Transport and attenuation of Salmonella enterica, fecal indicator bacteria and a poultry litter marker gene are correlated in soil columns

Occurrence, transmission and risks assessment of pathogens in aquatic environments accessible to humans

Pathogens are ubiquitously detected in various natural and engineered water systems, posing potential threats to public health. However, it remains unclear which human-accessible waters are hotspots for pathogens, how pathogens transmit to these waters, and what level of health risk associated with pathogens in these environments. This review collaboratively focuses and summarizes the contamination levels of pathogens on the 5 water systems accessible to humans (natural water, drinking water, recreational water, wastewater, and reclaimed water). Then, we showcase the pathways, influencing factors and simulation models of pathogens transmission and survival. Further, we compare the health risk levels of various pathogens through Quantitative Microbial Risk Assessment (QMRA), and assess the limitations of water-associated QMRA application. Pathogen levels in wastewater are consistently higher than in other water systems, with no significant variation for Cryptosporidium spp. among five water systems. Hydraulic conditions primarily govern the transmission of pathogens into human-accessible waters, while environmental factors such as temperature impact pathogens survival. The median and mean values of computed public health risk levels posed by pathogens consistently surpass safety thresholds, particularly in the context of recreational waters. Despite the highest pathogens levels found in wastewater, the calculated health risk is significantly lower than in other water systems. Except pathogens concentration, variables like the exposure mode, extent, and frequency are also crucial factors influencing the public health risk in water systems. This review shares valuable insights to the more accurate assessment and comprehensive management of public health risk in human-accessible water environments.

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.

Enterobacteria Survival, Percolation, and Leaching on Soil Fertilized with Swine Manure

Swine manure has a high load of pathogens, which can pose a risk to human and environmental health. In Brazil, studies evaluating the survival of pathogens in soil are scarce. Therefore, this study aimed to evaluate the survival, percolation, and leaching of enterobacteria in clayey soil after fertilization with swine manure. For this purpose, soil columns were fertilized with manure spiked with enterobacteria. The microorganisms' behavior was monitored in terms of survival, percolation, and leaching with and without rain. Soil samples were collected, and Escherichia coli and Salmonella enterica serovar Senftemberg were quantified. The results indicated that E. coli survived for a longer period (43 days) than S. senftemberg (14 days). E. coli percolated quickly through the soil, leaching 60 cm in less than 5 min during rainy events and remaining viable for up to 24 h after the rain. The results show the importance of treating manure effectively before being added to the soil. An efficient treatment could be anaerobic digestion, followed by a pond system. Considering the characteristics of swine-producing regions, the load of effluents applied to the soil may percolate, leach, or run off and consequently contaminate water bodies with pathogens.

Interactive removal of bacterial and viral particles during transport through low-cost filtering materials

Pathogen filtration is critically important for water sanitation. However, it is a big challenge to balance removal efficiency and filtering material cost. In this study, we quantified the removal processes of a bacterial strain Escherichia coli 652T7 and a model bacteriophage MS2 (ATCC 15597-B1) during their transport through columns containing iron filings (IF), calcined magnesite (CM), natural ore limestone (OL) or corn stalk biochar (BC) under saturated flow conditions. Experimental results showed that 99.98, 79.55, 63.79, and 62.59% of injected E. coli 652T7 and 98.78, 92.26, 68.79, and 69.82% of injected MS2 were removed by IF, CM, OL, and BC, respectively. The differences in removal percentage were attributed to the disparities of the microorganisms and filtering materials in surface function groups, surface charges, and surface morphology. Transport modeling with advection-dispersion equation (ADE) and interaction energy calculation with extended Derjaguin, Landau, Verwey, and Overbeek (XDLVO) model indicated that E. coli 652T7 and MS2 were mostly removed via irreversible attachment. In IF columns, E. coli 652T7 promoted the transport of MS2 but not vice versa. In CM columns, MS2 facilitated the transport of E. coli 652T7 and vice versa at a less extent. Such changes were a combined result of attachment site competition, steric effect, and mechanical straining. We found that the sum of the removal percentages of the two microorganisms in their respective transport experiments were similar to those calculated from their co-transport experiments. This result suggests that the removals were mainly limited by the attachment sites in the filtering materials.

