Persistence of fecal indicator bacteria in Santa Monica Bay beach sediments

Using bacterial and mitochondrial DNA markers to assess fecal pollution sources in stream water and sediments of a mixed land-use watershed

AIMS

Although stream bed sediment can be an important reservoir of fecal bacteria and pathogens, it is rarely analyzed when assessing microbial water quality. This study aims to identify fecal contamination sources in stream water and sediment and evaluates the impact of rainfall events on microbial water quality in a mixed land-use watershed.

METHODS AND RESULTS

Quantitative polymerase chain reaction was employed to quantify human-, cattle-, and chicken-associated genetic markers during dry and wet periods in the Middle Tallapoosa watershed in Alabama, USA. Human- and cattle-associated markers were consistently detected in water samples, irrespective of precipitation, whereas chicken-associated markers were predominantly found following significant rainfall events. In the sediment, all markers were detected at higher concentrations but with a lower frequency than in the water. Escherichia coli concentrations in water samples correlated significantly with 2-day antecedent rainfall and streamflow and were substantially lower than in the sediment.

CONCLUSIONS

Humans and cattle were the primary contamination sources in the study area, and runoff from storms and sediment contributed to fecal contamination in the streams.

Characterization of non-O157 enterohemorrhagic Escherichia coli isolated from different sources in Egypt

BACKGROUND

Enterohemorrhagic Escherichia coli (EHEC) O157 is implicated in serious food and water-borne diseases as hemorrhagic colitis (HC), and the potentially fatal hemolytic uremic syndrome (HUS). However, new players of non-O157 EHEC have been implicated in serious infections worldwide. This work aims at analyzing serotype and genotypic-based virulence profile of EHEC local isolates.

METHODS

A total of 335 samples were collected from different sources in Egypt. E. coli was isolated and subjected to serotyping. Non-O157 EHEC isolates were tested for virulence genes using PCR, phenotypic examination, phylogenetic typing, and molecular investigation by ERIC typing and MLST to disclose genetic relatedness of isolates. A heat map was used to identify potential associations between the origin of the isolates, their phenotypic and genotypic characteristics.

RESULTS

A total of 105 out of 335 isolates were identified as E. coli. Surprisingly, 49.5% of these isolates were EHEC, where O111, O91, O26 and O55 were the most prevalent serotypes including 38.46% from stool, 21.15% urine, 23.1% cheese, 9.62% meat products, 3.85% from both yogurt and sewage water. Screening 15 different virulence genes revealed that sheA, stx2 and eae were the most prevalent with abundance rates of 85%, 75% and 36%, respectively. Fifteen profiles of virulence gene association were identified, where the most abundant one was stx2/sheA (19%) followed by stx2/stx2g/sheA/eae (11.5%). Both stx2/sheA/eae and stx2/stx2g/sheA were equally distributed in 9.6% of total isolates. Phylogenetic typing revealed that pathogenic phylogroups B2 and D were detected among clinical isolates only. Forty-six different patterns were detected by ERIC genotyping. MLST resolved three sequence types of ST70, ST120 and ST394. The heat map showed that 21 isolates were of 70% similarity, 9 groups were of 100% clonality.

CONCLUSIONS

The prevalence of non-O157 EHEC pathotype was marginally higher among the food isolates compared to the clinical ones. The endemic ST120 was detected in cheese, necessitating crucial measures to prevent the spread of this clone. Clinical EHEC isolates exhibited a higher score, and combination of virulence genes compared to food and sewage water isolates, thereby posing a significant public health concern.

Vertical stratification and seasonality of fecal indicator bacteria in New York City playground sandboxes

Sandboxes in public play spaces afford a crucial opportunity for urban children to engage in naturalistic play that fosters development of cognitive, social, and motor skills. As open pits, sandboxes in New York City public playgrounds are potentially exposed to fecal inputs from various sources, including wild and domestic animals. A longitudinal study of thirteen sandboxes located in public playgrounds on the east side of Manhattan reveals ubiquity of the fecal indicator bacteria enterococci and Escherichia coli through all seasons. The highest concentrations of bacteria occur in surface sand (n = 42; mean enterococci 230 MPN/g and E. coli 182 MPN/g dry weight), with significantly lower levels at depths below the surface (n = 35; mean enterococci 21 MPN/g and E. coli 12 MPN/g dry weight), a stratification consistent with fecal loading at the surface. Generalized linear mixed models indicate that sand depth (surface vs. underlayers) is the most influential variable affecting bacterial levels (P <0.001 for both enterococci and E. coli), followed by sampling season (P <0.001 for both). Bacterial concentrations do not vary significantly as a function of playground location or ZIP code within the study area. Children's exposure while playing in sandboxes likely reaches 105 enterococci and 104E. coli in a typical play period. Microbial source tracking to identify fecal hosts reveals dog, bird, and human biomarkers in low concentrations. Open sandbox microcosms installed at ground level in the urban environment of Manhattan are fouled by enterococci and E. coli within two weeks, while adjacent closed microcosms exhibit no fecal contamination over a 33-day sampling period. Collectively, our results indicate that increasing the frequency of sand refills and covering sandboxes during times of disuse would be straightforward management strategies to mitigate fecal contamination in playground sandboxes.

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment

Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.

IMPORTANCE

Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.

Investigating Escherichia coli habitat transition from sediments to water in tropical urban lakes

Background

Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.

Methods

This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.

Results

The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g-1, and was about one order higher than in the water column (1 to 2,300 cfu mL-1). The habitat transition rates ranged from 0.03 to 0.41 h-1. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h-1. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.

Discussion

Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.

Mixoplankton and mixotrophy: future research priorities

Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.

