At some point in the past (several decades? centuries? earlier; the exact timeframe wasn't specified as far as I can recall) Earth had sent out ships to colonize other planets. These ships were designed to be operated by a human brain (surgically removed from its body and preserved by artificial means). Though there are similarities of premise with Anne McCaffrey's "Brainship" series, this is NOT one of those books. In this particular novel, at another unspecified interval after reaching this particular planet, something had happened to its (sun? other environmental factor?) that resulted in a mutation among the colonists. The people were now amphibious and somewhat telepathic. Here are some of the names I remember...."Gianna Rigoli Sarnoli" the original human name of the brain on this world's colony ship. "screamdeep" "waterjoyup" the parents of the story's main character. "poundgrayly" was a friend of theirs and "fishsinger" was the main character, iirc. in a flashback of "Gianna's there was mention of a "Penna" who was "Gianna's" sister and the person who had recommended her for the program. Does ANY of this sound familiar to anyone?
Scrolling through the pages it does appear to be about a cyborg spaceship. Also, the term "screamdeep" is in the book, so the odds are, this is it.
Also a similar story is The Lazarus effect, from Frank Herbets series Destination void. it has a ship operated by a brain trained in the lunar colony and crewd by clones, one of the clones (Raja Flatery) is the chaplain/psychaitrist and has a hipnotic trigger that will make him destroy the ship if they release a IA in the universe, they eventualy have to do so because the brain and its reverves go mad, and somehow he overcomes the trigger. Sometime later the Ship (capital H) drops the clones and the frozen colonists in a planet controled by a sentient seaweed that starts manipulating their genes and several types of mutants are created and the ship leaves. the last books are around another copys of the original clones that the ship left in orbit, and are found when the civilization of that world regained some space travel. raja flatery 2 or 3 has taken control of the world and is using all it's resources to build another Ship, with a human brain again to escape that world, and in the process is staining the world's resources and people to the breaking point, not helping is the fact that the "natives " worship the Ship and the seaweed , after being almost destroyed by the second or third generation is now alive and regaining conscience, it has created an "avatar made with human genes and the seaweed genes. it is to note that when the seaweed was almost destoyed the world went into a cataclysmic geological upheaval because the roots of the seaweed kept the tectonics and the sea currents controled.