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

Comparison of the Antibiotic Resistance of Escherichia coli Populations from Water and Biofilm in River Environments

Antibiotic-resistant, facultative pathogenic bacteria are commonly found in surface water; however, the factors influencing the spread and stabilization of antibiotic resistance in this habitat, particularly the role of biofilms, are not fully understood. The extent to which bacterial populations in biofilms or sediments exacerbate the problem for specific antibiotic classes or more broadly remains unanswered. In this study, we investigated the differences between the bacterial populations found in the surface water and sediment/biofilm of the Mur River and the Drava River in Austria. Samples of Escherichia coli were collected from both the water and sediment at two locations per river: upstream and downstream of urban areas that included a sewage treatment plant. The isolates were subjected to antimicrobial susceptibility testing against 21 antibiotics belonging to seven distinct classes. Additionally, isolates exhibiting either extended-spectrum beta-lactamase (ESBL) or carbapenemase phenotypes were further analyzed for specific antimicrobial resistance genes. E. coli isolates collected from all locations exhibited resistance to at least one of the tested antibiotics; on average, isolates from the Mur and Drava rivers showed 25.85% and 23.66% resistance, respectively. The most prevalent resistance observed was to ampicillin, amoxicillin-clavulanic acid, tetracycline, and nalidixic acid. Surprisingly, there was a similar proportion of resistant bacteria observed in both open water and sediment samples. The difference in resistance levels between the samples collected upstream and downstream of the cities was minimal. Out of all 831 isolates examined, 13 were identified as carrying ESBL genes, with 1 of these isolates also containing the gene for the KPC-2 carbapenemase. There were no significant differences between the biofilm (sediment) and open water samples in the occurrence of antibiotic resistance. For the E. coli populations in the examined rivers, the different factors in water and the sediment do not appear to influence the stability of resistance. No significant differences in antimicrobial resistance were observed between the bacterial populations collected from the biofilm (sediment) and open-water samples in either river. The different factors in water and the sediment do not appear to influence the stability of resistance. The minimal differences observed upstream and downstream of the cities could indicate that the river population already exhibits generalized resistance.

Differences in pathogenic community assembly processes and their interactions with bacterial communities in river and lake ecosystems

Pathogenic bacterial infections caused by water quality degradation are one of the most widespread environmental problems. Clarifying the structure of pathogens and their assembly mechanisms in lake ecosystems is vital to prevent the infestation of waterborne pathogens and maintain human health. However, the composition and assembly mechanisms of pathogenic bacterial communities in river and lake ecosystems are still poorly understood. In this study, we collected 17 water and 17 sediment samples from Lake Chaohu and its 11 inflow rivers. Sequencing of 16S rRNA genes was used to study bacterial pathogen communities. The results of the study showed that there was a significant difference (P < 0.05) in the composition of the pathogen community between riverine and lake habitats. Acinetobacter (36.49%) was the dominant bacterium in the river, whereas Flavobacterium (21.6%) was the most abundant bacterium in the lake. Deterministic processes (i.e., environmental filtering and species interaction) drove the assembly of pathogenic bacterial communities in the lake habitat, while stochastic processes shaped river pathogenic bacterial communities. Spearman correlation analysis showed that the α-diversity of bacterial communities was linearly and negatively linked to the relative abundance of pathogens. Having a higher bacterial community diversity had a suppressive effect on pathogen abundance. In addition, co-occurrence network analysis showed that bacterial communities were tightly linked to pathogenic bacteria. Pseudomonas aeruginosa and Salmonella enterica were identified as keystone species in an inflow water sampling network (W_FR), reducing the complexity of the network. These results provide a reference for assessments of water quality safety and pathogenic bacteria posing risks to human health in large freshwater lakes.

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

Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.

Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health

Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).