Environmental Injustice and Industrial Chicken Farming in Delaware

Potential disparities in the distribution of poultry CAFOs (confined animal feeding operations) and meat-processing facilities across Delaware were explored with regards to sociodemographic factors including race, ethnicity, and socioeconomic status. We conducted buffer analyses of CAFO host census tracts alongside sociodemographic data in order to explore populations in proximity to the Delaware chicken industry. We conducted a hotspot analysis of CAFOs to find areas with large concentrations of poultry operations and applied zero-inflation regression models to determine if there's a relationship between sociodemographic composition and number of CAFOs/meat- processing facilities in Delaware. Median household income was lower in CAFO host census tracts than all others, and also lower than the state median. A larger percentage of people living in poverty are in poultry CAFO hotspots (15.4 percent) compared to the state average (13.7 percent). Delaware's chicken industry disproportionately burdens low-wealth communities. Delaware policy-makers should employ environmental justice-oriented solutions to best serve impacted populations.

Modeling the vertical transport of antibiotic resistance genes in agricultural soils following manure application

Antibiotic resistance genes (ARGs) may be introduced to agricultural soil through the land application of cattle manure. During a rainfall event, manure-borne ARGs may infiltrate into subsurface soil and leach into groundwater. The objective of this study was to characterize and model the vertical transport of manure-borne ARGs through soil following the land application of beef cattle manure on soil surface. In this study, soil column experiments were conducted to evaluate the influence of manure application on subsurface transport of four ARGs: erm(C), erm(F), tet(O) and tet(Q). An attachment-detachment model with the decay of ARGs in the soil was used to simulate the breakthrough of ARGs in leachates from the control column (without manure) and treatment (with manure) soil columns. Results showed that the first-order attachment coefficient (k_a) was five to six orders of magnitude higher in the treatment column than in the control column. Conversely, the first-order detachment and decay coefficients (k_d and μ_s) were not significantly changed due to manure application. These findings suggest that in areas where manure is land-applied, some manure-borne bacteria-associated ARGs will be attached to the soil, instead of leaching to groundwater in near terms.

Particle fractionation controls Escherichia coli release from solid manure

Bacteria transport through soil is a complex process particularly when the cells are released from solid manures and co-transported with particles. This study focuses on understanding of the Escherichia coli release from different particle fractions (0.25-, 0.5-, 1-, and 2-mm) of solid manure and evaluating different influent boundary conditions during cell release from manure and when a solid manure is applied to the soil. The 0.25-mm and 2-mm particle sizes resulted a greater cell release compared to 0.5-mm and 1-mm fractions (p < 0.05). The shape and magnitude of the cell release curves (CRCs) from the original manure bulk were mainly influenced by the two 0.25-mm and 2-mm fractions, respectively. The arithmetic mean for normalizing the CRCs and the time variable- based normalized CRCs for the manure-treated soil were the robust variables in evaluation of the experimental data. However, a single maximum bacteria concentration could provide the realistic dataset for the modeling process. Evaluation of the root-mean-squared-error and Akaike criterion showed that the two- and three-parametric models are recommended for simulating the cell release from solid manure in comparison with one parametric models. This study also suggests considering separate microbial release evaluations, with regards to influent concentration, for manure and manure-treated soils to propose best management practices for controlling bacteria pollution. Further research will reveal the key roles of different woody components and soluble material ratios for the various solid manures in bacteria release.

