Use of microcosms to determine persistence of Escherichia coli in recreational coastal water and sediment and validation with in situ measurements

Examining the potential impacts of a coastal renourishment project on the presence and abundance of Escherichia coli

Erosion poses a significant threat to oceanic beaches worldwide. To combat this threat, management agencies often utilize renourishment, which supplements eroded beaches with offsite sand. This process can alter the physical characteristics of the beach and can influence the presence and abundance of microbial communities. In this study, we examined how an oceanic beach renourishment project may have impacted the presence and abundance of Escherichia coli (E. coli), a common bacteria species, and sand grain size, a sediment characteristic that can influence bacterial persistence. Using an observational field approach, we quantified the presence and abundance of E. coli in sand (from sub-tidal, intertidal, and dune zones on the beach) and water samples at study sites in both renourished and non-renourished sections of Folly Beach, South Carolina, USA in 2014 and 2015. In addition, we also measured how renourishment may have impacted sand grain size by quantifying the relative frequency of grain sizes (from sub-tidal, intertidal, and dune zones on the beach) at both renourished and non-renourished sites. Using this approach, we found that E. coli was present in sand samples in all zones of the beach and at each of our study sites in both years of sampling but never in water samples. Additionally, we found that in comparison to non-renourished sections, renourished sites had significantly higher abundances of E. coli and coarser sand grains in the intertidal zone, which is where renourished sand is typically placed. However, these differences were only present in 2014 and were not detected when we resampled the study sites in 2015. Collectively, our findings show that E. coli can be commonly found in this sandy beach microbial community. In addition, our results suggest that renourishment has the potential to alter both the physical structure of the beach and the microbial community but that these impacts may be short-lived.

Using machine learning models to predict the effects of seasonal fluxes on Plesiomonas shigelloides population density

Seasonal variations (SVs) affect the population density (PD), fate, and fitness of pathogens in environmental water resources and the public health impacts. Therefore, this study is aimed at applying machine learning intelligence (MLI) to predict the impacts of SVs on P. shigelloides population density (PDP) in the aquatic milieu. Physicochemical events (PEs) and PDP from three rivers acquired via standard microbiological and instrumental techniques across seasons were fitted to MLI algorithms (linear regression (LR), multiple linear regression (MR), random forest (RF), gradient boosted machine (GBM), neural network (NN), K-nearest neighbour (KNN), boosted regression tree (BRT), extreme gradient boosting (XGB) regression, support vector regression (SVR), decision tree regression (DTR), M5 pruned regression (M5P), artificial neural network (ANN) regression (with one 10-node hidden layer (ANN10), two 6- and 4-node hidden layers (ANN64), and two 5- and 5-node hidden layers (ANN55)), and elastic net regression (ENR)) to assess the implications of the SVs of PEs on aquatic PDP. The results showed that SVs significantly influenced PDP and PEs in the water (p < 0.0001), exhibiting a site-specific pattern. While MLI algorithms predicted PDP with differing absolute flux magnitudes for the contributing variables, DTR predicted the highest PDP value of 1.707 log unit, followed by XGB (1.637 log unit), but XGB (mean-squared-error (MSE) = 0.0025; root-mean-squared-error (RMSE) = 0.0501; R² =0.998; medium absolute deviation (MAD) = 0.0275) outperformed other models in terms of regression metrics. Temperature and total suspended solids (TSS) ranked first and second as significant factors in predicting PDP in 53.3% (8/15) and 40% (6/15), respectively, of the models, based on the RMSE loss after permutations. Additionally, season ranked third among the 7 models, and turbidity (TBS) ranked fourth at 26.7% (4/15), as the primary significant factor for predicting PDP in the aquatic milieu. The results of this investigation demonstrated that MLI predictive modelling techniques can promisingly be exploited to complement the repetitive laboratory-based monitoring of PDP and other pathogens, especially in low-resource settings, in response to seasonal fluxes and can provide insights into the potential public health risks of emerging pathogens and TSS pollution (e.g., nanoparticles and micro- and nanoplastics) in the aquatic milieu. The model outputs provide low-cost and effective early warning information to assist watershed managers and fish farmers in making appropriate decisions about water resource protection, aquaculture management, and sustainable public health protection.

Sanitary sewage overflows, boil water advisories, and emergency room and urgent care visits for gastrointestinal illness: a case-crossover study in South Carolina, USA, 2013-2017

BACKGROUND

Sanitary sewage overflows (SSOs) release raw sewage, which may contaminate the drinking water supply. Boil water advisories (BWAs) are issued during low or negative pressure events, alerting customers to potential contamination in the drinking water distribution system.

OBJECTIVE

We evaluated the associations between SSOs and BWAs and diagnoses of gastrointestinal (GI) illness in Columbia, South Carolina, and neighboring communities, 2013-2017.

METHODS

A symmetric bi-directional case-crossover study design was used to assess the role of SSOs and BWAs on Emergency Room and Urgent Care visits with a primary diagnosis of GI illness. Cases were considered exposed if an SSO or BWA occurred 0-4 days, 5-9 days, or 10-14 days prior to the diagnosis, within the same residential zip code. Effect modification was explored via stratification on participant-level factors (e.g., sex, race, age) and season (January-March versus April-December).

RESULTS

There were 830 SSOs, 423 BWAs, and 25,969 cases of GI illness. Highest numbers of SSOs, BWAs and GI cases were observed in a zip code where >80% of residents identified as Black or African-American. SSOs were associated with a 13% increase in the odds of a diagnosis for GI illness during the 0-4 day hazard period, compared to control periods (Odds Ratio: 1.13, 95% Confidence Interval: 1.09, 1.18), while no associations were observed during the other hazard periods. BWAs were not associated with increased or decreased odds of GI illness during all three hazard periods. However, in stratified analyses BWAs issued between January-March were associated with higher odds of GI illness, compared to advisories issued between April-December, in all three hazard periods.

SIGNIFICANCE

SSOs (all months) and BWAs (January-March) were associated with increased odds of a diagnosis of GI illness. Future research should examine sewage contamination of the drinking water distribution system, and mechanisms of sewage intrusion from SSOs.

IMPACT

Sewage contains pathogens, which cause gastrointestinal (GI) illness. In Columbia, South Carolina, USA, between 2013-2017, there were 830 sanitary sewage overflows (SSOs). There were also 423 boil water advisories, which were issued during negative pressure events. Using case-crossover design, SSOs (all months) and boil water advisories (January-March) were associated with increased odds of Emergency Room and Urgent Care diagnoses of GI illness, potentially due to contamination of the drinking water distribution system. Lastly, we identified a community where >80% of residents identified as Black or African-American, which experienced a disproportionate burden of sewage exposure, compared to the rest of Columbia.

Effective coastal Escherichia coli monitoring by unmanned aerial vehicles (UAV) thermal infrared images

Coastal Escherichia coli (E. coli) significantly influence ocean safety and public health, thus requiring an effective E. coli pollution monitoring. However conventional detection relying on manual field sampling is time-consuming. Here, this study established an E. coli estimation model based on thermal remote sensing of unmanned aerial vehicles (UAV). This model was developed against one-year comprehensive field work in a representative sandy beach and further validated against 50 beaches in Hong Kong to evaluate its applicability. The estimated E. coli concentrations were in a reliable agreement with direct measurements. For this model, this study deployed the radon-222 (²²²Rn) as a bridging tracer to couple UAV thermal images and coastal E. coli concentrations. Coastal ²²²Rn can be reflected on the UAV thermal images, and there was a good positive correlation between the ²²²Rn activity and coastal E. coli concentration via one-year field data. Hence, coupling the ²²²Rn activity estimated from UAV thermal images and the relationship between ²²²Rn and E. coli, this study can readily monitor coastal E. coli by UAV. These findings highlighted that UAV technology is an effective approach to measure the E. coli concentrations and can further pave the way for an efficient coastal E. coli monitoring and public health risk warning.

Turbidity and fecal indicator bacteria in recreational marine waters increase following the 2018 Woolsey Fire

Wildfires increase runoff and sediment yields that impact downstream ecosystems. While the effects of wildfire on stream water quality are well documented, oceanic responses to wildfire remain poorly understood. Therefore, this study investigated oceanic responses to the 2018 Woolsey Fire using satellite remote sensing and in situ data analyses. We examined 2016–2020 turbidity plume (n = 192) and 2008–2020 fecal indicator bacteria (FIB, n = 15,015) measurements at variable proximity to the Woolsey Fire. Shifts in coastal water quality were more pronounced in the “inside” region, which drained the burn area. The inside region experienced 2018–2019 plume surface area monthly means that were 10 and 9 times greater than 2016–2017 and 2017–2018 monthly means, respectively. Further, linear regressions showed that 2018–2019 three-day precipitation totals produced plumes of greater surface area. We also noted statistically significant increases in the inside region in 2018–2019 total coliform and Enterococcus monthly means that were 9 and 53 times greater than 2008–2018 monthly means, respectively. These results indicate that sediment and microbial inputs to coastal ecosystems can increase substantially post-wildfire at levels relevant to public and environmental health, and underscore the benefit of considering remote sensing and in situ measurements for water quality monitoring.

