If you want historical accounts, Mark Catesby's Natural History of Carolina, Florida and the Bahama Islands, based on fieldwork from the 1720s, is the earliest work by a "naturalist" on North America. UNC has Volumes I and II fully digitized.

As for pre-colonial stuff, Middle Tennessee State's Tanya Pierce recently put together a great edited volume Trends and Traditions in Southeastern Zooarchaeology. It's a got a sampling of everything from the Pleistocene to the 19th-century, but does focus a lot on subsistence, as does much of zooarchaeology. It's a good bibliographic reference to find more readings. I would also recommend the work of Dale Hutchinson at UNC, particularly Foraging, Farming, and Coastal Biocultural Adaptation in Late Prehistoric North Carolina. He's got several other publications that cover the intersection of humans and local flora and fauna. Elizabeth Reitz, at UGA, has worked extensively on marine- and aquatic-based subsistence if you're interested in that- I've not read any of her books to recommend specifically.