The subject invention provides microbe-based compositions comprising cultivated microorganisms and/or growth by-products thereof, as well as methods and systems for producing and using these compositions. More specifically, the subject invention provides microbe-based compositions comprising biologically pure yeast selected from the Pichia clade, and/or growth by-products thereof, such as biosurfactants, enzymes and solvents. Methods of using these compositions to enhance production in agriculture, horticulture, livestock rearing and aquaculture industries are also provided.