Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses

Abstract

Rivers are often challenged by fecal contaminations. The barrier effect of sediments against fecal bacteria was investigated through the use of a microbial source tracking (MST) toolbox, and by Next Generation Sequencing (NGS) of V5-V6 16S rRNA gene (rrs) sequences. Non-metric multi-dimensional scaling analysis of V5-V6 16S rRNA gene sequences differentiated bacteriomes according to their compartment of origin i.e., surface water against benthic and hyporheic sediments. Classification of these reads showed the most prevalent operating taxonomic units (OTU) to be allocated to Flavobacterium and Aquabacterium. Relative numbers of Gaiella, Haliangium, and Thermoleophilum OTU matched the observed differentiation of bacteriomes according to river compartments. OTU patterns were found impacted by combined sewer overflows (CSO) through an observed increase in diversity from the sewer to the hyporheic sediments. These changes appeared driven by direct transfers of bacterial contaminants from wastewaters but also by organic inputs favoring previously undetectable bacterial groups among sediments. These NGS datasets appeared more sensitive at tracking community changes than MST markers. The human-specific MST marker HF183 was strictly detected among CSO-impacted surface waters and not river bed sediments. The ruminant-specific DNA marker was more broadly distributed but intense bovine pollution was required to detect transfers from surface water to benthic and hyporheic sediments. Some OTU showed distribution patterns in line with these MST datasets such as those allocated to the Aeromonas, Acinetobacter, and Pseudomonas. Fecal indicators (Escherichia coli and total thermotolerant coliforms) were detected all over the river course but their concentrations were not correlated with MST ones. Overall, MST and NGS datasets suggested a poor colonization of river sediments by bovine and sewer bacterial contaminants. No environmental outbreak of these bacterial contaminants was detected.

Responses of streambed bacterial groups to cycles of low‐flow and erosive floods in a small peri‐urban stream

“…Therefore, WWO events represent huge delivery of faecal bacteria and pathogens in the river system. Other sources of faecal bacteria are also present in the catchment as indicated by Marti et al (2017), such as those coming from wild animals and livestocks (birds, cattle, horses, and goats), and organic soil amendments including composted manure in the rural areas.…”

“…The relative impact of WWO on the ecological state of small streams has been explored and shown to significantly modify river sediment microbiome organizations inferred from 16S rRNA polymerase chain reaction (PCR) gene products DNA sequences (Marti et al, 2017). These modifications were suggested to be linked to the nutrient inputs (organic‐C and N) discharged by CSOs.…”

“…This enrichment was reported for bacterial taxa allocated to the genus Aeromonas , Pseudomonas , and Acinetobacter , which are known to include pathogenic species. Furthermore, EC counts, indicative of faecal contamination, were found significant for most hyporheics sediments recovered downstream a CSO device (Marti et al, 2017). These allochthonous bacteria may persist during low‐flow periods when biotic (e.g., competition and predation) as well as abiotic factors (e.g., hydrological, physicochemical, and hydraulic factors) remain favourable.…”

“…River sediments and suspended matters (SMs) constitute biotopes driving the structuration of bacterial communities (e.g., Fischer, Wanner, & Pusch, 2002; Marti et al, 2017), but also a vector of dispersal in rivers (e.g., Ribolzi, Evrard, et al, 2016; Ribolzi, Rochelle‐Newall, et al, 2016). Analyses making use of microcosms showed faecal indicator bacteria (FIB) to have a lower die‐off rate in sediments than surface waters (Chandran et al, 2011; Craig, Fallowfield, & Cromar, 2004; Lee et al, 2011).…”

Thermotolerant coliform counts and nutrient levels as indicators of water quality in sub-Mediterranean karst river

“…Communal wastewaters contribute to increased phosphorus levels in surface waters [8]. Phosphorus is rarely found Cyclic variations in TTC numbers in water are attributed to water influx due to rainfalls [9][10][11]. However, according to the results obtained during fall and winter, it is clear that lower temperatures do not significantly impact decrease in TTC numbers.…”