Poikilothermic Animals as a Previously Unrecognized Source of Fecal Indicator Bacteria in a Backwater Ecosystem of a Large River

Traditional and new proposals for environmental microbial indicators-a review

The continuous increment in world population coupled with the greatest natural resource consumption and waste generation has an enormous impact on the environment. To date, using biological indicators (bioindicators) to evaluate the biological quality of natural environments is very common. Nonetheless, selecting those suitable for each ecosystem or contaminant is one of the most important issues for environmental sciences. Bacteria and helminths are mainly related to fecal contamination, while antibiotic-resistant bacteria, fungi, viruses, and microalgae are organisms used to determine deteriorated ecosystems by diverse contaminants. Nowadays, each bioindicator is used as a specific agent of different contaminant types, but detecting and quantifying these bioindicator microorganisms can be performed from simple microscopy and culture methods up to a complex procedure based on omic sciences. Developing new techniques based on the metabolism and physiological responses of traditional bioindicators is shown in a fast environmental sensitivity analysis. Therefore, the present review focuses on analyzing different bioindicators to facilitate developing suitable monitoring environmental systems according to different pollutant agents. The traditional and new methods proposed to detect and quantify different bioindicators are also discussed. Their vital role is considered in implementing efficient ecosystem bioprospection, restoration, and conservation strategies directed to natural resource management.

Gastropods as a source for fecal indicator bacteria in drinking water

Microbial water quality is routinely examined using the fecal indicator bacteria Escherichia coli, coliform bacteria and enterococci. Several practical cases in German drinking water distribution systems indicated invertebrates such as insects or gastropods as a source for the microbiological deterioration. Therefore, we examined three genera of Gastropoda (Arion, Helix and Cepaea) for the presence of fecal indictor bacteria in excreta using standard methods. Enterococci and coliform bacteria were detected in high concentrations (mean values of 1.5 × 106 and 6.3 × 106 per gram feces, respectively). E. coli was also detected, still specification revealed that what was assigned by standard ISO-methods to be E. coli was indeed a novel species of Buttiauxella, exhibiting β-D-glucuronidase activity, thus, explaining the false-positive results. Microbiome analyses confirmed the cultural results. Enterobacteriaceae were dominant in the samples, yet only very few sequences could be assigned to Escherichia. Our study suggests, that enterococci and coliform bacteria are an integral component in the gastropod microbiome, whereas E. coli might be derived from other sources with gastropods being a vector. The results further indicate, that the current concept of fecal indicator bacteria needs to be extended, as not only humans and homeothermic animals could be a source for fecal indictor bacteria, but also gastropods need to be taken into consideration.

Comparative Study of Flesh Quality, Blood Profile, Antioxidant Status, and Intestinal Microbiota of European Catfish (Silurus glanis) Cultivated in a Recirculating Aquaculture System (RAS) and Earthen Pond System

With the increasing demand for European catfish, traditional extensive growth methods in polyculture are no longer sufficient to meet market needs. Therefore, this study aimed to identify indicators for improving recirculating aquaculture system (RAS) technology by determining and comparing growth performance, flesh quality, blood profile, oxidative status, and intestinal microbiota parameters between fish cultivated in a RAS and an earthen pond. Results revealed that RAS-grown fish had a higher fat content compared to pond-grown fish, while no significant differences were found for growth parameters. Sensory analysis showed no significant difference in taste between the two groups. Blood composition analysis showed small differences. Oxidative status analyses showed higher catalase and glutathione peroxidase activities in RAS-grown fish and slightly higher superoxide dismutase activity in pond-grown fish. Microbial analysis showed differences in the intestinal microflora, with a higher total number of aerobic germs and anaerobic germs and a lower total number of sulfite-reducing clostridia in RAS-grown fish. This study provides valuable insights into the comparative performance of a RAS and a pond rearing system in European catfish production, potentially informing future growth technologies.

Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment

We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log₁₀ 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.

