Observed controls on resilience of groundwater to climate variability in sub-Saharan Africa.

Groundwater in sub-Saharan Africa supports livelihoods and poverty alleviation1,2, maintains vital ecosystems, and strongly influences terrestrial water and energy budgets3. Yet the hydrological processes that govern groundwater recharge and sustainability-and their sensitivity to climatic variability-are poorly constrained4,5. Given the absence of firm observational constraints, it remains to be seen whether model-based projections of decreased water resources in dry parts of the region4 are justified. Here we show, through analysis of multidecadal groundwater hydrographs across sub-Saharan Africa, that levels of aridity dictate the predominant recharge processes, whereas local hydrogeology influences the type and sensitivity of precipitation-recharge relationships. Recharge in some humid locations varies by as little as five per cent (by coefficient of variation) across a wide range of annual precipitation values. Other regions, by contrast, show roughly linear precipitation-recharge relationships, with precipitation thresholds (of roughly ten millimetres or less per day) governing the initiation of recharge. These thresholds tend to rise as aridity increases, and recharge in drylands is more episodic and increasingly dominated by focused recharge through losses from ephemeral overland flows. Extreme annual recharge is commonly associated with intense rainfall and flooding events, themselves often driven by large-scale climate controls. Intense precipitation, even during years of lower overall precipitation, produces some of the largest years of recharge in some dry subtropical locations. Our results therefore challenge the 'high certainty' consensus regarding decreasing water resources4 in such regions of sub-Saharan Africa. The potential resilience of groundwater to climate variability in many areas that is revealed by these precipitation-recharge relationships is essential for informing reliable predictions of climate-change impacts and adaptation strategies.

Seasonality of enteric viruses in groundwater-derived public water sources.

We investigated the seasonal prevalence of seven enteric viruses in groundwater-derived public water sources distributed across the dominant aquifers of England. Sampling targeted four periods in the hydrological cycle with typically varying microbial risks, as indicated using a decade of Escherichia coli prevalence data. Viruses were concentrated onsite by filtration of raw groundwater, and extracted nucleic acid (NA) was amplified by qPCR or RT-qPCR. Seven out of eight sources, all aquifers, and 31% of samples were positive for viral NA. The most frequently detected viral NA targets were Hepatitis A virus (17% samples, 63% sites), norovirus GI (14% samples, 38% sites), and Hepatitis E virus (7% samples, 25% sites). Viral NA presence was episodic, being most prevalent and at its highest concentration during November and January, the main groundwater recharge season, with 89% of all positive detects occurring during a rising water table. Seasonal norovirus NA detections matched its seasonal incidence within the population. Viral NA is arriving with groundwater recharge, as opposed to persisting for long-periods within the saturated zone. Neither total coliforms nor E. coli were significant predictors of viral NA presence-absence, and there was limited co-occurrence between viruses. Nevertheless, a source with an absence of E. coli in regularly collected historical data is unlikely to be at risk of viral contamination. To manage potential groundwater viral contamination via risk assessment, larger scale studies are required to understand key risk factors, with the evidence here suggesting viral NA is widespread across a range of typical microbial risk settings.

In-situ fluorescence spectroscopy is a more rapid and resilient indicator of faecal contamination risk in drinking water than faecal indicator organisms.

