Modeling microorganism transport and survival in the subsurface

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Assessing the risk of E. coli contamination from manure application in Chinese farmland by integrating machine learning and Phydrus

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.

Prediction of attachment efficiency using machine learning on a comprehensive database and its validation

Colloidal particles can attach to surfaces during transport, but the attachment depends on particle size, hydrodynamics, solid and water chemistry, and particulate matter. The attachment is quantified in filtration theory by measuring attachment or sticking efficiency (Alpha). A comprehensive Alpha database (2538 records) was built from experiments in the literature and used to develop a machine learning (ML) model to predict Alpha. The training (r-squared: 0.86) was performed using two random forests capable of handling missing data. A holdout dataset was used to validate the training (r-squared: 0.98), and the variable importance was explored for training and validation. Finally, an additional validation dataset was built from quartz crystal microbalance experiments using surface-modified polystyrene, poly (methyl methacrylate), and polyethylene. The experiments were performed in the absence or presence of humic acid. Full database regression (r-squared: 0.90) predicted Alpha for the additional validation with an r-squared of 0.23. Nevertheless, when the original database and the additional validation dataset were combined into a new database, both the training (r-squared: 0.95) and validation (r-squared: 0.70) increased. The developed ML model provides a data-driven prediction of Alpha over a big database and evaluates the significance of 22 input variables.

Granular media filtration for on-site treatment of greywater: A review

Rapid urbanization and industrialization have put pressure on water resources and centralized wastewater treatment facilities and the need for greywater treatment at decentralized levels is increasing. This paper reviews the studies that used granular filtration for the treatment of greywater. Filter media characteristics that helps in the selection of suitable sustainable and environmental friendly materials without compromising the quality of treated greywater is first reported. The effect of type of filter media, media size and media depth along with the effect of operating conditions are discussed in detail. The choice, role and effect of different pre-treatment alternatives to granular media filtration are also presented. The efficiency of the filters to remove different physicochemical and microbial parameters was compared with different reuse guidelines and standards. Reported studies indicate that not only filter media characteristics and operating conditions but also the quality of raw greywater significantly influence the filter performance. Based on the source of greywater and desired reuse option, different granular media filtration alternatives are suggested. Operation of filters with properly selected media at optimum conditions based on the source of greywater helps filter in achieve the different reuse standards.

Measuring and modeling the influence of salinity change on the transport behaviour of Escherichia coli through quartz sand

Pathogenic bacteria can be discharged in the environment through natural as well as anthropogenic activities. Once in the environment, they may contaminate soil and sediments and migrate towards water bodies. Transient chemical conditions may occur in soil/sediments and favor mobilization of bacteria, e.g., upon the reduction of salinity (or ionic strength). However, the magnitude of this phenomenon and its relationship with particle size is not well understood, yet. In this work, we investigated the transport of Escherichia coli under variable salinity conditions (between 1 and 20 part per thousand, ppt) and for different soil grain sizes (between 150 and 710 μm). A model developed in our group was applied in this work. It couples bacteria and salinity transport equations in order to account for transient water composition in the description of bacteria migration. The model was calibrated and validated with laboratory experiments. The tests were monitored continuously with UV-Vis spectroscopy, which allowed to record highly resolved concentration fronts. The results show that salinity increases the retardation of the bacteria. Upon salinity drop, a release of bacteria occurs forming a peak whose magnitude increases with salinity change. This effect becomes more important as the grain size decreases. Simulations suggest that the dominant retention mechanism is attachment for coarse sand and straining for fine sand. The retention can be reversed as the salinity is reduced causing a sudden bacteria mobilization. Such a behaviour may have important implications on microbial contamination of water bodies when soil/sediments undergo transient chemical conditions.

Transport of marine tracer phage particles in soil

Marine phages have been applied to trace ground- and surface water flows. Yet, information on their transport in soil and related particle intactness is limited. Here we compared the breakthrough of two lytic marine tracer phages (Pseudoalteromonas phages PSA-HM1 and PSA-HS2) with the commonly used Escherichia virus T4 in soil- and sand-filled laboratory percolation columns. All three phages showed high mass recoveries in the effluents and a higher transport velocity than non-reactive tracer Br^-. Comparison of effluent gene copy numbers (CN) to physically-determined phage particle counts or infectious phage counts showed that PSA-HM1 and PSA-HS2 retained high phage particle intactness (I_p > 81%), in contrast to T4 (I_p < 36%). Our data suggest that marine phages may be applied in soil to mimic the transport of (bio-) colloids or anthropogenic nanoparticles of similar traits. Quantitative PCR (qPCR) thereby allows for highly sensitive quantification and thus for the detection of even highly diluted marine tracer phages in environmental samples.

Improving safe sanitation practices using groundwater transport modelling and water quality monitoring data

In many developing countries, poorly constructed pit latrines are the primary source of groundwater contamination. Approaches are needed to identify site-specific separation distances between domestic wells and pit latrines. In this study, tracer transport simulations are combined with water quality monitoring data to identify separation distances in peri-urban Dar es Salaam. Bivariate correlation and linear regression models were used to find the relationships between (1) simulated tracer and distances from the wells to the nearest pit latrines (2) simulated tracer and observed contaminants (nitrate, E. coli, and total dissolved solids). The results showed a strong correlation between tracer with nitrate and E. coli, with Pearson coefficient (r) values of 0.80 and 0.79, but a weak correlation with total dissolved solids (TDS) (r = 0.23). A strong correlation between tracer and distance for shallow and deep wells (r = -0.96, -0.76) was found. Based on the soil type and aquifer properties in the area, wells must be placed at least 34 m from a pit latrine to minimize contamination. With recent advances in sensor technologies and the availability of low-cost sensors, linking simulated tracer with observed contaminant levels may provide an alternative first approach to quickly assess human health risks associated with groundwater contamination.