Highly variable removal of pathogens, antibiotic resistance genes, conventional fecal indicators and human-associated fecal source markers in a pilot-scale stormwater biofilter operated under realistic stormflow conditions

Green stormwater infrastructure systems, such as biofilters, provide many water quality and other environmental benefits, but their ability to remove human pathogens and antibiotic resistance genes (ARGs) from stormwater runoff is not well documented. In this study, a field scale biofilter in Southern California (USA) was simultaneously evaluated for the breakthrough of a conservative tracer (bromide), conventional fecal indicators, bacterial and viral human-associated fecal source markers (HF183, crAssphage, and PMMoV), ARGs, and bacterial and viral pathogens. When challenged with a 50:50 mixture of untreated sewage and stormwater (to mimic highly contaminated storm flow) the biofilter significantly removed (p < 0.05) 14 of 17 microbial markers and ARGsin descending order of concentration reduction: ermB (2.5 log(base 10) reduction) > Salmonella (2.3) > adenovirus (1.9) > coliphage (1.5) > crAssphage (1.2) > E. coli (1.0) ∼ 16S rRNA genes (1.0) ∼ fecal coliform (1.0) ∼ intl1 (1.0) > Enterococcus (0.9) ∼ MRSA (0.9) ∼ sul1 (0.9) > PMMoV (0.7) > Entero1A (0.5). No significant removal was observed for GenBac3, Campylobacter, and HF183. From the bromide data, we infer that 0.5 log-units of attenuation can be attributed to the dilution of incoming stormwater with water stored in the biofilter; removal above this threshold is presumably associated with non-conservative processes, such as physicochemical filtration, die-off, and predation. Our study documents high variability (>100-fold) in the removal of different microbial contaminants and ARGs by a field-scale stormwater biofilter operated under transient flow and raises further questions about the utility of human-associated fecal source markers as surrogates for pathogen removal.

Suspended particles are hotspots for pathogen-related bacteria and ARGs in coastal beach waters of northern China

Marine suspended particles are unique micro-habitats for diverse microbes and also hotspots of microbially metabolic activities. However, the association of bacterial pathogens, especially those carrying antibiotic resistance genes (ARGs), with these particles remain largely unknown in coastal habitats. This study investigated the distribution of pathogen-related bacteria and ARGs in particle-associated (PA) and free-living (FL) fractions of samples collected at three coastal beaches using NextGen sequencing and qPCR. Suspended particles were found to harbor significantly higher abundances of bacteria of pathogen-related genera and ARGs than their counterparts. Functional analysis of microbial community suggested that antibiotic biosynthetic pathways were also more abundant among PA microbiome comparing to FL microbial community, which further facilitated the spread of ARGs. Additionally, 13 pathogen-related genera co-occurred with ARG in PA fraction while only 2 pathogen-related genera co-occurred with ARGs in FL fraction. Overall, our research revealed suspended particles harbored more abundant pathogen-related genera and ARGs comparing with surrounding waters. Thus, suspended particles are hotspots for pathogen-related genera and ARGs and may pose a greater threat to human health in coastal beach.

Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network

Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.

Assessing environmental pollution levels in marinas

Despite the growing interest in recreational boating and the increasing number of marinas along the world's coastlines, environmental knowledge of these ecosystems is still very scarce. Detailed data of pollutants in marinas are necessary to provide a global approach of environmental risks in the context of international management strategies. In the present study, a set of 64 variables (30 in seawater and 34 in sediments) were measured to compare marinas from the Southern Iberian Peninsula (SIP). Uni and multivariate analyses showed significant differences among marinas, evidencing the importance of management on a local scale. The most relevant variables determining these differences were turbidity and the biocide Irgarol 1051 in seawater, and granulometry, hydrocarbons and faecal coliforms in sediment. The use of normalization techniques with Al or Fe, and the suitability of different methodologies to measure Total Organic Matter in marinas were also discussed. Additionally, we perform a comprehensive literature review of worldwide marina stressors and develop a simple and straightforward method for assessing environmental quality. The method was tested using SIP marinas and was based on the comparison of 15 selected sediment stressors with background values, concentrations of worldwide sediment quality guidelines (SQGs), and reference conditions/security thresholds established by the programme of coastal waters in port areas (ROM 5.1). A global score was assigned using a new proposed index, Marinas Environmental Pollution Index (MEPI), ranging from 0 to 150 points according to the environmental quality (<90: bad, 90-120: moderate, >120: good). MEPI of marinas from SIP ranged from 60 to 110 points indicating bad or moderate levels of pollution. Environmental quality is one of the decisive factors for awarding eco-labels or eco-certifications, such as Blue Flags in marinas. Therefore, pollution baseline information and environmental tools are mandatory for correct assignation of these awards and necessary for assessing the efficiency of management actions.

Selective survival of Escherichia coli phylotypes in freshwater beach sand

Escherichia coli is used as an indicator of fecal pollution at beaches despite evidence of long-term survival in sand. This work investigated the basis for survival of E. coli through field microcosm experiments and phylotypic characterization of more than >1400 E. coli isolated from sand, sewage, and gulls, enabling identification of long-surviving populations and environmental drivers of their persistence. Microcosms containing populations of E. coli from each source (n=176) were buried in the backshore of Lake Michigan for 45 & 96 days under several different nutrient treatments, including unaltered native sand, sterile autoclaved sand and baked nutrient depleted sand. Availability of carbon and nitrogen and competition with the indigenous community were major factors that influenced E. coli survival. E. coli Clermont phylotypes B1 and A were the most dominant phylotypes surviving seasonally (>6 weeks), regardless of source and nutrient treatment, whereas cryptic clade and D/E phylotypes survived over winter (>300 days). Autoclaved sand, presumably supplying nutrients through increased availability, promoted growth and the presence of the indigenous microbial community reduced this effect. Screening of 849 sand E. coli from four freshwater beaches demonstrated that B1, but also D/E, were the most common phylotypes recovered. Analysis by qPCR for the Gull2, Lachno3 and HB human markers demonstrated only 25% of the samples had evidence of gull waste and none of the samples had evidence of human waste. These findings suggest prevalence of E. coli in the sand could be attributed more to long term surviving populations than to new fecal pollution.IMPORTANCE Fecal pollution monitoring still relies upon the enumeration of E. coli, despite the fact that this organism can survive for prolonged periods and has been shown to be easily transported from sand into surrounding waters through waves and runoff, thus no longer represents recent fecal pollution events. Here, we experimentally demonstrate that regardless of host source, certain genetically distinct subgroups, or phylotypes, survive longer than others under conditions typical of Great Lakes beach sites. We found nutrients were a major driver of survival and could actually promote growth, and the presence of native microorganisms modulated these effects. These insights into the dynamics and drivers of survival will improve the interpretation of E. coli measurements at beaches and inform strategies that could focus on reducing nutrient inputs to beaches or maintaining a robust natural microbiome in beach sand.

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.

