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Knocking these animals out of the food chain will, in time, affect species relevant to fisheries.
She disputed an assessment by BP's compensation fund that the Gulf of Mexico will recover by the end of 2012.
Millions of barrels of oil spewed into the sea after a BP deepwater well ruptured in April 2010.
Professor Joye told the American Association for the Advancement of Science conference in Washington that it may be a decade before the full effects on the Gulf are apparent.
She said they concluded the layers had been deposited between June and September 2010 after it was discovered that no sign of sealife from samples taken in May remained.
Professor Joye and her colleagues used the Alvin submersible to explore the bottom-most layer of the water around the well head, known as the benthos.
"The impact on the benthos was devastating," she told BBC News.
"Filter-feeding organisms, invertebrate worms, corals, sea fans - all of those were substantially impacted - and by impacted, I mean essentially killed.
"Another critical point is that detrital feeders like sea cucumbers, brittle stars that wander around the bottom, I didn't see a living (sea cucumber) around on any of the wellhead dives. They're typically everywhere, and we saw none."
Organisms on the seafloor stimulate the activity of micro-organisms and oxygenate the sediments, two tasks at the bottom of the aquatic food chain that will inevitably have longer-term effects on species nearer the surface - including the ones we eat.
Professor Joye noted that after the Exxon Valdez spill, it took several years before it became clear that the herring industry had been destroyed.
As such, she disagrees with the assessment in February, by the administrator of BP's $20bn (£12bn) compensation fund, that the Gulf of Mexico will have recovered from the spill by the end of 2012.
"The Gulf is resilient," she said.
"I do believe that it will recover from this insult, but I don't think it's going to recover fully by 2012.
"I think it's going to be 2012 before we begin to really see the fisheries implications and repercussions from this."