Fate and transport in environmental quality

Changes in pollutant concentrations in environmental media occur both from pollutant transport in water or air and from local processes, such as adsorption, degradation, precipitation, straining, and so on. The terms "fate and transport" and "transport and fate" reflect the coupling of moving with the carrier media and biogeochemical processes describing local transformations or interactions. The Journal of Environmental Quality (JEQ) was one of the first to publish papers on fate and transport (F&T). This paper is a minireview written to commemorate the 50th anniversary of JEQ and show how the research interests, methodology, and public attention have been reflected in fate and transport publications in JEQ during the last 40 years. We report the statistics showing how the representation of different pollutant groups in papers changed with time. Major focus areas have included the effect of solution composition on F&T and concurrent F&T, the role of organic matter, and the relative role of different F&T pathways. The role of temporal and spatial heterogeneity has been studied at different scales. The value of long-term F&T studies and developments in modeling as the F&T research approach was amply demonstrated. Fate and transport studies have been an essential part of conservation measure evaluation and comparison and ecological risk assessment. For 50 years, JEQ has delivered new insights, methods, and applications related to F&T science. The importance of its service to society is recognized, and we look forward to new generations of F&T researchers presenting their contributions in JEQ.

Engineering modeling frameworks for microbial food safety at various scales

The landscape of mathematical model-based understanding of microbial food safety is wide and deep, covering interdisciplinary fields of food science, microbiology, physics, and engineering. With rapidly growing interest in such model-based approaches that increasingly include more fundamental mechanisms of microbial processes, there is a need to build a general framework that steers this evolutionary process by synthesizing literature spread over many disciplines. The framework proposed here shows four interconnected, complementary levels of microbial food processes covering sub-cellular scale, microbial population scale, food scale, and human population scale (risk). A continuum of completely mechanistic to completely empirical models, widely-used and emerging, are integrated into the framework; well-known predictive microbiology modeling being a part of this spectrum. The framework emphasizes fundamentals-based approaches that should get enriched over time, such as the basic building blocks of microbial population scale processes (attachment, migration, growth, death/inactivation and communication) and of food processes (e.g., heat and moisture transfer). A spectrum of models are included, for example, microbial population modeling covers traditional predictive microbiology models to individual-based models and cellular automata. The models are shown in sufficient quantitative detail to make obvious their coupling, or their integration over various levels. Guidelines to combine sub-processes over various spatial and time scales into a complete interdisciplinary and multiphysics model (i.e., a system) are provided, covering microbial growth/inactivation/transport and physical processes such as fluid flow and heat transfer. As food safety becomes increasingly predictive at various scales, this synthesis should provide its roadmap. This big picture and framework should be futuristic in driving novel research and educational approaches.

Storage and export of microbial biomass across the western Greenland Ice Sheet

The Greenland Ice Sheet harbours a wealth of microbial life, yet the total biomass stored or exported from its surface to downstream environments is unconstrained. Here, we quantify microbial abundance and cellular biomass flux within the near-surface weathering crust photic zone of the western sector of the ice sheet. Using groundwater techniques, we demonstrate that interstitial water flow is slow (~10⁻² m d⁻¹), while flow cytometry enumeration reveals this pathway delivers 5 × 10⁸ cells m⁻² d⁻¹ to supraglacial streams, equivalent to a carbon flux up to 250 g km⁻² d⁻¹. We infer that cellular carbon accumulation in the weathering crust exceeds fluvial export, promoting biomass sequestration, enhanced carbon cycling, and biological albedo reduction. We estimate that up to 37 kg km⁻² of cellular carbon is flushed from the weathering crust environment of the western Greenland Ice Sheet each summer, providing an appreciable flux to support heterotrophs and methanogenesis at the bed.

Microbes that colonise ice sheet surfaces are important to the carbon cycle, but their biomass and transport remains unquantified. Here, the authors reveal substantial microbial carbon fluxes across Greenland’s ice surface, in quantities that may sustain subglacial heterotrophs and fuel methanogenesis.

Analytical modeling of three-stage inactivation of viruses within droplets and solid porous particles

Various viruses can hide within fluid and solid structures and thus successfully cross different distances, causing the spread of viral infections. Analytical modeling of the triple treatment of virus within a small liquid droplet and within a solid porous particle is the basic research polygon of this paper. The three-stage treatment aims to maximize the efficacy of deactivating viruses indoors. In order to achieve this, viruses undergo treatment by infrared heating, ultraviolet deactivation and ionization-electrostatic deactivation by negative ions. When the droplets are treated with infrared heating, incomplete evaporation occurs, reducing their initial diameter by 10 times; an initial diameter of droplets is 0.01 mm, 0.03 mm and 0.05 mm. Thermal inactivation of viruses inside the droplets is almost negligible, due to short exposure time and a maximum temperature of 100 °C. On the other hand, when solid porous particles are heated to a much higher temperature at the same exposure time, this causes significant thermal inactivation of viruses inside them. Reducing the diameter of the droplet (due to evaporation) by 10 times causes a multiple increase in UV-C deactivation of viruses inside the droplets. The effect of UV-C radiation on viruses within solid porous particles is not included in this paper.