Surf zone microbiological water quality following emergency beach nourishment using sediments from a catastrophic debris flow

Urban disaster response requires disposal of complex wastes. This study regards a case wherein high intensity rainfall fell over a remote mountainous area previously burned by wildfire, generating debris flows that devastated a downstream town. Sanitary sewers and homes with septic systems were damaged, releasing human waste into the debris flow field. Contaminated sediments, with their high fecal indicator bacteria (FIB) concentrations, were cleared from public rights-of-way and creek channels by local authorities, then disposed onto distant Goleta Beach for beach nourishment, causing immediate surf zone microbiological water quality exceedances. To determine potential public health threats, disposed sediments and surf zone waters were sampled and analyzed-relative to reference samples of mountain soil and raw sewage-for FIB, pathogens, human (HF183) and other host- (Gull2 TaqMan, and DogBact) associated DNA-based fecal markers, and bacterial community 16S rRNA gene sequences. Approximately 20% of disposed sediment samples contained the HF183 marker; sequencing suggested that all samples were contaminated by sewage. In an initial sediment disposal period, surf zone waters harbored intestinal bacterial sequences that were shared with disposed sediments and sewage. Yet surf zone bacterial communities returned to mostly marine clades within weeks. Taken together, multiple conventional and DNA-based analyses informed this forensic assessment of human waste contamination. In the future, similar analyses could be used earlier in disaster response to guide sediment disposal decisions towards continuously protecting beachgoer health.

Status of faecal pollution in ports: A basin-wide investigation in the Adriatic Sea

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea.

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.

Comparative decay of sewage-associated marker genes in beach water and sediment in a subtropical region

There is a growing move towards using the quantitative polymerase chain (qPCR)-based sewage-associated marker genes to assess surface water quality. However, a lack of understanding about the persistence of many sewage-associated markers creates uncertainty for those tasked with investigating microbial water quality. In this study, we investigated the decay of two qPCR FIB [E. coli (EC), and Enterococcus spp. (ENT) 23S rRNA genes] and four sewage-associated microbial source tracking (MST) marker genes [human Bacteroides HF183 16S rRNA, adenovirus (HAdV), and polyomavirus (HPyV), and crAssphage, a recently described bacteriophage in feces], in outdoor mesocosms containing fresh and marine waters and their corresponding sediments. Decay rates of EC 23S rRNA, ENT 23S rRNA, and HF183 16S rRNA were significantly (p < 0.05) faster than the HAdV, HPyV and crAssphage markers in water samples from all mesocosms. In general, decay rates of bacterial targets were similar in the water columns of the studied mesocosms. Similarly, decay rates of viral targets were also alike in mesocosm water columns in relation to each other. The decay rates of FIB and sewage-associated markers were significantly faster in water samples compared to sediments in all three mesocosms. In the event of resuspension, FIB and marker genes from sediments can potentially recontaminate overlying waters. Thus, care should be taken when interpreting the occurrence of FIB and sewage-associated MST markers in water, which may have originated from sediments. The differential decay of these targets may also influence health outcomes and need to be considered in risk assessment models.

Assessment of local and regional strategies to control bacteria levels at beaches with consideration of impacts from climate change

The objective of this study was to evaluate relationships between local factors (beach geomorphology and management) and regional factors (infrastructure improvements and temperature changes) against levels of fecal indicator bacteria (FIB) at recreational beaches. Data were evaluated for 17 beaches located in Monroe County, Florida (Florida Keys), USA, including an assessment of sanitary infrastructure improvements using equivalent dwelling unit (EDU) connections. Results show that elevated FIB levels were associated with beach geomorphologies characterized by impeded flow and by beaches with lax management policies. The decrease in EDUs not connected coincided with a decrease in the fraction of days when bacteria levels were out of compliance. Multivariate factor analysis also identified beach management practices (presence of homeless and concession stands) as being associated with elevated FIB. Overall, results suggest that communities can utilize beach management strategies and infrastructure improvements to overcome the negative water quality impacts anticipated with climate change.

Determination of wild animal sources of fecal indicator bacteria by microbial source tracking (MST) influences regulatory decisions

Fecal indicator bacteria (FIB) are used to assess fecal pollution levels in surface water and are among the criteria used by regulatory agencies to determine water body impairment status. While FIB provide no information about pollution source, microbial source tracking (MST) does, which contributes to more direct and cost effective remediation efforts. We studied a watershed in Florida managed for wildlife conservation that historically exceeded the state regulatory guideline for fecal coliforms. We measured fecal coliforms, enterococci, a marker gene for avian feces (GFD), and a marker gene for human-associated Bacteroides (HF183) in sediment, vegetation, and water samples collected monthly from six sites over two years to: 1) assess the influence of site, temporal factors, and habitat (sediment, vegetation, and water) on FIB and MST marker concentrations, 2) test for correlations among FIB and MST markers, and 3) determine if avian feces and/or human sewage contributed to FIB levels. Sediment and vegetation had significantly higher concentrations of FIB and GFD compared to water and thus may serve as microbial reservoirs, providing unreliable indications of recent contamination. HF183 concentrations were greatest in water samples but were generally near the assay limit of detection. HF183-positive results were attributed to white-tailed deer (Odocoileus virginianus) feces, which provided a false indication of human sewage in this water body. FIB and GFD were positively correlated while FIB and HF183 were negatively correlated. We demonstrated that birds, not sewage, were the main source of FIB, thus avoiding implementation of a total maximum daily load program (TMDL). Our results demonstrate that the concomitant use of FIB and MST can improve decision-making and provide direction when water bodies are impaired, and provides a strategy for natural source exclusion in water bodies impacted by wild animal feces.

