The presently disclosed subject matter relates to Managed Ecosystem Fermentation (MEF) which is a continuous microbial process utilizing a managed ecosystem approach employing dozens to thousands of species of microorganisms, occurring in a controlled artificial environment and consuming organic materials without benefit of sterilization. The process of utilizing this fermentation for the consumption of organic materials on a continuous basis is within the scope of this disclosed subject matter. The process of separating chemicals as industrial chemicals from this fermentation on a continuous basis is within the scope of this disclosed subject matter. The process of separating biomass useful as high protein animal feed or fertilizer from this fermentation on a continuous (or semi-continuous) basis is within the scope of this disclosed subject matter.