Transport and retention of porous silicon-coated zero-valent iron in saturated porous media

Porous silicon-coated zero-valent iron (Fe⁰@p-SiO₂) is a promising material for in-situ contaminated groundwater remediation. However, investigations of factors that affect the transport of Fe⁰@p-SiO₂ remain incomplete. In the present study, Fe⁰@p-SiO₂ composites were prepared by a SiO₂-coated technology, and a series of column experiments were conducted to examine the effects of media size, ionic strength, and injection velocity and concentration on retention and transport in saturated porous media. Results showed that the obtained Fe⁰@p-SiO₂ is a core-shell composite with zero-valent iron as the core and porous silicon as the shell. Media size, injection velocity, Fe⁰ concentration, and ionic strength had a significant impact on the transport of Fe⁰@p-SiO₂. Fe⁰@p-SiO₂ effluent concentrations decreased with a smaller media size. Increasing initial particle concentration and ionic strength led to a decrease in particle transport. High particle retention was observed near the middle of the column, especially with high injection concentration. That was also observable in the condition of lower injection velocity or finer media. The results indicated that two transport behaviors during particles transport, which were "agglomeration-straining" and "detachment-re-migration". Moreover, the dominated mechanisms for Fe⁰@p-SiO₂ transport and retention in saturated porous media are hydrodynamic dispersion and interception. Given the results, in practical engineering applications, proper injection velocity and concentration should be selected depending on the pollution status of groundwater and the geochemical environment to ensure an effective in-situ reaction zone.

Groundwater pollution assessment in a coastal aquifer in Cape Coast, Ghana

This work presents an assessment of the chemico-physical and microbial quality of water samples from hand-dug wells in the shallow aquifer of three communities neighbouring the University of Cape Coast, Ghana. Sanitary risk inspection was undertaken at each well location and the physical parameters including electrical conductivity, pH, Dissolved Oxygen (DO) and etc. were measured in situ via probes. Microbial groundwater quality was analysed using membrane filtration method. Samples of water were analysed for the pollution indicator anions including chloride and nitrate. In addition, the possible persistence of bacteria in groundwater environments in the absence of predator organisms were studied and results fitted with exponential, second-order polynomial and linear distribution models. Sanitary risk inspection and microbial quality results indicate that all the wells were at risk and polluted with total coliforms from on-site sanitation. Twenty-five percent (7 out of 28) of the wells recorded DO concentration within acceptable limits of drinking water standards (> 5 mg/L). Average chloride concentration, 360.5 mg/L (range: 46 mg/L to 844 mg/L) and average electrical conductivity value of 1.5 mS/cm (range: 213 μS/cm to 2.7 mS/cm) were both higher than WHO recommended limits. Acidic conditions (pH < 6.5) were observed in water samples, indicating mineralisation of the aquifer. The high EC values and chloride content in groundwater were attributable to dry atmospheric aerosol deposition and possible mineral dissolution in the aquifer. Bacteria re-growth experiment results indicate that second-order polynomial distribution best describes bacteria inactivation rates in the absence of antagonist predators in our work. Extrapolation of time for complete inactivation of bacteria under groundwater environment ranged from 0.1 to 4 years indicating bacteria can persist in aquifers for long period of time. It was concluded that all the wells are at risk of pollution and polluted with faecal matter and atmospheric aerosols.

The Conjugation Window in an Escherichia coli K-12 Strain with an IncFII Plasmid

Many studies have examined the role that conjugation plays in disseminating antibiotic resistance genes in bacteria. However, relatively little research has quantitively examined and modeled the dynamics of conjugation under growing and nongrowing conditions beyond a couple of hours. We therefore examined growing and nongrowing cultures of Escherichia coli over a 24-h period to understand the dynamics of bacterial conjugation in the presence and absence of antibiotics with pUUH239.2, an IncFII plasmid containing multiantibiotic- and metal-resistant genes. Our data indicate that conjugation occurs after E. coli cells divide and before they have transitioned to a nongrowing phase. The result is that there is only a small window of opportunity for E. coli to conjugate with pUUH239.2 under both growing and nongrowing conditions. Only a very small percentage of the donor cells likely are capable of even undergoing conjugation, and not all transconjugants can become donor cells due to molecular regulatory controls and not being in the correct growth phase. Once a growing culture enters stationary phase, the number of capable donor cells decreases rapidly and conjugation slows to produce a plateau. Published models did not provide accurate descriptions of conjugation under nongrowing conditions. We present here a modified modeling approach that accurately describes observed conjugation behavior under growing and nongrowing conditions.IMPORTANCE There has been growing interest in horizontal gene transfer of antibiotic resistance plasmids as the antibiotic resistance crisis has worsened over the years. Most studies examining conjugation of bacterial plasmids focus on growing cultures of bacteria for short periods, but in the environment, most bacteria grow episodically and at much lower rates than in the laboratory. We examined conjugation of an IncFII antibiotic resistance plasmid in E. coli under growing and nongrowing conditions to understand the dynamics of conjugation under which the plasmid is transferred. We found that conjugation occurs in a narrow time frame when E. coli is transitioning from a growing to nongrowing phase and that the conjugation plateau develops because of a lack of capable donor cells in growing cultures. From an environmental aspect, our results suggest that episodic growth in nutrient-depleted environments could result in more conjugation than sustained growth in a nutrient rich environment.

Transport and retention of engineered silver nanoparticles in carbonate-rich sediments in the presence and absence of soil organic matter

The transport and retention behavior of polymer- (PVP-AgNP) and surfactant-stabilized (AgPURE) silver nanoparticles in carbonate-dominated saturated and unconsolidated porous media was studied at the laboratory scale. Initial column experiments were conducted to investigate the influence of chemical heterogeneity (CH) and nano-scale surface roughness (NR) arising from mixtures of clean, positively charged calcium carbonate sand (CCS), and negatively charged quartz sands. Additional column experiments were performed to elucidate the impact of CH and NR arising from the presence and absence of soil organic matter (SOM) on a natural carbonate-dominated aquifer material. The role of the nanoparticle capping agent was examined under all conditions tested in the column experiments. Nanoparticle transport was well described using a numerical model that facilitated blocking on one or two retention sites. Results demonstrate that an increase in CCS content in the artificially mixed porous medium leads to delayed breakthrough of the AgNPs, although AgPURE was much less affected by the CCS content than PVP-AgNPs. Interestingly, only a small portion of the solid surface area contributed to AgNP retention, even on positively charged CCS, due to the presence of NR which weakened the adhesive interaction. The presence of SOM enhanced the retention of AgPURE on the natural carbonate-dominated aquifer material, which can be a result of hydrophobic or hydrophilic interactions or due to cation bridging. Surprisingly, SOM had no significant impact on PVP-AgNP retention, which suggests that a reduction in electrostatic repulsion due to the presence of SOM outweighs the relative importance of other binding mechanisms. Our findings are important for future studies related to AgNP transport in shallow unconsolidated calcareous and siliceous sands.