Differential Sensitivity of Wetland-Derived Nitrogen Cycling Microorganisms to Copper Nanoparticles

Metallic nanoparticles (NPs), the most abundant nanomaterials in consumer and industrial products, are the most probable class to enter the environment. In this study, wetland-derived microcosms were incubated with copper nanoparticles (Cu-NP) and ionic CuCl₂ to investigate acute (10 days) and chronic (100 days) exposure towards nitrogen cycling microorganisms. The microbial ecology of wetlands play a crucial role in balancing nitrogen in pristine environments as well as in areas impacted by high nutrient loads (e.g., at wastewater effluent discharges). Gene abundance and expression changes were monitored using the GeoChip 5.0 high throughput functional gene microarray and metatranscriptomic shotgun sequencing (RNA-seq), respectively. After 10 days, the Cu-NP impacted microbial communities experienced structural shifts within microorganisms associated with dissimilatory nitrogen reduction accompanied by lower nitrate removal as compared to the unexposed controls. By day 100, these differences were largely resolved and nitrate removal was similar to the unexposed control. Furthermore, the Cu-NP exposed microcosms tolerated copper and were more resilient and adaptive than the unexposed controls based on the abundance and expression of other functions, including electron transfer, metal homeostasis, and stress response. These findings suggest sudden influxes of Cu-NPs into wetland systems may impair nitrogen removal initially, but long-term microbial shifts and functional redundancy would promote the net flux of total nitrogen out of the wetlands.

Evaluation of methods to sample fecal indicator bacteria in foreshore sand and pore water at freshwater beaches

Fecal indicator bacteria (FIB) are known to accumulate in foreshore beach sand and pore water (referred to as foreshore reservoir) where they act as a non-point source for contaminating adjacent surface waters. While guidelines exist for sampling surface waters at recreational beaches, there is no widely-accepted method to collect sand/sediment or pore water samples for FIB enumeration. The effect of different sampling strategies in quantifying the abundance of FIB in the foreshore reservoir is unclear. Sampling was conducted at six freshwater beaches with different sand types to evaluate sampling methods for characterizing the abundance of E. coli in the foreshore reservoir as well as the partitioning of E. coli between different components in the foreshore reservoir (pore water, saturated sand, unsaturated sand). Methods were evaluated for collection of pore water (drive point, shovel, and careful excavation), unsaturated sand (top 1 cm, top 5 cm), and saturated sand (sediment core, shovel, and careful excavation). Ankle-depth surface water samples were also collected for comparison. Pore water sampled with a shovel resulted in the highest observed E. coli concentrations (only statistically significant at fine sand beaches) and lowest variability compared to other sampling methods. Collection of the top 1 cm of unsaturated sand resulted in higher and more variable concentrations than the top 5 cm of sand. There were no statistical differences in E. coli concentrations when using different methods to sample the saturated sand. Overall, the unsaturated sand had the highest amount of E. coli when compared to saturated sand and pore water (considered on a bulk volumetric basis). The findings presented will help determine the appropriate sampling strategy for characterizing FIB abundance in the foreshore reservoir as a means of predicting its potential impact on nearshore surface water quality and public health risk.

Significance of beach geomorphology on fecal indicator bacteria levels

Large databases of fecal indicator bacteria (FIB) measurements are available for coastal waters. With the assistance of satellite imagery, we illustrated the power of assessing data for many sites by evaluating beach features such as geomorphology, distance from rivers and canals, presence of piers and causeways, and degree of urbanization coupled with the enterococci FIB database for the state of Florida. We found that beach geomorphology was the primary characteristic associated with enterococci levels that exceeded regulatory guidelines. Beaches in close proximity to marshes or within bays had higher enterococci exceedances in comparison to open coast beaches. For open coast beaches, greater enterococci exceedances were associated with nearby rivers and higher levels of urbanization. Piers and causeways had a minimal contribution, as their effect was often overwhelmed by beach geomorphology. Results can be used to understand the potential causes of elevated enterococci levels and to promote public health.

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.

Environmental Escherichia coli: ecology and public health implications-a review

Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through faeces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent faecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extraintestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a faecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics revealed the diversity and complexity of E. coli strains in various environments, which are affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments with regard to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.

Microbiological quality of water in a city with persistent and recurrent waterborne diseases under tropical sub-rural conditions: The case of Kikwit City, Democratic Republic of the Congo

The availability of safe drinking water in sub-Saharan countries remains a major challenge because poor sanitation has been the cause of various outbreaks of waterborne disease due to the poor microbiological quality of water used for domestic purposes. The faecal indicator bacteria (FIB) used in the present study included Escherichia coli (E. coli) and Enterococcus (ENT). FIB and aerobic mesophilic bacteria (AMB) were quantified during July 2015 (dry season) and November 2015 (rainy season) in order to assess the quality of drinking water from wells (n=3; P1-P3), and two rivers, the River Lukemi (RLK, n=3) and River Luini (RLN, n=2) in the city of Kikwit, which is located in the province of Kwilu in the Democratic Republic of the Congo. Kikwit is well known for its outbreaks of persistent and recurrent waterborne diseases including Entamoeba, Shigella, typhoid fever, cholera, and Ebola Viral Hemorrhagic Fever. Consequently, E. coli, ENT, and AMB were quantified in water samples according to the standard international methods for water quality determination using the membrane filtration method. The FIB characterization was performed for human-specific Bacteroides by PCR using specific primers. The results obtained revealed high FIB concentrations in river samples collected during both seasons. For example, E. coli respectively reached 4.3×10⁴ and 9.2×10⁴ CFU 100mL^-1 in the dry season and the wet season. ENT reached 5.3×10³ CFU 100mL^-1 during the dry season and 9.8×10³ CFU 100mL^-1 in the wet season. The pollution was significantly worse in the wet season compared to the dry season. Surprisingly, no faecal contamination was observed in well water samples collected in the dry season while E. coli and ENT were detected in all wells in the wet season with values of 6, 7, and 11CFUmL^-1 for E. coli in wells P1-P3, respectively and 3, 5, 9 CFU mL^-1for ENT in the same wells. Interestingly, the PCR assays for human-specific Bacteroides HF183/HF134 indicated that 97-100% captured in all analyses of isolated FIB were of human origin. The results indicate that contamination of E. coli, ENT, and AMB in the studied water resources increases during the wet season. This study improves understanding of the microbiological pollution of rivers and wells under tropical conditions and will guide future municipal/local government decisions on improving water quality in this region which is characterised by persistent and recurrent waterborne diseases. Although the epidemiology can be geographically localised, the effects of cross border transmission can be global. Therefore, the research results presented in this article form recommendations to municipalities/local authorities and the approach and procedures can be carried out in a similar environment.

