A genetically modified microorganism includes: an exogenous nucleic acid sequence encoding naphthalene dioxygenase (NDO), wherein the endogenous icd gene of the genetically modified microorganism is knocked out, in which the endogenous icd gene encodes isocitrate dehydrogenase (IDH), and wherein the genetically modified microorganism is capable of using glutamic acid and/or a salt thereof as a nitrogen source to grow and producing indigo dye.

A genetically modified microorganism includes: an exogenous nucleic acid sequence encoding naphthalene dioxygenase (NDO), wherein the endogenous icd gene of the genetically modified microorganism is knocked out, in which the endogenous icd gene encodes isocitrate dehydrogenase (IDH), and wherein the genetically modified microorganism is capable of using glutamic acid and/or a salt thereof as a nitrogen source to grow and producing indigo dye.

Dioxygenases and methods of biologically upgrading hydrocarbon streams, such as crude oil, using dioxygenases are provided herein. The dioxygenases can be used to remove impurities such as metals, heteroatoms, or asphaltenes from a hydrocarbon stream. In some cases, the dioxygenases can be chemically or genetically modified and can be used in different locations such as petroleum wells, pipes, reservoirs, tanks and/or reactors.