Chemotaxis Increases the Residence Time of Bacteria in Granular Media Containing Distributed Contaminant Sources

Coarse-graining bacterial diffusion in disordered media to surface states

Bacterial motility in spatially structured environments impacts a variety of natural and engineering processes. Constructing models to predict, control, and design bacterial motility for these processes remains challenging because bacteria and active swimmers have complex interactions with surfaces and because the precise environment geometry is unknown. Here, we present a method for deriving bacterial diffusion coefficients in disordered media in terms of cell and environmental parameters. The approach abstracts the dynamics in the full geometry to "surface states," which encode how cells interact with surfaces in the environment. Then, a long-time diffusion equation can be derived analytically from the state model. Applying this method to a run-and-tumble particle in a 2D Lorentz gas environment provides analytical predictions that show good agreement with particle simulations. Like past studies, we observe that the diffusivity depends nonmonotonically on the cell's run length. Using the analytical expressions, we derive the optimal run length, revealing an intuitive dependence on environmental length scales. Furthermore, we find that rescaling length and time by the average distance and time between trap events collapses all of the diffusivities onto a single curve, which we derive analytically. Thus, our approach extracts interpretable, macroscopic diffusive behavior from complex microscopic dynamics, and provides tools and intuitions for understanding bacterial diffusion in disordered media.

Microbial chemotaxis in degradation of xenobiotics: Current trends and opportunities

Chemotaxis, the directed movement of microbes in response to chemical gradients, plays a crucial role in the biodegradation of xenobiotics, such as pesticides, industrial chemicals, and pharmaceuticals, which pose significant environmental and health risks. Emerging trends in genomics, proteomics, and synthetic biology have advanced our understanding and control of these processes, thereby enabling the development of engineered microorganisms with tailored chemotactic responses and degradation capabilities. This process plays an essential physiological role in processes, such as surface sensing, biofilm formation, quorum detection, pathogenicity, colonization, symbiotic interactions with the host system, and plant growth promotion. Field applications have demonstrated the potential of bioremediation for cleaning contaminated environments. Therefore, it helps to increase the bioavailability of pollutants and enables bacteria to access distantly located pollutants. Despite considerable breakthroughs in decoding the regulatory mechanisms of bacterial chemotaxis, there are still gaps in knowledge that need to be resolved to harness its potential for sensing and degrading pollutants in the environment. This review covers the role of bacterial chemotaxis in the degradation of xenobiotics present in the environment, focusing on chemotaxis-based bacterial and microfluidic biosensors for environmental monitoring. Finally, we highlight the current challenges and future perspectives for developing more effective and sustainable strategies to mitigate the environmental impact of xenobiotics.

Taxis-enhanced mineralization and co-metabolism of PAHs by bacteria in micrometer-scale environments

Polycyclic aromatic hydrocarbons (PAHs) are associated with micropores in sediments and soils. This limits the bioaccessibility of these compounds via existing bioremediation technologies, as biodegradation is strongly influenced by the ability of bacteria to access different sizes of pores. In this work, we employed naphthalene and pyrene as model contaminants to evaluate the transformation capacity of the soil bacterium Pseudomonas putida G7 (2 × 1 μm) via mineralization and co-metabolic activity, respectively. Under non-growing conditions and in the absence of hydraulic flow, we examined how the tactic behavior of this motile bacterium influenced biodegradation of these two PAHs when passing through membranes with micrometer-sized pores (3 and 5 μm). The bacteria were spontaneously retained by the membranes, which blocked the contaminants away from a passive dosing source. However, the cells were mobilized through 5 μm pores after the application plant root exudate components (γ-aminobutyric acid, citrate and fructose) as strong chemoeffectors, which enhanced the mineralization of naphthalene and co-metabolism of pyrene. The tactic-mediated biodegradation enhancement did not occur through 3 μm pores, possibly due a physical constrain to the gradient sensing mechanism. Our results suggest that bacterial transport by chemotaxis may enhance the biotransformation of poorly bioaccessible contaminants present in micro-meter scale environments.