On Modeling Ensemble Transport of Metal Reducing Motile Bacteria

Many metal reducing bacteria are motile with their run-and-tumble behavior exhibiting series of flights and waiting-time spanning multiple orders of magnitude. While several models of bacterial processes do not consider their ensemble motion, some models treat motility using an advection diffusion equation (ADE). In this study, Geobacter and Pelosinus, two metal reducing species, are used in micromodel experiments for study of their motility characteristics. Trajectories of individual cells on the order of several seconds to few minutes in duration are analyzed to provide information on (1) the length of runs, and (2) time needed to complete a run (waiting or residence time). A Continuous Time Random Walk (CTRW) model to predict ensemble breakthrough plots is developed based on the motility statistics. The results of the CTRW model and an ADE model are compared with the real breakthrough plots obtained directly from the trajectories. The ADE model is shown to be insufficient, whereas a coupled CTRW model is found to be good at predicting breakthroughs at short distances and at early times, but not at late time and long distances. The inadequacies of the simple CTRW model can possibly be improved by accounting for correlation in run length and waiting time.

Impacts of a changing earth on microbial dynamics and human health risks in the continuum between beach water and sand

Although infectious disease risk from recreational exposure to waterborne pathogens has been an active area of research for decades, beach sand is a relatively unexplored habitat for the persistence of pathogens and fecal indicator bacteria (FIB). Beach sand, biofilms, and water all present unique advantages and challenges to pathogen introduction, growth, and persistence. These dynamics are further complicated by continuous exchange between sand and water habitats. Models of FIB and pathogen fate and transport at beaches can help predict the risk of infectious disease from beach use, but knowledge gaps with respect to decay and growth rates of pathogens in beach habitats impede robust modeling. Climatic variability adds further complexity to predictive modeling because extreme weather events, warming water, and sea level change may increase human exposure to waterborne pathogens and alter relationships between FIB and pathogens. In addition, population growth and urbanization will exacerbate contamination events and increase the potential for human exposure. The cumulative effects of anthropogenic changes will alter microbial population dynamics in beach habitats and the assumptions and relationships used in quantitative microbial risk assessment (QMRA) and process-based models. Here, we review our current understanding of microbial populations and transport dynamics across the sand-water continuum at beaches, how these dynamics can be modeled, and how global change factors (e.g., climate and land use) should be integrated into more accurate beachscape-based models.

Transport and retention of Shewanella oneidensis strain MR1 in water-saturated porous media with different grain-surface properties

Bacterium Shewanella oneidensis strain (MR1), a facultative microorganism that plays critical role in contaminant transformation and degradation, was used as an example to decipher the transport and retention of microorganisms in water-saturated porous media with different grain-surface properties and under different ionic compositions (i.e. Na⁺, Ca²⁺, and Mg²⁺). Dolomite and quartz sands, which contained different surface charge properties, were used as the representative minerals. Dolomite was selected because its surface charges are significantly affected by solution composition. The mobility of MR1 in the dolomite column was lower than that in the quartz column, because the lower energy barrier between MR1 and dolomite than that between MR1 and quartz, resulting in the larger retention of MR1 in the dolomite column. The breakthrough curves were well simulated by the two sites kinetic model with HYDRUS-1D. The maximum concentration of attached bacteria (S_max) were positively correlated to the ionic strength regardless of mineral types. The values of S_max were about 1.1-4.0 times larger in the MR1-dolomite system than that in the MR1-quartz system under different ionic strength conditions. The retention of the MR1 on dolomite surfaces in the presence of divalent cations Ca²⁺ is significantly higher than that on quartz surfaces primarily due to the larger electrostatic attraction energy between the MR1 and dolomite grains. The findings demonstrate that the porous media with the lower negative charge has the higher capacity for the retention and deposition of MR1, potentially affecting the transport of MR1 and other bacteria in the subsurface.

Natural source zone depletion of LNAPL: A critical review supporting modelling approaches

Natural source zone depletion (NSZD) of light non-aqueous phase liquids (LNAPLs) includes partitioning, transport and degradation of LNAPL components. NSZD is being considered as a site closure option during later stages of active remediation of LNAPL contaminated sites, and where LNAPL mass removal is limiting. To ensure NSZD meets compliance criteria and to design enhanced NSZD actions if required, residual risks posed by LNAPL and its long term behaviour require estimation. Prediction of long-term NSZD trends requires linking physicochemical partitioning and transport processes with bioprocesses at multiple scales within a modelling framework. Here we expand and build on the knowledge base of a recent review of NSZD, to establish the key processes and understanding required to model NSZD long term. We describe key challenges to our understanding, inclusive of the dominance of methanogenic or aerobic biodegradation processes, the potentially changeability of rates due to the weathering profile of LNAPL product types and ages, and linkages to underlying bioprocesses. We critically discuss different scales in subsurface simulation and modelling of NSZD. Focusing on processes at Darcy scale, 36 models addressing processes of importance to NSZD are investigated. We investigate the capabilities of models to accommodate more than 20 subsurface transport and transformation phenomena and present comparisons in several tables. We discuss the applicability of each group of models for specific site conditions.