Combining multi-isotopic and molecular source tracking methods to identify nitrate pollution sources in surface and groundwater

Nitrate (NO₃^-) pollution adversely impacts surface and groundwater quality. In recent decades, many countries have implemented measures to control and reduce anthropogenic nitrate pollution in water resources. However, to effectively implement mitigation measures at the origin of pollution,the source of nitrate must first be identified. The stable nitrogen and oxygen isotopes of NO₃^- (ẟ¹⁵N and ẟ¹⁸O) have been widely used to identify NO₃^- sources in water, and their combination with other stable isotopes such as boron (ẟ¹¹B) has further improved nitrate source identification. However, the use of these datasets has been limited due to their overlapping isotopic ranges, mixing between sources, and/or isotopic fractionation related to physicochemical processes. To overcome these limitations, we combined a multi-isotopic analysis with fecal indicator bacteria (FIB) and microbial source tracking (MST) techniques to improve nitrate origin identification. We applied this novel approach on 149 groundwater and 39 surface water samples distributed across Catalonia (NE Spain). A further 18 wastewater treatment plant (WWTP) effluents were also isotopically and biologically characterized. The groundwater and surface water results confirm that isotopes and MST analyses were complementary and provided more reliable information on the source of nitrate contamination. The isotope and MST data agreed or partially agreed in most of the samples evaluated (79 %). This approach was especially useful for nitrate pollution tracing in surface water but was also effective in groundwater samples influenced by organic nitrate pollution. Furthermore, the findings from the WWTP effluents suggest that the use of literature values to define the isotopic ranges of anthropogenic sources can constrain interpretations. We therefore recommend that local sources be isotopically characterized for accurate interpretations. For instance, the detection of MST inferred animal influence in some WWTP effluents, but the ẟ¹¹B values were higher than those reported in the literature for wastewater. The results of this study have been used by local water authorities to review uncertain cases and identify new vulnerable zones in Catalonia according to the European Nitrate Directive (91/676/CEE).

Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (∼4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwater and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments.IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.

Adsorption kinetics of the herbicide safeners, benoxacor and furilazole, to activated carbon and agricultural soils

Chloroacetamide herbicides, namely acetochlor and metolachlor, are common herbicides used on corn and soybean fields. Dichloroacetamide safeners, namely benoxacor and furilazole, are commonly used in formulations containing chloroacetamide herbicides. Extensive reports on adsorption of chloroacetamide herbicides are available, yet little information exists regarding adsorption potential of co-applied safeners. Herein, the adsorption and desorption characteristics of selected herbicide safeners to granular activated carbon (GAC) and in agricultural soils are reported. Further, soil column studies were performed to understand the leaching behaviour of the herbicide Dual II Magnum. Equilibrium sorption experiments of safeners to three agricultural soils and one GAC showed that adsorption was best fitted by the Freundlich isotherm. The Freundlich adsorption constant, K_f, for benoxacor and furilazole sorption onto three agricultural soils ranged from 0.1 to 0.27 and 0.1 to 0.13 (mg/g) × (mg/L)ˆ(1/n), respectively. The K_f for benoxacor and furilazole to GAC was 6.4 and 3.4 (mg/g) × (mg/L)ˆ(1/n), respectively, suggesting more favorable sorption of benoxacor to GAC than furilazole to GAC. The sorption to soils was reversible as almost 40%-90% of both safeners was desorbed from three soils. These results were validated in four replicated soil column studies, where S-metolachlor was shown to leach similarly to the safener benoxacor, originating from the herbicide formulation. The leaching of S-metolachlor and benoxacor was influenced by soil texture. Cumulatively, these results show that safeners will move through the environment to surface waters similarly to the active ingredients in herbicides, but may be removed during drinking water treatment via GAC.

