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Ecogenomic Sensor Enables Researchers to Monitor Oceans in Near Real Time

FT. LAUDERDALE, FLA. (GenomeWeb) — Researchers at the Monterey Bay Aquarium Research Institute have developed an instrument to collect and analyze seawater samples and the microbes within them to monitor ocean health.

At the Association for Biomolecular Resource Facilities meeting here, MBARI's James Birch described the development of a long-range autonomous underwater vehicle (AUV) from earlier, moored models. This vehicle houses an environmental sample processor (ESP) to analyze samples in situ as well as preserve samples for later tests in the lab. This new technology, he said, combines traditional oceanographic tools with ones used in the biomedical diagnostics and research fields.

The ocean covers 71 percentage of the Earth's surface, and oceanic phytoplankton generate about 70 percent of atmospheric oxygen, making them key microbes to study. Studying plankton, Birch noted, is an old proposal, and for decades boats have trawled along to determine what microbes are found where in the ocean.

Building on that, Birch said that if researchers can determine what the microbes are doing and where they are doing it, they could be used to gauge the health of the ocean.

"About 10 years ago, this concept of an ecogenomic sensor came into being," Birch said. The plan was to develop a sensor that would sit out in the ocean and report back on its findings.

But studying oceans and ocean life can be tricky, Birch noted, as even getting samples can be challenging. Deep waters are typically found far offshore where researchers and equipment are exposed to difficult weather and environmental conditions. In addition, the ocean is constantly in flux as currents and waves move microorganisms around a typically moored sensor.

The ESP developed by Birch and his colleagues collects samples for gene expression analysis. Seawater is filtered, cells lysed, and the contents exposed to a pre-prepared assay. The pre-prepared assay, he noted, relies on low-density DNA probes and protein arrays to gauge the presence and abundance of specific organisms, their genes, and metabolites. At the same time, the researchers developed a two-channel qPCR module to analyze gene expression, and they are working on folding in surface plasmon resonance and digital PCR capabilities.

By mooring two of these ESPs off the coast of Southern California, Birch and his colleagues were able to study recurrent algal blooms that occur there, but whose origin was unknown. An upwelling of water either brought algae up from the deep and exposed them to sunlight — making them "go bonkers," as Birch put it — or the algae were always present at the surface and the upwelling instead brought nutrients to the surface that then lead to an algal frenzy.

The AUV searches for the algae and its hallmark domoic acid, while also recording water temperatures. In their experiments, the MBARI researchers found that the algae didn't appear to be present until the water temperature fell, suggesting that the upwelling brought them to the surface.

Similarly, Birch and his colleagues used their ESP instrument to study a deepwater, active volcano that is west of Portland, Oregon. As this vent is some 1,600 meters below the surface in a high-pressure environment, they redesigned the sensor with a new titanium shell and intake system to handle the circumstances.

At two locations — one in the vent and one near where the ESP was moored — their analyses uncovered different assemblages of microbes. Their qPCR analysis, for instance, found that microbes near the deep vent had differential gene expression of ammonia oxidation genes.

However, Birch said that these efforts really only were able to detect events that had already happened upstream because the sensor is fixed in space, and the researchers determined they would need a more mobile sensor. 

To that end, they developed a mobile AUV — shaped like 10-foot-long missile — that can move in the waters with a cohort of microbes of interest. This AUV houses a redesigned ESP that uses integrated cartridges to either store or analyze samples.

The long-range AUV, Birch said, finished its fourth flight just a few weeks ago

The AUV flies in a yo-yo pattern, Birch said. Sensors in its nose detect pressure, temperature, depth, as well as chlorophyll levels. Once it finds a chlorophyll-containing layer, it's programmed to float along and collect samples. Then it dives 50 meters and collects samples there before collecting samples from the layer above the chlorophyll-containing layer. 

"The ability to control a long-range AUV — I could see [it] on my smartphone while at home — it was quite amazing," Birch said. "The ability to control it like that or have it autonomously respond, I think will transform oceanography," he added.