By Joan Slonczewski.
Wow. I really liked this book. It reminds me of Speaker for the Dead, actually.
The story concerns Prokaryon, a planet full of life inimical to unmodified humans--the environment has a high proportion of arsenic and other variations in chemistry which require extensive (and expensive) nanoengineered changes in physiology to adapt to. As a result, relatively few people have colonized it. The problem is that, although there has been no proof, many suspect the planet has "hidden masters" which are intelligent and may object to the human colonization. The problem is that no one has been able to find them, although the fact that it rains only after nightfall or when fires need to be put out is rather suspicious.
This book is the story of how they are found and how humans react to the first real alien species they've ever encountered. (There are also species like the aquatic Sharers in existence, but they seem to have been derived from humans via bioengineering rather than being completely alien.)
I liked this a lot, but the author doesn't seem to have published any new books recently (since 2000), though there are a few others out by her. They may be worth checking out.
Update: Just a few additional thoughts I had.
Favorite quote: "We're the Dancing People, and we'll dance to the stars!"
'jum has got to be the most interesting character. It's not entirely clear if she's mentally disabled in some way (idiot savant?) or just had a lonely childhood. Another fun quote from her: "What's one plus one?" "A little less than one and a half." Unusually, her strange form of addition doesn't seem to have any significance later in the book, although I certainly expected it to. She is quite delightful when she's not throwing rocks at people--see the dancing quote above! (Or maybe it has to do with the fact that she finally has her own friends.)
Another interesting point is how the sentients (robotic intelligences that have gained their own rights) also participate in the religion of the Spirit Caller brotherhood in the book. They seem to sincerely believe and pray. For that matter, the hidden masters also seem to have a religion, based on the questions they ask Rod (which are quite amusing; he ends up saying "Why are you asking me? I don't have the answers!")
Perhaps the biggest flaw in this book is the question of why Proteus wanted to terraform Prokaryon so badly. Surely there are plenty of uninhabited planets floating around that could be terraformed without destroying an amazing native ecosystem, environment and civilization? Especially if what he really wanted was lanthanide mines--I'm sure they could have been found in asteroids and other unoccupied space debris. I suppose one scene suggests he enjoys the feeling of power (playing God) that owning an occupied planet gives him, but the decision doesn't seem to make very good business sense.