The Effects of Low Concentrations and Long-Term Contamination by Sodium Dodecyl Sulfate on the Structure and Function of Bacterial Communities in the Lake-Terrestrial Ecotone

Due to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake-terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities due to its bacteriostatic properties. To investigate the effects of long-term discharge of sewage containing low concentrations of SDS on microorganisms in the lake-terrestrial ecotone, alterations in bacterial community structure, functional genes, and biomass were examined using a simulated continuous pollutant input. The results indicated the following: (1) The degradation rate of sodium dodecyl sulfate (SDS) by soil microorganisms in the lake-terrestrial ecotone under long-term and low concentrations of SDS stress ranged from 11 to 16 mg/kg·d. (2) The effects of low concentrations and long-term SDS stress on bacterial community structure and gene function in the lake-terrestrial ecotone differed significantly from those of short-term pollution. The damage to microbial-promoted material cycling in the lake-terrestrial ecotone was more severe; however, the proliferation of pathogenic bacteria remained continuously suppressed. (3) Soil bacteria in the lake-terrestrial ecotone responded to the stress of long-term and low concentrations of SDS primarily by enhancing chemotaxis and tolerance.

Soft matter physics of the ground beneath our feet

The soft part of the Earth's surface - the ground beneath our feet - constitutes the basis for life and natural resources, yet a general physical understanding of the ground is still lacking. In this critical time of climate change, cross-pollination of scientific approaches is urgently needed to better understand the behavior of our planet's surface. The major topics in current research in this area cross different disciplines, spanning geosciences, and various aspects of engineering, material sciences, physics, chemistry, and biology. Among these, soft matter physics has emerged as a fundamental nexus connecting and underpinning many research questions. This perspective article is a multi-voice effort to bring together different views and approaches, questions and insights, from researchers that work in this emerging area, the soft matter physics of the ground beneath our feet. In particular, we identify four major challenges concerned with the dynamics in and of the ground: (I) modeling from the grain scale, (II) near-criticality, (III) bridging scales, and (IV) life. For each challenge, we present a selection of topics by individual authors, providing specific context, recent advances, and open questions. Through this, we seek to provide an overview of the opportunities for the broad Soft Matter community to contribute to the fundamental understanding of the physics of the ground, strive towards a common language, and encourage new collaborations across the broad spectrum of scientists interested in the matter of the Earth's surface.

Propulsion of a three-sphere microrobot in a porous medium

Microorganisms and synthetic microswimmers often encounter complex environments consisting of networks of obstacles embedded into viscous fluids. Such settings include biological media, such as mucus with filamentous networks, as well as environmental scenarios, including wet soil and aquifers. A fundamental question in studying their locomotion is how the impermeability of these porous media impacts their propulsion performance compared with the case of that in a purely viscous fluid. Previous studies showed that the additional resistance due to the embedded obstacles leads to an enhanced propulsion of different types of swimmers, including undulatory swimmers, helical swimmers, and squirmers. In this paper, we employ a canonical three-sphere swimmer model to probe the impact of propulsion in porous media. The Brinkman equation is utilized to model a sparse network of stationary obstacles embedded into an incompressible Newtonian liquid. We present both a far-field theory and numerical simulations to characterize the propulsion performance of the swimmer in such porous media. In contrast to enhanced propulsion observed in other swimmer models, our results reveal that both the propulsion speed and efficiency of the three-sphere swimmer are largely reduced by the impermeability of the porous medium. We attribute the substantial reduction in propulsion performance to the screened hydrodynamic interactions among the spheres due to the more rapid spatial decays of flows in Brinkman media. These results highlight how enhanced or hindered propulsion in porous media is largely dependent on individual propulsion mechanisms. The specific example and physical insights provided here may guide the design of synthetic microswimmers for effective locomotion in porous media in their potential biological and environmental applications.

Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas

Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.

Taxis-mediated bacterial transport and its implication for the cometabolism of pyrene in a model aquifer

One of the main problems in contaminated soils is that many toxic substances, such as PAHs, which are found in areas close to aquifers and groundwater, are difficult to access and degrade via traditional methods of remediation. The use of controlled bacterial mobility through chemotaxis has been shown to be efficient in increasing the dispersion of pollutant-degrading organisms, increasing the biodegradation rates of pollutants. In this study, using percolation columns as model aquifers, the mobilization of the Pseudomonas putida G7 strain to a distant pyrene source was demonstrated using γ-aminobutyric acid and artificial root exudates as strong chemoeffectors. An increase in the biodegradation rates of the pollutant was observed relative to columns in which the tactic effector was not added. The presence of different metabolites was detected via a fraction collector associated with an HPLC system, providing evidence for the cometabolic capacity of strain G7. The use of chemotactic organisms can be an effective approach for the remediation of polluted sediments associated with aquifers and groundwaters, offering new possibilities for the treatment of contaminated aqueous areas.

Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.

Boundary design regulates the diffusion of active matter in heterogeneous environments

Physical boundaries play a key role in governing the overall transport properties of nearby self-propelled particles. In this work, we develop dispersion theories and conduct Brownian dynamics simulations to predict the coupling between surface accumulation and effective diffusivity of active particles in boundary-rich media. We focus on three models that are well-understood for passive systems: particle transport in (i) an array of fixed volume-excluding obstacles; (ii) a pore with spatially heterogeneous width; and (iii) a tortuous path with kinks and corners. While the impact of these entropic barriers on passive particle transport is well established, we find that these classical models of porous media flows break down due to the unique interplay between activity and the microstructure of the internal geometry. We study the activity-induced slowdown of effective diffusivity by formulating a Smoluchowski description of long-time self diffusivity which contains contributions from the density and fluctuation fields of the active particles. Particle-based and finite element simulations corroborate this perspective and reveal important nonequilibrium considerations of active transport.

The role of disorder in the motion of chiral active particles in the presence of obstacles

The presence of obstacles is intuitively expected to hinder the diffusive transport of active particles. However, for chiral active particles, a low density of obstacles near a surface can enhance their diffusive behavior. Here, we study numerically the role that disorder plays in determining the transport dynamics of chiral active particles on surfaces with obstacles. We consider different densities of regularly spaced obstacles and distinct types of disorder: noise in the dynamics of the particle, quenched noise in the positions of the obstacles as well as obstacle size polydispersity. We show that, depending on the type and strength of the disorder, the presence of obstacles can either enhance or hinder transport, and discuss implications for the control of active transport in disordered media.

Migration of active rings in porous media

Inspired by how the shape deformations in active organisms help them to migrate through disordered porous environments, we simulate active ring polymers in two-dimensional random porous media. Flexible and inextensible active ring polymers navigate smoothly through the disordered media. In contrast, semiflexible rings undergo transient trapping inside the pore space; the degree of trapping is inversely correlated with the increase in activity. We discover that flexible rings swell while inextensible and semiflexible rings monotonically shrink upon increasing the activity. Together, our findings identify the optimal migration of active ring polymers through porous media.

A biophysical threshold for biofilm formation

Bacteria are ubiquitous in our daily lives, either as motile planktonic cells or as immobilized surface-attached biofilms. These different phenotypic states play key roles in agriculture, environment, industry, and medicine; hence, it is critically important to be able to predict the conditions under which bacteria transition from one state to the other. Unfortunately, these transitions depend on a dizzyingly complex array of factors that are determined by the intrinsic properties of the individual cells as well as those of their surrounding environments, and are thus challenging to describe. To address this issue, here, we develop a generally-applicable biophysical model of the interplay between motility-mediated dispersal and biofilm formation under positive quorum sensing control. Using this model, we establish a universal rule predicting how the onset and extent of biofilm formation depend collectively on cell concentration and motility, nutrient diffusion and consumption, chemotactic sensing, and autoinducer production. Our work thus provides a key step toward quantitatively predicting and controlling biofilm formation in diverse and complex settings.

Influence of confinement on the spreading of bacterial populations

The spreading of bacterial populations is central to processes in agriculture, the environment, and medicine. However, existing models of spreading typically focus on cells in unconfined settings—despite the fact that many bacteria inhabit complex and crowded environments, such as soils, sediments, and biological tissues/gels, in which solid obstacles confine the cells and thereby strongly regulate population spreading. Here, we develop an extended version of the classic Keller-Segel model of bacterial spreading via motility that also incorporates cellular growth and division, and explicitly considers the influence of confinement in promoting both cell-solid and cell-cell collisions. Numerical simulations of this extended model demonstrate how confinement fundamentally alters the dynamics and morphology of spreading bacterial populations, in good agreement with recent experimental results. In particular, with increasing confinement, we find that cell-cell collisions increasingly hinder the initial formation and the long-time propagation speed of chemotactic pulses. Moreover, also with increasing confinement, we find that cellular growth and division plays an increasingly dominant role in driving population spreading—eventually leading to a transition from chemotactic spreading to growth-driven spreading via a slower, jammed front. This work thus provides a theoretical foundation for further investigations of the influence of confinement on bacterial spreading. More broadly, these results help to provide a framework to predict and control the dynamics of bacterial populations in complex and crowded environments.

