Decay of enteric microorganisms in biosolids-amended soil under wheat (Triticum aestivum) cultivation

Aging of colloidal contaminants and pathogens in the soil environment: Implications for nanoplastic and COVID-19 risk mitigation

Colloidal contaminants and pathogens are widely distributed in soil, whose tiny sizes and distinct surface properties render unique environmental behaviours. Because of aging, colloids can undergo dramatic changes in their physicochemical properties once in the soil environment, thus leading to diverse or even unpredictable environmental behaviour and fate. Herein, we provide a state-of-art review of colloid aging mechanisms and characteristics and implications for risk mitigation. First, we review aging-induced formation of colloidal contaminants and aging-associated changes. We place a special focus on emerging nanoplastic (NP) contaminants and associated physical, chemical, and biological aging processes in soil environments. Second, we assess aging and survival features of colloidal pathogens, especially viruses. Viruses in soils may survive from several days to months, or even several years in groundwater, depending on their rates of inactivation and the reversibility of attachment. Furthermore, we identify implications for risk mitigation based on aging mechanisms. Hotspots of (photo)chemical aging of NPs, including plastic gauzes at construction sites and randomly discarded plastic waste in rural areas, are identified as area requiring greater research attention. For COVID-19, we suggest taking greater care in regions where viruses are persist for long periods, such as cold climate regions. Soil amendment with quicklime (CaO) may act as an effective means for pathogen disinfection. Future risk mitigation of colloidal contaminants and pathogens relies on a better understanding of aging mechanisms and more sophisticated models accurately depicting processes in real soil environments.

Quantitative microbial human exposure model for faecal indicator bacteria and risk assessment of pathogenic Escherichia coli in surface runoff following application of dairy cattle slurry and co-digestate to grassland

Animal waste contains high numbers of microorganisms and therefore can present a potential biological threat to human health. During episodic rainfall events resulting in runoff, microorganisms in the waste and soil may migrate into surface runoff, contaminating surface water resources. A probabilistic human exposure (HE) model was created to determine exposure to faecal indicator bacteria (FIB): total coliforms (TC), E. coli and enterococci following application of bio-based fertiliser (dairy cattle slurry, digestate) to grassland; using a combination of experimental field results and literature-based data. This step was followed by a quantitative microbial risk assessment (QMRA) model for pathogenic E. coli based on a literature-based dose-response model. The results showed that the maximum daily HE (HE_daily) is associated with E. coli for unprocessed slurry (treatment T1) on day 1, the worst-case scenario where the simulated mean HE_daily was calculated as 2.84 CFU day ^-1. The results indicate that the overall annual probability of risk (P_annual) of illness from E. coli is very low or low based on the WHO safe-limit of P_annual as 10 ^-6. In the worst-case scenario, a moderate risk was estimated with simulated mean P_annual as 1.0 × 10 ^-5. Unpasteurised digestate application showed low risk on day 1 and 2 (1.651 × 10 ^-6, 1.167 × 10 ^-6, respectively). Pasteurised digestate showed very low risk in all scenarios. These results support the restriction imposed on applying bio-based fertiliser if there is any rain forecast within 48 h from the application time. This study proposes a future extension of the probabilistic model to include time, intensity, discharge, and distance-dependant dilution factor. The information generated from this model can help policymakers ensure the safety of surface water sources through the quality monitoring of FIB levels in bio-based fertiliser.

Impact of biosolids amendment and wastewater effluent irrigation on enteric antibiotic-resistant bacteria - a greenhouse study

