Aspects of the disclosure include the manufacture of non-naturally occurring bacteria for perchlorate bioremediation. An exemplary method includes determining a source bacteria having one or more source genes which code for perchlorate reduction and chlorite dismutase and determining a target bacteria that does not naturally include the source genes. A first sequence of deoxyribonucleic acid (DNA) is identified in the source genes that codes, in the source bacteria, for an ordered set of amino acids whose linear sequence results in a protein which breaks down perchlorates and a second sequence of DNA is determined which, if inserted into the target bacteria, would allow the target bacteria to code for the ordered set of amino acids. A gene package is built by replacing the first sequence of DNA with the second sequence of DNA and the gene package is inserted into the target bacteria, thereby forming a non-naturally occurring modified bacteria.