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This study aims to present a comprehensive study on the risks associated with the residual presence and transport of Escherichia coli (E. coli) in soil following the application of livestock manure in Chinese farmlands by integrating machine learning algorithms with mechanism-based models (Phydrus). We initially review 28 published papers to gather data on E. coli's die-off and attachment characteristics in soil. Machine learning models, including deep learning and gradient boosting machine, are employed to predict key parameters such as the die-off rate of E. coli and first-order attachment coefficient in soil. Then, Phydrus was used to simulate E. coli transport and survival in 23692 subregions in China. The model considered regional differences in E. coli residual risk and transport, influenced by soil properties, soil depths, precipitation, seasonal variations, and regional disparities. The findings indicate higher residual risks in regions such as the Northeast China, Eastern Qinghai-Tibet Plateau, and pronounced transport risks in the fringe of the Sichuan Basin fringe, the Loess Plateau, the North China Plain, the Northeast Plain, the Shigatse Basin, and the Shangri-La region. The study also demonstrates a significant reduction in both residual and transport risks one month after manure application, highlighting the importance of timing manure application and implementing region-specific standards. This research contributes to the broader understanding of pathogen behavior in agricultural soils and offers practical guidelines for managing the risks associated with manure use. This study's comprehensive method offers a potentially valuable tool for evaluating microbial contaminants in agricultural soils across the globe., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Traditional methods for assessing bacterial transport in soil or permeable sand aquifers, such as flow‐through experiments, breakthrough curve (BTC), and retention profile (RP) analysis, face challenges due to their complexity and the labor‐intensive nature of in situ implementations. This study seeks to address the question: How can the transport behavior of bacteria in soil be predicted in a simpler and more cost‐effective manner using RPs? We introduce an RP method designed to overcome these challenges by utilizing soil sampling at various depths to model bacterial breakthrough behaviors with greater efficiency. By employing the one‐site attachment/detachment model within the Hydrus 1D framework, our research compares the RP method (three RPs) against the conventional approach (BTC + RP), showcasing its efficacy through column experiments with bioluminescent Escherichia coli in humic acid‐coated sand. The results indicate that the accuracy of RP method aligns closely with traditional methods in predicting bacterial transport. This technique allows for the use of solid samples collected from a limited number of depths to predict breakthrough behaviors accurately, making it suitable for evaluating bacterial transport in settings such as farmlands, contaminated lands, riverbanks, and soil aquifer treatment systems. Our findings underscore the RP method's role in streamlining experimental procedures and its potential application in environmental science and agronomy. [ABSTRACT FROM AUTHOR]

Transport of pathogenic bacteria from land surface to groundwater is largely influenced by rainfall intensity and geochemical and structural heterogeneities of subsurface sediments at different depths. It has been assumed that the change in rainfall intensity has different effects on bacterial transport as a function of soil depth. In this study, repacked and intact column systems were used to investigate the influences of pore water velocity on the transport of Escherichia coli 652T7 through a loamy soil collected from varying soil depths. The soils differed in geochemical properties and soil structures. The concentrations of bacteria in soil and liquid samples were measured using plate counting method. The breakthrough percentages of E. coli 652T7 increased with pore water velocity at each depth in both intact and disturbed soils. Among the different soil depths, the largest velocity effect was observed for the transport through the top soil (0–5 cm) of both disturbed and intact soil profiles. This depth-dependent effect of pore water velocity was attributed to down gradients of soil organic matter (SOM) and iron oxide contents with depth because SOM and iron oxides were favorable for bacterial attachment on soil surfaces. In addition, less bacteria broke through the disturbed soil than through the intact soil at the same depth, and the pore water velocity effect was stronger with the disturbed than intact soils. Specifically, the maximum C/C0 (i.e., ratio of effluent to influent concentration) doubled (i.e., from 0.36 to 0.76) in the 0–5 cm intact soil columns and tripled (i.e., from 0.16 to 0.43) in the 0–5 cm repacked soil columns. This structure-dependent effect of pore water velocity was attributed to larger pore tortuosity and a narrower range of pore sizes in the disturbed soil than in the intact soil. These findings suggest that change in pore water velocity could trigger bacterial remobilization especially in surface soils, where more bacteria are retained relative to deep soils. Depth profile of pore water velocity effect in differently structured soils. [ABSTRACT FROM AUTHOR]