Reuse of wastewater effluent and biosolids in agriculture is essential to sustainable water and nutrient resource management practices. Wastewater and biosolids, however, are reportedly the recipients, reservoirs, and sources of antibiotic-resistant enteric pathogens. While decay rates of fecal bacterial indicators in soil are frequently studied, very few studies have reported on the persistence of the antibiotic-resistant sub-populations. Little is known about how multi-drug resistance phenotypes of enteric bacteria in agricultural soil change over time. In this study, germinated carrot seeds were planted in soil that received biosolids amendment and/or wastewater effluent irrigation in a greenhouse setting. We quantified total and antibiotic-resistant fecal bacterial indicators (Escherichia coli and enterococci) weekly in soil and total E. coli at harvest (day 77) on carrots. Antibiotic susceptibility of 121 E. coli and 110 enterococci collected isolates were determined. E. coli or enterococci were not recovered from the soil without biosolids amendment regardless of the irrigation water source. After biosolids amendment, soil E. coli and enterococci concentrations increased more than 3 log₁₀ CFU/g-TS within the first week, declined slowly over time, but stayed above the detection limit (0.39 CFU/g-TS) over the entirety of the study. No statistical difference was found between effluent wastewater or water irrigation in soil total and antibiotic-resistant E. coli and enterococci concentrations or carrots E. coli levels. Soil antibiotic-resistant E. coli and enterococci decayed significantly faster than total E. coli and enterococci. Moreover, the prevalence of multi-drug resistant (resistance to three or more antibiotics) E. coli declined significantly over time, while almost all collected enterococci isolates showed multi-drug resistance phenotypes. At harvest, E. coli were present on carrots; the majority of which were resistant to ampicillin. The survival of antibiotic-resistant enteric bacteria in soil and on harvested carrots indicates there are transmission risks associated with biosolids amendment use in root crops.

Strain, Soil-Type, Irrigation Regimen, and Poultry Litter Influence Salmonella Survival and Die-off in Agricultural Soils

The use of untreated biological soil amendments of animal origin (BSAAO) have been identified as one potential mechanism for the dissemination and persistence of Salmonella in the produce growing environment. Data on factors influencing Salmonella concentration in amended soils are therefore needed. The objectives here were to (i) compare die-off between 12 Salmonella strains following inoculation in amended soil and (ii) characterize any significant effects associated with soil-type, irrigation regimen, and amendment on Salmonella survival and die-off. Three greenhouse trials were performed using a randomized complete block design. Each strain (~4 log CFU/g) was homogenized with amended or non-amended sandy-loam or clay-loam soil. Salmonella levels were enumerated in 25 g samples 0, 0.167 (4 h), 1, 2, 4, 7, 10, 14, 21, 28, 56, 84, 112, 168, 210, 252, and 336 days post-inoculation (dpi), or until two consecutive samples were enrichment negative. Regression analysis was performed between strain, soil-type, irrigation, and (i) time to last detect (survival) and (ii) concentration at each time-point (die-off rate). Similar effects of strain, irrigation, soil-type, and amendment were identified using the survival and die-off models. Strain explained up to 18% of the variance in survival, and up to 19% of variance in die-off rate. On average Salmonella survived for 129 days in amended soils, however, Salmonella survived, on average, 30 days longer in clay-loam soils than sandy-loam soils [95% Confidence interval (CI) = 45, 15], with survival time ranging from 84 to 210 days for the individual strains during daily irrigation. When strain-specific associations were investigated using regression trees, S. Javiana and S. Saintpaul were found to survive longer in sandy-loam soil, whereas most of the other strains survived longer in clay-loam soil. Salmonella also survived, on average, 128 days longer when irrigated weekly, compared to daily (CI = 101, 154), and 89 days longer in amended soils, than non-amended soils (CI = 61, 116). Overall, this study provides insight into Salmonella survival following contamination of field soils by BSAAO. Specifically, Salmonella survival may be strain-specific as affected by both soil characteristics and management practices. These data can assist in risk assessment and strain selection for use in challenge and validation studies.