The spreading of bacteria through their environments critically impacts our everyday lives; it can be harmful, underlying the progression of infections and spoilage of foods, or can be beneficial, enabling the delivery of therapeutics, sustaining plant growth, and remediating polluted terrain. In all these cases, bacteria typically inhabit crowded environments, such as soils, sediments, and biological tissues/gels, in which solid obstacles confine the cells and regulate their spreading. However, existing models of spreading typically focus on cells in unconfined settings, and thus are frequently not applicable to cells in more complex environments. Here, we address this gap in knowledge by extending the classic Keller-Segel model of bacterial spreading via motility to also incorporate cellular growth and division, and explicitly consider the influence of confinement. Through numerical simulations of this extended model, we show how confinement fundamentally alters the dynamics and morphology of spreading bacterial populations—in particular, driving a transition from chemotactic spreading of motile cells to growth-driven spreading via a slower, jammed front. These results provide a foundation for further investigations of the influence of confinement on bacterial spreading, both by yielding testable predictions for future experiments, and by providing guidelines to predict and control the dynamics of bacterial populations in complex and crowded environments.

Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production

Pit mud is a typical artificial ecosystem for Chinese liquor production. Clostridium inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of Clostridium increased with pit mud quality, further influencing the quality of baijiu.

Microbial communities in petroleum-contaminated sites: Structure and metabolisms

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

A geometric criterion for the optimal spreading of active polymers in porous media

Efficient navigation through disordered, porous environments poses a major challenge for swimming microorganisms and future synthetic cargo-carriers. We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with experiments of Escherichia coli, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. Our findings show that the spreading of active agents in porous media can be optimized by tuning their run lengths, which we rationalize using a coarse-grained model. More significantly, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. Our criterion unifies results for porous media with disparate pore sizes and shapes and for run-and-tumble polymers. It thus provides a fundamental principle for optimal transport of active agents in densely-packed biological and environmental settings.

Bioremediation perspectives and progress in petroleum pollution in the marine environment: a review

The marine environment is often affected by petroleum hydrocarbon pollution due to industrial activities and petroleum accidents. This pollution has recalcitrant and persistent compounds that pose a high risk to the ecological system and human health. For this reason, the world claims to seek to clean up these pollutants. Bioremediation is an attractive approach for removing petroleum pollution. It is considered a low-cost and highly effective approach with fewer side effects compared to chemical and physical techniques. This depends on the metabolic capability of microorganisms involved in the degradation of hydrocarbons through enzymatic reactions. Bioremediation activities mostly depend on environmental conditions such as temperature, pH, salinity, pressure, and nutrition availability. Understanding the effects of environmental conditions on microbial hydrocarbon degraders and microbial interactions with hydrocarbon compounds could be assessed for the successful degradation of petroleum pollution. The current review provides a critical view of petroleum pollution in seawater, the bioavailability of petroleum compounds, the contribution of microorganisms in petroleum degradation, and the mechanisms of degradation under aerobic and anaerobic conditions. We consider different biodegradation approaches such as biostimulation, bioaugmentation, and phytoremediation.

The Only Chemoreceptor Encoded by che Operon Affects the Chemotactic Response of Agrobacterium to Various Chemoeffectors

Chemoreceptor (also called methyl-accepting chemotaxis protein, MCP) is the leading signal protein in the chemotaxis signaling pathway. MCP senses and binds chemoeffectors, specifically, and transmits the sensed signal to downstream proteins of the chemotaxis signaling system. The genome of Agrobacterium fabrum (previously, tumefaciens) C58 predicts that a total of 20 genes can encode MCP, but only the MCP-encoding gene atu0514 is located inside the che operon. Hence, the identification of the exact function of atu0514-encoding chemoreceptor (here, named as MCP₅₁₄) will be very important for us to understand more deeply the chemotaxis signal transduction mechanism of A. fabrum. The deletion of atu0514 significantly decreased the chemotactic migration of A. fabrum in a swim plate. The test of atu0514-deletion mutant (Δ514) chemotaxis toward single chemicals showed that the deficiency of MCP₅₁₄ significantly weakened the chemotactic response of A. fabrum to four various chemicals, sucrose, valine, citric acid and acetosyringone (AS), but did not completely abolish the chemotactic response. MCP₅₁₄ was localized at cell poles although it lacks a transmembrane (TM) region and is predicted to be a cytoplasmic chemoreceptor. The replacement of residue Phe328 showed that the helical structure in the hairpin subdomain of MCP₅₁₄ is a direct determinant for the cellular localization of MCP₅₁₄. Single respective replacements of key residues indicated that residues Asn336 and Val353 play a key role in maintaining the chemotactic function of MCP₅₁₄.