Distribution and Differential Survival of Traditional and Alternative Indicators of Fecal Pollution at Freshwater Beaches

Alternative indicators have been developed that can be used to identify host sources of fecal pollution, yet little is known about how their distribution and fate compare to traditional indicators. Escherichia coli and enterococci were widely distributed at the six beaches studied and were detected in almost 95% of water samples (n = 422) and 100% of sand samples (n = 400). Berm sand contained the largest amount of E. coli (P < 0.01), whereas levels of enterococci were highest in the backshore (P < 0.01). E. coli and enterococci were the lowest in water, using a weight-to-volume comparison. The gull-associated Catellicoccus marimammalium (Gull2) marker was found in over 80% of water samples, regardless of E. coli levels, and in 25% of sand samples. Human-associated Bacteroides (HB) and Lachnospiraceae (Lachno2) were detected in only 2.4% of water samples collected under baseflow and post-rain conditions but produced a robust signal after a combined sewage overflow, despite low E. coli concentrations. Burdens of E. coli and enterococci in water and sand were disproportionately high in relation to alternative indicators when comparing environmental samples to source material. In microcosm studies, Gull2, HB, and Lachno2 quantitative PCR (qPCR) signals were reduced twice as quickly as those from E. coli and enterococci and approximately 20% faster than signals from culturable E. coli High concentrations of alternative indicators in source material illustrated their high sensitivity for the identification of fecal sources; however, differential survival and the potential for long-term persistence of traditional fecal indicators complicate the use of alternative indicator data to account for the levels of E. coli and enterococci in environmental samples.

IMPORTANCE

E. coli and enterococci are general indicators of fecal pollution and may persist in beach sand, making their use problematic for many applications. This study demonstrates that gull fecal pollution is widespread at Great Lakes beaches, whereas human and ruminant contamination is evident only after major rain events. An exploration of sand as a reservoir for indicators found that E. coli was ubiquitous, while gull host markers were detected in only 25% of samples. In situ sand beach microcosms provided decay rate constants for E. coli and enterococci relative to alternative indicators, which establish comparative benchmarks that would be helpful to distinguish recent from past pollution. Overall, alternative indicators are useful for identifying sources and assessing potentially high health risk contamination events; however, beach managers should be cautious in attempting to directly link their detection to the levels of E. coli or enterococci.

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.

Sediment characteristics and microbiological contamination of beach sand - A case-study in the archipelago of Madeira

Beach sand can harbour pathogenic and opportunistic microorganisms, as well as faecal indicator bacteria that influence directly the bathing water quality. Pathogenic and opportunistic microorganisms often raise concern of exposure during beach related recreational activities. In this work, three different types of sandy beaches (natural basaltic, natural calcareous and artificial calcareous) of the Archipelago of Madeira (Portugal) were sampled for bacterial and fungal contaminants and grain size distribution, during four years (2010-2013). Following an extreme weather event in 2010, the faecal indicator bacteria levels spiked, returning to base levels shortly thereafter. The same phenomenon occurred with fungi, where potentially pathogenic fungi were the dominant group. Yeast-like fungi and dermatophytes were, however, mainly associated to months of higher usage by recreational users. Statistical analysis showed higher contamination of sediment in artificial beaches compared to natural beaches and granulometry and chemical composition of sand did not influence in the microbial loads. Instead, bather density and the influence of coastal protection structures needed to maintain the volume of artificial beach sand regarding the removal potential of wave induced currents are obvious influencing factors.

Decay rates of faecal indicator bacteria from sewage and ovine faeces in brackish and freshwater microcosms with contrasting suspended particulate matter concentrations

To safeguard human health, legislative measures require the monitoring of faecal indicator bacteria (FIB) concentrations in recreational and shellfish waters. Consequently, numerous studies have focussed on FIB survival in the water column and more recently in estuarine sediments. However, there is a paucity of information regarding the influence of contrasting suspended particulate matter (SPM) concentrations on the survival of FIB in the water column of estuaries. Here, microcosms containing freshwater or brackish water with low, high and extreme SPM concentrations were inoculated with sewage and ovine faeces and the decay rate of Escherichia coli, coliforms and enterococci were determined by enumeration over five consecutive days. E. coli derived from ovine faeces proliferated and persisted at high levels in both freshwater and brackish microcosms (no decay), whereas ovine enterococci demonstrated a net decay over the duration of the experiment. Furthermore, SPM concentration had a significant effect on the decay rates of both E. coli and enterococci from ovine faeces in brackish microcosms, but decay rate was greater at low SPM concentrations for E. coli, whereas the opposite was observed for enterococci, whose decay rates increased as SPM concentration increased. E. coli, enterococci and coliforms derived from wastewater demonstrated a net decay in both freshwater and brackish microcosms, with contrasting effects of SPM concentration on decay rate. In addition, some FIB groups demonstrated contrasting responses (decay or proliferation) in the first 24h following inoculation into freshwater versus brackish microcosms. Overall, SPM concentrations influenced the proliferation and decay rates of FIB in brackish waters, but had minimal influence in freshwater. These results demonstrate that the survival rates of FIB in aquatic environments are system specific, species and source dependent, and influenced by SPM concentration. This study has important implications for catchment-based risk assessments and source apportionment of FIB pollution in aquatic environments.

Modeling spatiotemporal bacterial variability with meteorological and watershed land-use characteristics

Bacteria are a primary contaminant in natural surface water. The instream concentration of fecal coliform, a potential indicator of pathogens, is influenced by meteorological conditions and land-use characteristics. However, the relationships between these conditions and fecal coliforms are not fully understood. Furthermore, the sources of large variability in fecal coliform counts, e.g., temporal or spatial sources, remain unexplained, especially at large scales. This study proposes the use of Bayesian overdispersed Poisson models, whereby the combined effects of temperature, rainfall, and land-use characteristics on fecal coliform concentration are quantified with predictive uncertainty, and the sources of variability in fecal coliform concentration are assessed. The models were developed using 8-year weekly observations of fecal coliforms obtained from the Wachusett Reservoir watershed in Massachusetts, USA. The results highlight the importance of interactions among meteorological and land-use characteristics in controlling the instream fecal coliform concentration; the increase in fecal coliform concentration with temperature increase was more drastic when rainfall occurred. Also, the responses of fecal coliforms to temperature increases were more pronounced in forest-dominated than in urban-dominated areas. In contrast, the fecal coliform concentration increased more rapidly with rainfall increases in urban-dominated than in forest-dominated areas. The models also demonstrate that among the sources of variability, the monthly component made the most significant contribution to the variability in fecal coliform concentrations. Our results suggest that seasonally dependent processes, including surface runoff, are critical factors that regulate fecal coliform concentration in streams.

