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There has been a large output of genomic data in ecological studies of centralised wastewater treatment plants over the past number of years. One significant collaboration of Danish and Swedish research institutions lead to the development of the Microbes of Activated Sludge and Anaerobic Digesters (MiDAS 4) global taxonomic database. The database has been an effective tool in understanding centralised systems, however, there has been no known application of this tool in understanding the ecology of organisms in the on-site wastewater treatment systems. The growth of microbial mats or "biomats" has been identified as an essential component in the attenuation of pollutants within the soil treatment unit (STU) of conventional on-site wastewater treatment systems (OWTSs). Two research sites were employed to determine the influence of the pre-treatment of raw-domestic wastewater on these communities. The STUs at each of the two sites were split, whereby half received effluent directly from septic tanks, and half received more highly treated effluents from packaged aerobic treatment systems [a coconut husk media filter on one site, and a rotating biodisc contactor (RBC) on the other site]. Effluents from the RBC had a higher level of pre-treatment [~90% Total Organic Carbon (TOC) removal], compared to the media filter (~60% TOC removal). These sites' biomat were sampled two-dimensionally in respect of distance and depth, to configure ecological data with changes in the volumetric water content values which had been used successfully as an indicator of the location of the biomat. A total of 92 samples were obtained from both STU locations and characterized by MiDAS taxonomic database. Our study has shown that the biomats receiving primary or untreated effluent have less pronounced increases in denitrifiers compared to the biomats receiving treated or partially treated effluent. but biomats receiving primary effluents have been found to be capable of removing six times the amount of total nitrogen. This suggests that the increases in functional richness within the STU are secondary to bioclogging, as metabolic rates could be limited by hydraulic conductivity.