Indicator organisms such as Escherichia coli (E. coli) and enterococci are used to evaluate the fecal contamination of surface waters and infer the risk to public health. This risk includes the presence of pathogenic bacteria, protozoa, and viruses all of which may persist in the environment for extended periods of time (Bell, Kase et al 2021, Rzeżutka, Cook 2004). Extensive analysis of New Zealand water quality data from 1998–2007 showed that water quality was highly variable; waterways in rural and urban areas generally had reduced water quality compared to native forest areas (Ballantine, Booker, et al. 2010, van Bunnik, Pollock, et al. 2007). Fecal contamination of waterways may occur either directly (such as accidental or deliberate discharge of untreated sewage, inadequately treated discharge from wastewater treatment plants, livestock access to waterways) or in-directly (such as surface run-off from paddocks or fields to waterways). A range of measures can reduce direct contamination such as exclusion of livestock from rivers and adequate treatment of wastewater, but mitigation of diffuse/indirect pollution is more difficult. In rivers, microorganisms may settle out of the water column and remain in the sediment until a disturbance (e.g., flooding, dredging or recreational activity) causes their resuspension. Generally, microbes which are attached to sediments have been shown to survive longer than those free in suspension (Burton, Gunnison, et al. 1987, Jamieson, Joy, et al. 2005, Oliver, Clegg, et al. 2007, Walters, Katzl, et al. 2014) and sediments accumulate in the riverbed and act as a reservoir for bacterial indicators and pathogens (Devane, Moriarty, et al. 2014, Haller, Poté, et al. 2009).
Currently, fecal contamination of recreational water and thus public health risk is assessed by microbial analysis targeting fecal indicators in samples collected directly from the water column. In New Zealand, the Recreational Water Quality Guidelines apply thresholds to categorize results into ‘meet guidelines’ (acceptable water quality of ≤ 260 cfu E. coli 100 mL− 1), ‘alert level’ (< 260 cfu and > 550 cfu E. coli 100 mL− 1) and ‘action level’ (≥ 550 cfu E. coli 100 mL− 1) (Table 4). According to these categories public health risk associated with recreational water use is assessed and action taken if necessary. ‘Alert level’ triggers a sanitary survey to report on sources of contamination while ‘action level’ requires erecting signs and informing the public that a public health problem exists. This approach assumes that the majority of microorganisms are free-floating and not associated with sediment particles. The impairment of water quality due to resuspension of riverbed sediment has long been proposed (Jamieson, Joy, et al. 2005, Nagels, Valstar, et al. 2002). It is known that sediments can store substantial quantities of microorganisms which, under flood conditions, are released into the water (Muirhead, Davies-Colley, et al. 2004, Nagels, Valstar, et al. 2002).
Sediments can contain 100 to 1000 times as many fecal indicator bacteria as overlying water (Ashbolt, Grohmann, et al. 1993, Davies, Long, et al. 1995, Pachepsky, Shelton 2011, van Donsel, Geldreich 1971). Moreover, microorganisms can show enhanced growth in sediments compared to water (Anderson, Whitlock, et al. 2005, Pote, Haller, et al. 2009). High organic content, small grain size, protection from predation, and helpful water temperatures (Anderson, Whitlock, et al. 2005, Davies, Long, et al. 1995, Fish and Pettibone, 1995) all likely enhance the prevalence and growth rates of microorganisms in sediments. Thus, sediments are very likely to be reservoirs of microbes posing public health risks which should be considered for inclusion in recreational water testing guidelines.
Accumulation of microorganisms in sediments and their release into the water column under natural conditions is continuous and influenced primarily by river flows (Pachepsky, Shelton 2011). Under flood conditions, bacteria contained within the pore water of the sediment are rapidly released. Thus, peak microbial loadings of flooded rivers are closely related to turbidity and the rising limb of hydrographs, prior to peak flows (Karimaee-Tabarestani and Zarrati, 2015, Nagels, Davies-Colley, et al. 2002). Release of E. coli from sediments can also continue after high flows before returning to rates associated with base flow conditions (Yakirevich, Pachepsky, et al. 2013), highlighting the continual flux of microbes in a stream after sediment disturbance. This continual flux may result in simultaneous deposition and re-suspension of microorganisms during base flow (Drummond, Davies-Colley, et al. 2014, Drummond, Davies-Colley, et al. 2015). Studies concerning microbial communities in the hyporheic zones of rivers (i.e., the porous riverbed below the sediment surface) during baseflow conditions have focused mainly on the ecology and microbial diversity, rather than movement of microorganisms in and out of the hyporheic zone (Feris, Ramsey, et al. 2003, Griebler and Lueders, 2009). We propose that sediment disturbing events during base flow will increase levels of water column pathogens similarly as they do during high flow events. Most recreational activities such as swimming and paddling take place under base flow conditions and stirring up sediments may expose people to pathogenic microorganisms. We investigated 30 rivers in Canterbury, New Zealand, with regards to the impact of simulated recreational disturbance of sediments on microbial water quality during base flow conditions, as well as the influence of the surrounding land use. Current regulations of recreational water quality lack pathogen indicator measurements in sediments. Therefore, we aimed to provide evidence that routine sediment sampling in addition to water sampling may provide a more accurate measure for recreational water quality guidelines to protect public health.