Faecal indicator organisms (FIOs) are limited in their ability to protect public health from the microbial contamination of drinking water because of their transience and time required to deliver a result. We evaluated alternative rapid, and potentially more resilient, approaches against a benchmark FIO of thermotolerant coliforms (TTCs) to characterise faecal contamination over 14 months at 40 groundwater sources in a Ugandan town. Rapid approaches included: in-situ tryptophan-like fluorescence (TLF), humic-like fluorescence (HLF), turbidity; sanitary inspections; and total bacterial cells by flow cytometry. TTCs varied widely in six sampling visits: a third of sources tested both positive and negative, 50% of sources had a range of at least 720 cfu/100 mL, and a two-day heavy rainfall event increased median TTCs five-fold. Using source medians, TLF was the best predictor in logistic regression models of TTCs ≥10 cfu/100 mL (AUC 0.88) and best correlated to TTC enumeration (ρs 0.81), with HLF performing similarly. Relationships between TLF or HLF and TTCs were stronger in the wet season than the dry season, when TLF and HLF were instead more associated with total bacterial cells. Source rank-order between sampling rounds was considerably more consistent, according to cross-correlations, using TLF or HLF (min ρs 0.81) than TTCs (min ρs 0.34). Furthermore, dry season TLF and HLF cross-correlated more strongly (ρs 0.68) than dry season TTCs (ρs 0.50) with wet season TTCs, when TTCs were elevated. In-situ TLF or HLF are more rapid and resilient indicators of faecal contamination risk than TTCs.

Changes in global groundwater organic carbon driven by climate change and urbanization.

Climate change and urbanization can increase pressures on groundwater resources, but little is known about how groundwater quality will change. Here, we use a global synthesis (n = 9,404) to reveal the drivers of dissolved organic carbon (DOC), which is an important component of water chemistry and substrate for microorganisms that control biogeochemical reactions. Dissolved inorganic chemistry, local climate and land use explained ~ 31% of observed variability in groundwater DOC, whilst aquifer age explained an additional 16%. We identify a 19% increase in DOC associated with urban land cover. We predict major groundwater DOC increases following changes in precipitation and temperature in key areas relying on groundwater. Climate change and conversion of natural or agricultural areas to urban areas will decrease groundwater quality and increase water treatment costs, compounding existing constraints on groundwater resources.

In-situ fluorescence spectroscopy indicates total bacterial abundance and dissolved organic carbon.

We explore in-situ fluorescence spectroscopy as an instantaneous indicator of total bacterial abundance and faecal contamination in drinking water. Eighty-four samples were collected outside of the recharge season from groundwater-derived water sources in Dakar, Senegal. Samples were analysed for tryptophan-like (TLF) and humic-like (HLF) fluorescence in-situ, total bacterial cells by flow cytometry, and potential indicators of faecal contamination such as thermotolerant coliforms (TTCs), nitrate, and in a subset of 22 samples, dissolved organic carbon (DOC). Significant single-predictor linear regression models demonstrated that total bacterial cells were the most effective predictor of TLF, followed by on-site sanitation density; TTCs were not a significant predictor. An optimum multiple-predictor model of TLF incorporated total bacterial cells, nitrate, nitrite, on-site sanitation density, and sulphate (r2 0.68). HLF was similarly related to the same parameters as TLF, with total bacterial cells being the best correlated (ρs 0.64). In the subset of 22 sources, DOC clustered with TLF, HLF, and total bacterial cells, and a linear regression model demonstrated HLF was the best predictor of DOC (r2 0.84). The intergranular nature of the aquifer, timing of the study, and/or non-uniqueness of the signal to TTCs can explain the significant associations between TLF/HLF and indicators of faecal contamination such as on-site sanitation density and nutrients but not TTCs. The bacterial population that relates to TLF/HLF is likely to be a subsurface community that develops in-situ based on the availability of organic matter originating from faecal sources. In-situ fluorescence spectroscopy instantly indicates a drinking water source is impacted by faecal contamination but it remains unclear how that relates specifically to microbial risk in this setting.

Tryptophan-like and humic-like fluorophores are extracellular in groundwater: implications as real-time faecal indicators.

