Exploring bacterial pathogen community dynamics in freshwater beach sediments: A tale of two lakes

Abstract

Pathogenic bacteria associated with freshwater ecosystems can pose significant health risks particularly where recreational water use is popular. Common water quality assessments involve quantifying indicator Escherichia coli within the water column but neglect to consider physical and geochemical factors and contributions from the sediment. In this study, we used high-throughput sequencing to investigate sediment microbial communities at four freshwater public beaches in southern Ontario, Canada and analysed community structure, function, and gene expression with relation to geographical characteristics. Our results indicate that beach sediments at the sediment-water interface could serve as potential sources of bacterial contamination under low-energy environments with tightly packed small sediment particles compared with high-energy environments. Further, the absence of pathogens but expression of pathogenic transcripts suggests occurrence of alternate gene acquisition. Pathogenicity at these locations included expression of Salmonella virulence factors, genes involved in pertussis, and antimicrobial resistance. Finally, we introduce a proposed universal bacterial pathogen model to consider the combined and synergistic processes used by these microbes. To our knowledge, this is the first study of its kind to investigate chemolithotrophic activity related to pathogens within bed sediment at freshwater beaches. This work helps advance current understanding of health risks in these environments.

Microbe–sediment interactions in Great Lakes recreational waters: Implications for human health risk

“…Microbes belonging to the Bacteroides genus are abundant in the gut and faeces of many warm-blooded animals and have become a common target in MST of environmental samples (Ahmed et al, 2016;G omez-Doñate et al, 2016). Therefore, we expected expression levels for this target to be among the highest for our environmental dataset, especially at the more contaminated locations (i.e., BR and KV) as previously reported (VanMensel et al, 2020(VanMensel et al, , 2022.…”

“…Although expression was not as prevalent as Bacteroides MST targets, FIB_Enterococcus was detected in the dataset with values ranging from 1.78 to 4.89 log copies/g, and FIB_Ecoli ranging from 2.97 to 5.09 log copies/g. With the concern that deposited sediment in aquatic systems may represent a reservoir of pathogenic microbes (Baker et al, 2021;Korajkic et al, 2019;VanMensel et al, 2020), our results that FIB transcripts were isolated from SS reveals added concern for the role that sediment plays regarding human health and safety in recreational waters, such as mobility.…”

“…Frequent beach closures often result in this area due to high levels of FIB and blue‐green algae detected in the water column. Six public beaches in WEC were selected for this study based on historical water quality data reported by the WEC Health Unit (WECHU, http://www.wechu.org) and built off locations previously selected for metatranscriptomic investigation of bacterial gene expression associated with the bed (VanMensel et al, 2020) and SS (VanMensel et al, 2022).…”

“…Surface bed sediment samples were collected from the nearshore (i.e., swimming zone) of local public beaches; four located on the north shore of Lake Erie (Holiday Conservation Beach [HD], Lakeside Beach in Kingsville [KV], Seaside Beach in Leamington [LE] and Point Pelee Northwest Beach [PP]), and two situated on the southern shoreline of Lake St. Clair (Sandpoint Beach [SP] and West Belle River Beach [BR]). All bed sediment samples were collected via sediment coring, as previously described (VanMensel et al, 2020) and denote several time points representing a spatiotemporal study throughout the 2017 swimming season (June through September) of the WEC local public beaches (Table S1). Total suspended solids were collected seasonally (spring, summer and fall) in 2017 from the nearshore zone of KV and BR beaches as well as from their adjacent tributaries (Mill Creek and Belle River, respectively; Table S1).…”

“…Total RNA concentrations were determined using either the Agilent 2100 Bioanalyzer (Agilent Technologies) or fluorometrically using the Qubit 2.0 Fluorometer and RNA Broad-Range Assay kit (Thermo Fisher Scientific) (Table S2). Select samples were tested for RNA quality assurance using the Bioanalyzer, previously published (VanMensel et al, 2020(VanMensel et al, , 2022. Typically, the RNA integrity number (RIN) was 6.0 or greater.…”