Transport of bacteriophage MS2 and PRD1 in saturated dune sand under suboxic conditions

Soil passage of (pretreated) surface water to remove pathogenic microorganisms is a highly efficient process under oxic conditions, reducing microorganism concentrations about 8 log¹⁰ within tens of meters. However, under anoxic conditions, it has been shown that removal of microorganisms can be limited very much. Setback distances for adequate protection of natural groundwater may, therefore, be too short if anoxic conditions apply. Because removal of microorganisms under suboxic conditions is unknown, this research investigated removal of bacteriophage MS2 and PRD1 by soil passage under suboxic conditions at field scale. At the field location (dune area), one injection well and six monitoring wells were installed at different depths along three suboxic flow lines, where oxygen concentrations ranged from 0.4 to 1.7 mg/l and nitrate concentrations ranged from 13 to 16 mg/L. PRD1 and MS2 were injected directly at the corresponding depths and their removal in each flow line was determined. The highest bacteriophage removal was observed in the top layer, with about 9 log removal of MS2, and 7 log removal of PRD1 after 16 meters of aquifer transport. Less removal was observed at 12 m below surface, probably due to a higher groundwater velocity in this coarser grained layer. MS2 was removed more effectively than PRD1 under all conditions. Due to short travel times, inactivation of the phages was limited and the reported log removal was mainly associated with attachment of phages to the aquifer matrix. This study shows that attachment of MS2 and PRD1 is similar for oxic and suboxic sandy aquifers, and, therefore, setback distances used for sandy aquifers under oxic and suboxic conditions provide a similar level of safety. Sticking efficiency and the attachment rate coefficient, as measures for virus attachment, were evaluated as a function of the physico-chemical conditions.

Applying Quantitative Molecular Tools for Virus Transport Studies: Opportunities and Challenges

Bacteriophages have been used in soil column studies for the last several decades as surrogates to study the fate and transport behavior of enteric viruses in groundwater. However, recent studies have shown that the transport behavior of bacteriophages and enteric viruses in porous media can be very different. The next generation of virus transport science must therefore provide more data on mobility of enteric viruses and the relationship between transport behaviors of enteric viruses and bacteriophages. To achieve this new paradigm, labor intensity devoted to enteric virus quantification method must be reduced. Recent studies applied quantitative polymerase chain reaction (qPCR) to column filtration experiments to study the transport behavior of human adenovirus (HAdV) in porous media under a variety of conditions. A similar approach can be used to study the transport of other enteric viruses such as norovirus. Analyzing the column samples with both qPCR and culture assays and applying multiplex qPCR to study cotransport behavior of more than one virus will provide information to under-explored areas in virus transport science. Both nucleic acid extraction kits and one-step lysis protocols have been used in these column studies to extract viral nucleic acid for qPCR quantification. The pros and cons of both methods are compared herein and solutions for overcoming problems are suggested. As better understanding of the transport behavior of enteric viruses is clearly needed, we strongly advocate for application of rapid molecular tools in future studies as well as optimization of protocols to overcome their current limitations.

Continuum-based models and concepts for the transport of nanoparticles in saturated porous media: A state-of-the-science review

Environmental applications of nanoparticles (NP) increasingly result in widespread NP distribution within porous media where they are subject to various concurrent transport mechanisms including irreversible deposition, attachment/detachment (equilibrium or kinetic), agglomeration, physical straining, site-blocking, ripening, and size exclusion. Fundamental research in NP transport is typically conducted at small scale, and theoretical mechanistic modeling of particle transport in porous media faces challenges when considering the simultaneous effects of transport mechanisms. Continuum modeling approaches, in contrast, are scalable across various scales ranging from column experiments to aquifer. They have also been able to successfully describe the simultaneous occurrence of various transport mechanisms of NP in porous media such as blocking/straining or agglomeration/deposition/detachment. However, the diversity of model equations developed by different authors and the lack of effective approaches for their validation present obstacles to the successful robust application of these models for describing or predicting NP transport phenomena. This review aims to describe consistently all the important NP transport mechanisms along with their representative mathematical continuum models as found in the current scientific literature. Detailed characterizations of each transport phenomenon in regards to their manifestation in the column experiment outcomes, i.e., breakthrough curve (BTC) and residual concentration profile (RCP), are presented to facilitate future interpretations of BTCs and RCPs. The review highlights two NP transport mechanisms, agglomeration and size exclusion, which are potentially of great importance in controlling the fate and transport of NP in the subsurface media yet have been widely neglected in many existing modeling studies. A critical limitation of the continuum modeling approach is the number of parameters used upon application to larger scales and when a series of transport mechanisms are involved. We investigate the use of simplifying assumptions, such as the equilibrium assumption, in modeling the attachment/detachment mechanisms within a continuum modelling framework. While acknowledging criticisms about the use of this assumption for NP deposition on a mechanistic (process) basis, we found that its use as a description of dynamic deposition behavior in a continuum model yields broadly similar results to those arising from a kinetic model. Furthermore, we show that in two dimensional (2-D) continuum models the modeling efficiency based on the Akaike information criterion (AIC) is enhanced for equilibrium vs kinetic with no significant reduction in model performance. This is because fewer parameters are needed for the equilibrium model compared to the kinetic model. Two major transport regimes are identified in the transport of NP within porous media. The first regime is characterized by higher particle-surface attachment affinity than particle-particle attachment affinity, and operative transport mechanisms of physicochemical filtration, blocking, and physical retention. The second regime is characterized by the domination of particle-particle attachment tendency over particle-surface affinity. In this regime although physicochemical filtration as well as straining may still be operative, ripening is predominant together with agglomeration and further subsequent retention. In both regimes careful assessment of NP fate and transport is necessary since certain combinations of concurrent transport phenomena leading to large migration distances are possible in either case.

