Metagenomics reveals seasonality of human pathogenic bacteria from hand-dug well water in the Cuvelai Etosha Basin of Namibia

Namibia is a large country with a population slightly above 2 million of which 73% live in rural areas. It is the driest country in sub-Saharan Africa with unpredictable rainfall patterns which occur between October and May. The Cuvelai Etosha Basin is a rural setting in which most people depend on groundwater to circumvent water scarcity by the construction of hand-dug wells. Communities consume hand-dug well water throughout the year without; knowledge of its safety, and treatment prior to use. Hence, this study aimed at evaluating the seasonal safety and quality of hand-dug well water for human consumption. A 16S rRNA metagenomics study was conducted to explore the influence of season on the human pathogenic bacterial species richness, diversity, evenness and abundance in the hand-dug wells. Bacterial pathogens were identified and analysis revealed no significant difference in species richness and diversity, and a significant difference in species evenness and abundance between the wet and dry seasons. Hence, seasonality had an influence on human bacterial pathogens evenness and abundance but had no influence on species richness and diversity. In addition, the water in hand-dug wells of the Cuvelai Etosha Basin is not safe for consumption and domestic use unless sanitized. It is recommended that efforts should be made to treat the water prior to use, and hand-dug wells should be properly constructed to reduce contamination

Partitioning of water between differently sized shrubs and potential groundwater recharge in a semiarid savanna in Namibia

Introduction: Many semiarid regions around the world are presently experiencing significant changes in both climatic conditions and vegetation. This includes a disturbed coexistence between grasses and bushes also known as bush encroachment, and altered precipitation patterns with larger rain events. Fewer, more intense precipitation events might promote groundwater recharge, but depending on the structure of the vegetation also encourage further woody encroachment.Materials and Methods: In this study, we investigated how patterns and sources of water uptake of Acacia mellifera (blackthorn), an important encroaching woody plant in southern African savannas, are associated with the intensity of rain events and the size of individual shrubs. The study was conducted at a commercial cattle farm in the semiarid Kalahari in Namibia (MAP 250 mm/a). We used soil moisture dynamics in different depths and natural stable isotopes as markers of water sources. Xylem water of fifteen differently sized individuals during eight rain events was extracted using a Scholander pressure bomb.Results and Discussion: Results suggest the main rooting activity zone of A. mellifera in 50 and 75 cm soil depth but a reasonable water uptake from 10 and 25 cm. Any apparent uptake pattern seems to be driven by water availability, not time in the season. Bushes prefer the deeper soil layers after heavier rain events, indicating some evidence for the classical Walter’s two-layer hypothesis. However, rain events up to a threshold of 6 mm/day cause shallower depths of use and suggest several phases of intense competition with perennial grasses. The temporal uptake pattern does not depend on shrub size, suggesting a fast upwards water flow inside. δ2H and δ18O values in xylem water indicate that larger shrubs rely less on upper and very deep soil water than smaller shrubs. It supports the hypothesis that in environments where soil moisture is highly variable in the upper soil layers, the early investment in a deep tap-root to exploit deeper, more reliable water sources could reduce the probability of mortality during the establishment phase. Nevertheless, independent of size and time in the season, bushes do not compete with potential groundwater recharge. In a savanna encroached by A. mellifera, groundwater will most likely be affected indirectly

In situ unsaturated zone water stable isotope (2H and 18O) measurements in semi-arid environments: A soil water balance

© 2016 Author(s). Stable isotopes (deuterium, 2H, and oxygen-18, 18O) of soil water were measured in the field using a liquid water isotope analyzer (tunable off-axis integrated cavity output spectroscope, OA-ICOS, LGR) and commercially available soil gas probes (BGL-30, UMS, Munich) in the semi-arid Cuvelai-Etosha Basin (CEB), Namibia. Results support the applicability of an in situ measurement system for the determination of stable isotopes in soil pore water. High spatial and temporal resolution was achieved in the study area with reasonable accuracy and measurements were in agreement with laboratory-based cryogenic vacuum extraction and subsequent cavity ring-down laser spectroscopic isotope analysis (CRDS, L2120-i, Picarro Inc.). After drift and span correction of the in situ isotope data, precision for over 140 measurements taken during two consecutive field campaigns (June and November 2014) was 1.8 and 0.48 ‰ for δ2H and δ18O, respectively. Mean measurement trueness is determined using quality check standards and was 5 and 0.3 ‰ for δ2H and δ18O, respectively. The isotope depth profiles are used quantitatively to calculate a soil water balance. The contribution of transpiration to total evapotranspiration ranged between 72 and 92 %. Shortly after a rain event, the contribution of transpiration was much lower, at 35 to 50 %. Potential limitations of such an in situ system are related to environmental conditions which could be minimized by using a temperature-controlled chamber for the laser spectrometer. Further, the applicability of the system using previously oven-dried soil material might be limited by physicochemical soil properties (i.e., clay minerals). Uncertainty in the in situ system is suggested to be reduced by improving the calibration procedure and further studying fractionation effects influencing the isotope ratios in the soil water, especially at low water contents. Furthermore, the influence of soil-respired CO2 on isotope values within the root zone could not be deduced from the data