Retention modes of manure-fecal coliforms in soil under saturated hydraulic condition

Manures are important soil nutrient conditioners and source of several pathogenic bacteria that potentially contribute to groundwater and surface water pollution. The best management practices need a solid understanding of manure sources, concentrations, and strategies to limit the number of bacteria in natural soil environment. In this study, a series of soil column experiments were conducted to investigate how bacteria mobility can potentially be influenced by retention mechanisms while moving through undisturbed saturated soil. This was assessed by bacteria retention profiles and mobility indices including the maximum transported (C_max-T) and retained (C_max-R) concentrations, filtration coefficient (λ_f) and the maximum depth of bacteria transport (Z_max). Three different soil samples (sandy, loamy and silty clay loam) were enriched with three types of manures (cow, sheep, and poultry), placed on top of three soil columns (16 cm diameter, 30 cm height) with an equivalent of 10 Mg ha^-1 (dry basis) summing up to a total of 36 columns. Leaching was performed under saturated steady-state conditions (i.e., 1.62 cm min^-1) for a duration of 4 pore volumes. After percolation, soil columns were sliced into six 5-cm interval layers and slices were characterized for retained bacteria. Results showed irregular exponential or quasi-exponential bacteria retention profiles for cow and sheep manures, whereas uniform-shaped profiles occurred for poultry manure. The latter variant also switched to exponential shape for the sandy soil at the highest and lowest C_max-T and C_max-R values due to higher pore water velocity. The λ_f and the Z_max values were also found to be affected by soil texture and manure origin. The λ_f was higher for poultry manure due to higher free-cell transport of bacteria most probably induced by higher amount of soluble mobile components. However, the greater amounts of transported wooden materials released from cow and sheep manures acted as harbors for bacteria. Accordingly, the filtration rate decreased and tailing effects for bacteria transport increased. The results also suggest that the practices and strategies for using manures could be optimized according to the respective transport behavior to manage the bacteria retention with respect to soil and manure types to reduce soil and water pollution.

Fecal pollution: new trends and challenges in microbial source tracking using next-generation sequencing

In this minireview, we expand upon traditional microbial source tracking (MST) methods by discussing two recently developed, next-generation-sequencing (NGS)-based MST approaches to identify sources of fecal pollution in recreational waters. One method defines operational taxonomic units (OTUs) that are specific to a fecal source, e.g., humans and animals or shared among multiple fecal sources to determine the magnitude and likely source association of fecal pollution. The other method uses SourceTracker, a program using a Bayesian algorithm, to determine which OTUs have contributed to an environmental community based on the composition of microbial communities in multiple fecal sources. Contemporary NGS-based MST tools offer a promising avenue to rapidly characterize fecal source contributions for water monitoring and remediation efforts at a broader and more efficient scale than previous molecular MST methods. However, both NGS methods require optimized sequence processing methodologies (e.g. quality filtering and clustering algorithms) and are influenced by primer selection for amplicon sequencing. Therefore, care must be taken when extrapolating data or combining datasets. Furthermore, traditional limitations of library-dependent MST methods, including differential decay of source material in environmental waters and spatiotemporal variation in source communities, remain to be fully understood. Nevertheless, increasing use of these methods, as well as expanding fecal taxon libraries representative of source communities, will help improve the accuracy of these methods and provide promising tools for future MST investigations.

Chrysomya megacephala larvae feeding favourably influences manure microbiome, heavy metal stability and greenhouse gas emissions

Chrysomya megacephala is a saprophagous fly whose larvae can compost manure and yield biomass and bio‐fertilizer simultaneously. However, there are concerns for the safety of the composting system, that is risk of diseases spread by way of manure pathogens, residue of harmful metals and emission of greenhouse gases. Microbiota analysis and heavy metal speciation by European Communities Bureau of Reference were evaluated in raw, C. megacephala‐composted and natural stacked swine manure to survey pathogenic bacterial changes and mobility of lead and cadmium in manure after C. megacephala feeding; the emission rate of CH₄ and N₂O from manure during C. megacephala composting and natural stacking was also measured. C. megacephala composting altered manure microbiota, reduced the risk of pathogenic bacteria and maintained the stability, and microbiota changes might be associated with heavy metal fractions, especially in Pseudomonas and Prevotella. In addition, C. megacephala‐composting significantly reduced the emission rate of CH₄ and N₂O in comparing with natural stacking situation and the first two days should be the crucial period for CH₄ and N₂O emission measurement for manure treatment by C. megacephala. Moreover, OTU26 and Betaproteobacteria were changed after C. megacephala composting which might play a role in emission of CH₄ and N₂O, respectively.

