Escherichia coli, as an indicator of fecal contamination, can move from manure-amended soil to groundwater under rainfall or irrigation events. Predicting its vertical transport in the subsurface is essential for the development of engineering solutions to reduce the risk of microbiological contamination. In this study, we collected 377 datasets from 61 published papers addressing E. coli transport through saturated porous media and trained six types of machine learning algorithms to predict bacterial transport. Eight variables, including bacterial concentration, porous medium type, median grain size, ionic strength, pore water velocity, column length, saturated hydraulic conductivity, and organic matter content were used as input variables while the first-order attachment coefficient and spatial removal rate were set as target variables. The eight input variables have low correlations with the target variables, namely, they cannot predict target variables independently. However, using the predictive models, input variables can effectively predict the target variables. For scenarios with higher bacterial retention, such as smaller median grain size, the predictive models showed better performance. Among six types of machine learning algorithms, Gradient Boosting Machine and Extreme Gradient Boosting outperformed other algorithms. In most predictive models, pore water velocity, ionic strength, median grain size, and column length showed higher importance than other input variables. This study provided a valuable tool to evaluate the transport risk of E.coli in the subsurface under saturated water flow conditions. It also proved the feasibility of data-driven methods that could be used for predicting other contaminants\' transport in the environment.

Monitoring the dynamics of bacteria in porous media is of great significance to understand the bacterial transport and the interplay between bacteria and environmental factors. In this study, we reported a non-invasive, real-time, and efficient method to quantify bioluminescent bacterial concentration in water and sand media during flow-through experiments. First, 27 column experiments were conducted, and the bacterial transport was monitored using a real-time bioluminescent imaging system. Next, we quantified the bacterial concentration in water and sand media using two methods-viable count and bioluminescent count. The principle of the bioluminescent count in sand media was, for a given bioluminescence image, the total number of bacteria was proportionally allocated to each segment according to its bioluminescence intensity. We then compared the bacterial concentration for the two methods and found a good linear correlation between the bioluminescent count and viable count. Finally, the effects of porous media surface coating, pore water velocity, and ionic strength on the bioluminescent count in sand media were investigated, and the results showed that the bioluminescence counting accuracy was most affected by surface coating, followed by ionic strength, and was hardly affected by pore water velocity. Overall, the study proved that the bioluminescent count was a reliable method to quantify bacterial concentration in water (106 to 2 × 108 cell mL-1) or sand media (5 × 106-5 × 108 cell cm-3). This approach also offers a new way of thinking for in situ bacterial enumeration in two-dimensional devices such as 2D flow cells, microfluidic devices, and rhizoboxes.

Surface-associated bacterial communities flourish in nature and in the body of animal hosts with abundant macromolecular polymers. It is unclear how the endowed viscoelasticity of polymeric fluids influences bacterial motile behavior in such environments. Here, we combined experiment and theory to study near-surface swimming of flagellated bacteria in viscoelastic polymer fluids. In contrast to the swimming behavior in Newtonian fluids, we discovered that cells swim in less curved trajectories and display reduced near-surface accumulation. Using a theoretical analysis of the non-Newtonian hydrodynamic forces, we demonstrated the existence of a generic lift force acting on a rotating filament near a rigid surface, which arises from the elastic tension generated along curved flow streamlines. This viscoelastic lift force weakens the hydrodynamic interaction between flagellated swimmers and solid surfaces and contributes to a decrease in surface accumulation. Our findings reveal previously unrecognized facets of bacterial transport and surface exploration in polymer-rich environments that are pertinent to diverse microbial processes and may inform the design of artificial microswimmers capable of navigating through complex geometries.

Bacteria often respond to dynamic soil environment through the secretion of extracellular polymeric substances (EPS). The EPS modifies cell surface properties and soil pore-scale hydration status, which in turn, influences bacteria transport in soil. However, the effect of soil particle size and EPS-mediated surface properties on bacterial transport in the soil is not well understood. In this study, the simultaneous impacts of EPS and collector size on Escherichia coli (E. coli) transport and deposition in a sand column were investigated. E. coli transport experiments were carried out under steady-state flow in saturated columns packed with quartz sand with different size ranges, including 0.300-0.425 mm (sand-I), 0.212-0.300 mm (sand-II), 0.106-0.150 mm (sand-III) and 0.075-0.106 mm (sand-IV). Bacterial retention increased with decreasing sand collector size, suggesting that straining played an important role in fine-textured media. Both experiment and simulation results showed a clear drop in the retention rate of the bacterial population with the presence of additional EPS (200 mg L-1) (EPS+). The inhibited retention of cells in sand columns under EPS+ scenario was likely attributed to enhanced bacteria hydrophilicity and electrostatic repulsion between cells and sand particles as well as reduced straining. Calculations of the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) interactions energies revealed that high repulsive energy barrier existed between bacterial cells and sand particles in EPS+ environment, primarily due to high repulsive electrostatic force and Lewis acid-base force, as well as low attractive Lifshitz-van der Waals force, which retarded bacterial population deposition. Steric stabilization of EPS would also prevent the approaching of cells close to the quartz surface and thereby hinder cell attachment. This study was the first to show that EPS reduced bacterial straining in saturated porous media. These findings provide new insight into the functional effects of extrinsic EPS on bacterial transport behavior in the saturated soil environment, e.g., aquifers.

