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Researchers discover new digestive strategy in shipworms

An international research team led by Dan Distel, director of the Ocean Genome Legacy Center of New England Biolabs at Northeastern University, has discovered a novel digestive strategy in shipworms. The breakthrough, the researchers say, may also be a game-changer for the industrial production of clean biofuels.

To start, it’s important to note that shipworms, the so-called “termites of the sea,” aren’t actually worms—they’re bizarre clams that look like worms. Similar to termites, they use enzymes made by bacteria to aid in the break down wood for nutrition. But the researchers found that the enzymes shipworms use to break down wood don’t originate in gut bacteria; in fact, they’re far removed from it, instead the enzymes are made by symbiotic bacteria stored inside specialized cells in their the gills and then transported to the gut.

Their research was published online Monday afternoon in the Early Edition of the journal Proceedings of the National Academy of Sciences. Distel collaborated with researchers at institutions across the United States as well as in France and the Philippines. The National Science Foundation, the U.S. Department of Energy’s Joint Genome Institute, the Fogarty International Center at the National Institutes of Health, and New England BioLabs supported this research.

Distel, a research professor at Northeastern’s Marine Science Center, said no other animal in the world relies on bacteria outside of its digestive system to produce its digestive enzymes and no other intracellular bacterium is known to produce enzymes that function in the outside world of the host. In fact, he said digestive strategies don’t differ much between organisms, particularly those that eat wood or plant material.

“You don’t hear about the discovery of new digestive strategies very often,” he said. “It just doesn’t happen.”

The research team, which included former OGL research scientists Roberta O’Connor (Tufts Medical Center), Jennifer Fung (Bolt Threads Inc.), and Koty Sharp (Eckerd College), examined shipworms from Puget Sound in northwestern Washington. First, the researchers used genomics to sequence the genomes of the gill bacteria and to identify the genes predicted to be involved in breaking down plant matter. Then, they searched the gut in hopes of finding proteins there that were encoded in genomes of the gill bacteria. From their examination, the researchers did in fact find these proteins.

What’s more, Distel said the team found nearly 1,000 different genes in the gills that could be involved in breaking down wood. In the gut, they found about 45 of these same genes. “This was a key finding,” he said, “because we can identify the small number of enzymes that are actually involved in breaking down wood in gut, and that gives us a list of candidates that you can start to look at to find commercially-viable enzymes.”

Distel said a key area where this work could yield potential commercial benefits is in biofuel production. These enzymes, he said, are interesting because they convert plant biomass, or cellulose, into sugar, which can be used to make biofuels like ethanol. The U.S. government has mandated that 36 billion gallons of cellulosic biofuel be produced annually by 2022, and Distel said nearly half of this supply will be expected to come from cellulosic feedstocks—mainly agricultural waste like cornstalks. The USDA estimates that as much as one-third of America’s transportation fuel demand could be met by cellulosic biomass. But Distel said the main bottleneck preventing the commercial success of cellulosic ethanol is the lack of enzymes necessary to cheaply and efficiently convert cellulose to sugar.

Enter the shipworm.

In terms of next steps, the researchers plan to investigate exactly how these important digestive enzymes are transported from shipworms’ gills to the gut.

Distel also oversees the Ocean Genome Legacy, a public biorepository of DNA samples from marine life that re-located last year to Northeastern’s Marine Science Center in Nahant, Massachusetts. He said these findings further exemplify the need to study marine life and its many mysteries.

“This is why it’s so important that we as researchers look at oceans,” Distel said. “It yields so many unexpected benefits.”