Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa
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ORIGINAL PAPER
Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa Angel Valverde1,3,4 · Errol D. Cason1,2 · Alba Gómez‑Arias1 · Derya Bozkale4 · Danny Govender5,6 · Eddie Riddell5,7 · Don Cowan4 Received: 17 September 2019 / Revised: 6 August 2020 / Accepted: 2 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Human activities such as agriculture and mining are leading causes of water pollution worldwide. Individual contaminants are known to negatively affect microbial communities. However, the effect of multifaceted pollution on these communities is less well understood. We investigated, using next-generation sequencing of the 16S rRNA genes, the effects of multisource (i.e., fertilizer industry and mining) chronic pollution on bacterial and archaeal communities in water and sediments from the Olifants River catchment, South Africa. Water samples showed less microbial species diversity than sediments and both habitats displayed different microbial communities. Within each of these habitats, pollution had no effect on alpha diversity but shaped the microbial composition and taxonomy-based predicted functions. Certain prokaryotic taxa and functional groups were indicative of different degrees of pollution. Heterotrophic taxa (e.g., Flavobacterium sp.) and sulphur-oxidizing bacteria (i.e., Thiobacillus sp.) were indicators of pollution in water and sediments, respectively. Ultimately, this information could be used to develop microbial indicators of water quality degradation. Keywords Chronic pollution · Microbial communities · River sediments · 16S rRNA gene sequencing
Introduction Pollution has been identified as the main pressure affecting freshwater systems and resources around the world (Vörösmarty et al. 2010). Water pollution can result from different anthropogenic activities, including mining and fertilizer industry. Discharged mine water negatively impacts Communicated by Erko stackebrandt. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00203-020-02035-2) contains supplementary material, which is available to authorized users. * Angel Valverde [email protected] 1
Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
2
Department of Animal‑, Wildlife‑, and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
3
Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Consejo Superior de Investigaciones Científicas, Salamanca, Spain
aquatic environments by increasing the levels of suspended solids, leading to mobilization of elements such as iron, copper, manganese and zinc and also altering the pH of the receiving water (Baker and Banfield 2003). On the other hand, chemical fertilizers containing phosphorus and nitrogen contributes to eutrophication, one of the leading causes of degraded water quality worldwide (Dodds 2006). Mi
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