The plastic Trojan horse: Biofilms increase microplastic uptake in marine filter feeders impacting microbial transfer and organism health

Microplastic pollution has become a major source of concern, with a large body of literature surrounding the impacts of microplastic ingestion by biota. However, many of these studies utilise virgin microbeads, which are not reflective of environmental microplastics that are rapidly colonised with microbial communities (plastisphere) in marine ecosystems. It is a concern therefore that current evidence of the impacts of microplastics on biota are unrepresentative of the environmental microplastic pollution. In this study, uptake and bioaccumulation of both virgin and Escherichia coli coated microplastics, by European native oysters (Ostrea edulis) were compared, and the physiological responses of oysters to the exposure were investigated. The uptake of E. coli coated microplastics was found to be significantly higher than the uptake of virgin microplastics, with average concentrations of 42.3 ± 23.5 no. g^-1 and 11.4 ± 0.6 no. g^-1 microbeads found in oysters exposed to coated and virgin microplastics, respectively. This suggests that environmental microplastic uptake into the marine trophic web by benthic filter feeders may be greater than previously thought. The oxygen consumption and respiration rate of oysters exposed to E. coli coated microplastics increased significantly over time, whilst virgin microplastics did not produce any measurable significant physiological responses. However, less than 0.5% of the total amount of administered microbeads were retained by all oysters, suggesting a limited residence time within the organisms. Although microplastics did not bioaccumulate in oyster tissues in the short-term, microorganisms assimilated by the ingestion of coated microplastics may be transferred to higher trophic levels. This poses a risk, not only for wildlife, but also for food safety and human health. The capacity to carry pathogens and expose a wide range of organisms to them means microplastics may have an important role as vectors for disease.

Variability of E. coli in streambed sediment and its implication for sediment sampling

E. coli is the number one cause for water quality impairments in rivers and streams in South Dakota and the United States. Stream bottom sediments can be a reservoir for bacteria, including pathogenic organisms and fecal indicator bacteria (FIB), due to the favorable conditions provided by sediments for survival. Despite this, little is known about the variability of E. coli in sediments which should be considered when developing a sampling regime. This study examines the spatial variability of E. coli in sediment across the stream cross-section, the temporal stability of E. coli in sediment samples, and the implications for sediment sampling and processing. Five locations were sampled for sediment E. coli along two tributaries to the Big Sioux River in eastern South Dakota, four along Skunk Creek (Sk1, Sk2, Sk3, and Sk4), and one in Sixmile Creek (SM). In Skunk Creek, site Sk1 has direct cattle access where the other three sites (Sk2, Sk3, and Sk4) are under Seasonal Riparian Area Management (SRAM), a strategy that limits the cattle access to the stream. E. coli concentrations in the sediment ranged from 4 to 997 CFU g^-1 (8.5 × 10² to 2.1 × 10⁵ CFU 100 mL^-1). The highest and lowest E. coli concentrations observed were at sites Sk1 and Sk4, respectively. The E. coli concentration decreased from the upstream cattle crossing site (Sk1) through the downstream SRAM sites. Analyzing the stream cross-section analysis revealed no significant difference in E. coli concentration between the edge and the middle of the stream. Sediment samples can be held up to 24 h after sample collection in refrigerated conditions (37 °F) in the majority of cases (80%) without significant changes in E. coli concentrations. The sample size analysis indicated the spatial variability of E. coli across the stream cross-section is high and a single grab sample may not be able to provide adequate representation of E. coli concentrations in sediment without substantial error. The findings provide insight for designing E. coli monitoring projects and promote the awareness of unconventional sources of microbiological water quality impairment which are often overlooked.

Decay Rate of Escherichia coli in a Mountainous Tropical Headwater Wetland

Surface water contamination by pathogen bacteria remains a threat to public health in the rural areas of developing countries. Fecal indicator bacteria (FIB) like Escherichia coli (E. coli) are widely used to assess water contamination, but their behavior in tropical ecosystems is poorly documented. Our study focused on headwater wetlands which are likely to play a key role in stream water purification of fecal pollutants. Our main objectives were to: (i) evaluate decay rates (k) of the total, particle-attached and free-living E. coli; (ii) quantify the relative importance of solar radiation exposition and suspended particles deposition on k; and (iii) investigate E. coli survival in the deposited sediment. We installed and monitored 12 mesocosms, 4500 mL each, across the main headwater wetland of the Houay Pano catchment, northern Lao People’s Democratic Republic (Lao PDR), for 8 days. The four treatments with triplicates were: sediment deposition-light (DL); sediment deposition-dark (DD); sediment resuspension-light (RL); and sediment resuspension-dark (RD). Particle-attached bacteria predominated in all mesocosms (97 ± 6%). Decay rates ranged from 1.43 ± 0.15 to 1.17 ± 0.13 day−1 for DL and DD treatments, and from 0.50 ± 0.15 to −0.14 ± 0.37 day−1 for RL and RD treatments. Deposition processes accounted for an average of 92% of E. coli stock reduction, while solar radiation accounted for around 2% over the experiment duration. The sampling of E. coli by temporary resuspension of the deposited sediment showed k values close to zero, suggesting potential survival or even growth of bacteria in the sediment. The present findings may help parameterizing hydrological and water quality models in a tropical context.

Pathogen and Surrogate Survival in Relation to Fecal Indicator Bacteria in Freshwater Mesocosms

The microbial quality of agricultural water for fresh produce production is determined by the presence of the fecal indicator bacterium (FIB) Escherichia coli, despite poor correlations with pathogen presence. Additional FIB, such as enterococci, have been utilized for assessing water quality. The study objective was to determine the survival times (first time to detect zero or censored) of FIB (E. coli and enterococci), surrogates (Listeria innocua, Listeria seeligeri, Salmonella enterica serovar Typhimurium, and PRD1), and pathogens (four strains each of pathogenic E. coli and Listeria monocytogenes and five Salmonella serovars) simultaneously inoculated in freshwater mesocosms exposed to diel and seasonal variations. Six separate mesocosm experiments were conducted for ≤28 days each season, with samples (sediment/water) collected each day for the first 7 days and weekly thereafter. Microorganisms survived significantly longer in sediment than in water (hazard ratio [HR] for water/sediment is 2.2; 95% confidence interval [CI], 1.79 to 2.71). Also, FIB E. coli survived significantly longer than FIB enterococcus (HR for enterococci/E. coli is 12.9 [95% CI, 8.18 to 20.37]) after adjusting for the sediment/water and lake/river effects. Differences in the area under the curve (calculated from log CFU or PFU over time) were used to assess pathogen and surrogate survival in relation to FIB. Despite sample type (sediment/water) and seasonal influences, survival rates of pathogenic Salmonella serovars were similar to those of FIB E. coli, and survival rates of L. monocytogenes and pathogenic E. coli were similar to those of FIB enterococci. Further investigation of microbial survival in water and sediment is needed to determine which surrogates are best suited to assess pathogen survival in agricultural water used in irrigation water for fresh produce. IMPORTANCE Contamination of fresh produce via agricultural water is well established. This research demonstrates that survival of fecal indicator bacteria, pathogenic microorganisms, and other bacterial and viral surrogates in freshwater differs by sample type (sediment/water) and season. Our work highlights potential risks associated with pathogen accumulation and survival in sediment and the possibility for resuspension and contamination of agricultural water used in fresh produce production. Specifically, a greater microbial persistence in sediments than in water over time was observed, along with differences in survival among microorganisms in relation to the fecal indicator bacteria E. coli and enterococci. Previous studies compared data among microbial groups in different environments. Conversely, fecal indicator bacteria, surrogates, and pathogenic microorganisms were assessed within the same water and sediment mesocosms in the present study during four seasons, better representing the agricultural aquatic environment. These data should be considered when agricultural microbial water quality criteria in fresh produce operations are being determined.

Effects of hydrological regime and land use on in-stream Escherichia coli concentration in the Mekong basin, Lao PDR

In the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination using Escherichia coli as fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extreme E. coli concentrations occurring during the rainy season. The highest E. coli concentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province.