Effect of Low Energy Waves on the Accumulation and Transport of Fecal Indicator Bacteria in Sand and Pore Water at Freshwater Beaches

Elevated fecal indicator bacteria (FIB) in beach sand and pore water represent an important nonpoint source of contamination to surface waters. This study examines the physical processes governing the accumulation and distribution of FIB in a beach aquifer. Field data indicate E. coli and enterococci can be transported 1 and 2 m, respectively, below the water table. Data were used to calibrate a numerical model whereby FIB are delivered to a beach aquifer by wave-induced infiltration across the beach face. Simulations indicate FIB rapidly accumulate in a beach aquifer with FIB primarily associated with sand rather than freely residing in the pore water. Simulated transport of E. coli in a beach aquifer is complex and does not correlate with conservative tracer transport. Beaches with higher wave-induced infiltration rate and vertical infiltration velocity (i.e., beaches with higher beach slope and wave height, and lower terrestrial groundwater discharge) had greater E. coli accumulation and E. coli was transported deeper below the beach face. For certain beach conditions, the amount of FIB accumulated in sand over 5-6 days was found to be sufficient to trigger a beach advisory if eroded to surface water.

Transport of Fecal Indicators from Beach Sand to the Surf Zone by Recirculating Seawater: Laboratory Experiments and Numerical Modeling

Recirculating seawater is an important component of submarine groundwater discharge, yet its role in transporting microbial contaminants from beach sand to coastal water is unknown. This study investigated the extent to which recirculating seawater carries fecal indicators, Enterococcus and bird-associated Catellicoccus, through the beach subsurface. Laboratory experiments and numerical modeling were performed to characterize the transport of fecal indicators suspended in seawater through medium-grained beach sand under transient and saturated flow conditions. Enterococcus was measured both by culture (cENT) and DNA assay (tENT), and Catellicoccus (CAT) by DNA assay. There were differences between transport of tENT and CAT compared to cENT through laboratory columns containing beach sands. Under transient flow conditions, first-order attachment rate coefficients (k_att) of DNA markers were greater (∼10 h^-1) than k_att of cENT (∼1 h^-1), although under saturated conditions k_att values were similar (∼1 h^-1). First-order detachment rate coefficients, k_det, of DNA markers were greater (∼1 h^-1) than k_det of cENT (∼0.1h^-1) under both types of flow conditions. Incorporating the rate coefficients into field-scale subsurface transport simulations showed that, in this sand type, the contribution of recirculating seawater to surf zone contamination is likely to be minimal unless bird feces are deposited close to the land-sea interface.

Do Goethite Surfaces Really Control the Transport and Retention of Multi-Walled Carbon Nanotubes in Chemically Heterogeneous Porous Media?

Transport and retention behavior of multi-walled carbon nanotubes (MWCNTs) was studied in mixtures of negatively charged quartz sand (QS) and positively charged goethite-coated sand (GQS) to assess the role of chemical heterogeneity. The linear equilibrium sorption model provided a good description of batch results, and the distribution coefficients (K_D) drastically increased with the GQS fraction that was electrostatically favorable for retention. Similarly, retention of MWCNTs increased with the GQS fraction in packed column experiments. However, calculated values of K_D on GQS were around 2 orders of magnitude smaller in batch than packed column experiments due to differences in lever arms associated with hydrodynamic and adhesive torques at microscopic roughness locations. Furthermore, the fraction of the sand surface area that was favorable for retention (S_f) was much smaller than the GQS fraction because nanoscale roughness produced shallow interactions that were susceptible to removal. These observations indicate that only a minor fraction of the GQS was favorable for MWCNT retention. These same observations held for several different sand sizes. Column breakthrough curves were always well described using an advective-dispersive transport model that included retention and blocking. However, depth-dependent retention also needed to be included to accurately describe the retention profile when the GQS fraction was small. Results from this research indicate that roughness primarily controlled the retention of MWCNTs, although goethite surfaces played an important secondary role.

Transport and retention of bacteria and viruses in biochar-amended sand

The transport and retention of Escherichia coli and bacteriophages (PRD1, MS2 and ФX174), as surrogates for human pathogenic bacteria and viruses, respectively, were studied in the sand that was amended with several types of biochar produced from various feedstocks. Batch and column studies were conducted to distinguish between the role of attachment and straining in microbe retention during transport. Batch experiments conducted at various solution chemistries showed negligible attachment of viruses and bacteria to biochar before or after chemical activation. At any given solution ionic strength, the attachment of viruses to sand was significantly higher than that of biochar, whereas bacteria showed no attachment to either sand or biochar. Consistent with batch results, biochar addition (10% w/w) to sand reduced virus retention in the column experiments, suggesting a potential negative impact of biochar application to soil on virus removal. In contrast, the retention of bacteria was enhanced in biochar-amended sand columns. However, elimination of the fine fraction (<60μm) of biochar particles in biochar-amended sand columns significantly reduced bacteria retention. Results from batch and column experiments suggest that land application of biochar may only play a role in microbe retention via straining, by alteration of pore size distribution, and not via attachment. Consequently, the particle size distribution of biochar and sediments is a more important factor than type of biochar in determining whether land application of biochar enhances or diminishes microbial retention.

Use of aerobic spores as a surrogate for cryptosporidium oocysts in drinking water supplies

Waterborne illnesses are a growing concern among health and regulatory agencies worldwide. The United States Environmental Protection Agency has established several rules to combat the contamination of water supplies by cryptosporidium oocysts, however, the detection and study of cryptosporidium oocysts is hampered by methodological and financial constraints. As a result, numerous surrogates for cryptosporidium oocysts have been proposed by the scientific community and efforts are underway to evaluate many of the proposed surrogates. The purpose of this review is to evaluate the suitability of aerobic bacterial spores to serve as a surrogate for cryptosporidium oocysts in identifying contaminated drinking waters. To accomplish this we present a comparison of the biology and life cycles of aerobic spores and oocysts and compare their physical properties. An analysis of their surface properties is presented along with a review of the literature in regards to the transport, survival, and prevalence of aerobic spores and oocysts in the saturated subsurface environment. Aerobic spores and oocysts share many commonalities with regard to biology and survivability, and the environmental prevalence and ease of detection make aerobic spores a promising surrogate for cryptosporidium oocysts in surface and groundwater. However, the long-term transport and release of aerobic spores still needs to be further studied, and compared with available oocyst information. In addition, the surface properties and environmental interactions of spores are known to be highly dependent on the spore taxa and purification procedures, and additional research is needed to address these issues in the context of transport.

