A method is described for recovering resources from a microbe supporting environment such as a water treatment system, comprising the steps of using microbial DNA sequencing to analyze the microbiome of the microbe supporting environment and identifying adjustments to the microbial content of the microbiome that will be useful in extracting resources from the microbe supporting environment such as a water treatment system, wherein the resources extracted can include, for example, methane released by microbes, nitrogen, phosphorus, or other contaminants generated by microbes, and/or clean water obtained by removing contaminants in a water treatment system.