A method of remediating an effluent containing livestock waste comprising: establishing a stratified lagoon of effluent containing livestock waste, the lagoon being divided into a set of horizontal sub-portions at different levels (levels 1 to 7) in the lagoon according to an oxygen gradient, each sub-portion of the lagoon having a different concentration of dissolved oxygen, the concentration of dissolved oxygen being inversely proportional to the distance of the subportion from the surface of the lagoon; establishing a stratified incubator comprising a set of horizontal sub-portions at different levels (levels 1 to 7) in the incubator according to an oxygen gradient, each sub-portion of the incubator having a different concentration of dissolved oxygen, and each sub-portion of the incubator corresponding to a sub-portion of the lagoon having a substantially similar dissolved oxygen concentration being inversely proportional to the distance of the sub-portion from the surface of the lagoon; transmitting a volume of effluent from each sub-portion of the lagoon to the corresponding sub-portion of the incubator having a substantially similar concentration of dissolved oxygen as said sub-portion of the lagoon; generating a first remediated volume of effluent in said corresponding sub-portion of the incubator responsive to proliferating a first microorganism which uses a first compound in said volume of effluent as substrate for growth, the first microorganism enabling a first chemical reaction which alters the first compound; transmitting said first remediated volume of effluent and said first micro-organism from said corresponding sub-portion of the incubator to the corresponding sub-portion of the lagoon having a substantially similar concentration of dissolved oxygen as said corresponding sub-portion of the incubator; and generating a second remediated volume of effluent in said corresponding sub-portion of the lagoon responsive to proliferating said first micro-organism. establishing a stratified lagoon of effluent containing livestock waste, the lagoon being divided into a set of horizontal sub-portions at different levels (levels 1 to 7) in the lagoon according to an oxygen gradient, each sub-portion of the lagoon having a different concentration of dissolved oxygen, the concentration of dissolved oxygen being inversely proportional to the distance of the subportion from the surface of the lagoon; establishing a stratified incubator comprising a set of horizontal sub-portions at different levels (levels 1 to 7) in the incubator according to an oxygen gradient, each sub-portion of the incubator having a different concentration of dissolved oxygen, and each sub-portion of the incubator corresponding to a sub-portion of the lagoon having a substantially similar dissolved oxygen concentration being inversely proportional to the distance of the sub-portion from the surface of the lagoon; transmitting a volume of effluent from each sub-portion of the lagoon to the corresponding sub-portion of the incubator having a substantially similar concentration of dissolved oxygen as said sub-portion of the lagoon; generating a first remediated volume of effluent in said corresponding sub-portion of the incubator responsive to proliferating a first microorganism which uses a first compound in said volume of effluent as substrate for growth, the first microorganism enabling a first chemical reaction which alters the first compound; transmitting said first remediated volume of effluent and said first micro-organism from said corresponding sub-portion of the incubator to the corresponding sub-portion of the lagoon having a substantially similar concentration of dissolved oxygen as said corresponding sub-portion of the incubator; and generating a second remediated volume of effluent in said corresponding sub-portion of the lagoon responsive to proliferating said first micro-organism.