Critical role of surface roughness on colloid retention and release in porous media

This paper examines the critical role of surface roughness (both nano- and micro-scale) on the processes of colloid retention and release in porous media under steady-state and transient chemical conditions. Nanoscale surface roughness (NSR) in the order of a few nanometers, which is common on natural solid surfaces, was incorporated into extended-DLVO calculations to quantify the magnitudes of interaction energy parameters (e.g. the energy barrier to attachment, ΔΦa , and detachment, ΔΦd , from a primary minimum). This information was subsequently used to explain the behavior of colloid retention and release in column and batch experiments under different ionic strength (IS) and pH conditions. Results demonstrated that the density and height of NSR significantly influenced the interaction energy parameters and consequently the extent and kinetics of colloid retention and release. In particular, values of ΔΦa and ΔΦd significantly decreased in the presence of NSR. Therefore, consistent with findings of column experiments, colloid retention in the primary minimum was predicted to occur at some specific locations on the sand surface, even at low IS conditions. However, NSR yielded a much weaker primary minimum interaction compared with that of smooth surfaces. Colloid release from primary minima upon decreasing IS and increasing pH was attributed to the impact of NSR on the values of ΔΦd . Pronounced differences in the amount of colloid retention in batch and column experiments indicated that primary minimum interactions were weak even at high IS conditions. Negligible colloid retention in batch experiments was attributed to hydrodynamic torques overcoming adhesive torques, whereas significant colloid retention in column experiments was attributed to nano- and micro-scale roughness which would dramatically alter the lever arms associated with hydrodynamic and adhesive torques.

Determining Parameters and Mechanisms of Colloid Retention and Release in Porous Media

A modeling framework is presented to determine fundamental parameters and controlling mechanisms of colloid (microbes, clays, and nanoparticles) retention and release on surfaces of porous media that exhibit wide distributions of nanoscale chemical heterogeneity, nano- to microscale roughness, and pore water velocity. Primary and/or secondary minimum interactions in the zone of electrostatic influence were determined over the heterogeneous solid surface. The Maxwellian kinetic energy model was subsequently employed to determine the probability of immobilization and diffusive release of colloids from each of these minima. In addition, a balance of applied hydrodynamic and resisting adhesive torques was conducted to determine locations of immobilization and hydrodynamic release in the presence of spatially variable water flow and microscopic roughness. Locations for retention had to satisfy both energy and torque balance conditions for immobilization, whereas release could occur either due to diffusion or hydrodynamics. Summation of energy and torque balance results over the elementary surface area of the porous medium provided estimates for colloid retention and release parameters that are critical to predicting environmental fate, including the sticking and release efficiencies and the maximum concentration of retained colloids on the solid phase. Nanoscale roughness and chemical heterogeneity produced localized primary minimum interactions that controlled long-term retention, even when mean chemical conditions were unfavorable. Microscopic roughness played a dominant role in colloid retention under low ionic strength and high hydrodynamic conditions, especially for larger colloids.

Colloid release and clogging in porous media: Effects of solution ionic strength and flow velocity

The release and retention of in-situ colloids in aquifers play an important role in the sustainable operation of managed aquifer recharge (MAR) schemes. The processes of colloid release, retention, and associated permeability changes in consolidated aquifer sediments were studied by displacing native groundwater with reverse osmosis-treated (RO) water at various flow velocities. Significant amounts of colloid release occurred when: (i) the native groundwater was displaced by RO-water with a low ionic strength (IS), and (ii) the flow velocity was increased in a stepwise manner. The amount of colloid release and associated permeability reduction upon RO-water injection depended on the initial clay content of the core. The concentration of released colloids was relatively low and the permeability reduction was negligible for the core sample with a low clay content of about 1.3%. In contrast, core samples with about 6 and 7.5% clay content exhibited: (i) close to two orders of magnitude increase in effluent colloid concentration and (ii) more than 65% permeability reduction. Incremental improvement in the core permeability was achieved when the flow velocity increased, whereas a short flow interruption provided a considerable increase in the core permeability. This dependence of colloid release and permeability changes on flow velocity and colloid concentration was consistent with colloid retention and release at pore constrictions due to the mechanism of hydrodynamic bridging. A mathematical model was formulated to describe the processes of colloid release, transport, retention at pore constrictions, and subsequent permeability changes. Our experimental and modeling results indicated that only a small fraction of the in-situ colloids was released for any given change in the IS or flow velocity. Comparison of the fitted and experimentally measured effluent colloid concentrations and associated changes in the core permeability showed good agreement, indicating that the essential physics were accurately captured by the model.

Microbial Transport and Fate in the Subsurface Environment: Introduction to the Special Section

Microorganisms constitute an almost exclusive form of life in the earth's subsurface environment (not including caves), particularly at depths exceeding the soil horizon. While of broad interest to ecology and geology, scientific interest in the fate and transport of microorganisms, particularly those introduced through the anthropogenic environment, has focused on understanding the subsurface environment as a pathway for human pathogens and on optimizing the use of microbial organisms for remediation of potable groundwater. This special section, inspired by the 2014 Ninth International Symposium for Subsurface Microbiology, brings together recent efforts to better understand the spatiotemporal occurrence of anthropogenic microbial groundwater contamination and the fate and transport of microbes in the subsurface environment: in soils, deep unsaturated zones, and within aquifer systems. Work includes field reconnaissance, controlled laboratory studies to improve our understanding of specific fate and transport processes, and the development and application of improved mechanistic understanding of microbial fate and transport processes in the subsurface environment. The findings confirm and also challenge the limitations of our current understanding of highly complex microbial fate and transport processes across spatiotemporal scales in the subsurface environment; they also add to the increasing knowledge base to improve our ability to protect drinking water resources and perform in situ environmental remediation.

