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Relatives of passengers on AirAsia Flight 8501 in Surabaya, Indonesia, react to the breaking news of debris and bodies being found on Dec. 30, 2014.ROBERTUS PUDYANTO/Getty Images

Indonesians reacted with grief and shock on Tuesday as bloated bodies and debris were discovered in the Java Sea, painfully ending the mystery of AirAsia Flight 8501, which crashed with 162 people aboard.

An initial group of six bodies recovered, swollen but intact, did not have life jackets on. Indonesian television showed a half-naked bloated body of a man whose shirt partly covered his head. The images sent a spasm of pain through family members watching together in a waiting room at the Surabaya airport.

Ifan Joko, 54, said he was still hoping for a miracle. His brother, Charlie Gunawan, along with his wife, their three children and two other family members, were travelling to Singapore on the plane to ring in the New Year. "I know the plane has crashed, but I cannot believe my brother and his family are dead," he said, wiping a tear. "... We still pray they are alive."

(AirAsia Flight 8501: What we know so far about the plane's disappearance)

THE SEARCH: SHALLOW WATERS, BUT MURKY CHALLENGES

Searchers combing the Java Sea to find and recover debris and bodies from the AirAsia jet that crashed there have the advantage of working in much shallower waters than those found in the open ocean, but also face challenges that include monsoons, murkiness and trash.

Erik van Sebille, an oceanographer at the University of New South Wales in Sydney, said the Java Sea is 100 times shallower than the remote stretch of Indian Ocean where searchers are still looking for another missing plane, Malaysia Airlines Flight 370. "It makes the search much simpler," he said.

But because the monsoon season is underway, he said, there's likely to be lots of rain that will wash sediment into rivers that feed into the sea and make it murky. And he said the abundance of fishing in the region will make it harder for spotter planes to distinguish trash from any plane debris.

David Gallo, the director of special projects at the Woods Hole Oceanographic Institution in Woods Hole, Massachusetts, said the challenge of locating the wreckage or black boxes remains huge.

Gallo said the area where searchers are looking for the AirAsia jet might appear much narrower and more contained than the area for Flight 370, but is still enormous: "bigger than West Virginia and South Carolina combined," he said. That is about the same size as Indonesia's Java province.

"There is nothing easy about this," Gallo said.