Comparison of the occurrence and survival of fecal indicator bacteria in recreational sand between urban beach, playground and sandbox settings in Toronto, Ontario

While beach sands are increasingly being studied as a reservoir of fecal indicator bacteria (FIB), less is known about the occurrence of FIB in other recreational sands (i.e., sandboxes and playgrounds). In this study, different culture-based FIB enumeration techniques were compared and microbial source tracking assays were conducted on recreational sand samples from beaches, playgrounds and sandboxes around Toronto, ON. FIB were detected in every sand sample (n=104) with concentrations not changing significantly over the five month sampling period. Concentrations of FIB and a gull-specific DNA marker were significantly higher in foreshore beach sands, and indicated these were a more significant reservoir of FIB contamination than sandbox or playground sands. Human- and dog-specific contamination markers were not detected. All culture-based FIB enumeration techniques were consistent in identifying the elevated FIB concentrations associated with foreshore beach sands. However, significant differences between differential agar media, IDEXX and Aquagenx Compartment Bag Test were observed, with DC media and Enterolert being the most sensitive methods to detect Escherichia coli and enterococci, respectively. To better understand the elevated occurrence of E. coli in foreshore sands, microcosm survival experiments were conducted at two different temperatures (15 °C and 28 °C) using non-sterile saturated foreshore beach sands collected from two urban freshwater beaches with different sand type (fine grain and sand-cobble). Microcosms were inoculated with a mixture of eight sand-derived E. coli strains and sampled over a 28-day period. E. coli levels were found to decline in all microcosms, although survival was significantly greater in the finer sand and at the cooler temperature (15 °C). These results indicate that FIB can be widespread in any type of recreational sand and, while E. coli can survive for many weeks, it is most likely to accumulate in cooler fine-grain sand as occurs below the foreshore sand surface.

New Antimicrobially Amended Media for Improved Nonpoint Source Bacterial Pollution Treatment

Nonpoint source pollution (NPS) such as stormwater runoff may introduce high loads of bacteria, impairing surface water bodies. The existing filter materials in stormwater best management practices (BMP) are typically not designed to inactivate bacteria. Herein, novel filtration media were extensively tested for microbial load reduction in stormwater runoff. Red cedar wood chips (RC) were amended with different loadings of either 3-(trihydroxysilyl) propyldimethyloctadecyl ammonium chloride (TPA) or silver nanoparticles (AgNP). Under batch conditions at 25 °C, log10 removal values (LRV) up to 3.71 ± 0.38 (mean ± standard error) for TPA-RC and 2.25 ± 1.00 for AgNP-RC were achieved for Escherichia coli (E. coli), whereas unmodified RC achieved less than 0.5 LRV. Similar trends were observed at 17.5 °C, however at low temperature (10 °C) no statistically significant difference in E. coli inactivation between modified and unmodified RC was detected. Inactivation kinetic studies show that TPA-RC has higher inactivation rate constants compared to AgNP-RC. Under dynamic flow conditions a mass balance approach indicates that even after remobilization up to 99.8% of E. coli removal using 9 mg/g TPA-RC compared to 64.8% for unmodified RC. This study demonstrates that RC wood chips amended with antimicrobial compounds show promising applications as filtration material for the reduction of microbiological contamination load in stormwater runoff.

Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater

The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater.

Influence of wave action on the partitioning and transport of unattached and floc-associated bacteria in fresh water

The dynamic interaction of bacteria within bed sediment and suspended sediment (i.e., floc) in a wave-dominated beach environment was assessed using a laboratory wave flume. The influence of shear stress (wave energy) on bacterial concentrations and on the partitioning and transport of unattached and floc-associated bacteria was investigated. The study showed that increasing wave energy (0.60 and 5.35 N/s) resulted in a 0.5 to 1.5 log increase in unattached cells of the test bacterium Pseudomonas sp. strain CTO7::gfp-2 in the water column. There was a positive correlation between the bacterial concentrations in water and the total suspended solids, with the latter increasing from values of near 0 to up to 200 mg/L over the same wave energy increase. The median equivalent spherical diameter of flocs in suspension also increased by an order of magnitude in all experimental trials. Under both low (0.60 N/s) and high (5.35 N/s) energy regime, bacteria were shown to preferentially associate with flocs upon cessation of wave activity. The results suggest that collecting water samples during periods of low wave action for the purpose of monitoring the microbiological quality of water may underestimate bacterial concentrations partly because of an inability to account for the effect of shear stress on the erosion and mobilization of bacteria from bed sediment to the water column. This highlights the need to develop a more comprehensive beach analysis strategy that not only addresses presently uncharacterized shores and sediments but also recognizes the importance of eroded flocs as a vector for the transport of bacteria in aquatic environments.

Contribution of sand-associated enterococci to dry weather water quality

Culturable enterococci and a suite of environmental variables were collected during a predominantly dry summer at a beach impacted by nonpoint source pollution. These data were used to evaluate sands as a source of enterococci to nearshore waters, and to assess the relationship between environmental factors and dry-weather enterococci abundance. Best-fit multiple linear regressions used environmental variables to explain more than half of the observed variation in enterococci in water and dry sands. Notably, during dry weather the abundance of enterococci in dry sands at the mean high-tide line was significantly positively related to sand moisture content (ranging from <1-4%), and the daily mean ENT in water could be predicted by a linear regression with turbidity alone. Temperature was also positively correlated with ENT abundance in this study, which may indicate an important role of seasonal warming in temperate regions. Inundation by spring tides was the primary rewetting mechanism that sustained culturable enterococci populations in high-tide sands. Tidal forcing modulated the abundance of enterococci in the water, as both turbidity and enterococci were elevated during ebb and flood tides. The probability of samples violating the single-sample maximum was significantly greater when collected during periods with increased tidal range: spring ebb and flood tides. Tidal forcing also affected groundwater mixing zones, mobilizing enterococci from sand to water. These data show that routine monitoring programs using discrete enterococci measurements may be biased by tides and other environmental factors, providing a flawed basis for beach closure decisions.

