Biofiltration relies on microbial degradation of the contaminants to maintain the absorptive capacity of the filter media. Biofilters are extensively used to treat gas streams with multiple contaminants with different chemical properties. This study investigates the co-removal of dimethyl disulphide (DMDS) and ammonia from a gas stream using compost based biofilters. Pure cultures of 'Thiobacillus thioparus' (ATTC 8158), ' Nitrosomonas europaea' (ATTC 25978) and 'Nitrobacter winogradskyi ' (ATTC 25391) were used to inoculate the media. 'T. thioparus ' is capable of oxidizing DMDS to sulphate, while 'N. europaea ' and 'N. winogradskyi' perform the two stage autotrophic oxidation of ammonia do nitrate, nitrification. A quantitative polymerase chain reaction (PCR) method was developed to allow tracking of 'T. thioparus' and 'N. europaea' in the filter media. The PCR method developed used most probably number (MPN) statistics to make population estimates from a series of positive/negative tests conducted on series dilutions of DNA extracted from the filter media. The MPN-PCR method had a lower detection limit of 100 cells per gram of dry media and an upper detection limit of 10 9 cells per gram of dry media, with a 95% confidence factor of 4.67. ' T. thioparus' populations observed in the media samples ranged from 7.9 * 102 to 1.3 * 108 cells per gram of dry media. 'N. europaea' populations in the media samples ranged from 1.6 * 103 to 6.3 * 104 cells per gram of dry media. 'In situ' activity rates for ' T. thioparus' change significantly, 95% confidence level, from 2.6 * 10-10 grams sulphur per cell during growth phase to 4.4 * 10-13 grams sulphur per cell during stationary phase. 'T. thioparus' was inhibited by ammonia levels as low as 50 ppmv in the gas phase, but if DMDS removal was established prior to ammonia addition chemical removal of the ammonia prevented this inhibitory effect. Autotrophic nitrifiers persisted in the biofilters treating ammonia only and ammonia in combination with DMDS, while populations in the biofilters treating DMDS only dropped below detection. While they persisted there is evidence that they may not be responsible for the observed ammonia removal. In the combined treatments the sulphate produced from the DMDS oxidation was sufficient to account for all of the observed ammonia removal. Other evidence, including preliminary denaturing gradient gel electrophoresis (DGGE) analysis, suggests that heterotrophic nitrifiers may be making a significant contribution to the biofiltration of ammonia.