Rare earth elements in uranium ore deposits from Namibia: A nuclear forensics tool

Rare earth elements (REE) concentrations and pattern remains largely unchanged during the process of milling and can thus provide strong evidence of the origin of the material. The aim of this study was to determine the rare earth elements in uranium ore deposits as a nuclear forensics tool. Uranium ore from three mines were collected and analyzed using an inductively coupled plasma mass spectrometry (ICP-MS) to determine the concentrations of rare earth elements. A non-parametric Kruskal-Wallis test and a pair wise comparison test was used to test for significant difference in the concentration of REEs between the mines followed by principal component analysis (PCA). The REE concentration were normalized with C1-Chondrite values to determine the REE pattern. The total concentration of the REE ranged from 131.38 to 161.77 ppb, 266.27 to 840.37 ppb, 177.86 to231.51 for Mine 1, 2 and 3, respectively. The mean ∑REE obtained was in the order M2>M3>M1. The pairwise comparison test of the pair M1 and M2 was found to be less than 0.05, indicating a significant difference in the samples. The REE pattern is mostly similar for all the ore samples with pronounce Eu anomaly, enriched LREE and depleted flat HREE. The PCA results indicates that the ore samples can be distinguished from each other

Evaporation loss along the Calueque-Oshakati Canal in the Cuvelai-Etosha Basin (Northern Namibia): Evidence from stable isotopes and hydrochemistry

© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. Since 1973, Kunene River water has been carried from the Calueque reservoir in Angola along a 160 km open concrete canal to the town of Oshakati in the central part of the Cuvelai-Etosha Basin and has been supplying drinking water to the most densely populated rural area of Namibia. Despite its importance for the region, intra-seasonal water quality and the technical condition of the canal are not routinely checked. Water samples were collected during four field campaigns right before the onset of the rainy season (November 2013 and 2014), and after the rainy season (June 2014 and May 2015), at 16 sites along the canal for stable water isotopes (deuterium, oxygen-17 and oxygen-18) and hydrochemical analyses. The isotope patterns and chemical composition of the canal water is discussed in comparison to local rain, Kunene source water, surface water and groundwater. Clear isotope enrichment indicates evaporative loss of water. A Craig–Gordon model was used to estimate water loss. The loss increases with distance from the source with a maximum of up to 10 %, depending on the season. The results are discussed in context of water availability, vulnerability and water resources management in this water-scarce area

Toward the sustainable use of groundwater springs: A case study from Namibia

-The water supply in drylands mainly relies on groundwater, making it a crucial resource. Springs in southern Africa are often underutilized, and are neither protected nor monitored. Thus, the aim of this study was to evaluate their quality in a sample area in northwestern Namibia and to propose solutions for the sustainable use of springs. In total, 35 springs and hot springs were evaluated in the study area located in the drier part of Namibia (Pmean = 150–400 mm/year), an area highly impacted by ongoing climate change with longer and more frequent drought seasons. The springs there are mostly uncaptured and the discharge is in the form of surface runoff, which is mainly lost to the atmosphere by evaporation. Most of the studied springs were perennial, despite a severe drought period. Local communities rely on the springs mainly for livestock and human consumption, as well as for irrigation. However, 71% of the springs do not have any protective measures. The temperature, pH, conductivity and alkalinity were tested in situ. In total, 20 samples were collected and analyzed for major ions (boron, fluoride, silica and strontium) and total dissolved solids (TDS). The physical and inorganic results mostly indicated good and excellent quality water for human consumption, while the hot springs tended to have poor water quality in terms of Namibian standards, indicating that the water was not fit for human consumption

