Digestion strategy in shipworms holds potential for biofuels

By Northeastern University | November 13, 2014

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 recently published 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.”