Fluorescent natural organic matter at tryptophan-like (TLF) and humic-like fluorescence (HLF) peaks is associated with the presence and enumeration of faecal indicator bacteria in groundwater. We hypothesise, however, that it is predominantly extracellular material that fluoresces at these wavelengths, not bacterial cells. We quantified total (unfiltered) and extracellular (filtered at < 0.22 µm) TLF and HLF in 140 groundwater sources across a range of urban population densities in Kenya, Malawi, Senegal, and Uganda. Where changes in fluorescence occurred following filtration they were correlated with potential controlling variables. A significant reduction in TLF following filtration (ΔTLF) was observed across the entire dataset, although the majority of the signal remained and thus considered extracellular (median 96.9%). ΔTLF was only significant in more urbanised study areas where TLF was greatest. Beneath Dakar, Senegal, ΔTLF was significantly correlated to total bacterial cells (ρs 0.51). No significant change in HLF following filtration across all data indicates these fluorophores are extracellular. Our results suggest that TLF and HLF are more mobile than faecal indicator bacteria and larger pathogens in groundwater, as the predominantly extracellular fluorophores are less prone to straining. Consequently, TLF/HLF are more precautionary indicators of microbial risks than faecal indicator bacteria in groundwater-derived drinking water.

Real-time detection of faecally contaminated drinking water with tryptophan-like fluorescence: defining threshold values.

We assess the use of fluorescent dissolved organic matter at excitation-emission wavelengths of 280nm and 360nm, termed tryptophan-like fluorescence (TLF), as an indicator of faecally contaminated drinking water. A significant logistic regression model was developed using TLF as a predictor of thermotolerant coliforms (TTCs) using data from groundwater- and surface water-derived drinking water sources in India, Malawi, South Africa and Zambia. A TLF threshold of 1.3ppb dissolved tryptophan was selected to classify TTC contamination. Validation of the TLF threshold indicated a false-negative error rate of 15% and a false-positive error rate of 18%. The threshold was unsuccessful at classifying contaminated sources containing <10 TTC cfu per 100mL, which we consider the current limit of detection. If only sources above this limit were classified, the false-negative error rate was very low at 4%. TLF intensity was very strongly correlated with TTC concentration (ρs=0.80). A higher threshold of 6.9ppb dissolved tryptophan is proposed to indicate heavily contaminated sources (≥100 TTC cfu per 100mL). Current commercially available fluorimeters are easy-to-use, suitable for use online and in remote environments, require neither reagents nor consumables, and crucially provide an instantaneous reading. TLF measurements are not appreciably impaired by common intereferents, such as pH, turbidity and temperature, within typical natural ranges. The technology is a viable option for the real-time screening of faecally contaminated drinking water globally.

Using boreholes as windows into groundwater ecosystems.

Groundwater ecosystems remain poorly understood yet may provide ecosystem services, make a unique contribution to biodiversity and contain useful bio-indicators of water quality. Little is known about ecosystem variability, the distribution of invertebrates within aquifers, or how representative boreholes are of aquifers. We addressed these issues using borehole imaging and single borehole dilution tests to identify three potential aquifer habitats (fractures, fissures or conduits) intercepted by two Chalk boreholes at different depths beneath the surface (34 to 98 m). These habitats were characterised by sampling the invertebrates, microbiology and hydrochemistry using a packer system to isolate them. Samples were taken with progressively increasing pumped volume to assess differences between borehole and aquifer communities. The study provides a new conceptual framework to infer the origin of water, invertebrates and microbes sampled from boreholes. It demonstrates that pumping 5 m(3) at 0.4-1.8 l/sec was sufficient to entrain invertebrates from five to tens of metres into the aquifer during these packer tests. Invertebrates and bacteria were more abundant in the boreholes than in the aquifer, with associated water chemistry variations indicating that boreholes act as sites of enhanced biogeochemical cycling. There was some variability in invertebrate abundance and bacterial community structure between habitats, indicating ecological heterogeneity within the aquifer. However, invertebrates were captured in all aquifer samples, and bacterial abundance, major ion chemistry and dissolved oxygen remained similar. Therefore the study demonstrates that in the Chalk, ecosystems comprising bacteria and invertebrates extend from around the water table to 70 m below it. Hydrogeological techniques provide excellent scope for tackling outstanding questions in groundwater ecology, provided an appropriate conceptual hydrogeological understanding is applied.