The Native Microbial Community of Gastropod-Associated Phasmarhabditis Species Across Central and Southern California

Nematodes in the genus Phasmarhabditis can infect and kill slugs and snails, which are important agricultural pests. This useful trait has been commercialized by the corporation BASF after they mass produced a product labeled Nemaslug®. The product contains Phasmarhabditis hermaphrodita, which has been cultured with Moraxella osloensis, a bacterial strain that was originally thought to be responsible for causing mortality in slugs and snails. The exact mechanism leading to death in a Phasmarhabditis infected host is unknown but may involve contributions from nematode-associated bacteria. The naturally occurring microbial community of Phasmarhabditis is unexplored; the previous Phasmarhabditis microbial community studies have focused on laboratory grown or commercially reared nematodes, and in order to obtain a deeper understanding of the parasite and its host interactions, it is crucial to characterize the natural microbial communities associated with this organism in the wild. We sampled Phasmarhabditis californica, Phasmarhabditis hermaphrodita, and Phasmarhabditis papillosa directly from their habitats in Central and Southern California nurseries and garden centers and identified their native microbial community via 16S amplicon sequencing. We found that the Phasmarhabditis microbial community was influenced by species, location, and possibly gastropod host from which the nematode was collected. The predominant bacteria of the Phasmarhabditis isolates collected included Shewanella, Clostridium perfringens, Aeromonadaceae, Pseudomonadaceae, and Acinetobacter. Phasmarhabditis papillosa isolates exhibited an enrichment with species belonging to Acinetobacter or Pseudomonadaceae. However, further research must be performed to determine if this is due to the location of isolate collection or a species specific microbial community pattern. More work on the natural microbial community of Phasmarhabditis is needed to determine the role of bacteria in nematode virulence.

Assessment of Human Health Risks in Tropical Environmental Waters with Microbial Source Tracking Markers

Human specific microbial source tracking (MST) markers which are highly specific to human waste contamination offer the advantage of better association with human pathogens than traditional microbial indicators. However, the performance of these MST markers may vary across different geographical regions. The magnitude of MST markers also plays an important role in interpreting the health risks. This study aims to (i) validate the specificity and sensitivity of human markers for tropical urban catchments; (ii) identify the threshold concentrations of MST markers, i.e. human polyomaviruses (HPyVs), Bacteroides thetaiotaomicron (B. theta) and Methanobrevibacter smithii (M. smithii), that correspond to the acceptable gastrointestinal (GI) illness risks associated with swimming using the QMRA approach; and (iii) validate the threshold concentrations of MST markers using the surveillance data obtained from the tropical urban environment. Among the three MST markers, HPyVs showed the highest specificity (100%) to sewage samples, followed by M. smithii (97%) and B. theta (90%). All MST markers showed 100% sensitivity towards sewage contamination, with B. theta present in highest abundance in sewage, followed by HPyVs and M. smithii. This study demonstrates a risk-based framework to identify the threshold concentrations of MST markers associated with GI illness risks in environmental waters by considering two main influencing factors (i.e. decay and dilution factors). This study successfully validated the B. theta threshold concentration range (581 to 8073 GC/100 mL) with field data (370 to 6500 GC/100 mL) in estimating GI illness risks with an Enterococcus model. Field data showed that the MST markers at threshold concentrations were able to classify the safe level in more than 83% of the samples, according to GI illness risks from Enterococcus and adenovirus. The study also highlighted the lack of associations between MST markers and GI illness risks from norovirus. With comprehensive information on specificity, sensitivity and threshold concentrations of MST markers, increasing confidence can be placed on identifying human source contamination and evaluating the health risks posed in environmental waters in Singapore.

Microbial faecal pollution of river water in a watershed of tropical Ethiopian highlands is driven by diffuse pollution sources

Tropical communities in the developing world depend heavily on riverine systems for their socioeconomic development. However, these resources are poorly protected from diffuse pollution, and there is a lack of quantitative information regarding the microbial pollution characteristics of riverine water, despite frequently reported gastrointestinal diseases. The aim of our study was to apply faecal taxation (i.e., faecal pellet counting in representative test areas to estimate the potential availability of diffuse pollution sources) in combination with a detailed microbiological faecal pollution analysis in a riverine environment to elucidate the importance of diffuse pollution. To realize this approach, ambient faecal pellets, a multiparametric data set for standard faecal indicator bacteria (SFIB), including Escherichia coli, Clostridium perfringens spores and enterococci from catchment soil and river water, and a number of riverine water physicochemical variables were analysed during a one-year cycle. We demonstrated that the abundance of ambient faecal pellets, which were consistently counted at reference sites in the catchment, was associated with faecal pollution in the river water. Water SFIB, dissolved oxygen, nutrients, conductivity and total suspended solids were strongly linked with the abundance of ambient faecal pellets in the river catchment, as demonstrated by principal component analysis (PCA). Elevated concentrations of SFIB in the riverine water in the absence of rainfall also suggested the direct input of faecal bacteria into the riverine water by livestock (e.g., during watering) and humans (e.g., during bathing). Statistical analyses further revealed that the microbiological water quality of the investigated riverine water was not influenced by SFIB potentially occurring in the soil. This study demonstrates the importance of diffuse faecal pollution sources as major drivers of the microbiological quality of riverine water in the Ethiopian highlands. In addition, the new successfully applied integrated approach could be very useful for developing predictive models, which would aid in forecasting riverine microbiological quality in tropical developing countries.