Investigating chemical and microbial functional indicators of nutrient retention capacity in greenhouse stormwater retention ponds in southwestern Ontario, Canada

The tributaries flowing through Leamington, Ontario are unique in the Canadian Lake Erie watershed due to the broad spatial extent of greenhouse operations, which more than doubled in size and density from 2011 to 2022. These greenhouse operations are considered to be potential nutrient point sources with respect to observed nutrient concentrations in tributaries adjacent to greenhouse stormwater retention ponds (GSWPs). Identifying causal factors of nutrient release, whether this be chemical or biological, within these ponds may be critical for mitigating their impact on the watershed and ultimately the receiving waters of Lake Erie. Specifically, phosphorus and nitrogen accumulation in freshwater ponds can contribute to environmental damage proximal to adjacent streams, serving as a potential catalyst for algal blooms and eutrophication. This study compared correlations between the water column N:P stoichiometry, sediment nutrient retention capacity, and drivers of microbial metabolism within GSWP sediments. Correlations between water column TN:TP ratios and sediment nutrient retention capacity were observed, suggesting an interplay between N and P in terms of nutrient limitation. Further, clear shifts were observed in the bacterial metabolic pathways analyzed through metatranscriptomics. Specifically, genes related to nitrogen fixation, nitrification and denitrification, and other metabolic processes involving sulfur and methane showed differential expression depending on the condition of the respective pond (i.e., naturalized wetland vs. dredged, eutrophic pond). Collectively, this research serves to highlight the interconnected role of chemical-biological processes particularly as they relate to significant ecosystem processes such as nutrient loading and retention dynamics in impaired freshwater systems.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

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

The introduction and proliferation of pathogenic organisms in aquatic systems is a serious global issue that consequently leads to economic, financial, and health concerns. Health and safety related to recreational water use is typically monitored through water quality assessments that are outdated and can be misleading. These traditional methods focus on broad taxa groups, provide no insight into the active community or source of contamination, and the sediment compartments (bed and suspended) are often overlooked. To bridge this knowledge gap, our study aimed to 1) examine the metatranscriptome of the microbial community associated with suspended sediment (SS) in freshwater systems; 2) explore the influence of SS in tributaries to the littoral zone of the receiving lake; and 3) compare the SS fraction with previously reported nearshore bed sediment data. Samples were collected seasonally from Lake St. Clair and Lake Erie. Beaches in this region are influenced by both agriculture runoff and continued urban expansion. Results show that both adjacent tributary and beach SS have similar microbial functional diversity and are strongly correlated by site and season. We identified expression of transcripts encoding sequences with similarities to genes involved in nine bacterial infectious disease pathways, including legionellosis (sdhA) and Vibrio cholerae pathogenesis. According to MG-RAST gene categories, lake samples typically showed higher overall expression (p < 0.05) of transcripts with similarities to genes involved in infectious disease pathways compared to the tributaries, with summer upregulated (p < 0.05) compared to fall. Our data suggests SS acts as a strong vector for pathogen transport, making this facet an important area for further research as it pertains to human health regarding recreational water use. To our knowledge, this work is the first to investigate SS in aquatic microbial communities using metatranscriptomic analyses and has significant potential to help address growing issues of microbial contamination impacting freshwater security.

Investigating the microbial dynamics of microcystin-LR degradation in Lake Erie sand

Cyanobacterial blooms and the associated hepatotoxins produced (e.g., microcystins, MCs) create a significant human health risk in freshwater lakes around the world, including Lake Erie. Though various physical and chemical treatment options are utilized, these are costly and their effectiveness decreases when other organics are present. Laboratory studies have identified a remediation option based on a mlr gene operon that can systematically degrade this toxin; however, studies on Lake Erie have been unable to amplify mlr genes from MC-degrading bacteria. These results suggest that either existing primers may be inefficient for broad identification of the mlr genes or that MC degradation genes and/or pathways may vary among bacterial taxa. To investigate the dynamics of the Lake Erie microbial community involved in the degradation of microcystin-LR (MC-LR), a flow-through column experiment using collected beach sand was conducted over a period of six weeks. Increasing concentrations of lake water spiked with MC-LR were continuously delivered to both biotic and abiotic (sterilized) sand columns, with influent and effluent MC-LR concentrations measured by LC-MS/MS. Despite the toxin concentrations far exceeding natural conditions during a bloom event (maximum dosage = 15.4 μg/L), MC-LR was completely removed within 21 h of contact time in the biotic columns. Stimulation of community taxa during the degradation process included Burkholderiaceae, Illumatobacteraceae, Pseudomonadaceae, Rhodocyclaceae and Nitrosomonadaceae. The overall results suggest several critical species may be required for the most complete and effective degradation of MC-LR.

Next generation sequencing approaches to evaluate water and wastewater quality

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.

Diel Dynamics of Freshwater Bacterial Communities at Beaches in Lake Erie and Lake St. Clair, Windsor, Ontario

Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.