The New York Times reports that team of scientists from the University of Athens and the University of East Anglia determined this by using microscopy and x-rays to scan the mineral content. They found that these "columns" and "paved floors" were actually created as early as 5 million years ago by methane seeping from the sea floor, which microbes then helped to oxidize and form a type of dolomite cement known as concretion. While this phenomenon is rare in such shallow waters (the "ruins" were found about 7 to 15 feet below the surface), it's a more common occurrence in deeper waters.