Genetic Microbial Source Tracking Support QMRA Modeling for a Riverine Wetland Drinking Water Resource

Riverine wetlands are important natural habitats and contain valuable drinking water resources. The transport of human- and animal-associated fecal pathogens into the surface water bodies poses potential risks to water safety. The aim of this study was to develop a new integrative modeling approach supported by microbial source tracking (MST) markers for quantifying the transport pathways of two important reference pathogens, Cryptosporidium and Giardia, from external (allochthonous) and internal (autochthonous) fecal sources in riverine wetlands considering safe drinking water production. The probabilistic-deterministic model QMRAcatch (v 1.1 python backwater) was modified and extended to account for short-time variations in flow and microbial transport at hourly time steps. As input to the model, we determined the discharge rates, volumes and inundated areas of the backwater channel based on 2-D hydrodynamic flow simulations. To test if we considered all relevant fecal pollution sources and transport pathways, we validated QMRAcatch using measured concentrations of human, ruminant, pig and bird associated MST markers as well as E. coli in a Danube wetland area from 2010 to 2015. For the model validation, we obtained MST marker decay rates in water from the literature, adjusted them within confidence limits, and simulated the MST marker concentrations in the backwater channel, resulting in mean absolute errors of < 0.7 log₁₀ particles/L (Kruskal–Wallis p > 0.05). In the scenarios, we investigated (i) the impact of river discharges into the backwater channel (allochthonous sources), (ii) the resuspension of pathogens from animal fecal deposits in inundated areas, and (iii) the pathogen release from animal fecal deposits after rainfall (autochthonous sources). Autochthonous and allochthonous human and animal sources resulted in mean loads and concentrations of Cryptosporidium and Giardia (oo)cysts in the backwater channel of 3–13 × 10⁹ particles/hour and 0.4–1.2 particles/L during floods and rainfall events, and in required pathogen treatment reductions to achieve safe drinking water of 5.0–6.2 log₁₀. The integrative modeling approach supports the sustainable and proactive drinking water safety management of alluvial backwater areas.

Evaluation of groundwater bacterial community composition to inform waterborne pathogen vulnerability assessments

Microbial water quality evaluations are essential for determining the vulnerability of subsurface drinking water sources to fecal pathogen intrusion. Rather than directly monitor waterborne pathogens using culture- or enumeration-based techniques, the potential of assessing bacterial community using 16S rRNA gene amplicon sequencing to support these evaluations was investigated. A framework for analyzing 16S rRNA gene amplicon sequencing results featuring negative-binomial generalized linear models is demonstrated, and applied to bacterial taxa sequences in purge water samples collected from a shallow, highly aerobic, unconfined aquifer. Bacterial taxa relevant as indicators of fecal source and surface connectivity were examined using this approach. Observed sequences of Escherichia, a genus suggestive of fecal source, were consistently detected but not confirmed by culture-based methods. On the other hand, episodic appearance of anaerobic taxa sequences in this highly aerobic environment, namely Clostridia and Bacteroides, warrants further investigation as potential indicators of fecal contamination. Betaproteobacteria sequences varied significantly on a seasonal basis, and therefore may be linked to understanding surface-water groundwater interactions at this site. However, sequences that are often encountered in surface water bodies (Cyanobacteria and Flavobacteriia) were notably absent or present at very low levels, suggesting that microbial transport from surface-derived sources may be rather limited. This work demonstrates the utility of 16S rRNA gene amplicon sequencing for contextualizing and complementing conventional microbial techniques, allowing for hypotheses about source and transport processes to be tested and refined.

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.

