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San Diego researchers have new way to gauge ocean life

Sardines clump together in a school of the small fish in the Gulf of California in this undated photo
Octavio Aburto
Scripps Institution of Oceanography
Sardines clump together in a school of the small fish in the Gulf of California in this undated photo

San Diego scientists are pioneering a new way to measure the strength of the smallest creatures and plants in the ocean.

Tools developed for genetic research are giving oceanographers a better glance at the diversity of the microscopic parts that make up the ocean’s basic food web.

Scripps Institution of Oceanography’s Chase James calls the technique meta-barcoding. Researchers take samples, filter them, then scan them for DNA from microscopic plants and animals.


“If you ever work in a grocery store and you’re making sure you’re taking stock of the inventory, you would go around and scan all the barcodes in the grocery store, right?” said James, a graduate student at the Scripps Institution of Oceanography and the study’s lead author. “And that’s basically what we’re doing, but in the ocean.”

The results, published in the Journal Nature Communications, give researchers a more complete picture of the ocean’s health.

It also helps improve understanding about changes that are happening in the food web because of climate change.

James says scientists began taking ocean samples in 2014, following along on a long running study of ocean currents known as the California Cooperative Oceanic Fisheries Investigations (CALCOFI), which was established to track the sardine fishery.

“One of the powerful aspects of working with the CALCOFI program is that we are also collecting data (about) where certain commercially important fisheries are. Like tuna and certain marine mammal surveys,” said Andrew Allen, a computational biologist at the Scripps Institute of Oceanography and the J. Craig Venter Institute.


Seven years of ocean sampling created a data record that can be used to track changes over time, and it also points to the differences between the new sample technique and other sampling methods tracking the ocean’s life.

The team is also working on putting their data analysis approach to use on historical samples of ocean water that was previously analyzed using other older methods.

“Roughly 35% to 40% of the diversity that we find regionally, we don’t find globally,” James said. “And so this is kind of an immense depository, regionally, that suggests that these global snapshots aren’t really capturing the local, the regional diversity.”