Microbes are responsible for key parts of the process that generates natural gas, but during its recovery, they are the enemy.
Sulfate reducing bacteria – which use sulfate ions in the water for energy – spit out sulfide, a toxic molecule that “sours” the gas product. To combat this process, biocides like formaldehyde and gluteraldehyde are thrown down the pipe in an attempt to preserve a usable product.
The environmental complications of microbial involvement are thus twofold. Initially, the toxic biocides inevitably leak into the surrounding rock and aquifers, and since these poisons are non-specific, there’s a lot of collateral damage. Later on, after older wells are abandoned, sulfate reducers come back with a vengeance, generating acidic byproducts that can corrode pipes and release heavy metals.