Study of Evolution of Microbiological Properties in Sewage Sludge-Amended Soils: A Pilot Experience

Large amounts of sewage sludge are generated in urban wastewater treatment plants and used as fertilizer in agriculture due to its characteristics. They can contain contaminants such as heavy metals and pathogenic microorganisms. The objective of this research work is to study, in real conditions, the evolution of microbial concentration in agricultural soils fertilized by biologically treated sewage sludge. The sludge (6.25 tons Ha-1) was applied in two agricultural soils with different textures and crops. A microbiological (total coliforms, Escherichia coli, Staphylococcus aureus, Enterococcus sp., Pseudomonas sp., Salmonella sp. and total mesophylls) and physical-chemical characterization of the sludge, soils and irrigation water were carried out. The evolution of these parameters during sowing, growth and harvesting of crops was studied. Initially, sewage sludge had a higher concentration of microorganisms than soils. Irrigation water also contained microorganisms, fewer than sewage sludge amendment but not negligible. After amendment, there were no differences in the microbiological evolution in the two types of soil. In general, bacterial concentrations after crop harvest were lower than bacterial concentrations detected before sewage sludge amendment. Consequently, the application of sludge from water treatment processes did not worsen the microbiological quality of agricultural soil in this study at real conditions.

Environmental Drivers for Persistence of Escherichia coli and Salmonella in Manure-Amended Soils: A Meta-Analysis

ABSTRACT

Application of organic amendments to agricultural land improves soil quality and provides nutrients essential for plant growth; however, they are also a reservoir for zoonotic pathogens whose presence poses a significant risk to public health. The persistence of bacteria in manure-amended soil, and differences in manure handling practices, are important issues from a food safety perspective. The primary objective of this study was to quantitatively summarize the variations in the rate of decline of Escherichia coli and Salmonella spp. in manure-amended soil under laboratory and field conditions, and to assess the impact of environmental factors. Available literature data on persistence of E. coli and Salmonella spp. in manure-amended soil from 42 primary research studies were extracted and statistically analyzed using a mixed-effect regression model. The results indicated that temperature (soil and air combined) was the most prominent factor affecting persistence of both E. coli and Salmonella spp. under laboratory conditions (P < 0.001), and of E. coli under field conditions (P < 0.05). The time required for a log reduction of E. coli under field conditions was significantly higher at low temperature (0 to 10°C) than at high temperature (greater than 20°C) (P < 0.05). In addition, application method was identified as a significant factor, with manure incorporation to soil inducing longer survival compared with surface application by approximately 1.2 times. The significant variation observed among primary research studies of bacterial persistence has highlighted that mitigation strategies associated with the use of manures in fresh produce production need to be improved by addressing factors such as climate, soil management, application method, and initial microbial levels. These findings may be used to support guidelines establishing exclusion periods between manure fertilization and the grazing or harvesting of crops, and may be useful for the generation of quantitative microbial risk models for fresh produce.

HIGHLIGHTS

Soil contamination of a public park by human and canine mastadenovirus, as well as hookworms and Toxocara spp eggs

Public parks are leisure environments widely used by both, adults and children, often accompained by their pets. Soil contamination of these environments by enteric viruses and intestinal parasites occurs through these animals feces. The aim of this work was to detect Carnivore protoparvovirus 1 (CPV-1) and different species of Mastadenovirus in soils samples from a park located in a medium-sized city in Brazil and evaluate the presence of helminth eggs and larvae in 18 points of a public park soil samples, as well as feces found on this site during six months. Parasitological analyzes were conducted through flotation and sedimentation techniques, and polymerase chain reaction (PCR) was used for viral detection. Of the 216 soil and 16 feces samples, 49% (106/216) and 12% (2/16) were positivefor nematodes larvae, respectively, through sedimentation techniques. Toxocara spp eggs were found in one soil sample and one feces sample, Trichuris spp eggs were found in only one feces sample and Hookworms eggs were found in four soil samples. After reconstruction work in the streets near the park, 30% (64/216) of the samples were positive for Human Mastadenovirus C (HAdV-C), 1.4% (3/216) for HAdV-E and 0.4% (1/216) for Canine Mastadenovirus A (CAdV-A). The parasitic forms found in this study have demonstrated that the contamination of the park’s soil pose a threat to human and animal health. This was the first study to report the presence of HAdVs and CAdVs in soil samples.

