Do you have access to a machine that can measure atomic fluorescence?

To measure Hg(0), scientists will flush a sample with air or nitrogen into a Hg(0) trap. Some atomic fluorescence analyzers will come with these very sensitive gold Hg(0) traps, which are great for measuring low levels of Hg(0). If you don't have gold traps, you can make a liquid trap out of potassium permanganate and sulfuric acid. Permanganate traps are not as sensitive as gold traps, but with mercury reducing bacteria you don't need your trap to be very sensitive.

maybe you can use lumix RA915+ to measure element mercury 

reference:Mercury Reduction and Cell-Surface Adsorption by Geobacter

sulfurreducens PCA

You can measure the reduced Hg2+ indirectly. For example, measure Hg2+ at 0 h, then again measure Hg2+ after incubation period. You can subtract the final Hg2+ concentration from initial Hg2+ concentration and you will know how much is lost as Hg0.

You can follow one of our recent publication

doi:10.1016/j.chemosphere.2015.08.061