Elucidating fecal pollution patterns in alluvial water resources by linking standard fecal indicator bacteria to river connectivity and genetic microbial source tracking

A novel concept for fecal pollution analysis was applied at alluvial water resources to substantially extend the information provided by fecal indicator bacteria (FIB). FIB data were linked to river connectivity and genetic microbial source tracking (MST). The concept was demonstrated at the Danube River and its associated backwater area downstream of the city of Vienna, using a comprehensive 3-year data set (10 selected sites, n = 317 samples). Enumeration of Escherichia coli (ISO 16649-2), intestinal enterococci (ISO 7899-2) and Clostridium perfringens (ISO 14189) revealed a patchy distribution for the investigation area. Based on these parameters alone a clear interpretation of the observed fecal contamination patterns was not possible. Comparison of FIB concentrations to river connectivity allowed defining sites with dominating versus rare fecal pollution influence from the River Danube. A strong connectivity gradient at the selected backwater sites became obvious by 2D hydrodynamic surface water modeling, ranging from 278 days (25%) down to 5 days (<1%) of hydraulic connectivity to the River Danube within the 3-year study period. Human sewage pollution could be identified as the dominating fecal source at the highly connected sites by adding information from MST analysis. In contrast, animal fecal pollution proofed to be dominating in areas with low river connectivity. The selection of genetic MST markers was focusing on potentially important pollution sources in the backwater area, using human (BacHum, HF183II), ruminant (BacR) and pig (Pig2Bac) -associated quantitative PCR assays. The presented approach is assumed to be useful to characterize alluvial water resources for water safety management throughout the globe, by allocating fecal pollution to autochthonous, allochthonous, human or animal contamination components. The established river connectivity metric is not limited to bacterial fecal pollution, but can be applied to any type of chemical and microbiological contamination.

An agent-based model that simulates the spatio-temporal dynamics of sources and transfer mechanisms contributing faecal indicator organisms to streams. Part 2: Application to a small agricultural catchment

The new Model for the Agent-based simulation of Faecal Indicator Organisms (MAFIO) is applied to a small (0.42 km²) Scottish agricultural catchment to simulate the dynamics of E. coli arising from sheep and cattle farming, in order to provide a proof-of-concept. The hydrological environment for MAFIO was simulated by the "best" ensemble run of the tracer-aided ecohydrological model EcH₂O-iso, obtained through multi-criteria calibration to stream discharge (MAE: 1.37 L s^-1) and spatially-distributed stable isotope data (MAE: 1.14-3.02‰) for the period April-December 2017. MAFIO was then applied for the period June-August for which twice-weekly E. coli loads were quantified at up to three sites along the stream. Performance in simulating these data suggested the model has skill in capturing the transfer of faecal indicator organisms (FIOs) from livestock to streams via the processes of direct deposition, transport in overland flow and seepage from areas of degraded soil. Furthermore, its agent-based structure allowed source areas, transfer mechanisms and host animals contributing FIOs to the stream to be quantified. Such information is likely to have substantial value in the context of designing and spatially-targeting mitigation measures against impaired microbial water quality. This study also revealed, however, that avenues exist for improving process conceptualisation in MAFIO (e.g. to include FIO contributions from wildlife) and highlighted the need to quantitatively assess how uncertainty in the spatial extent of surface flow paths in the simulated hydrological environment may affect FIO simulations. Despite the consequent status of MAFIO as a research-level model, its encouraging performance in this proof-of-concept study suggests the model has significant potential for eventual incorporation into decision support frameworks.

Viral and Bacterial Fecal Indicators in Untreated Wastewater across the Contiguous United States Exhibit Geospatial Trends

Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United States are sparse. We report geospatial trends of cultivated bacteriophage (somatic, F⁺, and total coliphages and GB-124 phage), as well as genetic markers targeting polyomavirus, enterococci, E. coli, Bacteroidetes, and human-associated Bacteroides spp. (HF183/BacR287 and HumM2) in 49 primary influent sewage samples collected from facilities across the contiguous United States. Samples were selected from rural and urban facilities spanning broad latitude, longitude, elevation, and air temperature gradients by using a geographic information system stratified random site selection procedure. Most indicators in sewage demonstrated a remarkable similarity in concentration regardless of location. However, some exhibited predictable shifts in concentration based on either facility elevation or local air temperature. Geospatial patterns identified in this study, or the absence of such patterns, may have several impacts on the direction of future water quality management research, as well as the selection of alternative metrics to estimate sewage pollution on a national scale.IMPORTANCE This study provides multiple insights to consider for the application of bacterial and viral indicators in sewage to surface water quality monitoring across the contiguous United States, ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirmed that crAssphage genetic markers occur at a higher average concentration than key human-associated Bacteroides spp. on a national scale. Geospatial testing also suggested that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial trends in untreated sewage represents an important step toward the validation of these newer methods for future water quality monitoring applications. In addition, the large paired-measurement data set reported here affords the opportunity to conduct a range of secondary analyses, such as the generation of new or updated quantitative microbial risk assessment models used to estimate public health risk.