Metagenomic analysis of microbial communities from hand-dug wells in the Cuvelai-Etosha Basin, Namibia

Abstract

The total surface area of planet earth is about 510 million Km2 and about 71% of this area is water and the remaining 29% is formed by land mass. The proportion of water is much higher, as it is a major component of physiological existence and includes all types of natural water resources; oceans, seas, rivers, lakes and groundwater. Africa has about 64% water coverage, which is the lowest among the continents in the world. This situation retards the development of most African countries because water is crucial for social-economic development and this situation demands that African countries explore the use of groundwater and rainfall in addition to surface water. Water scarcity is commonly experienced in southern Africa due to the increased arid conditions and unpredictable rainfall patterns. The region has countries such as Botswana, Angola and Zambia with unpredictable rainfall patterns while Namibia is a desert country with short rain and long dry seasons. The Cuvelai Etosha Basin of Namibia is a rural setting in which most people depend on groundwater to circumvent water scarcity by the construction of hand-dug wells. However, groundwater presents another problem because it is saline in most parts of the basin and the situation is worsened by lack of perennial rivers within the regions. A Metagenomics and culturing study was conducted to explore the bacterial communities in hand-dug well water of the Cuvelai Etosha Basin and its safety for human and livestock consumption. The influence of hand-dug well type, region and season on bacterial; colony forming units, coliforms and particular genera, phyla, species richness, diversity and evenness, human and livestock pathogens, zoonotic pathogens, and grey bacteria was revealed. The dominant bacterial phyla and major water physicochemical parameters influencing phyla abundance were determined leading to conclusions; hand-dug well type and region does not influence the subjects investigated except for colony forming unitss that are influenced by hand-dug well type. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Cyanobacteria are dominant and main physicochemical factors influencing their abundance were phosphate, manganese, potential of hydrogen, and temperature. Seasonality did not affect coliforms and Proteus species presence, bacterial species diversity and evenness except richness and abundance. The wet season had pronounced abundances of human, livestock and zoonotic pathogens and grey bacteria. Overall, Cuvelai Etosha Basin hand-dug well water is not safe for human and livestock consumption unless sanitized. Keywords: Bacteria, Cuvelai Etosha Basin, hand-dug wells, metagenomics, water