Decay rates of Escherichia coli, Enterococcus spp., F-specific bacteriophage MS2, somatic coliphage and human adenovirus in facultative pond sludge

The purpose of this study was to evaluate the efficacy of a waste stabilization pond (WSP) system to reduce pathogen contaminants in sludge. This included examining the factors that influence the fate and concentration of human pathogens and their indicators in two sludge layers. The decay rates of five study microorganisms were determined under in-situ conditions at a WSP. The background levels of fecal origin microorganisms were consistently detected (ranging: Escherichia coli 10⁴ to 10⁶, enterococci 10¹ to 10³, F-specific bacteriophage (MS2) 10¹ to 10³ and somatic coliphage 10¹ to 10⁴ colony-forming units (CFU) mL^-1, as well as 10¹ to 10² human adenovirus gene copies mL^-1) in the primary facultative pond. Among microorganisms tested, the bacteria generally decayed faster than adenovirus and bacteriophage, particularly in the upper sludge layer. Due to the observed regrowth of E. coli, it may have a limited value as an indicator for pathogen removal in the wastewater stabilization ponds. The abundance of E. coli numbers within the pond biome followed changes in pond temperature over time. The results of the study suggest that viruses could survive for a long time, particularly in deeper layers (>1 metre) in the sludge, during winter months (T₉₀ = 156 d). The presence of human pathogens in WSP sludge, in particular viruses, may be a barrier to its beneficial reuse in agriculture. The results indicate that additional treatment of sludge may be required to mitigate potential public health risks from reuse of sludge for agricultural purposes.

Comparative Assessment of BGM and PLC/PRF/5 Cell Lines for Enteric Virus Detection in Biosolids

The buffalo green monkey (BGM) cell line is required for the detection of enteric viruses in biosolids through a total culturable viral assay (TCVA) by the United States Environmental Protection Agency. In the present study, BGM and PLC/PRF/5 cell lines were evaluated for TCVA and for their use in determining the incidence of adenoviruses and enteroviruses in raw sludge and Class B biosolids. Six raw sludge and 17 Class B biosolid samples were collected from 13 wastewater treatment plants from seven U.S. states. Samples were processed via organic flocculation and concentrate volumes equivalent to 4 g total solids were assayed on BGM and PLC/PRF/5 cells. Cell monolayers were observed for cytopathic effect (CPE) after two 14-days passages. Cell lysates were tested for the presence of adenoviruses and enteroviruses by PCR or RT-PCR. The PLC/PRF/5 cells detected more culturable viruses than the BGM cells by CPE (73.9% vs. 56.5%, respectively). 52% of the samples were positive for CPE using both cell lines. No viruses were detected in either cell line by PCR in flasks in which CPE was not observed. No adenoviruses were detected in 13 CPE-positive samples from BGM lysates. In contrast, of the 17 samples exhibiting CPE on PLC/PRF/5 cells, 14 were positive for adenoviruses (82.4%). In conclusion, PLC/PRF/5 cells were superior for the detection of adenoviruses in both raw sludge and Class B biosolids. Thus, the use of BGM cells alone for TCVA may underestimate the viral concentration in sludge/biosolid samples.

A quantitative microbial risk assessment model for total coliforms and E. coli in surface runoff following application of biosolids to grassland

In Ireland, the land application of biosolids is the preferred option of disposing of municipal sewage waste. Biosolids provide nutrients in the form of nitrogen, phosphorus, potassium and increases organic matter. It is also an economic way for a country to dispose of its municipal waste. However, biosolids may potentially contain a wide range of pathogens, and following rainfall events, may be transported in surface runoff and pose a potential risk to human health. Thus, a quantitative risk assessment model was developed to estimate potential pathogens in surface water and the environmental fate of the pathogens following dilution, residence time in a stream, die-off rate, drinking water treatment and human exposure. Surface runoff water quality data was provided by project partners. Three types of biosolids, anaerobically digested (AD), lime stabilised (LS), and thermally dried (TD)) were applied on micro plots. Rainfall was simulated at three time intervals (24, 48 and 360 h) following land application. It was assumed that this water entered a nearby stream and was directly abstracted for drinking water. Consumption data for drinking water and body weight was obtained from an Irish study and assigned distributions. Two dose response models for probability of illness were considered for total and faecal coliform exposure incorporating two different exposure scenarios (healthy populations and immuno-compromised populations). The simulated annual risk of illness for healthy populations was below the US EPA and World Health Organisation tolerable level of risk (10^-4 and 10^-6, respectively). However, immuno-compromised populations may still be at risk as levels were greater than the tolerable level of risk for that subpopulation. The sensitivity analysis highlighted the importance of residence time in a stream on the bacterial die-off rate.