Particle association of Enterococcus sp. increases growth rates and simulated persistence in water columns of varying light attenuation and turbulent diffusivity

Predicting water quality and the human health risks associated with sewage-derived microbes requires understanding the fate and transport of these contaminants. Sewage-derived pathogen risks are typically assessed and monitored by measuring concentrations of fecal indicating bacteria (FIB), like Enterococcus sp. Previous research demonstrated that a high fraction of FIB is particle-associated, which can alter FIB dynamics within secondary water bodies. In this study, we experimentally quantified the effect of particle association on dark, temperature- and light-dependent growth and sinking rates of enterococci. Particle association significantly increased dark growth rates, light-dependent growth rates (i.e. decreased mortality), and sinking rates, relative to free-living enterococci. Simulations using a novel, 1-dimensional model parameterized by these rates indicate greater persistence (T₉₀) for particle-associated enterococci in water bodies across a wide range of diffuse attenuation coefficients of light (K_d) and turbulent diffusivity (D) values. In addition, persistence of both fractions increased in simulated turbid and turbulent waters, compared to clear and/or quiescent conditions. Simulated persistence of both fractions also increased when enterococci discharges occurred later in a diel cycle (towards sunset, as opposed to sunrise), especially for the free-living population, because later discharges under our model conditions allowed both fractions to mix deeper before inactivation via sunlight. Model sensitivity testing revealed that T₉₀ variability was greatest when dark growth rates were altered, suggesting that future empirical studies should focus on quantifying these rates for free-living and particle-associated sewage-derived microbes. Despite greater sensitivity of T₉₀ to variability in dark growth rates, omitting light-dependent growth rates from simulations dramatically influenced T₉₀ values. Our results demonstrate that particle association can increase enterococci persistence in receiving waters and highlight the importance of incorporating particle association in future water quality models.

Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring

In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.

COVID-19 Pandemic Consequences on Coastal Water Quality Using WST Sentinel-3 Data: Case of Tangier, Morocco

The west coast of Tangier, in northern Morocco, has been affected by industrial wastewater discharge that reaches the ocean through the Boukhalef river. Therefore, the Jbila and Sidikacem beaches near to the Boukhalef river mouth have been classified as polluted for many years. With the aim of determining the COVID-19 pandemic consequences on the Tangier coastal environment, a linear model using Sentinel 3 water surface temperature (WST) has been tested in several locations. Data from April 2019 and April 2020, before and during the COVID-19 pandemic related emergency status in Morocco, were compared. The results from April 2019 showed high WST values and consequently, the poorest water quality in the sites closest to the Boukhalef river mouth. On the other hand, the results from April 2020 showed normal WST values and high water quality in the same study area. These results illustrate the usefulness of Sentinel 3 WST for the estimation of bathing water quality on the west coast of Tangier. The study shows the positive impact of the COVID-19 pandemic consequences on the coastal environment quality in the study area and indicates the importance of decreasing the industrial discharge on the west coast of Tangier. The same methodology could be used in decision-making processes and to reduce cost, time and human resources for coastal monitoring systems. We demonstrate the potential of using the Sentinel 3 data for coastal waters monitoring, as well as the need for stricter controls of pollutant discharges into the world’s rivers.

Prevalence of indicator and potential pathogenic bacterial groups in the Chapora bay-estuarine system, Goa, central west coast of India

This paper describes the prevalence of indicator and pathogenic bacterial groups in water and sediments in OSZ-offshore, ISZ-inshore, IEZ-inner estuary, and UEZ-upper estuary along the river Chapora, central west coast of India, which is influenced by anthropogenic inputs. The abundance of indicator bacterial groups such as total coliforms and Escherichia coli-like organisms in water ranged from non-detectable (ND) to 10³ colony-forming units (CFU)/mL. In contrast, their abundance in the sediments was six orders magnitude higher than water (ND to 10⁹ CFU/g). The abundance of potential pathogenic bacteria in water and sediment samples ranged from ND to 10³ CFU/mL and from ND to 10⁹ CFU/g respectively, with Shigella-like organisms (SHLO) being the most abundant. In the surface waters, SHLO and Pseudomonas aeruginosa-like organisms (PALO) and in bottom waters, Vibrio parahaemolyticus-like organism and PALO increased progressively from OSZ to UEZ. In contrast, Proteus/Klebsiella-like organisms (PKLO) showed a reverse trend. Amongst all four zones, IEZ was the most contaminated in terms of the higher abundance of indicator and potential pathogenic bacterial populations as corroborated by significantly lower water quality index value. Principal component analysis performed using physico-chemical variables and bacterial groups to reduce data set variability revealed that a different set of parameters contributed differently to the total variation in each zone. Considering the eco-sensitivity of the river Chapora, the results of the present study call for precautionary measures to minimize the degree of anthropogenic inputs.

Marine sediment toxicity: A focus on micro- and mesocosms towards remediation

Micro- and/or mesocosms are experimental tools bringing ecologically relevant components of the natural environment under controlled conditions closest to the real world, without losing the advantage of reliable reference conditions and replications, providing a link between laboratory studies and filed studies in natural environments. Here, for the first time, a formal comparison of different types of mesocosm applied to the study of marine contaminants is offered, considering that pollution of coastal areas represented a major concern in the last decades because of the abundance of discharged toxic substances. In particular, the structural characteristics of micro- and mesocosms (m-cosms) used to study marine contaminated sediments were reviewed, focusing on their advantages/disadvantages. Their potentiality to investigate sediment remediation have been discussed, offering new perspective on how the use of m-cosms can be useful for the development of practical application in the development of solutions for contaminated sediment management in the contaminated marine environment.

Differential Transport of Escherichia coli Isolates Compared to Abiotic Tracers in a Karst Aquifer

Lack of filtration and rapid transport of groundwater and particulate matter make karst aquifers susceptible to bacterial contamination. This study utilized quantitative polymerase chain reaction (qPCR) to examine the transport and attenuation of two nonvirulent isolates of Escherichia coli (E. coli) in relation to traditional groundwater tracers (rhodamine WT dye and 1-µm diameter latex microspheres) in a karst-conduit aquifer in central Kentucky. Bacterial isolates were labeled with stable isotopes (¹⁵ N and ¹³ C). All tracers were detected more than 6 km downstream from the injection site and demonstrated overlapping breakthrough curves, with differential transport observed between the two bacterial strains. The E. coli isolate containing the kps gene (low attachment) arrived at sampling sites 1.25 to 36 h prior to the bacterial isolate containing the iha gene (high attachment) and was detected in samples collected following storm events in which the iha isolate was not detected. The storage potential of contaminants within karst systems was demonstrated by the remobilization of all tracers during storm events more than 1 month after injection. Bacteria-sized microspheres were more easily remobilized during periods of increased discharge compared to other tracers. The study demonstrated that molecular biology techniques such as qPCR can be utilized as a sensitive analysis of bacterial tracers in karst aquifers and may prove to be a more sensitive analytical technique than stable isotope analysis for field-scale traces.

Vancomycin resistance plasmids affect persistence of Enterococcus faecium in water

Vancomycin resistant enterococci (VRE) cause 20,000 infections annually in the United States, most of which are nosocomial. Recent findings of VRE in sewage-contaminated surface waters demonstrate an alternate route of human exposure, and a possible setting for horizontal gene exchange facilitated by plasmids and other mobile genetic elements. Maintenance of antibiotic resistance genes and proteins may, however, present a fitness cost in the absence of selective pressure, particularly in habitats such as environmental waters that are not optimal for gut-associated bacteria. Nutrient levels, which are transiently elevated following sewage spills, may also affect survival. We tested the hypotheses that nutrients and/or plasmids conferring vancomycin resistance affect Enterococcus faecium survival in river water by measuring decay of strains that differed only by their plasmid, under natural and augmented nutrient conditions. In natural river water, decay rate (log₁₀ reduction) correlated directly with plasmid size; however, plasmid presence and size had no effect on decay rate when nutrients levels were augmented. Under natural nutrient levels, the vancomycin-resistant strain with the largest plasmid (200 kb) decayed significantly more rapidly than the plasmid-less, susceptible parent strain, in contrast to similar decay rates among strains under augmented nutrient conditions. This work is among the first to show that plasmids conferring antibiotic resistance affect fitness of Enterococcus species in secondary habitats such as surface water. The nutrient-dependent nature of the fitness cost suggests that conveyance of VRE to environmental waters in nutrient-rich sewage may prolong survival of these pathogens, providing greater opportunity for host infection and/or horizontal gene transfer.

