Quantitative analysis of transverse bacterial migration induced by chemotaxis in a packed column with structured physical heterogeneity

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.

Response of a new rumen-derived Bacillus licheniformis to different carbon sources

Introduction

Bacillus licheniformis (B. licheniformis) is a microorganism with a wide range of probiotic properties and applications. Isolation and identification of novel strains is a major aspect of microbial research. Besides, different carbon sources have varying effects on B. licheniformis in regulating the microenvironment, and these mechanisms need to be investigated further.

Methods

In this study, we isolated and identified a new strain of B. licheniformis from bovine rumen fluid and named it B. licheniformis NXU98. The strain was treated with two distinct carbon sources-microcrystalline cellulose (MC) and cellobiose (CB). A combination of transcriptome and proteome analyses was used to investigate different carbon source effects.

Results

The results showed that B. licheniformis NXU98 ABC transporter proteins, antibiotic synthesis, flagellar assembly, cellulase-related pathways, and proteins were significantly upregulated in the MC treatment compared to the CB treatment, and lactate metabolism was inhibited. In addition, we used MC as a distinct carbon source to enhance the antibacterial ability of B. licheniformis NXU98, to improve its disease resistance, and to regulate the rumen microenvironment.

Discussion

Our research provides a potential new probiotic for feed research and a theoretical basis for investigating the mechanisms by which bacteria respond to different carbon sources.

Surface tension coupled non-uniformly imposed flows modulate the activity of reproducing chemotactic bacteria in porous media

This paper investigates a non-homogeneous two-dimensional model for reproducing chemotactic bacteria, immersed in a porous medium that experiences non-uniformly imposed flows. It is shown that independently of the form of the fluid velocity field, the compressible/incompressible nature of the fluid significantly shifts the Turing stability-instability transition line. In dry media, Gaussian perturbations travel faster than the hyperbolic secant ones, yet the latter exhibit better stability properties. The system becomes highly unstable under strong flows and high surface tension. Approximated solutions recovered by injecting Gaussian perturbations overgrow, in addition to triggering concentric breathing features that split the medium into high and low-density domains. Secant perturbations on the other hand scatter slowly and form patterns of non-uniformly distributed peaks for strong flows and high surface tension. These results emphasize that Gaussian perturbations strongly modulate the activity of bacteria, hence can be exploited to perform fast spreading in environments with changing properties. In this sense, Gaussian profiles are better candidates to explain quick bacterial responses to external factors. Secant-type approximated solutions slowly modulate the bacterial activity, hence are better alternatives to dive into weak bacterial progressions in heterogeneous media.

Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media

Oil pollution in soil-groundwater systems is difficult to remove, and a large amount of residual oil is trapped in the low permeable layer of the heterogeneous aquifer. Aromatic hydrocarbons in oil have high toxicity and low solubility in water, which are harmful to the ecological environment. Chemotactic degrading bacteria can perceive the concentration gradient of non-aqueous phase liquid (NAPL) pollutants in the groundwater environment, and enrich and proliferate around the pollutants, thus achieving a more efficient and thorough remediation effect. However, the existing theoretical models are relatively simple. The physical fields of oil–water two-phase flow and oil-phase solute convection and diffusion in water are not coupled, which further restricts the accuracy of studies on bacterial chemotaxis to NAPL. In this study, geometric models based on the actual microfluidic experimental study were constructed. Based on the phase field model, diffusion convection equation and chemotaxis velocity equation, the effects of heterogeneity of porous media, wall wettability and groundwater flow rate on the residual oil and the concentration distribution of chemotaxis bacteria were studied. Under all of the simulation conditions, the residual oil in the high permeable area was significantly lower than that in the low permeable area, and the wall hydrophilicity enhanced the water flooding effect. Chemotactic bacteria could react to the concentration gradient of pollutants dissolved into water in the oil phase, and enrich near the oil–water interface with high concentration of NAPL, and the density of chemotactic bacteria at the oil–water interface can be up to 1.8–2 times higher than that in the water phase at flow rates from 1.13 to 6.78 m/d.

Spatial variations, source apportionment and potential ecological risks of polycyclic aromatic hydrocarbons and synthetic musks in river sediments in Shanghai, China

The aims of this study were to investigate the levels, possible sources and potential ecological risks of 26 polycyclic aromatic hydrocarbons (PAHs) including highly carcinogenic dibenzopyrene (DBP) isomers and 4 synthetic musks (SMs) in river sediments from Shanghai. 74 sediment samples were collected from the Huangpu River and its main tributaries. The total concentrations ranged from 52.0 to 11400 ng g^-1 for Σ₂₆PAHs, 25.1-9910 ng g^-1 for 16 USEPA priority PAHs (Σ₁₆PAHs), 0.769-384 ng g^-1 for Σ₄DBPs, and 0.080-63.3 ng g^-1 for Σ₄SMs, respectively. Seven sources of PAHs in river sediments were identified by positive matrix factorization (PMF) model. Coal combustion, vehicle and creosote were the major emission sources for PAHs. SMs came mainly from domestic and industrial wastewaters. The toxic equivalent quantities of the benzo[a]pyrene (TEQ_BaP) ranged from 7.64 to 3920 ng g^-1 for Σ₂₄PAHs, 2.07-1150 ng g^-1 for Σ₁₆PAHs, and 5.53-3150 ng g^-1 for Σ₄DBPs. The TEQ_BaP of Σ₄DBPs made up 73.9% of Σ₂₄PAHs, which indicated that DBPs were the major carcinogenic contributors to total PAHs in sediments. According to sediment quality guidelines (SQGs) and mean PEL-Q values, the risks posed by PAHs in sediments were at medium level at most sampling sites, and SMs posed a low ecological risk to sediment-dwelling organisms in Shanghai.

