Identifying chemolithotrophic and pathogenic-related gene expression within suspended sediment flocs in freshwater environments: A metatranscriptomic assessment

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.…”

“…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).…”

“…Total RNA from sediment was extracted using the RNeasy PowerSoil Total RNA kits (Qiagen), following the manufacturer's instructions including slight modifications as previously described (VanMensel et al, 2020), with sample weight 2 or 5 g and final pellet resuspended in 50 or 60 μL RNase‐free water for suspended and bed sediment samples, respectively. Sample weight was different for suspended and bed sediment due to differing concentrations of isolated RNA; specifically, SS was fine‐grained, cohesive sediment (i.e., D 50 < 35 μm; VanMensel et al, 2022) and consequently held greater concentrations of biomass compared with bed sediment samples. RNase inhibitor (Invitrogen) was added to the resuspended pellet to minimize degradation.…”

“…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). These samples were acquired using a water pump and a continuous flow centrifuge as previously described (VanMensel et al, 2022). Overall, 172 bed sediment samples and 32 SS samples were selected for targeted transcriptomics, totalling 204 samples processed on the OpenArray ® chips.…”

“…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.…”