Distribution and persistence of Escherichia coli and Enterococci in stream bed and bank sediments from two urban streams in Houston, TX

The purpose of this research was to determine if Escherichia coli and enterococci in streambed and bank sediments from two urban bayous, Buffalo Bayou and White Oak Bayou, in Houston, TX, USA are a significant source of the chronically high levels of these bacteria in the overlying water. The watersheds of the bayous lie within highly urbanized areas of Greater Houston and there is primary recreational contact with the public. Extensive sampling of the watersheds was conducted from 2008 to 2010. Both fecal indicator bacteria were found at ≥ 10(4)MPNgdry wt.(-1) concentrations in the upper 1cm of sediment cores with declines by orders of magnitude at 15 and 30 cm sediment horizons and in some cases 60 cm, but, nonetheless, indicating that they can remain viable even at depth. No interannual variation was observed. And, there was no correlation with percent organic matter, however there was moderate correlation (R(2)=0.12; p=0.001) of E. coli with sediment moisture. In sediments, most E. coli and enterococci in Buffalo Bayou (76%) and White Oak Bayou (87.5%) were associated with fine sand grains (60 to 250 μm). In the water column, E. coli was associated, in roughly equal percentages, with particle sizes <10, 10-25, 25-63, and ≥ 63 μm (21.9, 25.6, 30.4, and 32.9%, respectively). Enterococci were mostly attached to particle sizes in the ranges of 10-25μm (36.0%) and 25-63 μm (31.1%) as well as ≥ 63 μm (37.7%) (p=0.0001). Fingerprinting of E. coli isolates from both bayous with Rep-PCR and the BOX A1R primer was used to demonstrate translocation of sediments from the upper to lower watersheds.

Assessment of pathogenic bacteria in water and sediment from a water reservoir under tropical conditions (Lake Ma Vallée), Kinshasa Democratic Republic of Congo

This study was conducted to assess potential human health risks presented by pathogenic bacteria in a protected multi-use lake-reservoir (Lake Ma Vallée) located in west of Kinshasa, Democratic Republic of Congo (DRC). Water and surface sediments from several points of the Lake were collected during summer. Microbial analysis was performed for Escherichia coli, Enterococcus (ENT), Pseudomonas species and heterotrophic plate counts. PCR amplification was performed for the confirmation of E. coli, ENT, Pseudomonas spp. and Pseudomonas aeruginosa isolated from samples. The results reveal low concentration of bacteria in water column of the lake, the bacterial quantification results observed in this study for the water column were below the recommended limits, according to WHO and the European Directive 2006/7/CE, for bathing water. However, high concentration of bacteria was observed in the sediment samples; the values of 2.65 × 10(3), 6.35 × 10(3), 3.27 × 10(3) and 3.60 × 10(8) CFU g(-1) of dry sediment for E. coli, ENT, Pseudomonas spp. and heterotrophic plate counts, respectively. The results of this study indicate that sediments of the Lake Ma Vallée can constitute a reservoir of pathogenic microorganisms which can persist in the lake. Possible resuspension of faecal indicator bacteria and pathogens would affect water quality and may increase health risks to the population during recreational activities. Our results indicate that the microbial sediment analysis provides complementary and important information for assessing sanitary quality of surface water under tropical conditions.

Persistence of fecal indicator bacteria in sediment of an oligotrophic river: comparing large and lab-scale flume systems

In this study, both a lab and a large-scale flume system were used to investigate the survival of fecal indicator bacteria (FIB) in bed sediments of an alpine oligotrophic river. To determine the influence of substratum on persistence, survival within 3-cm-deep substratum cages versus on thin, biofilm-covered ceramic tiles was tested. Moreover, the impact of bed shear stress on survival in bed sediments was explored. It was seen that in the lab-scale flume having a very low bed shear stress (0.3 N m(-2)), E. coli and enterococci survival in 3-cm-deep substratum cages was nearly the same as in a thin biofilm (200 μm). However, in the large-scale flume system characterized by a bed shear stress of 9 N m(-2), the added protection of the deeper substratum cages promoted considerably longer survival of E. coli and enterococci than the thin biofilm. Additionally, the FIB removal mechanisms in the two flume systems varied. At the lab-scale, enterococci was seen to persist twice as long as E. coli, while in the large-scale flume the two FIB were removed at the same rate. A comparison of qPCR analyses performed in both flumes suggests that bed sediment erosion and the influence of grazers/predators were responsible for FIB removal from the sediments in the large-scale flume, whereas in the lab flume FIB inactivation caused removal. These results indicate that hydraulic parameters such as bed shear stress as well as the presence of macroinvertebrates in a system are both important factors to consider when designing flumes as they can significantly impact FIB persistence in sediments of fast-flowing, alpine streams.

Microbes in Beach Sands: Integrating Environment, Ecology and Public Health

Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area.

Decay of genetic markers for fecal bacterial indicators and pathogens in sand from Lake Superior

Beach sands impact water quality and pathogen loads, however, the comparative decay of the fecal indicator bacteria (FIB) Enterococcus spp. and Escherichia coli, and pathogens in freshwater sand have not been examined. In this study, freshwater sand microcosms were inoculated with sewage and pure cultures of bacterial pathogens to compare relative decay rates. The abundance of culturable Enterococcus spp. and E. coli, genetic markers for Enterococcus spp. (Entero1), total Bacteroides (AllBac), and human-specific Bacteroides (HF183), and genetic markers for the pathogens Campylobacter jejuni, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella enterica subsp. enterica serovar Typhimurium, and Shigella flexneri were monitored over the course of two weeks using conventional culture methods and quantitative PCR (qPCR). The effect of moisture on the persistence of culturable FIB and all genetic markers was also determined. In addition, propidium monoazide (PMA) treatment was used to examine differences in the persistence of total genetic markers and those from live cells. Decay rates were statistically compared using Tukey's test. Moisture had a significant (p ≤ 0.05) effect on the decay rates of culturable indicator bacteria, total AllBac markers, and genetic markers for FIB, Salmonella, and MRSA from live cells. At 14% sand moisture, the decay rate of total markers was slower than that of live cells for all qPCR assays, but at 28% moisture, there was no difference in the decay rates of total and live markers for any assay. AllBac and MRSA markers increased in sand at 28% moisture, probably indicating cellular growth. Overall, culturable FIB and HF183 had decay rates that were most comparable to the bacterial pathogen markers examined in this study, whereas Entero1 and AllBac rarely exhibited decay rates similar to the bacterial pathogens in this study. The choice of FIB for assessment of fecal contamination in freshwater sand should take into account the pathogen of concern and sand moisture conditions.

