and other people always thought that was an insurmountable challenge,” he said. “Now we are detecting so many different types of organisms. We are the only ones in the world who can deliver that kind of capability.”