Challenges to implementing environmental-DNA monitoring in Namibia

By identifying fragments of DNA in the environment, eDNA approaches present a promising tool for monitoring biodiversity in a cost-effective way. This is particularly pertinent for countries where traditional morphological monitoring has been sparse. The first step to realising the potential of eDNA is to develop methodologies that are adapted to local conditions. Here, we test field and laboratory eDNA protocols (aqueous and sediment samples) in a range of semi-arid ecosystems in Namibia. We successfully gathered eDNA data on a broad suite of organisms at multiple trophic levels (including algae, invertebrates and bacteria) but identified two key challenges to the implementation of eDNA methods in the region: 1) high turbidity requires a tailored sampling technique and 2) identification of taxa by eDNA methods is currently constrained by a lack of reference data. We hope this work will guide the deployment of eDNA biomonitoring in the arid ecosystems of Namibia and neighbouring countries

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 budgets. Yet the hydrological processes that govern groundwater recharge and sustainability—and their sensitivity to climatic variability—are poorly constrained4. 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 resources 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

Determining the source water and active root depth of woody plants using a deuterium tracer at a Savannah site in northern Stampriet Basin, Namibia

Woody plants play a significant role in the global water cycle through water uptake by roots and evapotranspiration. A deuterium tracer was used to assess the active root depths for Salvia mellifera and Boscia albitrunca in the Ebenhaezer area (western Namibia). The tracer was inserted at different soil depths in December 2016. Xylem cores were obtained using an increment borer, and transpired water was collected using transpiration bags zipped around the plants’ leaves. Groundwater was collected from boreholes. Soil samples were collected after the rainy season using a hand auger. Xylem and soil water were extracted using a cryogenic vacuum extraction method and analysed for stable water isotopes. Only one S. mellifera transpiration sample showed a high deuterium content (516‰) where the tracer was inserted at 2.5-m soil depth. Elevated deuterium contents were observed in two S. mellifera xylem samples; tracer had been applied at 2.5 and 3 m depth (yielding 35 and 31‰ deuterium, respectively), which constitutes a possible active-root depth range for S. mellifera. At the end of the study period (May 2017), the average δ18O value for B. albitrunca xylem samples was similar to that of groundwater. The δ18O value for S. mellifera was between that of soil water and groundwater, indicating that this species uses groundwater and soil water available for groundwater recharge. Determination of the active root depth and source water for these species would help improve hydrological modelling by incorporating the influence of woody plants on groundwater recharge

Reconstructing rainfall using dryland dunes: Assessing the suitability of the southern Kalahari for unsaturated zone hydrostratigraphies

Time-series of dryland rainfall over 100-1000 s of years are scarce but are needed to underpin improved predictions under future climate change. Dryland sand dunes are established Quaternary geomorphic archives, which also contain pore moisture as part of the unsaturated zone (USZ), with chemical tracers that provide a novel proxy for palaeomoisture. Chloride depth profiles, converted using a mass balance approach to temporal records, are known as hydrostratigraphies. Evaporative enrichment of meteoric chloride occurs in the near-surface zone and the established signature gets transported vertically via infiltration. This study explores the potential for this approach for southern Kalahari vegetated linear dunes comparing twelve (10-12 m deep) hydrostratigraphies across space and sampled in different years (2011, 2013, and 2016). Three further profiles sampled close to an interdune pan demonstrate that additional chloride is added locally to the dune closest to the pan. The remaining hydrostratigraphies show variable trends, with four broad groupings, leading us to suggest this region is unsuitable for this approach. Insights into this variable behavior were sought from simulating liquid and vapor flux using STEMMUS (Simultaneous Transfer of Energy, Mass and Momentum in Unsaturated Soil). Simulations suggest the mixing zone can reach 10 m thick, which helps account for the variation in hydrostratigraphies. Heterogeneity may also arise from spatially-heterogenous receipt of convective rainfall events and non-uniform vegetation cover. Furthermore, the vegetated nature of the landscape leads to less uniform moisture movement within the dune sands. We call for future applications to include site-specific insights into moisture dynamics. Stone A, Zeng Y, Yu L, van der Ploeg M and Wanke H (2022), Reconstructing rainfall using dryland dunes: Assessing the suitability of the southern Kalahari for unsaturated zone hydrostratigraphies