Persistence and Decay of Fecal Microbiota in Aquatic Habitats

Fecal microorganisms can enter water bodies in diverse ways, including runoff, sewage discharge, and direct fecal deposition. Once in water, the microorganisms experience conditions that are very different from intestinal habitats. The transition from host to aquatic environment may lead to rapid inactivation, some degree of persistence, or growth. Microorganisms may remain planktonic, be deposited in sediment, wash up on beaches, or attach to aquatic vegetation. Each of these habitats offers a panoply of different stressors or advantages, including UV light exposure, temperature fluctuations, salinity, nutrient availability, and biotic interactions with the indigenous microbiota (e.g., predation and/or competition). The host sources of fecal microorganisms are likewise numerous, including wildlife, pets, livestock, and humans. Most of these microorganisms are unlikely to affect human health, but certain taxa can cause waterborne disease. Others signal increased probability of pathogen presence, e.g., the fecal indicator bacteria Escherichia coli and enterococci and bacteriophages, or act as fecal source identifiers (microbial source tracking markers). The effects of environmental factors on decay are frequently inconsistent across microbial species, fecal sources, and measurement strategies (e.g., culture versus molecular). Therefore, broad generalizations about the fate of fecal microorganisms in aquatic environments are problematic, compromising efforts to predict microbial decay and health risk from contamination events. This review summarizes the recent literature on decay of fecal microorganisms in aquatic environments, recognizes defensible generalizations, and identifies knowledge gaps that may provide particularly fruitful avenues for obtaining a better understanding of the fates of these organisms in aquatic environments.

Modelling the effects of physicochemical variables and anthropogenic activities as ecological drivers of Plesiomonas shigelloides distribution and freshwaters quality

Spatio-temporal distribution of pathogens in freshwater is driven by environmental variables (EVs), natural, and human-induced activities and the spread of infections and disease outbreaks are triggered significantly by these processes. The role of EVs and anthropogenic activities on the distribution of Plesiomonas shigelloides is not well understood; hence this study aimed at modelling the effects of EVs and anthropogenic gradients on the densities of Plesiomonas in freshwaters and freshwater quality. Three freshwaters were sampled from February to December 2017. The EVs and Plesiomonas densities of the freshwaters were determined using standard techniques, while partial least square path modelling and correlation analysis were performed on the data collected. Factors underpinning the quality of the freshwaters were identified through principal component analysis (PCA). Most EVs fell within the bounds of recommended permissible limits except turbidity, TSS, salinity and TDS. Results revealed a significant increase of Plesiomonas densities with an increase in the magnitude of path coefficients and intensities of anthropogenic activities along the freshwaters. The distribution of Plesiomonas correlated with temperature (r = 0.69, p < 0.01), TSS (r = 0.30, p < 0.01), TBS (r = 0.28, p < 0.01), and BOD (r = 0.39, p < 0.01). Similarly, a significant correlation existed between conductivity and TDS (r = 0.97, p < 0.01) and salinity (r = 0.99, p < 0.01). Network analysis of EVs identified three closed networks essential for freshwaters quality and Plesiomonas distribution with nodes of variables under synergistic latent influences. Overall, PCA identified four drivers of the freshwater quality and in part, Plesiomonas density; namely, nutrient loading; thermal and organic pollutions, aesthetic pollution, and pH modulators. Higher component score indicated a greater impact of nutrient loading on the freshwater quality. The study concluded that Plesiomonas distribution is largely shaped by anthropogenic gradients and EVs in rivers, and these may play a major role in its dissemination along freshwater milieus.

Assessing Risk of E. coli Resuspension from Intertidal Estuarine Sediments: Implications for Water Quality

Estuarine sediments are a reservoir for faecal bacteria, such as E. coli, where they reside at greater concentrations and for longer periods than in the overlying water. Faecal bacteria in sediments do not usually pose significant risk to human health until resuspended into the water column, where transmission routes to humans are facilitated. The erosion resistance and corresponding E. coli loading of intertidal estuarine sediments was monitored in two Scottish estuaries to identify sediments that posed a risk of resuspending large amounts of E. coli. In addition, models were constructed in an attempt to identify sediment characteristics leading to higher erosion resistance. Sediments that exhibited low erosion resistance and a high E. coli loading occurred in the upper- and mid-reaches of the estuaries where sediments had higher organic content and smaller particle sizes, and arose predominantly during winter and autumn, with some incidences during summer. Models using sediment characteristics explained 57.2% and 35.7% of sediment shear strength and surface stability variance respectively, with organic matter content and season being important factors for both. However large proportions of the variance remained unexplained. Sediments that posed a risk of resuspending high amounts of faecal bacteria could be characterised by season and sediment type, and this should be considered in the future modelling of bathing water quality.

Depth-Dependent Response of Fecal Indicator Bacteria in Sediments to Changes in Water Column Nutrient Levels

Concentrations of in bottom sediments can influence the assessment of microbial stream water quality. Runoff events bring nutrients to streams that can support the growth of in sediments. The objective of this work was to evaluate depth-dependent changes in populations after nutrients are introduced to the water column. Bovine feces were collected fresh and mixed into sediment. Studies were performed in a microcosm system with continuous flow of synthetic stream water over inoculated sediment. Dilutions of autoclaved bovine manure were added to water on Day 16 at two concentrations, and KBr tracer was introduced into the water column to evaluate ion diffusion. Concentrations of , total coliforms, and total aerobic heterotrophic bacteria, along with orthophosphate-P and ammonium N, were monitored in water and sediment for 32 d. Sediment samples were analyzed in 0- to 1-cm and 1- to 3-cm sectioned depths. Concentrations of and total coliforms in top sediments were approximately one order of magnitude greater than in bottom sediments throughout the experiment. Introduction of nutrients to the water column triggered an increase of nutrient levels in both top and bottom sediments and increased concentrations of bacteria in the water. However, the added nutrients had a limited effect on in sediment where bacterial inactivation continued. Vertical gradients of concentrations in sediments persisted during the inactivation periods both before and after nutrient addition to the water column.

Differential decay and prediction of persistence of Enterococcus spp. and Escherichia coli culturable cells and molecular markers in freshwater and seawater environments

To quantify the impact of fecal pollution on the microbiological bathing water quality, predictive modeling is being increasingly used in which the decay rate of the fecal indicators plays an important role. The decay of sewage-sourced enterococci and Escherichia coli culturable cells and their associated molecular markers (16SrRNA) quantified by Quantitative Reverse transcription PCR were measured in controlled microcosms as well in in situ conditions using different water types, from marine waters to fresh waters with intermediate salinity. All bacterial decays were fitted to a first order decay model. In the laboratory study, the light radiation was the most influent factor affecting E. coli and enterococci survival by culture methods although environmental conditions weakly impacted the decay of molecular markers. The results also indicated differential persistence of genetic markers and culturable organisms of fecal indicator bacteria in different water systems. For each bacteria indicator and analytical method, four equations were obtained to predict the time required to have a 90% reduction (T90) according irradiance, salinity and temperature parameters. The weighted model RMSE (Root Mean Square Error) calculated for all field experiments showed that quantification obtained with the equations defined by laboratory-based study compared reasonably well with in-situ observed quantification (0.4 and 0.2 log by standard culture methods for E. coli and Enterococcus spp. and 0.6 and 0.3 log by RT-qPCR for E. coli and Enterococcus spp. respectively). The modeling tool can be used to predict the presence of fecal pollution in marine and fresh waters in combination with either culture based- or rapid molecular methods.

Determination of Bathing Water Quality Using Thermal Images Landsat 8 on the West Coast of Tangier: Preliminary Results

Bathing water quality has been monitored in the west coast of Tangier, Morocco due to increased urban and industrial discharge through the Boukhalef river, using in-situ bacteriological measurements which demand high economical and temporal costs. In this study, Landsat 8 Thermal Infrared Sensor (TIRS) images were used as an alternative to the classical method, for determining bathing water quality to help decision makers obtain up-to-date and cost-effective information for coastal environment protection. For this purpose, during spring and summer 2017, seven sampling points were examined in terms of bacteriological parameters: Total Coliforms (TC), Faecal Coliforms (FC), Intestinal Enterococci (IE) and Escherichia coli (E. coli). Also, a spatial-temporal analysis was performed in this temporal window to detect temperature anomalies and their spatial distribution along the coastal bathing area. In addition, a relationship between in-situ bacteriological parameter measurements and temperature from satellite images was analyzed. The results of the water temperature distribution showed the highest values next to the Boukhalef river mouth, as well as the poorest water quality according to in-situ measurements, while lower values and better water quality status were observed moving away from the Boukhalef river mouth. The relationship between water temperature and bacterial concentration showed a high correlation coefficient (R2 = 0.85). Consequently, the model development approaches used may be useful in estimating bacterial concentration in coastal bathing areas and can serve to create a monitoring system to support decision makers in the protection actions of the coast.

