Electronic Thesis and Dissertation Repository


Doctor of Philosophy




Dr. Gordon Southam


Potholes are weathering features, of various sizes and shapes, which are found in exposed rock surfaces that lack vegetative and soil cover. Biofilms associated with the ephemeral aquatic pothole environments of the Colorado Plateau were examined as initial and intermediate stages of colonisation of arid, oligotrophic rock surfaces.

Imaging of the interface between pothole biofilms and their host rock revealed features of biological weathering; chiefly, the breakdown of silicate minerals and precipitation of clay and carbonate minerals. High pH measured in pothole water reflected deposition of secondary carbonate minerals at some locations and indicated the development of high pH microenvironments that were responsible for actively weathering the host rock. Further, the biologically-affected crust of pothole host rock contained relatively less SiO2 and more CaO bearing minerals than the abiotic host rock, indicating that the activity of the biofilm was weathering silicate minerals while at the same time precipitating calcite.

The nutritional requirements of the biofilms were not fully met by rain water, and were supplemented by sources already present in the pothole. The aqueous geochemistry of potholes under artificial oligotrophic conditions indicated that the biofilm was active, obtained nutrients directly from sediment and the host rock, and was able to influence water chemistry without nutrients derived from rain. The sampling of potholes filled with water from rain events found that wind-blown nutrients were an important contribution from storms.

Imaging of pothole biofilms revealed novel adaptations to nutrient-limited conditions, such as microcolonies of cells and dense webs of extracellular polymeric substances, which suggested a high level of resilience in the endemic communities.

Environmental 16s rRNA analysis of three different biofilms showed that sediment accumulation is key to species diversity: deep potholes (that can retain water for longer periods, but do not have much soil) supported bacterial communities similar in diversity to biofilms on bare rock, whereas biofilms from potholes with soils hosted a much more diverse community of heterotrophic bacteria. The increase in diversity as potholes accumulate sediment underlined the importance of soil formation in the desert environment.