In situ monitoring techniques can provide new insight into bacterial transport after inoculating exogenous bacteria into contaminated soils for bioremediation. A real-time and non-destructive optical sensor (the optrode) was employed to monitor in situ transport of two fluorescently labelled bacteria - Green Fluorescent Protein (Gfp)-labelled, hydrophilic Pseudomonas putida and Tomato Fluorescent Protein (td)-labelled, hydrophobic Rhodococcus erythropolis, in a saturated sand column with and without rhamnolipid surfactant. In situ measurements were made at three sampling ports in the column with the optrode in two sets of column experiments. In Experiment 1, liquid samples were extracted for ex situ analyses (plate counts and fluorescence), while in Experiment 2 no liquid samples were extracted. Extracting liquid samples for ex situ analyses in Experiment 1 disturbed in situ measurements; in situ measured bacterial concentrations were lower, or a significant lag in breakthrough occurred relative to ex situ measurements. In Experiment 2, the optrode worked well in monitoring bacterial transport, which gave consistent transport parameters at each sampling port. Moreover, the optrode enabled the impact of bacterial hydrophobicity and rhamnolipid surfactant on bacterial transport to be observed. Specifically, hydrophilic P. putida was transported faster through the column than hydrophobic R. erythropolis; we infer from this result that fewer P. putida cells adsorb to sand particles than do R. erythropolis cells. The rhamnolipid surfactant enhanced the transport of both hydrophilic and hydrophobic bacteria. These two observations are consistent with Lifshitz-van der Waals forces and acid-base interactions between bacteria and sand.

The geological conditions of the contaminated sites will affect the migration of microorganisms in the underground environment. In order to study the effect of low-permeability lens on bacterial transport, green fluorescent protein labeling combined with light transmission method was used to reveal the bacterial transport in the heterogeneous aquifer. The experiment has the advantages of real-time monitoring and no disturbance. The results showed that the bacteria gave priority to bypass the lens to flow away. The lens had a significant effect on hindering the bacterial transport due to adsorption and straining. The larger permeability coefficient ratio between the bulk media and the low-permeability lens was, the more obvious the obstruction was. AN-1 cannot enter the lens until the ratio decreased to the order of 102. With the increase of the flow velocity, the bacterial plume changed a lot. The higher flow velocity reduced the adsorption and retention of AN-1 to the media, resulting in some microorganisms remaining in the pores washed down. When the flow came to 2.0 m·d-1, AN-1 cannot adhere to the media due to the excessive fluid shear stress.

In order to manage and control the pathogen release from waste streams of various municipal, industrial, and agricultural pollution sources, it is crucial to investigate the impact of release pathways of such contaminants on their fate and transport in groundwater, especially in respect to natural heterogeneities encountered in aquifers. In this laboratory scale study, we investigate the impacts of different release scenarios of Escherichia coli bacteria, including spatially distributed surface recharge and single-point deep injection, as well as mono-pulse and continuous injection on the transport of Escherichia coli within both single-layered and multilayer aquifers. The results demonstrate earlier arrival of bacteria breakthrough curve (BTC) than conservative solute within a single-layer system with textural and continuum scale heterogeneities, attributed to size exclusion mechanism and preferential flow paths. Size exclusion may be responsible for multiple peaked BTCs observed in all cases of mono-pulse injection of bacteria through both single layer and multi-layer systems. The higher breakthrough of bacteria suspension introduced through a distributed source compared to the point source injection at the same flow rate (19% and 53% in middle and top layers, respectively) suggests that natural hydrologic events such as storm may be more influential in the transport of pathogens in soils than point injections of bacteria in engineering applications such as bioremediation. Moreover, our results reveal that the concentration of the semi-steady state breakthrough formed under distributed and continuous injection condition increases significantly with an increase in the recharge flow rate. This would suggest that a variation in hydrologic conditions can significantly mobilize pathogens which are already deposited in soils.

Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L-1), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).

Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below ∼4 m. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of 6 m. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths. Deep fracture communities contained a higher relative abundance of aerobes and plant material decomposers like Nitrospirae, Acidobacteria and Planctomycetes than adjacent matrix sediments. Similarly, analyses of the relative abundances of archaeal amoA, nirK and dsrB genes indicated transition from aerobic to anaerobic nitrogen and sulphur cycling at greater depth in preferential flow paths than in matrix sediments. Preferential flow paths in the top 260 cm contained more indicator operational taxonomic units from the plough layer community than the matrix sediments. This study indicates that the availability of oxygen and organic matter and downward transport of bacteria shape bacterial communities in preferential flow paths, and suggests that their lifestyles differ from those of bacteria in matrix communities.

Mammals produce volatile odours that convey different types of societal information. In Homo sapiens, this is now recognised as body odour, a key chemical component of which is the sulphurous thioalcohol, 3-methyl-3-sulfanylhexan-1-ol (3M3SH). Volatile 3M3SH is produced in the underarm as a result of specific microbial activity, which act on the odourless dipeptide-containing malodour precursor molecule, S-Cys-Gly-3M3SH, secreted in the axilla (underarm) during colonisation. The mechanism by which these bacteria recognise S-Cys-Gly-3M3SH and produce body odour is still poorly understood. Here we report the structural and biochemical basis of bacterial transport of S-Cys-Gly-3M3SH by Staphylococcus hominis, which is converted to the sulphurous thioalcohol component 3M3SH in the bacterial cytoplasm, before being released into the environment. Knowledge of the molecular basis of precursor transport, essential for body odour formation, provides a novel opportunity to design specific inhibitors of malodour production in humans.