Characterizing Aquifer Heterogeneity Using Bacterial and Bacteriophage Tracers

Gravel aquifers act as important potable water sources in central western Europe, yet they are subject to numerous contamination pressures. Compositional and textural heterogeneity makes protection zone delineation around groundwater supplies in these units challenging; artificial tracer testing aids characterization. This paper reappraises previous tracer test results in light of new geological and microbiological data. Comparative passive gradient testing, using a fluorescent solute (Uranine), virus (H40/1 bacteriophage), and comparably sized bacterial tracers and , was used to investigate a calcareous gravel aquifer's ability to remove microbiological contaminants at a test site near Munich, Germany. Test results revealed relative recoveries could exceed those of H40/1 at monitoring wells, 10 m and 20 m from an injection well, by almost four times; recoveries varied by a factor of up to three between wells. Application of filtration theory suggested greater attenuation of H40/1 relative to similarly charged occurred due to differences in microorganism size, while estimated collision efficiencies appeared comparable. By contrast, more positively charged experienced greater attenuation at one monitoring point, while lower attenuation rates at the second location indicated the influence of geochemical heterogeneity. Test findings proved consistent with observations from nearby fresh outcrops that suggested thin open framework gravel beds dominated mass transport in the aquifer, while discrete intervals containing stained clasts reflect localized geochemical heterogeneity. Study results highlight the utility of reconciling outcrop observations with artificial tracer test responses, using microbiological tracers with well-defined properties, to characterize aquifer heterogeneity.

Dynamics of suspended and attached aerobic toluene degraders in small-scale flow-through sediment systems under growth and starvation conditions

The microbially mediated reactions, that are responsible for field-scale natural attenuation of organic pollutants, are governed by the concurrent presence of a degrading microbial community, suitable energy and carbon sources, electron acceptors, as well as nutrients. The temporal lack of one of these essential components for microbial activity, arising from transient environmental conditions, might potentially impair in situ biodegradation. This study presents results of small scale flow-through experiments aimed at ascertaining the effects of substrate-starvation periods on the aerobic degradation of toluene by Pseudomonas putida F1. During the course of the experiments, concentrations of attached and mobile bacteria, as well as toluene and oxygen were monitored. Results from a fitted reactive-transport model, along with the observed profiles, show the ability of attached cells to survive substrate-starvation periods of up to four months and suggest a highly dynamic exchange between attached and mobile cells under growth conditions and negligible cell detachment under substrate-starvation conditions. Upon reinstatement of toluene, it was readily degraded without a significant lag period, even after a starvation period of 130 days. Our experimental and modeling results strongly suggest that aerobic biodegradation of BTEX-hydrocarbons at contaminated field sites is not hampered by intermittent starvation periods of up to four months.

Mimicking filtration and transport of rotavirus and adenovirus in sand media using DNA-labeled, protein-coated silica nanoparticles

Rotavirus (RoV) and adenovirus (AdV) are important viral pathogens for the risk analysis of drinking water. Despite this, little is known about their retention and transport behaviors in porous media due to a lack of representative surrogates. We developed RoV and AdV surrogates by covalently coupling 70-nm sized silica nanoparticles with specific proteins and a DNA marker for sensitive detection. Filtration experiments using beach sand columns demonstrated the similarity of the surrogates' concentrations, filtration efficiencies and attachment kinetics to those of the target viruses. The surrogates showed the same magnitude of concentration reduction as the viruses. Conversely, MS2 phage (a traditional virus model) over-predicted concentrations of AdV and RoV by 1- and 2-orders of magnitude respectively. The surrogates remained stable in size, surface charge and DNA concentration for at least one year. They can be easily and rapidly detected down to a single particle. Preliminary tests suggest that they were readily detectable in a number of environmental waters and treated effluent. With up-scaling validation in pilot trials, the surrogates developed here could be a cost-effective new tool for studying virus retention and transport in porous media. Examples include assessing filter efficacy in water and wastewater treatment, tracking virus migration in groundwater after effluent land disposal, and establishing safe setback distances for groundwater protection.

An explanation for differences in the process of colloid adsorption in batch and column studies

It is essential to understand the mechanisms that control virus and bacteria removal in the subsurface environment to assess the risk of groundwater contamination with fecal microorganisms. This study was conducted to explicitly provide a critical and systematic comparison between batch and column experiments. The aim was to investigate the underlying factors causing the commonly observed discrepancies in colloid adsorption process in column and batch systems. We examined the colloid adsorption behavior of four different sizes of carboxylate-modified latex (CML) microspheres, as surrogates for viruses and bacteria, on quartz sand in batch and column experiments over a wide range of solution ionic strengths (IS). Our results show that adsorption of colloids in batch systems should be considered as an irreversible attachment because the attachment/detachment model was found to be inadequate in describing the batch results. An irreversible attachment-blocking model was found to accurately describe the results of both batch and column experiments. The rate of attachment was found to depend highly on colloid size, solution IS and the fraction of the sand surface area favorable for attachment (Sf). The rate of attachment and Sf values were different in batch and column experiments due to differences in the hydrodynamic of the system, and the role of surface roughness and pore structure on colloid attachment. Results from column and batch experiments were generally not comparable, especially for larger colloids (≥0.5μm). Predictions based on classical DLVO theory were found to inadequately describe interaction energies between colloids and sand surfaces.