Escherichia coli has long been used as an indicator of recent faecal contamination in a water body.  However, little is known concerning the extent to which conditions in the external environment shape the genetic structure and diversity of E. coli communities in the species’ secondary habitat.  Septic tanks represent a good system with which to investigate E. coli community structure in environments external to the host.  For a given septic tank, the source of the faecal inputs are largely unambiguous and temporally, relatively constant.  Yet the physio-chemical conditions in the septic tank will vary seasonally, with the type of septic system, and with the exact nature of the non-faecal inputs.

Samples were taken from 66 septic tanks on rural residential properties in the Canberra region of NSW, Australia.  Samples were processed and plated onto MacConkey agar and up to 44 isolates were characterised per tank.  Phylogenetic group membership of isolates was determined by quadruplex PCR and genetic diversity was determined by rep-PCR fingerprinting.  Physical and chemical analyses included temperature, pH, and conductivity; as well, ammonium, nitrate, phosphate, and surfactant concentrations were determined.  Richness (the number of genotypes) and the Shannon diversity index were used to assess the extent to which E. coli community diversity varied with the physio-chemical conditions of the septic tank.

More than 700 E. coli isolates representing 270 distinct genotypes were recovered. Septic tanks were most frequently dominated by phylogroup A strains (34%), whilst phylogroup B2 strains were only dominant in 19% of the tanks. The median number of distinct genotypes per tank was 2.6 (range 1-16).  There was no relationship between the number of people providing inputs to the tank and genotype diversity.  Physio-chemical conditions of the septic tanks were found to influence E. coli diversity; genotype diversity increased with increasing ammonium concentration, but declined with increasing pH.  The results demonstrate that selection is an important determinant of E. coli genetic structure in its secondary habitats.