Finding novel chemoreceptors that specifically sense and trigger chemotaxis toward polycyclic aromatic hydrocarbons in Novosphingobium pentaromativorans US6-1

Bacterial chemotaxis can improve the efficiency of aromatic compound degradation, however, knowledge of how bacteria sense high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs), is limited. Here, the chemotactic responses of Novosphingobium pentaromativorans US6-1 to 9 aromatic compounds were investigated. The results showed that US6-1 chemotactically responded to phenanthrene (PHE), pyrene (PYR), benzo[a]pyrene (BaP) and their six metabolites. Six methyl-accepting chemotaxis proteins (MCPs) were annotated from US6-1 genome, four of which contained putative ligand-binding domains (LBDs). To confirm whether these four MCPs were involved in triggering chemotaxis toward PAHs, the MCP mutants were constructed. Observations showed a loss of the chemotactic responses to benzoate, phthalate, PHE and BaP only in the mutant ∆mcp03030. Surface plasmon resonance (SPR) assays further confirmed that MCP03030LBD specifically bound phthalate, PHE, PYR and BaP, while MCP18870LBD bound only PYR. The mutant ∆mcp03030-∆mcp18870 was then constructed and was shown to have lost the chemotactic response to 5 aromatic compounds. Combined with the effects of outer membrane transporter deletion on chemotaxis and MCP deletion on the PAH degradation, our study demonstrated that the chemoreceptors MCP03030 and MCP18870 can recognize PAHs and their metabolites in the periplasm, triggering metabolism-dependent and metabolism-independent chemotaxis, and be linked with HMW-PAH biodegradation.

Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media

The fate and transport of bacteria in porous media are essential for bioremediation and water quality control. However, the influence of biological activities like extracellular electron transfer (EET) and swimming motility toward granular media on cell transport remains unknown. Here, electroactive bacteria with higher Fe(III) reduction abilities were found to demonstrate greater retention in ferrihydrite-coated sand. Increasing the concentrations of the electron donor (1-10 mM lactate), shuttle (0-50 μM anthraquinone-2,6-disulfonate), and acceptor (ferrihydrite, MnO₂, or biochar) under flow conditions significantly reduced Shewanella oneidensis MR-1's mobility through redox-active porous media. The deficiency of EET ability or flagellar motion and inhibition of intracellular proton motive force, all of which are essential for energy taxis, enhanced MR-1's transport. It was proposed that EET could facilitate MR-1 to sense, tactically move toward, and attach on redox-active media surface, eventually improving its retention. Positive linear correlations were established among parameters describing MR-1's energy taxis ability (relative taxis index), cell transport behavior (dispersion coefficient and relative change of effluent percentage), and redox activity of media surface (reduction potential or electron-accepting rate), providing novel insights into the critical impacts of bacterial microscale motility on macroscale cell transport through porous media.

In silico analysis of the chemotactic system of Agrobacterium tumefaciens

Agrobacterium tumefaciens is an efficient tool for creating transgenic host plants. The first step in the genetic transformation process involves A. tumefaciens chemotaxis, which is crucial to the survival of A. tumefaciens in changeable, harsh and even contaminated soil environments. However, a systematic study of its chemotactic signalling pathway is still lacking. In this study, the distribution and classification of chemotactic genes in the model A. tumefaciens C58 and 21 other strains were annotated. Local blast was used for comparative genomics, and hmmer was used for predicting protein domains. Chemotactic phenotypes for knockout mutants of ternary signalling complexes in A. tumefaciens C58 were evaluated using a swim agar plate. A major cluster, in which chemotaxis genes were consistently organized as MCP (methyl-accepting chemotaxis protein), CheS, CheY1, CheA, CheR, CheB, CheY2 and CheD, was found in A. tumefaciens, but two coupling CheW proteins were located outside the 'che' cluster. In the ternary signalling complexes, the absence of MCP atu0514 significantly impaired A. tumefaciens chemotaxis, and the absence of CheA (atu0517) or the deletion of both CheWs abolished chemotaxis. A total of 465 MCPs were found in the 22 strains, and the cytoplasmic domains of these MCPs were composed of 38 heptad repeats. A high homology was observed between the chemotactic systems of the 22 A. tumefaciens strains with individual differences in the gene and receptor protein distributions, possibly related to their ecological niches. This preliminary study demonstrates the chemotactic system of A. tumefaciens, and provides some reference for A. tumefaciens sensing and chemotaxis to exogenous signals.