Soil geochemical and structural heterogeneities are coupled in influencing the fate and transport of viruses in soil profiles. Only the soil layer at a certain depth, where viruses have least mobility, determines the total flux and distance of virus transport. However, few studies have addressed the dependence of virus transport on soil depths. This dependence is mostly due to the gradients of geochemistry, soil structure, and solution chemistry along the soil profile. We employed intact soil columns (5 cm in length, 4.5 cm in inner diameter) from three depths (5–10 cm, 35–40 cm, and 65–70 cm) to investigate the transport of two very different model viruses: 1) MS2; a hydrophobic, negatively charged, less aggregated phage of E. coli , and 2) ΦX174; a hydrophilic, positively charged (pH=6.58 ± 0.21), highly aggregated phage of E. coli as a function of depth. The breakthrough of both viruses increased with soil depth in both 10 mM and 40 mM NaCl solutions. The mobility of MS2 was greater than ΦX174 at 5–10 cm and 35–40 cm depths, but the mobility of ΦX174 increased much faster than MS2 with soil depth and surpassed MS2 mobility in the soil of 65–70 cm depth. The effect of ionic strength on the mobility of nanosized MS2 decreased with soil depth because of decreased soil organic matter (SOM) content. The decreased SOM lessened ionic strength sensitivity via a hydrophobicity-reduced Lewis acid-base attraction mechanism. In comparison, ΦX174 viruses showed an overall weaker response to ionic strength change since they were aggregated into microsized particles in the experimental solutions and thereby subjected to mechanical straining in the intact soils. The elevated straining effect counteracted the electrostatically facilitated transport of ΦX174. These findings suggest that soil amendments with organic matter might be low cost, effective measures for reducing virus transport through soil profiles. [Display omitted] • Viral mobility increases with soil depth. • Soil organic matter is key to limiting viral spread. • Soil organic matter reduces viral sensitivity to ionic strength. • Nanosized viruses have high environmental risks. • Mobility of aggregated viruses is dominated by straining than electrostatic forces. [ABSTRACT FROM AUTHOR]

[Display omitted] • A non-invasive imaging technique was developed for real-time bacterial observation. • Depth for maximum bacterial retention shifted with time under unsaturated flow. • Bacterial retention decreased exponentially with travel distance at lower velocity. • Bacterial retention decreased multi-exponentially with distance at higher velocity. This study investigated the transport and retention of bioluminescent Escherichia coli strain 652T7 under different pore water velocities (8.7 cm h−1 and 13.0 cm h−1) and pore water saturations (85% and 100%) utilizing a non-invasive, real-time bioluminescent imaging technique. Under saturated flow conditions, the concentrations of retained bioluminescent E. coli 652T7 decreased exponentially with distance from the source at the lower velocity but decreased non-exponentially at the higher velocity. Under unsaturated flow conditions, pore water velocity had no significant effect on bacterial breakthrough concentration; however, the concentrations of retained cells were maximal at a significant distance from the source (non-monotonic). The distance from source of the maximum concentration increased from 2.4-cm at 1.05 pore volumes to 4.3-cm at 3.15 pore volumes, indicating slow translation of bacterial down-gradient under unsaturated flow conditions. That conditions were modestly unfavorable to attachment at the solid-water interface (SWI) was indicated by deposition rate coefficients being greater (by a factor of four) for simulations versus experiments, and by significant repulsive barriers to attachment at both the SWI (260 kT) and the air–water interface (AWI, fully repulsive). The inferred slow translation under unsaturated flow conditions therefore reflects either accumulation without arrest in the secondary minimum at the SWI and/or capillary interaction at the AWI. This non-invasive bioluminescence method yielded real-time quantitative observation of bacterial distribution from source and demonstrated contrasting transport behaviors previously obtained solely via more laborious methods with limited spatio-temporal observation. [ABSTRACT FROM AUTHOR]

[Display omitted] • Bacterial mobility increased with soil depth. • Soil disturbance increased bacterial dispersion. • Intact soil structure was favorable to bacterial transport. • Soil organic matter, iron oxides, and zeta potential are key to bacterial transport. Pathogenic bacteria, widely present in septic tanks, sewage sludges, and wastewater, can move through the subsurface environment to pollute drinking water. Bacterial transport behaviors vary with soil properties and are subject to soil pore networking. In this study, we investigated the transport of Escherichia coli 652T7 through intact and disturbed soils collected from different soil depths (0−5 cm, 5−10 cm, 10−15 cm, and 15−20 cm). The results obtained under steady-state saturated flow conditions demonstrated significant influences of soil depth and soil structure on the transport of E. coli 652T7. The breakthrough percentages of E. coli 652T7 from the intact soil cores increased with soil depth from 36 % at 0−5 cm to 63 % at 5−10 cm, 83 % at 10−15 cm, and 100 % at 15−20 cm. A similar trend was observed for the breakthrough from the repacked soil cores except with lower percentages (i.e., 16 % at 0−5 cm, 49 % at 5−10 cm, 76 % at 10−15 cm, and 86 % at 15−20 cm). Such an increase with soil depth was attributed to a combined effect of decreases in soil organic matter content (from 3.84 % to 2.47 %), free iron oxides (from 142.25 mg kg−1 to 110.66 mg kg−1), and zeta potential (from −17.6 mV to −29.0 mV) with soil depth. The larger breakthrough percentages of E. coli 652T7 from the intact than the repacked soil cores are speculated due to the existence of larger macropores, lower pore connectivity density, and reduced access to attachment sites in the intact soils than in the disturbed soils. Overall, this study suggests that tillage and organic amendments might be effective measures for reducing bacterial movement in soils. [ABSTRACT FROM AUTHOR]