Patterns of sediment-associated fecal indicator bacteria in an urban estuary: Benthic-pelagic coupling and implications for shoreline water quality

Estuarine and coastal waterways are commonly monitored for fecal and sewage contamination to protect recreator health and ecosystem functions. Such monitoring programs commonly rely on cultivation-based counts of fecal indicator bacteria (FIB) in water column samples. Recent studies demonstrate that sediments and beach sands can be heavily colonized by FIB, and that settling and resuspension of colonized particles may significantly influence the distribution of FIB in the water column. However, measurements of sediment FIB are rarely incorporated into monitoring programs, and geographic surveys of sediment FIB are uncommon. In this study, the distribution of FIB and the extent of benthic-pelagic FIB coupling were examined in the urbanized, lower Hudson River Estuary. Using cultivation-based enumeration, two commonly-measured FIB, enterococci and Escherichia coli, were widely distributed in both sediment and water, and were positively correlated with each other. The taxonomic identity of FIB isolates from water and sediment was confirmed by DNA sequencing. The geometric mean of FIB concentration in sediment was correlated with both the geometric mean of FIB in water samples from the same locations and with sediment organic carbon. These two positive associations likely reflect water as the FIB source for underlying sediments, and longer FIB persistence in the sediments compared to the water, respectively. The relative representation of other fecal associated bacterial genera in sediment, determined by 16S rRNA gene sequencing, increased with the sequence representation of the two FIB, supporting the value of these FIB for assessing sediment contamination. Experimental resuspension of sediment increased shoreline water column FIB concentrations, which may explain why shoreline water samples had higher average FIB concentrations than samples collected nearby but further from shore. In combination, these results demonstrate extensive benthic-pelagic coupling of FIB in an urbanized estuary and highlight the importance of sediment FIB distribution and ecology when interpreting water quality monitoring data.

The Environmental Impact of Cattle Access to Watercourses: A Review

The degradation of freshwater resources and loss of freshwater biodiversity by anthropogenic activities, including agriculture, are of major global concern. Together with diffuse pollutants, point sources, such as where cattle have direct access to riparian margins and watercourses, can potentially present significant environmental challenges. These can include impacts on stream morphology, increased sedimentation, nutrient additions, microbial contamination, and impacts on aquatic biota. Mitigation measures aimed at reducing these frequently include reducing the amount of time cattle spend in riparian margins and watercourses. This is often accomplished through the provision of an alternative water supply and grazing management, or even cattle exclusion measures. Although a number of studies refer to potential negative impacts, there has been little attempt to review previous research on this topic. The key aim of this paper is to collate and review these disparate studies, as well as those relating to the effectiveness of mitigation measures. Although it is difficult to draw generalizations from studies due to the inherent variability between and within catchments, evidence pertaining to impacts in relation to sedimentation, pathogens, and riparian margin vegetation were strong. Conclusions in relation to impacts on stream morphology and nutrient parameters were less clear, whereas studies on responses of macroinvertebrate communities were particularly variable, with differences due to cattle access difficult to separate from catchment scale effects. A greater understanding of the impact of cattle access on watercourses under varying conditions will help inform policymakers on the cost effectiveness of existing management criteria and will help in revising existing measures.

Rapid Colorimetric Detection of Bacterial Species through the Capture of Gold Nanoparticles by Chimeric Phages

Rapid, inexpensive, and sensitive detection of bacterial pathogens is an important goal for several aspects of human health and safety. We present a simple strategy for detecting a variety of bacterial species based on the interaction between bacterial cells and the viruses that infect them (phages). We engineer phage M13 to display the receptor-binding protein from a phage that naturally targets the desired bacteria. Thiolation of the engineered phages allows the binding of gold nanoparticles, which aggregate on the phages and act as a signal amplifier, resulting in a visible color change due to alteration of surface plasmon resonance properties. We demonstrate the detection of two strains of Escherichia coli, the human pathogens Pseudomonas aeruginosa and Vibrio cholerae, and two strains of the plant pathogen Xanthomonas campestris. The assay can detect ∼100 cells with no cross-reactivity found among the Gram-negative bacterial species tested here. The assay can be performed in less than an hour and is robust to different media, including seawater and human serum. This strategy combines highly evolved biological materials with the optical properties of gold nanoparticles to achieve the simple, sensitive, and specific detection of bacterial species.

The putative functions of lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment

Escherichia coli colonizes various body parts of animal hosts as a commensal and a pathogen. It can also persist in the external environment in the absence of fecal pollution. It remains unclear how this species has evolved to adapt to such contrasting habitats. Lysogeny plays pivotal roles in the diversification of the phenotypic and ecologic characters of E. coli as a symbiont. We hypothesized that lysogeny could also confer fitness to survival in the external environment. To test this hypothesis, we used the induced phages of an E. coli strain originating from marine sediment to infect a fecal E. coli strain to obtain an isogenic lysogen of the latter. The three strains were tested for survivorship in microcosms of seawater, marine sediment and sediment interstitial water as well as swimming motility, glycogen accumulation, biofilm formation, substrate utilization and stress resistance. The results indicate that lysogenic infection led to tractable changes in many of the ecophysiological attributes tested. Particularly, the lysogen had better survivorship in the microcosms and had a substrate utilization profile resembling the sediment strain more than the wild type fecal strain. Our findings provide new insights into the understanding of how E. coli survives in the natural environment.

River water analysis using a multiparametric approach: Portuguese river as a case study

The Ave River in northern Portugal has a history of riverbanks and water quality degradation. The river water quality was assessed by physicochemical, biological (macroinvertebrates) and microbiological (Enterococcus spp. and Escherichia coli) parameters in six locations (A-F, point A being the nearest to the source) throughout its course during a year. Epilithic biofilms were studied through polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Antimicrobial susceptibility testing helped with selecting isolates (n = 149 E. coli and n = 86 enterococci) for further genetic characterization. Pursuant to physicochemical and macroinvertebrates-based parameters, the river water was of reasonable quality according to European legislation (Directive 2000/60/EC). However, the microbiological analysis showed increased fecal contamination downstream from point C. At point D, four carbapenem-resistant E. coli isolates were recovered. Paradoxically, point D was classified as a point of 'Good Water Quality' according to macroinvertebrates results. Point F presented the highest contamination level and incidence of multidrug-resistant (MDR) isolates in the water column (13 MDR enterococci out of 39 and 33 MDR E. coli out of 97). Epilithic biofilms showed higher diversity in pristine points (A and B). Thus, biological and microbiological parameters used to assess the water quality led to divergent results; an outcome that reinforces the need for a holistic evaluation.

Assessment of Bacterial Accumulation and Environmental Factors in Sentinel Oysters and Estuarine Water Quality from the Phang Nga Estuary Area in Thailand

This study characterized microbiological and chemical contamination of oyster meat and estuarine water in Phang Nga, Thailand. Pooled oyster meats (n = 144), estuarine waters (n = 96) and environmental parameters were collected from March, 2016 to February, 2017, and assessed for levels of total coliforms (TC), fecal coliforms (FC), Escherichia coli (EC), and Vibrio parahaemolyticus (VP), presence of Salmonella and Shigella and levels of heavy metals (Mn, Pb and Cd). The prevalence of TC, FC and EC were in 99.3%, 94.4% and 93.1% of oyster meat and 94.8%, 79.2%, and 78.1% of water, respectively. The average VP levels was 8.5 × 10⁷ most probable number (MPN)/g oyster. Prevalence of Shigella and Salmonella in the pooled oysters were 7.6% and 30.6%, respectively. The dominant Salmonella serovars were Paratyphi B followed by Seremban, and Kentucky. In contrast, the prevalence of Shigella were 27.1%, but Salmonella was not detected in estuarine water. Factors statistically associated with EC accumulation in oyster were level of FC, 7-day average precipitation, temperature, relative humidity, and presence of Salmonella in the sample. The optimal cutoff value of EC to predict Salmonella in oyster was 420 MPN/g. Results indicate this area has relatively safe levels of heavy metals, whereas bacterial contamination was very high for oysters.