Crowding-Enhanced Diffusion: An Exact Theory for Highly Entangled Self-Propelled Stiff Filaments

We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a remarkable increase of the effective diffusivity upon increasing the filament number density by more than one order of magnitude. This counterintuitive "crowded is faster" behavior can be rationalized by extending the concept of a confining tube pioneered by Doi and Edwards for highly entangled, crowded, passive to active systems. We predict a scaling theory for the effective diffusivity as a function of the Péclet number and the filament number density. Subsequently, we show that an exact expression derived for a single self-propelled filament with motility parameters as input can predict the nontrivial spatiotemporal dynamics over the entire range of length and timescales. In particular, our theory captures short-time diffusion, directed swimming motion at intermediate times, and the transition to complete orientational relaxation at long times.

Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere

Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.

Confinement and activity regulate bacterial motion in porous media

Understanding how bacteria move in porous media is critical to applications in healthcare, agriculture, environmental remediation, and chemical sensing. Recent work has demonstrated that E. coli, which moves by run-and-tumble dynamics in a homogeneous medium, exhibits a new form of motility when confined in a disordered porous medium: hopping-and-trapping motility, in which cells perform rapid, directed hops punctuated by intervals of slow, undirected trapping. Here, we use direct visualization to shed light on how these processes depend on pore-scale confinement and cellular activity. We find that hopping is determined by pore-scale confinement, and is independent of cellular activity; by contrast, trapping is determined by the competition between pore-scale confinement and cellular activity, as predicted by an entropic trapping model. These results thus help to elucidate the factors that regulate bacterial motion in porous media, and could help aid the development of new models of motility in heterogeneous environments.

Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through 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).

Bacterial hopping and trapping in porous media

Diverse processes-e.g. bioremediation, biofertilization, and microbial drug delivery-rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown due to the opacity of typical 3D media. As a result, models of migration are limited and often employ ad hoc assumptions. Here we reveal that the paradigm of run-and-tumble motility is dramatically altered in a porous medium. By directly visualizing individual Escherichia coli, we find that the cells are intermittently and transiently trapped as they navigate the pore space, exhibiting diffusive behavior at long time scales. The trapping durations and the lengths of "hops" between traps are broadly distributed, reminiscent of transport in diverse other disordered systems; nevertheless, we show that these quantities can together predict the long-time bacterial translational diffusivity. Our work thus provides a revised picture of bacterial motility in complex media and yields principles for predicting cellular migration.

Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip

The group of imidazolinone herbicides, widely used for weed control, is hazardous to some sensitive rotational crops. Thus, rapid elimination of imidazolinones from contaminated soil is significant for the environment. Biodegradation studies have demonstrated the ability of chemotaxis to enhance the biodegradation of pollutants. In this study, we used our newly developed SlipChip device for chemotactic sorting and a microfluidic streak plate device for bacterial cultivation as a new pipeline for screening imidazolinone degraders. The degradation efficiencies of an enrichment consortium and a chemotaxis consortium were determined by HPLC-MS/MS. Both consortia degraded all tested imidazolinones, with the highest efficiency (71.8%) for imazethapyr, and the chemotaxis consortium degraded these compounds approximately 10% more efficiently than the enrichment consortium. Moreover, the community diversities of the enrichment consortium and the chemotaxis consortium were analyzed by 16S rRNA gene amplicon sequencing. The results indicated that members of genus Ochrobactrum primarily contribute to the degradation of imidazolinones. This work proved that chemotaxis toward biodegradable pollutants increases their bioavailability and enhances the biodegradation rate. It also provided a new way to screen effective pollutant degraders and can be applied for the selective isolation of other chemotactic species from environmental samples.