Different Behavior of Enteric Bacteria and Viruses in Clay and Sandy Soils after Biofertilization with Swine Digestate

Enteric pathogens from biofertilizer can accumulate in the soil, subsequently contaminating water and crops. We evaluated the survival, percolation and leaching of model enteric pathogens in clay and sandy soils after biofertilization with swine digestate: PhiX-174, mengovirus (vMC0), Salmonella enterica Typhimurium and Escherichia coli O157:H7 were used as biomarkers. The survival of vMC0 and PhiX-174 in clay soil was significantly lower than in sandy soil (iT90 values of 10.520 ± 0.600 vs. 21.270 ± 1.100 and 12.040 ± 0.010 vs. 43.470 ± 1.300, respectively) and PhiX-174 showed faster percolation and leaching in sandy soil than clay soil (iT90 values of 0.46 and 2.43, respectively). S. enterica Typhimurium was percolated and inactivated more slowly than E. coli O157:H7 (iT90 values of 9.340 ± 0.200 vs. 6.620 ± 0.500 and 11.900 ± 0.900 vs. 10.750 ± 0.900 in clay and sandy soils, respectively), such that E. coli O157:H7 was transferred more quickly to the deeper layers of both soils evaluated (percolation). Our findings suggest that E. coli O157:H7 may serve as a useful microbial biomarker of depth contamination and leaching in clay and sandy soil and that bacteriophage could be used as an indicator of enteric pathogen persistence. Our study contributes to development of predictive models for enteric pathogen behavior in soils, and for potential water and food contamination associated with biofertilization, useful for risk management and mitigation in swine digestate recycling.

Importance of Soil Amendments: Survival of Bacterial Pathogens in Manure and Compost Used as Organic Fertilizers

Biological soil amendments (BSAs) such as manure and compost are frequently used as organic fertilizers to improve the physical and chemical properties of soils. However, BSAs have been known to be a reservoir for enteric bacterial pathogens such as enterohemorrhagic Escherichia coli (EHEC), Salmonella spp., and Listeria spp. There are numerous mechanisms by which manure may transfer pathogens to growing fruits and vegetables, and several outbreaks of infections have been linked to manure-related contamination of leafy greens. In the United States several commodity-specific guidelines and current and proposed federal rules exist to provide guidance on the application of BSAs as fertilizers to soils, some of which require an interval between the application of manure to soils and the harvest of fruits and vegetables. This review examines the survival, persistence, and regrowth/resuscitation of bacterial pathogens in manure, biosolids, and composts. Moisture, along with climate and the physicochemical properties of soil, manure, or compost, plays a significant role in the ability of pathogens to persist and resuscitate in amended soils. Adaptation of enteric bacterial pathogens to the nonhost environment of soils may also extend their persistence in manure- or compost-amended soils. The presence of antibiotic-resistance genes in soils may also be increased by manure application. Overall, BSAs applied as fertilizers to soils can support the survival and regrowth of pathogens. BSAs should be handled and applied in a manner that reduces the prevalence of pathogens in soils and the likelihood of transfer of food-borne pathogens to fruits and vegetables. This review will focus on two BSAs—raw manure and composted manure (and other feedstocks)—and predominantly on the survival of enteric bacterial pathogens in BSAs as applied to soils as organic fertilizers.