Escherichia coli Concentration as a Function of Stream Order and Watershed Size

This research examines the relationship of concentrations to stream order and watershed size and considers the implications on water quality standards. To assess geospatial effects, data were obtained from 743 monitoring stations in the Central Great Plains, Cross Timbers, and South Central Plains ecoregions of Texas and Oklahoma. Median and geometric mean concentrations were analyzed for correlation with stream order and watershed size at each site. Comparison of the three ecoregions revealed concentrations were highest in the westernmost Central Great Plains and lowest in the easternmost South Central Plains. Similarly, the strength of 's correlation with stream order and watershed area decreased with ecoregion moving west to east. Thus, incorporating ecoregion approaches when defining stream water quality standards is supported. Analysis showed no significant relationship of stream order or watershed size to concentrations in least-impacted watersheds (i.e., watersheds with minimal wastewater discharge and urbanization). Conversely, analysis of data from all sites showed a weak negative relationship between concentration and stream order and watershed size, with concentration generally decreasing with increasing stream order and watershed size. However, variability in smaller watersheds and lower-order streams supports continued use of site-specific studies to determine appropriate standards. Three-parameter exponential models provided an approach to estimate concentrations using Shreve stream order and watershed area and identify outlier streams potentially affected by anthropogenic activities where further investigation or remediation may be warranted.

Alteration of host-pathogen interactions in the wake of climate change - Increasing risk for shellfish associated infections?

The potential for climate-related spread of infectious diseases through marine systems has been highlighted in several reports. With this review we want to draw attention to less recognized mechanisms behind vector-borne transmission pathways to humans. We have focused on how the immune systems of edible marine shellfish, the blue mussels and Norway lobsters, are affected by climate related environmental stressors. Future ocean acidification (OA) and warming due to climate change constitute a gradually increasing persistent stress with negative trade-off for many organisms. In addition, the stress of recurrent hypoxia, inducing high levels of bioavailable manganese (Mn) is likely to increase in line with climate change. We summarized that OA, hypoxia and elevated levels of Mn did have an overall negative effect on immunity, in some cases also with synergistic effects. On the other hand, moderate increase in temperature seems to have a stimulating effect on antimicrobial activity and may in a future warming scenario counteract the negative effects. However, rising sea surface temperature and climate events causing high land run-off promote the abundance of naturally occurring pathogenic Vibrio and will in addition, bring enteric pathogens which are circulating in society into coastal waters. Moreover, the observed impairments of the immune defense enhance the persistence and occurrence of pathogens in shellfish. This may increase the risk for direct transmission of pathogens to consumers. It is thus essential that in the wake of climate change, sanitary control of coastal waters and seafood must recognize and adapt to the expected alteration of host-pathogen interactions.

Use of Molecular Markers to Compare Escherichia coli Transport with Traditional Groundwater Tracers in Epikarst

Bacterial contamination of karst aquifers is a global concern as water quality deteriorates in the face of decreasing water security. Traditional abiotic groundwater tracers, which do not exhibit surface properties similar to bacteria, may not be good proxies for risk assessment of bacterial transport in karst environments. This study examined the transport and attenuation of two isolates of in relation to traditional groundwater tracers (rhodamine WT dye and 1-μm-diam. latex microspheres) through ∼30 m of epikarst in western Kentucky. Differential movement of the four tracers was observed, with tracer behavior dependent on flow conditions. Dye arrived at the sampling site prior to particulates. Molecular biology techniques successfully detected bacteria in the cave and showed attenuation was greater for a bacterial isolate with high attachment efficiency compared with an isolate known to have low attachment efficiency. Microspheres were first detected simultaneously with the low-attachment isolate but attained maximum concentrations during increases in discharge >11 d post-injection. Bacteria were remobilized by storm events >60 d after injection, illustrating the storage capacity of epikarst with regard to potential contaminants. The two bacterial strains were not transported at the same rate within the epikarst, showing breakthroughs during differing storm events and illustrating the importance of cell surface chemistry in the prediction of microorganism movement. Moreover, this study has shown that molecular analysis can be successfully used to target, quantify, and track introduced microbial tracers in karst terrains.

Genetic relatedness of faecal coliforms and enterococci bacteria isolated from water and sediments of the Apies River, Gauteng, South Africa

To date, the microbiological quality of river sediments and its impact on water resources are not included in the water quality monitoring assessment. Therefore, the aim of this study was to establish genetic relatedness between faecal coliforms and enterococci isolated from the river water and riverbed sediments of Apies River to better understand the genetic similarity of microorganisms between the sediment and water phases. Indicator bacteria were subjected to a molecular study, which consisted of PCR amplification and sequence analysis of the 16S rRNA and 23S rRNA gene using specific primers for faecal coliforms and enterococci, respectively. Results revealed that the Apies River had high faecal pollution levels with enterococci showing low to moderate correlation coefficient (r² values ranged from 0.2605 to 0.7499) compared to the faecal coliforms which showed zero to low correlation (r² values ranged from 0.0027 to 0.1407) indicating that enterococci may be better indicator than faecal coliforms for detecting faecal contamination in riverbed sediments. The phylogenetic tree of faecal coliforms revealed a 98% homology among their nucleotide sequences confirming the close genetic relatedness between river water and riverbed sediment isolates. The phylogenetic tree of the enterococci showed that Enterococcus faecalis and Enterococcus faecium are the predominant species found in both river water and riverbed sediments with bootstrap values of ≥99%. A high degree of genetic relatedness between sediment and water isolates indicated a possible common ancestry and transmission pathway. We recommend the microbial monitoring of riverbed sediments as it harbours more diverse microbial community and once resuspended may cause health and environmental problems.

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation

The CrbS/R system is a two-component signal transduction system that regulates acetate utilization in Vibrio cholerae, P. aeruginosa, and P. entomophila. CrbS is a hybrid histidine kinase that belongs to a recently identified family, in which the signaling domain is fused to an SLC5 solute symporter domain through aSTAC domain. Upon activation by CrbS, CrbR activates transcription of the acs gene, which encodes an acetyl-CoA synthase (ACS), and the actP gene, which encodes an acetate/solute symporter. In this work, we characterized the CrbS/R system in Pseudomonas fluorescens SBW25. Through the quantitative proteome analysis of different mutants, we were able to identify a new set of genes under its control, which play an important role during growth on acetate. These results led us to the identification of a conserved DNA motif in the putative promoter region of acetate-utilization genes in the Gammaproteobacteria that is essential for the CrbR-mediated transcriptional activation of genes under acetate-utilizing conditions. Finally, we took advantage of the existence of a second SLC5-containing two-component signal transduction system in P. fluorescens, CbrA/B, to demonstrate that the activation of the response regulator by the histidine kinase is not dependent on substrate transport through the SLC5 domain.

Microcosms for evaluating microbial indicator persistence and mobilization in fluvial sediments during rainfall events

Mediterranean rivers, which are subject to long, dry periods and heavy rainfall events, could be particularly useful for understanding future climate scenarios. This study generated microcosms that mimicked riverbank sediment resuspension into the water of a typical Mediterranean river as a consequence of heavy rainfall. The mobilization and inactivation of six fecal pollution indicators and microbial source tracking markers were evaluated. The T₉₀ values in the sediments were: 4 days for sorbitol-fermenting Bifidobacterium, 11 days for culturable E. coli, 36 days for bacteriophages infecting Bacteroides thetaiotaomicron strain GA17 and more than 42 days for qPCR-detected E. coli, somatic coliphages and sulfite-reducing clostridia spores. Bacteriophages and bacteria showed different resuspension and sedimentation patterns. The data obtained could be used in predictive models to assess the effects of climate change on surface water quality. Pathogen mobilization into the water column poses a risk for humans, animals and the natural environment, and breaches the One Health approach.