Impact of Chemoeffectors on Bacterial Motility, Transport, and Contaminant Degradation in Sand-Filled Percolation Columns

Chemoeffector-mediated bacterial motility and tactic swimming are major drivers for contaminant accessibility and biodegradation at submillimeter scales. In sand-filled percolated columns we tested how and to what degree chemoeffectors influenced bacterial transport and thereby promoted accessibility and degradation of distantly located ¹⁴C-naphthalene (NAH) at the centimeter scale. Sunflower root exudates and silver nanoparticles (AgNPs) were used as chemoeffectors to stimulate opposing effects of motility and tactic swimming of NAH-degrading Pseudomonas putida G7. Sunflower exudates prompted smooth bacterial movement and positive taxis, while AgNPs induced tortuous movement and repellent responses. Compared to chemoeffector-free controls exudates reduced deposition and stimulated bacterial transport during percolation experiments. AgNPs, however, provoked bacterial deposition and concomitant saturation of the collector surfaces (filter blocking) that led to progressively increased percolation of cells. Despite mechanistic differences, both motility patterns supported bacterial transport and promoted mineralization rates of NAH desorbing from a source placed at the column outlet. Observed mineralization rates in the presence of the chemoeffectors were 5-fold higher than those in their absence and similar to NAH-mineralization in well-stirred batch assays. Our results indicate that chemically mediated, small-scale bacterial motility patterns may become relevant for long-distance bacterial transport and the biodegradation of patchy contaminants at higher scales, respectively.

Chemotaxis Increases the Retention of Bacteria in Porous Media with Residual NAPL Entrapment

Chemotaxis has the potential to decrease the persistence of nonaqueous phase liquid (NAPL) contaminants in aquifers by allowing pollutant-degrading bacteria to move toward sources of contamination and thus influence dissolution. This experimental study investigated the migratory response of chemotactic bacteria to a distribution of residual NAPL ganglia entrapped within a laboratory-scale sand column under continuous-flow at a superficial velocity of 0.05 cm/min. Naphthalene dissolved in a model NAPL 2,2,4,4,6,8,8-heptamethylnonane partitioned into the aqueous phase to create localized chemoattractant gradients throughout the column. A pulse mixture of equal concentrations of Pseudomonas putida G7, a strain chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a nonchemotactic mutant, was introduced to the column and effluent bacterial concentrations were measured with time. Breakthrough curves (BTCs) for the two strains were noticeably different upon visual inspection. Differences in BTCs (compared to nonchemotactic controls) were quantified in terms of percent recovery and were statistically significant ( p < 0.01). Chemotaxis reduced percent recovery in the effluent by 45% thereby increasing the population of bacteria that were retained within the column in the vicinity of residual NAPL contaminants. An increase in flow rate to a superficial velocity of 0.25 cm/min did not diminish cell retention associated with the chemotactic effect.

Two Agrobacterium tumefaciens CheW Proteins Are Incorporated into One Chemosensory Pathway with Different Efficiencies

Agrobacterium tumefaciens is the agent that causes crown gall tumor disease on more than 140 species of dicotyledonous plants. Chemotaxis of A. tumefaciens toward the wound sites of the host plant is the first step to recognize the host. CheW is a coupling protein that bridges the histidine kinase CheA and the chemoreceptors to form the chemotaxis core signaling complex and plays a crucial role in the assembly and function of the large chemosensory array. Unlike all previously reported chemotaxis systems, A. tumefaciens has only one major che operon but two cheW homologs (atu2075 as cheW₁ and atu2617 as cheW₂) on unlinked loci. The in-frame deletion of either cheW gene significantly affects A. tumefaciens chemotaxis but does not abolish the chemotaxis, unless both cheW genes were deleted. The effect of cheW₂ deletion on the chemotaxis is more severe than that of cheW₁ deletion. Either CheW can interact with CheA and couple it to the cell poles. The promoter activity of cheW₂ is always higher than that of cheW₁ under all of the tested conditions. When two cheW genes were adjusted to the same expression level by using the identical promoter, the difference between the effects of two CheW proteins on the chemotaxis still existed. Therefore, we envision that both the different molecular ratio of two CheW proteins in cell and the different affinities of two CheW proteins with CheA and chemoreceptors result in the efficiency difference of two CheW proteins in functioning in the large chemosensory array.