Environmental and animal-associated enterococci

Enterococci are generally commensal bacteria inhabiting the gastrointestinal tract of humans and animals. They have, however, been implicated as the etiological agent of a variety of illnesses and nosocomial infections. In addition to pathogenic potential, there is growing concern regarding the incidence of antibiotic resistance and genetic exchange among Enterococcus spp. within and among a variety of animal hosts. While primarily considered an enteric group, extra-enteric habitats in which enterococci persist and potentially grow have been studied for decades. Although many biotic (e.g., predation) and abiotic (e.g., sunlight, nutrients, and salinity) stressors have been thought to limit the success of enterococci in these secondary habitats, a growing body of evidence suggests that certain strains may become naturalized to environmental habitats. Enterococci have also been used for decades as indicators of fecal contamination in recreational waters where increased concentrations of this group have been linked to the incidence of illness in humans following recreational use of these waters. Persistence of enterococci in secondary habitats, however, suggests that their presence in ambient waters may prove to be a poor indicator of actual risks to public health. In this chapter, we provide a review of the existing body of literature concerning animal host associations, genetic exchange is reviewed, and emphasis is placed on the growing body of evidence for the persistence and growth of enterococci in secondary habitats.

The impact of major earthquakes and subsequent sewage discharges on the microbial quality of water and sediments in an urban river

A series of large earthquakes struck the city of Christchurch, New Zealand in 2010-2011. Major damage sustained by the sewerage infrastructure required direct discharge of up to 38,000 m(3)/day of raw sewage into the Avon River of Christchurch for approximately six months. This allowed evaluation of the relationship between concentrations of indicator microorganisms (Escherichia coli, Clostridium perfringens and F-RNA phage) and pathogens (Campylobacter, Giardia and Cryptosporidium) in recreational water and sediment both during and post-cessation of sewage discharges. Giardia was the pathogen found most frequently in river water and sediment, although Campylobacter was found at higher levels in water samples. E. coli levels in water above 550 CFU/100 mL were associated with increased likelihood of detection of Campylobacter, Giardia and Cryptosporidium, supporting the use of E. coli as a reliable indicator for public health risk. The strength of the correlation of microbial indicators with pathogen detection in water decreased in the following order: E. coli>F-RNA phage>C. perfringens. All the microorganisms assayed in this study could be recovered from sediments. C. perfringens was observed to accumulate in sediments, which may have confounded its usefulness as an indicator of fresh sewage discharge. F-RNA phage, however, did not appear to accumulate in sediment and in conjunction with E. coli, may have potential as an indicator of recent human sewage discharge in freshwater. There is evidence to support the low-level persistence of Cryptosporidium and Giardia, but not Campylobacter, in river sediments after cessation of sewage discharges. In the event of disturbances of the sediment, it is highly probable that there could be re-mobilisation of microorganisms beyond the sediment-water exchange processes occurring under base flow conditions. Re-suspension events do, therefore, increase the potential risk to human health for those who participate in recreational and work-related activities in the river environment.

Influence of resuspension on the fate of fecal indicator bacteria in large-scale flumes mimicking an oligotrophic river

In this study, large-scale flume systems simulating an oligotrophic river were used to explore the fate and transport of the fecal indicator bacteria (FIB) Escherichia coli and enterococci following a combined sewer overflow (CSO). Specifically, the removal pattern of FIB from the water column was examined as well as deposition onto the flume bed. Finally, the impact that a sudden increase in bed shear stress has on FIB in the water column was investigated. The large-scale flumes utilized in this study proved extremely useful for our investigations as they very closely approximated conditions within the Isar River (Munich, Germany). By using both natural substratum and fresh river water, as well as a flow velocity of nearly 1 m s(-1) at a water depth of roughly 0.5 m, shear stresses typical of the Isar River (9 N m(-2)) were achieved. As a result, scaling effects were appreciably reduced. In our flume system, UV inactivation played only a minimal role in overall FIB removal. Therefore, we were able to more precisely investigate other mechanisms which result in FIB removal from the water column. From the two standard FIB removal experiments following a CSO, the removal rate coefficient (k) of 0.2 h(-1) was identified for both E. coli and enterococci in the water column. An increase in the bed shear stress led to more than a 150% rise in total suspended solid (TSS) levels in the water column. These elevated TSS levels (≈ 50 mg l(-1)) increased the persistence of suspended FIB in the water column by 20 h (k = 0.05 h(-1)). This indicates that higher TSS loads resulting from resuspended bed sediments can significantly expand the area that is impacted by a CSO event. At lower TSS loads (<20 mg l(-1)) deposition onto the flume bed did not contribute significantly to FIB removal from the water column. Any deposition which did occur did not result in a net accumulation of culturable FIB in the benthic biofilm.

Enterococci in the environment

Enterococci are common, commensal members of gut communities in mammals and birds, yet they are also opportunistic pathogens that cause millions of human and animal infections annually. Because they are shed in human and animal feces, are readily culturable, and predict human health risks from exposure to polluted recreational waters, they are used as surrogates for waterborne pathogens and as fecal indicator bacteria (FIB) in research and in water quality testing throughout the world. Evidence from several decades of research demonstrates, however, that enterococci may be present in high densities in the absence of obvious fecal sources and that environmental reservoirs of these FIB are important sources and sinks, with the potential to impact water quality. This review focuses on the distribution and microbial ecology of enterococci in environmental (secondary) habitats, including the effect of environmental stressors; an outline of their known and apparent sources, sinks, and fluxes; and an overview of the use of enterococci as FIB. Finally, the significance of emerging methodologies, such as microbial source tracking (MST) and empirical predictive models, as tools in water quality monitoring is addressed. The mounting evidence for widespread extraenteric sources and reservoirs of enterococci demonstrates the versatility of the genus Enterococcus and argues for the necessity of a better understanding of their ecology in natural environments, as well as their roles as opportunistic pathogens and indicators of human pathogens.