Microbial communities in an ephemeral stream system and the implications of saline mine discharge

Abstract

The Fitzroy River Basin (FRB), Queensland, contains the largest coal reserve in Australia. Driven by an increasing need to conserve fresh water, coal mine operators in the region have placed significant emphasis on reducing freshwater use by implementing water re-use. As a consequence, the salinity of stored water on mine sites has increased due to accumulation of salts through evaporation, groundwater input and mine operations. When excess water is discharged into the environment, this reduced water quality may constitute an environmental risk to the receiving ecosystem. Reports on the impact of mine site discharge highlighted the lack of data on potential impacts of saline discharge on the aquatic environment following flood events in 2007/08. The FRB is a semi-arid region in which the river systems only flow for a few months a year. In such intermittent rivers, major biogeochemical cycling occurs in river sediments and is largely driven by microbial metabolic processes. These microbial processes are of particular importance in maintaining downstream water quality and healthy functioning of the aquatic ecosystem. Current assessment tools do not capture nutrient cycles mediated by microorganisms, but instead focus on the impacts of larger organisms such as fish and macroinvertebrates. There is a need for a combined approach which includes assessing potential impacts on ecosystem processes. Little is known on the effects of salinity on ecosystem processes mediated by microorganisms in freshwater systems and insights have largely been inferred from comparisons with other ecosystems such as estuarine and marine environments. Further, most research has been conducted on perennial streams and little is known on microbial ecology and nutrient cycling in ephemeral streams. The aim of this thesis was to gain insights into microbial communities and ecosystem processes in an ephemeral stream system to guide management decisions in the context of saline water discharge from coal mines. The thesis was guided by two objectives: 1) to examine microbial community distribution in an ephemeral river system; and 2) to investigate the effect of increased salinity on selected ecosystem processes. The first objective, to examine microbial community distribution in an ephemeral river system (The Upper Isaac catchment, located within the FRB), used a field-based approach to build on the conceptual understanding of microbial communities and microbially driven ecosystem processes. To gain an understanding of microbial distribution, the habitats within the Upper Isaac Catchment were characterised. This provided a framework under which microbial community distribution could be examined. Habitat characterisation was based on physical environmental parameters, for which key habitat characteristics were the presence/absence of surface water in relation to seasonal flow, levels of detritus in stream beds and substrate type. Using 16S rRNA pyrosequencing, key microbial groups were identified; such as high abundances of spore forming bacteria indicating resistance to sediment desiccation and microorganisms associated with nutrient poor conditions. The distribution of these microorganisms showed that microbial communities could be predicted by habitat characteristics. Microbial community composition and their ecological functions were strongly influenced by the physical and chemical conditions; principally the presence and absence of surface water, detritus, depth and water quality parameters such as pH and ammonia. Nitrification in low detritus sediments was one of the major ecosystem processes, and the potential co-occurrence of nitrifiers and anammox was observed. The main driver of heterotrophic activity appeared to be localised hotspots of organic deposition as a result of seasonal flow. The second objective was to investigate the effect of increased salinity on potential rates of nitrification, denitrification and methanogenesis. Process rate measurements were undertaken under controlled laboratory incubations. Reduced potential rates of nitrification occurred at 10,000 µS/cm and no inhibition of increased salinity was observed for denitrification and methanogenesis at salinities up to 5000 µS/cm. The characterisation of microbial communities in the Upper Isaac Catchment has made a significant contribution to the development of a conceptual understanding of microbial communities and ecosystem processes in ephemeral streams. With microbial communities differing between habitat types; these findings provide a framework within the Upper Isaac Catchment for selecting both future sites for monitoring changes in microbial communities/ecosystem conditions and discharge locations with the capacity to process water that is higher in salinity and/or nutrients.