Pollution shapes the microbial communities in river water and sediments from the Olifants River catchment, South Africa

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.

Multi-compartment impact of micropollutants and particularly antibiotics on bacterial communities using environmental DNA at river basin-level

“…Sediment-bacterial communities exhibited significantly higher alpha-diversities (described as Chao1- and Shannon-indices as well as eveness) than bacterial communities inhabiting water and biofilm, which had similar levels of alpha diversity (Dunn’s test, p -adjusted□<□0.05; Figure 2). These findings are consistent with previous studies, all showing that sediments harbour in general greater bacterial biodiversity (Lozupone and Knight, 2007; Valverde et al, 2021), and that water and biofilm habitats both display lower alpha diversity levels (Walters and Martiny, 2020). This pattern is driven by the greater heterogeneity of sediments, in comparison to water and biofilms, resulting in spatially/resource-driven niche partitioning, which increases bacterial alpha diversity (Gibbons and Gilbert, 2015).…”

“…We identified significant dissimilarities between bacterial communities in water, biofilm, and sediment compartments (Figure S4; PERMANOVA test, p -adjusted < 0.001). Consistent with previous studies (Garner et al, 2016; Valverde et al, 2021), sediment bacterial communities displayed dissimilarities across different sampling sites with distinct pollution pressure (PERMANOVA test, p - adjusted < 0.001). Reference sites positively correlated with phosphate and light and negatively with nitrate, micropollutants (CAChems), and antibiotic stress (TU MIC ) (Figure 3A).…”

“…We assessed the diversity of bacterial communities sampled simultaneously from water, biofilms, and sediments in tributaries and the main river course of the River Aconcagua basin. Our study complements previous works that focussed on single compartments i.e., water (Li et al, 2023;Mansfeldt et al, 2020), biofilm (Aubertheau et al, 2017;Chonova et al, 2018;Freixa et al, 2020), sediment (Gao et al, 2019;Haller et al, 2011;Shao et al, 2023;Xie et al, 2016;Zhang et al, 2022), or on water and sediment together (Drury et al, 2013;Guo et al, 2016;Ibekwe et al, 2016;Valverde et al, 2021).…”

“…Bacteroidetes had high median relative abundances primarily in water and biofilm (∼15% in each), whereas Actinobacteria showed significantly higher median relative abundance in sediment (25%) and Cyanobacteria in biofilms (40%) (Figure S3). The same phyla were also the most prevalent in sediment and water samples exposed to chronic pollution derived from fertiliser industry and mining (Valverde et al, 2021). In terms of the dynamic of these phyla across different sampling sites, Bacteroidetes had higher relative abundances along the main river course and tributaries which have been characterised by higher micropollutants concentrations (Inostroza et al, 2024, 2023b).…”

“…Studies that consider broader spatial distributions have also reported a reduced diversity of bacterial communities that inhabit areas characterised by urban and agricultural land use, compared to reference areas (Ibekwe et al, 2016;Li et al, 2023). However, it is important to note that other studies that compared sites up-and downstream of WWTPs did not find significant biodiversity differences (Mansfeldt et al, 2020) and changes in bacterial community composition in areas of agricultural and industrial land use were attributed to chemical pollution in water and sediment (Valverde et al, 2021). Indeed, significant associations have been described between micropollutant concentrations and alterations in bacterial communities in water samples, but not in sediments in mixed land use areas (Gao et al, 2019).…”