Bacterial mobilization and transport through manure enriched soils: Experiment and modeling

A precise evaluation of bacteria transport and mathematical investigations are useful for best management practices in agroecosystems. In this study, using laboratory experiments and modeling approaches, we assess the transport of bacteria released from three types of manure (cow, sheep, and poultry) to find the importance of the common manures in agricultural activities in soil and water pollution. Thirty six intact soil columns with different textures (sandy, loamy, and silty clay loam) were sampled. Fecal coliform leaching from layers of the manures on the soil surface was conducted under steady-state saturated flow conditions at 20 °C for up to four Pore Volumes (PVs). Separate leaching experiments were conducted to obtain the initial concentrations of bacteria released from the manures (Co). Influent (Co) and effluent (C) bacteria concentrations were measured by the plate-count method and the normalized concentrations (C/C0) were plotted versus PV representing the breakthrough curves (BTCs). Transport parameters were predicted using the attachment/detachment model (two-kinetic site) in HYDRUS-1D. Simulations fitted well the experimental data (R² = 0.50-0.96). The attachment, detachment, and straining coefficients of bacteria were more influenced by the soils treated with cow manure compared to the sheep and poultry manures. Influent curves of fecal coliforms from the manures (leached without soil) illustrated that the poultry manure had the highest potential to pollute the effluent water from the soils in term of concentration, but the BTCs and simulated data related to the treated soils illustrated that the physical shape of cow manure was more important to both straining and detachment of bacteria back into the soil solution. Detachment trends of bacteria were observed through loam and silty clay loam soils treated with cow manure compared to the cow manure enriched sandy soil. We conclude that management strategies must specifically minimize the effect of fecal coliform concentrations before field application, especially for the combination of poultry and cow manures, which has higher solubility and tailing behavior, respectively. Interestingly, the addition of sheep manure with all three soils had the lowest mobilization of bacteria. We also suggest studying the chemistry of soil solution affected by manures to present all relevant information which affect bacterial movement through soils during leaching.

Identification of Factors Affecting Fecal Pollution in Beaver Lake Reservoir

Standard methods for the evaluation of recreational water quality rely on generic bacterial indicators such as . However, does not provide enough information to determine fecal source or public health risk. The stsudy objective was to determine factors influencing the presence of and host-specific markers (HSM) from upstream to downstream in Beaver Lake Reservoir (BLR). From February 2014 to September 2015, 420 base flow and rain event samples were collected from seven sites-two sites from streams (White River [WR] and War Eagle Creek) draining into BLR and five sites from within BLR. Each sample was analyzed for and by quantitative polymerase chain reaction for HSM related to human, bovine, and poultry. The data indicate that overall levels of were significantly greater in the WR and significantly lower at the most downstream sampling location in BLR. is more likely present during spring (adjusted odds ratio [aOR] = 1.86), at the WR sampling site (aOR = 3.39), or during a rain event (aOR = 2.73). Moreover, the HSM HumM2 is more likely present (aOR = 1.99) when is present. These same factors were associated with concentrations >126 most probable number 100 mL (aOR = 2.76-12.48), except the poultry marker CL was more likely associated (aOR = 3.81) than HumM2. This study revealed that both seasonal and locational factors are important variables for fecal pollution in BLR. Moreover, these same factors may apply to fecal pollution in manmade reservoirs within similar types of watersheds across the United States, as well as internationally.