Modeling Transport of Chemotactic Bacteria in Granular Media with Distributed Contaminant Sources

Chemotaxis has the potential to improve bioremediation strategies by enhancing the transport of pollutant-degrading bacteria to the source of contamination, leading to increased pollutant accessibility and biodegradation. This computational study extends work reported previously in the literature to include predictions of chemotactic bacterial migration in response to multiple localized contaminant sources within porous media. An advection-dispersion model, in which chemotaxis was represented explicitly as an additional advection-like term, was employed to simulate the transport of bacteria within a sand-packed column containing a distribution of chemoattractant sources. Simulation results provided insight into attractant and bacterial distributions within the column. In particular, it was found that chemotactic bacteria exhibited a distinct biased migration toward contaminant sources that resulted in a 30% decrease in cell recovery, and concomitantly an enhanced retention within the sand column, compared to the nonchemotactic control. Model results were consistent with experimental observations. Parametric studies were conducted to provide insight into the influence of chemotaxis parameters on bacterial migration and cell percent recovery. The model results provide a better understanding of the effect of chemotaxis on bacterial transport in response to distributed contaminant sources.

Is there any crosstalk between the chemotaxis and virulence induction signaling in Agrobacterium tumefaciens?

Agrobacterium tumefaciens, a soil-born phytopathogenic bacterium, is well known as a nature's engineer due to its ability to genetically transform the host by transferring a DNA fragment (called T-DNA) from its Ti plasmid to host-cell genome. To combat the harsh soil environment and seek the appropriate host, A. tumefaciens can sense and be attracted by a large number of chemical compounds released by wounded host. As a member of α-proteobacterium, A. tumefaciens has a chemotaxis system different from that found in Escherichia coli, since many chemoattractants for A. tumefaciens chemotaxis are virulence (vir) inducers. However, advances in the study of the chemotaxis paradigm, E. coli chemotaxis system, have provided enough information to analyze the A. tumefaciens chemotaxis. At low concentration, chemoattractants elicit A. tumefaciens chemotaxis and attract the species to the wound sites of the host. At high concentration, chemoattractants induce the expression of virulence genes and trigger T-DNA transfer. Recent studies on the VirA and ChvE of the vir-induction system provide some evidences to support the crosstalk between chemotaxis and vir-induction. This review compares the core components of chemotaxis signaling system of A. tumefaciens with those observed in other species, discusses the connection between chemotaxis and vir-induction in A. tumefaciens, and proposes a model depicting the signaling crosstalk between chemotaxis and vir-induction.

Influence of 3-Chloroaniline on the Biofilm Lifestyle of Comamonas testosteroni and Its Implications on Bioaugmentation

Bioaugmentation has been frequently proposed in wastewater and soil treatment to remove toxic aromatic compounds. The performance of bioaugmentation is affected by a number of biological and environmental factors, including the interaction between the target pollutant and the augmented bacterial cells. In this study, using Comamonas testosteroni and 3-chloroaniline (3-CA) as the model organism and target pollutant, we explored the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our results showed that the exposure to 3-CA greatly reduced the retention of C. testosteroni cells in packed-bed bioreactors (from 22% to 15% after three pore volumes), which could be attributed to the altered bacterial motility and cell surface hydrophobicity. To further understand the molecular mechanisms, we employed an integrated genomic and transcriptomic analysis to examine the influence of 3-CA on the expression of genes important to the biofilm lifestyle of C. testosteroni We found that exposure to 3-CA reduced the intracellular c-di-GMP level by downregulating the expression of genes encoding c-di-GMP synthases and induced massive cell dispersal from the biofilms. Our findings provide novel environmental implications on bioaugmentation, particularly in biofilm reactors, for the treatment of wastewater containing recalcitrant industrial pollutants.

IMPORTANCE

Bioaugmentation is a bioremediation approach that often has been described in the literature but has almost never been successfully applied in practice. Many biological and environmental factors influence the overall performance of bioaugmentation. Among these, the interaction between the target pollutant and the augmented bacterial cells is one of the most important factors. In this study, we revealed the influence of toxic aromatic pollutants on the biofilm lifestyle of bacteria capable of degrading aromatic compounds toward a better understanding of cell-pollutant interaction in bioaugmentation. Our findings provide novel environmental implications on bioaugmentation for the treatment of wastewater containing recalcitrant industrial pollutants; in particular, the exposure to toxic pollutants may reduce the retention of augmented organisms in biofilm reactors by reducing the c-di-GMP level, and approaches to elevating or maintaining a high c-di-GMP level may be promising to establish and maintain sustainable bioaugmentation activity.