While FGD systems are able to mitigate the air pollution caused by SOx gasses, calcium-sulfur solids and FGD wastewater must be treated for various constituents before release into the environment. Selenium is an essential micronutrient to many organisms, but the concentration between beneficial and toxic levels of selenium differs by one order of magnitude. One of the constituents requiring treatment is selenium, a non-metal contaminant which in recent years has come to be known as a problem from coal processing activities. The selenium in these waste streams, much like other industrial waste streams, are subjected to regulation by the United States Environmental Protection Agency (EPA). In 2015, the EPA published the Effluent Limitation Guidelines (ELG) rule. In FGD systems untreated selenium concentrations are approximately 3000 µg/L. The ELG rule by the EPA has regulated the effluent concentrations to be 12 µg/L for existing sources and 5 µg/L for new sources.

Biological treatment for selenium removal is deployed at the industrial scale. Most biological treatment for selenium removal is targeted to reduce selenium oxyanions into elemental selenium. In order for this reaction to occur, selenate and selenite have to be the most energetically favorable electron acceptors in the system. Little is known on the microbes that are able to carry out such reactions, but it is suspected that more than one species are able to reduce selenium oxyanions in FGD systems.

NETL has demonstrated microorganisms naturally present in FGD effluent can be enriched for selenate and selenite reducers. The two key microorganisms were found capable of reducing 99% of the dissolved selenate, and one key microorganism was found capable of reducing 95% of the dissolved selenite.  The final product was imaged to be elemental selenium nanospheres and were observed to be formed both intercellularly and extracellularly. Work is ongoing to optimize this selenium reduction, and further characterize the metabolic function of these microorganisms and the final selenium product.