Effect of freshwater sediment characteristics on the persistence of fecal indicator bacteria and genetic markers within a Southern California watershed

In this study, the aging of culturable FIB and DNA representing genetic markers for Enterococcus spp. (ENT1A), general Bacteroides (GB3), and human-associated Bacteroides (HF183) in freshwater sediments was evaluated. Freshwater sediment was collected from four different sites within the upper and lower reach of the Topanga Creek Watershed and two additional comparator sites within the Santa Monica Bay, for a total of six sites. Untreated (ambient) and oven-dried (reduced microbiota) sediment was inoculated with 5% sewage and artificial freshwater. Microcosms were held for a 21-day period and sampled on day 0, 1, 3, 5, 7, 12, and 21. There were substantial differences in decay among the sediments tested, and decay rates were related to sediment characteristics. In the ambient sediments, smaller particle size and higher levels of organic matter and nutrients (nitrogen and phosphorus) were associated with increased persistence of the GB3 marker and culturable Escherichia coli (cEC) and enterococci (cENT). The HF183 marker exhibited decay rates of -0.50 to -0.96 day^-1, which was 2-5 times faster in certain ambient sediments than decay of culturable FIB and the ENT1A and GB3 markers. The ENT1A and GB3 markers decayed at rates of between -0.07 and -0.28 and -0.10 to -0.44 day^-1, and cEC and cENT decayed at rates of between -0.22 and -0.81 and -0.03 and -0.40 day^-1, respectively. In the oven-dried sediments, increased persistence of all indicators and potential for limited growth of culturable FIB and the GB3 and ENT1A markers was observed. A simplified two-box model using the HF183 marker and cENT decay rates generated from the microcosm experiments was applied to two reaches within the Topanga Canyon watershed in order to provide context for the variability in decay rates observed. The model predicted lower ambient concentrations of enterococci in sediment in the upper (90 MPN g^-1) versus lower Topanga watershed (530 MPN g^-1) and low ambient levels of the HF183 marker (below the LLOQ) in sediments in both lower and upper watersheds. It is important to consider the variability in the persistence of genetic markers and FIB when evaluating indicators of fecal contamination in sediments, even within one watershed.

Riverbed Sediments as Reservoirs of Multiple Vibrio cholerae Virulence-Associated Genes: A Potential Trigger for Cholera Outbreaks in Developing Countries

Africa remains the most cholera stricken continent in the world as many people lacking access to safe drinking water rely mostly on polluted rivers as their main water sources. However, studies in these countries investigating the presence of Vibrio cholerae in aquatic environments have paid little attention to bed sediments. Also, information on the presence of virulence-associated genes (VAGs) in environmental ctx-negative V. cholerae strains in this region is lacking. Thus, we investigated the presence of V. cholerae VAGs in water and riverbed sediment of the Apies River, South Africa. Altogether, 120 samples (60 water and 60 sediment samples) collected from ten sites on the river (January and February 2014) were analysed using PCR. Of the 120 samples, 37 sediment and 31 water samples were positive for at least one of the genes investigated. The haemolysin gene (hlyA) was the most isolated gene. The cholera toxin (ctxAB) and non-O1 heat-stable (stn/sto) genes were not detected. Genes were frequently detected at sites influenced by human activities. Thus, identification of V. cholerae VAGs in sediments suggests the possible presence of V. cholerae and identifies sediments of the Apies River as a reservoir for potentially pathogenic V. cholerae with possible public health implications.

Microbial Remobilisation on Riverbed Sediment Disturbance in Experimental Flumes and a Human-Impacted River: Implication for Water Resource Management and Public Health in Developing Sub-Saharan African Countries

Resuspension of sediment-borne microorganisms (including pathogens) into the water column could increase the health risk for those using river water for different purposes. In the present work, we (1) investigated the effect of sediment disturbance on microbial resuspension from riverbed sediments in laboratory flow-chambers and in the Apies River, Gauteng, South Africa; and (2) estimated flow conditions for sediment-borne microorganism entrainment/resuspension in the river. For mechanical disturbance, the top 2 cm of the sediment in flow-chambers was manually stirred. Simulating sudden discharge into the river, water (3 L) was poured within 30 s into the chambers at a 45° angle to the chamber width. In the field, sediment was disturbed by raking the riverbed and by cows crossing in the river. Water samples before and after sediment disturbance were analysed for Escherichia coli. Sediment disturbance caused an increase in water E. coli counts by up to 7.9-35.8 times original values. Using Shields criterion, river-flow of 0.15-0.69 m³/s could cause bed particle entrainment; while ~1.57-7.23 m³/s would cause resuspension. Thus, sediment disturbance in the Apies River would resuspend E. coli (and pathogens), with possible negative health implications for communities using such water. Therefore, monitoring surface water bodies should include microbial sediment quality.

Indicator bacteria community in seawater and coastal sediment: the Persian Gulf as a case

BACKGROUND

The aim of present work was to assess the concentration levels as well as vertical distribution of indicator bacteria including total coliform, fecal coliform, Pseudomonas aeruginosa, and Heterotrophic Plate Count (HPC) in the marine environment (seawater and coastal sediments) and evaluate the correlation between indicator bacteria and some physicochemical parameters of surface sediments as well as seawaters.

METHODS

A total number of 48 seawater and sediment samples were taken from 8 stations (each site 6 times with an interval time of 2 weeks) between June and September 2014. Seawater and sediment samples were collected from 30 cm under the surface samples and different sediment depths (0, 4, 7, 10, 15, and 20 cm) respectively, along the Persian Gulf in Bushehr coastal areas.

RESULTS

Based on the results, the average numbers of bacterial indicators including total coliform, fecal coliform, and Pseudomonas aeruginosa as well as HPC in seawater samples were 1238.13, 150.87, 8.22 MPN/100 ml and 1742.91 CFU/ml, respectively, and in sediment samples at different depths (from 0-20 cm) varied between 25 × 10³ to 51.67 × 10³, 5.63 × 10³ to 12.46 × 10³, 17.33 to 65 MPN/100 ml, 36 × 10³ to 147.5 × 10³ CFU/ml, respectively. There were no statistically significant relationships between the indicator organism concentration levels with temperature as well as pH value of seawater. A reverse correlation was found between the level of indicator bacteria and salinity of seawater samples. Also results revealed that the sediment texture influenced abundance of indicators bacteria in sediments. As the concentration levels of indicators bacteria were higher in muddy sediments compare with sandy ones.

CONCLUSION

Result conducted Bushehr coastal sediments constitute a reservoir of indicator bacteria, therefore, whole of the indicators determined were distinguished to be present in higher levels in sediments than in the overlying seawater. It was concluded that the concentration levels of microbial indicators decreased with depth in sediments. Except total coliform, the numbers of other bacteria including fecal coliform, Pseudomonas aeruginosa and HPC bacteria significantly declined in the depth between 10 and 15 cm.

Elucidation of the tidal influence on bacterial populations in a monsoon influenced estuary through simultaneous observations

The influence of tides on bacterial populations in a monsoon influenced tropical estuary was assessed through fine resolution sampling (1 to 3 h) during spring and neap tides from mouth to the freshwater end at four stations during pre-monsoon, monsoon and post-monsoon seasons. Higher abundance of total bacterial count (TBC) in surface water near the river mouth, compared to the upstream, during pre-monsoon was followed by an opposite scenario during the monsoon When seasonally compared, it was during the post-monsoon season when TBC in surface water was highest, with simultaneous decrease in their count in the river sediment. The total viable bacterial count (TVC) was influenced by the depth-wise stratification of salinity, which varied with tidal fluctuation, usually high and low during the neap and spring tides respectively. The abundance of both the autochthonous Vibrio spp. and allochthonous coliform bacteria was influenced by the concentrations of dissolved nutrients and suspended particulate matter (SPM). It is concluded that depending on the interplay of riverine discharge and tidal amplitude, sediment re-suspension mediated increase in SPM significantly regulates bacteria populations in the estuarine water, urging the need of systematic regular monitoring for better prediction of related hazards, including those associated with the rise in pathogenic Vibrio spp. in the changing climatic scenarios.

Presence and survival of culturable Campylobacter spp. and Escherichia coli in a temperate urban estuary

Urban estuaries throughout the world typically contain elevated levels of faecal contamination, the extent of which is generally assessed using faecal indicator organisms (FIO) such as Escherichia coli. This study assesses whether the bacterial FIO, E. coli is a suitable surrogate for Campylobacter spp., in estuaries. The presence and survival dynamics of culturable E. coli and Campylobacter spp. are compared in the water column, bank sediments and bed sediments of the Yarra River estuary (located in Melbourne, Australia). The presence of E. coli did not necessarily indicate detectable levels of Campylobacter spp. in the water column, bed and bank sediments, but the inactivation rates of the two bacteria were similar in the water column. A key finding of the study is that E. coli and Campylobacter spp. can survive for up to 14days in the water column and up to 21days in the bed and bank sediments of the estuary. Preliminary data presented in this study also suggests that the inactivation rates of the two bacteria may be similar in bed and bank sediments. This undermines previous hypotheses that Campylobacter spp. cannot survive outside of its host and indicates that public health risks can persist in aquatic systems for up to three weeks after the initial contamination event.

