Widespread contamination of ground and surface water with nitrate (NO₃^-) and perchlorate (ClO₄ ^-) has been recorded in many US states. Nitrate and perchlorate are soluble anions that are known to affect human health. This dissertation presents the results of three studies of biological reduction ClO₄ ^- and NO₃^- using autotrophic bacteria.

In the first study, hydrogenotrophic (H₂ oxidizing) denitrifiers were inoculated into two hollow fiber membrane bioreactors (HFMB), which were set up in different configurations (I and II). In Configuration I, H ₂ passed through the lumen of the fibers and nitrified water flowed through the shell. In Configuration II, liquid flowed through the lumen and H₂ through the shell. Complete denitrification was achieved in both systems with pH and biomass control at hydraulic retention times (HRT) of 8.3 and 1.5 hours for configurations I and II, respectively. Influent dissolved oxygen (DO) did not inhibit denitrification.

The second study investigated reduction of NO₃^- and ClO₄^- in ion exchange (IX) brines using halophilic-hydrogenotrophic bacteria in a HFMB (Configuration II). Continuous operation of the HFMB resulted in partial denitrification (30%) of the brines. Batch HFMB operation resulted in average removal efficiencies of 30% and 42% for NO₃^- and ClO₄^-, respectively.

The third study investigated ClO₄^- reduction using Sulfur Utilizing Perchlorate Reducing Bacteria (SUPeRB). SUPeRB cultures reduced 5-20 mg/L ClO₄^- to < 0.5 mg/L at varying salinities (0-30 g/L NaCl). Perchlorate (8-0.01 mg/L) reduction was achieved in packed bed reactors (PBR) inoculated with SUPeRB and filled with S° pellets and crushed oyster shells at empty bed contact times of 8-13 hours for low and high ClO₄^- concentrations, respectively. Decreased ClO₄^- removal efficiency was observed at increased recirculation velocity and with small S⁰ particle sizes. Influent DO or NO₃^- did not inhibit overall ClO₄^- removal.