Competitive Survival of Escherichia coli, Vibrio cholerae, Salmonella typhimurium and Shigella dysenteriae in Riverbed Sediments

Studies on the survival of bacterial enteric pathogens in riverbed sediments have mostly focused on individual organisms. Reports on the competitive survival of these pathogens in riverbed sediments under the same experimental setup are limited. We investigated the survival of Escherichia coli, Salmonella enterica ser. Typhimurium, Vibrio cholerae and Shigella dysenteriae in riverbed sediments of the Apies River. Experiments were performed in flow chambers containing three sediment types and connected to aquarium pumps immersed in river water to maintain continuous water circulation. Each chamber was inoculated with ~10⁷ CFU/mL (final concentration) of each microorganism and kept at 4, 20 and 30 °C. Chambers were sampled on days 0, 1, 2, 7, 14 and 28. At 4 °C, only E. coli and S. typhimurium survived throughout the 28 experimental days. V. cholerae had the shortest survival time at this temperature and was not detected in any of the sediment chambers 24 h after inoculation. S. dysenteriae only survived until day 7. At an increased temperature of 20 °C, only S. dysenteriae was not detected on day 28 of the experiment. At 30 °C, V. cholerae and Salmonella survived longer (28 days) than E. coli (14 days) and S. dysenteriae (4 days). Vibrio cholerae was shown to have the highest T ₉₀ values (32 days) in all sediment types at 20 and 30 °C. We conclude that the sediments of the Apies River present a favourable environment for the survival of indicator and pathogenic bacteria depending on the prevailing temperature.

Watershed Assessment with Beach Microbial Source Tracking and Outcomes of Resulting Gull Management

Total maximum daily load (TMDL) implementation at a southern California beach involved ultraviolet treatment of watershed drainage that provided >97% reduction in fecal indicator bacteria (FIB) concentrations. However, this pollutant control measure did not provide sufficient improvement of beach water quality, prompting further assessment. Investigation included microbial source tracking (MST) for human, gull, and canine fecal sources, monitoring of enterococci and fecal coliform, and measurement of chemical and physical water quality parameters for samples collected from watershed, groundwater, and beach sites, including a beach scour pond and tidal creek. FIB variability remained poorly modeled in regression analysis. However, MST revealed correlations between FIB and gull source tracking markers, leading to recommendations to manage gulls as a pollutant source. Beach conditions were followed for three years after implementation of a best management practice (BMP) to abate gulls using a falconry program for the beach and an upland landfill. The gull abatement BMP was associated with improved beach water quality, and this appears to be the first report of falconry in the context of TMDL implementation. Overall, MST data enabled management action despite an inability to fully model FIB dynamics in the coupled watershed-beach system.

Examining the Colonization and Survival of E. coli from Varying Host Sources in Drainage Basin Sediments and Stormwater

It is widely understood that stormwater drainage has a significant impact on the health of tidal creek systems via regular inputs of runoff from the surrounding watershed. Due to this hydrologic connection, contamination of the upstream drainage basin will have a direct effect on estuaries and tidal creeks that often act as receiving waters. This study focuses on the importance of drainage basin sediments as they enhance the persistence and transport of the fecal indicator bacteria E. coli within a watershed. Experiments presented use microcosm environments with drainage basin sediments and stormwater to investigate E. coli colonization of stagnant waters and to examine the importance of host sources to bacterial survival. A novel method for establishing microcosms using environmental sediments with in situ bacterial populations and sterile overlying waters is used to examine E. coli colonization of the water column in the absence of flow. Colonization of sterile sediment environments also is examined using two common host sources (human and avian). Each experiment uses sediments of varying grain size and organic content to examine the influence of physical characteristics on bacterial prevalence. Results suggest host source of bacteria may be more important to initial bacterial colonization while physical characteristics of drainage basin sediments better explains extended E. coli persistence. Findings also suggest an indirect control of water column bacterial concentration by sediment type and erodibility.

Occurrence of diarrhoeagenic Escherichia coli virulence genes in water and bed sediments of a river used by communities in Gauteng, South Africa

In most developing countries, especially in Southern Africa, little is known about the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes in riverbed sediments. The present study sought to investigate the presence of DEC virulence genes in riverbed sediments of the Apies River, a river used by many communities in Gauteng, South Africa. Water and sediment samples were collected from the river between July and August 2013 (dry season) and also between January and February 2014 (wet season) following standard procedures. Isolation of E. coli was done using the Colilert®-18 Quanti-Tray® 2000 system. DNA was extracted from E. coli isolates using the InstaGene™ matrix from Bio-Rad and used as template DNA for real-time PCR. Water pH, temperature, dissolved oxygen, electrical conductivity and turbidity were measured in situ. Over 59 % of 180 samples analysed were positive for at least one of the seven DEC virulence genes investigated. The eaeA gene was the most isolated gene (29.44 %) while the ipaH gene the least isolated (8.33 %). The ipaH gene (p = 0.012) and the ST gene (stIa, p = 0.0001, and stIb, p = 0.019) were positively correlated with temperature. The detection of diarrhoeagenic E. coli virulence genes in the sediments of the Apies River shows that the sediments of this river might not only be a reservoir of faecal indicator bacteria like E. coli but also pathogenic strains of this bacterium. These organisms could represent a public health risk for poor communities relying on this water source for various purposes such as drinking and recreational use. There is therefore an urgent need to monitor these DEC pathotypes especially in areas without adequate water supplies.

Historical Associations of Molecular Measurements of Escherichia coli and Enterococci to Anthropogenic Activities and Climate Variables in Freshwater Sediment Cores

This study investigated the long-term associations of anthropogenic (sedimentary P, C, and N concentrations, and human population in the watershed), and climatic variables (air temperature, and river discharge) with Escherichia coli uidA and enterococci 23S rRNA concentrations in sediment cores from Anchor Bay (AB) in Lake St. Clair, and near the mouth of the Clinton River (CR), Michigan. Calendar year was estimated from vertical abundances of (137)Cs. The AB and CR cores spanned c.1760-2012 and c.1895-2012, respectively. There were steady state concentrations of enterococci in AB during c.1760-c.1860 and c.1910-c.2003 at ∼0.1 × 10(5) and ∼2.0 × 10(5) cell equivalents (CE) per g-dry wt, respectively. Enterococci concentrations in CR increased toward present day, and ranged from ∼0.03 × 10(5) to 9.9 × 10(5) CE/g-dry wt. The E. coli concentrations in CR and AB increased toward present day, and ranged from 0.14 × 10(7) to 1.7 × 10(7) CE/g-dry wt, and 1.8 × 10(6) to 8.5 × 10(6) CE/g-dry wt, respectively. Enterococci was associated with population and river discharge, while E. coli was associated with population, air temperature, and N and C concentrations (p < 0.05). Sediments retain records of the abundance of fecal indicator bacteria, and offer a way to evaluate responses to increased population, nutrient loading, and environmental policies.

Seasonal variability of faecal indicator bacteria numbers and die-off rates in the Red River basin, North Viet Nam

The Red River is the second largest river in Viet Nam and constitutes the main water source for a large percentage of the population of North Viet Nam. Here we present the results of an annual survey of Escherichia coli (EC) and Total Coliforms (TC) in the Red River basin, North Viet Nam. The objective of this work was to obtain information on faecal indicator bacteria (FIB) numbers over an annual cycle and, secondly, to determine the die-off rates of these bacterial indicators. Monthly observations at 10 stations from July 2013–June 2014 showed that TC and EC reached as high as 39100 cfu (colony forming units) 100 ml⁻¹ and 15300 colonies 100 ml⁻¹, respectively. We observed a significant seasonal difference for TC (p < 0.05) with numbers being higher during the wet season. In contrast, no significant seasonal difference was found for EC. The FIB die-off rates ranged from 0.01 d⁻¹ to a maximum of 1.13 d⁻¹ for EC and from 0.17 d⁻¹ to 1.33 d⁻¹ for TC. Die-off rates were significantly higher for free bacteria than for total (free + particle attached) bacteria, suggesting that particle attachment provided a certain level of protection to FIB in this system.

To swim or not to swim? A disagreement between microbial indicators on beach water quality assessment in Hong Kong

The USEPA and the WHO now advocate the use of enterococci as indicators for marine water quality. This study investigated the outcomes for Hong Kong beach water quality assessment by comparing enterococcus measures with data from the HKEPD's monitoring programme. Six beaches were tested once every 2-3 months from November 2013 to June 2014 in order to identify the most contaminated sites, followed by intensive water sampling in sites found to have the highest enterococci densities (Clear Water Bay Second and Golden) every five to six days for six sampling events over a 30-day period in 2014. The geometric means of enterococci were found to be 124 and 41 cfu/100 mL at Clear Water Bay Second and Golden respectively, indicating that there may be higher risks of illness associated with swimming at both beaches than previously known. Moreover, beach sediments contained higher concentrations of enterococci than water, and warrant further study.