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.

An alternative smooth particle hydrodynamics formulation to simulate chemotaxis in porous media

Chemotaxis, the microorganisms autonomous motility along or against the concentration gradients of a chemical species, is an important, yet often neglected factor controlling the transport of bacteria through saturated porous media. For example, chemotactic bacteria could enhance bioremediation by directing their own motion to residual contaminants trapped in low hydraulic conductive zones of contaminated aquifers. The aim of the present work is to develop an accurate numerical scheme to model chemotaxis in saturated porous media and other advective dominating flow systems. We propose to model chemotaxis by using a new class of meshless Lagrangian particle methods we recently developed for applications in fluid mechanics. The method is based on the Smooth Particle Hydrodynamics (SPH) formulation of (Ben Moussa et al., Int Ser Numer Math, 13(1):29-62, 2006), combined with a new Weighted Essentially Non-Oscillatory (WENO) reconstruction technique on moving point clouds in multiple space dimensions. The purpose of this new numerical scheme is to fully exploit the advantages of SPH among traditional mesh-based and mesh-free schemes and to overcome drawbacks related to the use of standard SPH for modeling chemotaxis in porous media. First, we test the new scheme against analytical reference solutions. Then, under the assumption of complete mixing at the Darcy scale, we perform two-dimensional conservative solute transport simulations under steady-state flow conditions, to show the capability of the proposed new scheme to model chemotaxis.

Swimming Motility Reduces Deposition to Silica Surfaces

The transport and fate of bacteria in porous media is influenced by physicochemical and biological properties. This study investigated the effect of swimming motility on the attachment of cells to silica surfaces through comprehensive analysis of cell deposition in model porous media. Distinct motilities were quantified for different strains using global and cluster-based statistical analyses of microscopic images taken under no-flow condition. The wild-type, flagellated strain DJ showed strong swimming as a result of the actively swimming subpopulation whose average speed was 25.6 μm/s; the impaired swimming of strain DJ77 was attributed to the lower average speed of 17.4 μm/s in its actively swimming subpopulation; and both the nonflagellated JZ52 and chemically treated DJ cells were nonmotile. The approach and deposition of these bacterial cells were analyzed in porous media setups, including single-collector radial stagnation point flow cells (RSPF) and two-dimensional multiple-collector micromodels under well-defined hydrodynamic conditions. In RSPF experiments, both swimming and nonmotile cells moved with the flow when at a distance ≥20 μm above the collector surface. Closer to the surface, DJ cells showed both horizontal and vertical movement, limiting their contact with the surface, while chemically treated DJ cells moved with the flow to reach the surface. These results explain how wild-type swimming reduces attachment. In agreement, the deposition in micromodels was also lowest for DJ compared with those for DJ77 and JZ52. Wild-type swimming specifically reduced deposition on the upstream surfaces of the micromodel collectors. Conducted under environmentally relevant hydrodynamic conditions, the results suggest that swimming motility is an important characteristic for bacterial deposition and transport in the environment.

Occurrence, sources and health risk assessment of polycyclic aromatic hydrocarbons in urban (Pudong) and suburban soils from Shanghai in China

A comprehensive investigation was conducted to the urban (Pudong) and suburban soils in Shanghai. A total of 154 soil samples were analyzed for 26 PAHs including highly carcinogenic dibenzopyrenes (DBPs). The total concentrations ranged from 25.8 to 7380 μg kg(-1) for Σ26PAHs and 18.8 to 6320 μg kg(-1) for 16 USEPA priority PAHs (Σ16PAHs), respectively. The BaP toxic equivalent (BaPeq) concentrations were between 6.41 and 2880 μg kg(-1) for Σ24PAHs, 1.11 and 620 μg kg(-1) for Σ16PAHs and 2.72 and 2250 μg kg(-1) for Σ4DBPs. The high PAH contamination in green land soils might originate mainly from local road traffic and industrial activities, and sewage sludge application or waste water irrigation for soil. Seven sources of soil PAHs in Shanghai were identified by positive matrix factorization (PMF) model. The mean risk quotient (m-RQ) values indicated that there were medium to high ecological risks in 9.10% of soil samples, pyrene (Pyr), benzo[b]fluoranthene (BbF) and benz[a]anthracene (BaA) were the major ecological risk drivers under agricultural use. The cancer risk (CR) values were within the acceptable range at 35.7%, 35.1% and 31.2% of sampling sites for children, youths and adults, respectively. The total lifetime carcinogenic risk (TLCR) values at 57.8% of sampling sites were within the acceptable range. Overall, cancer risks of soil PAHs in all sampling sites in the studied area were below the highest acceptable risk, suggesting that soil PAHs are unlikely to pose a significant cancer risk for population based on ingestion, dermal contact and inhalation exposure pathways.

Laboratory research aimed at closing the gaps in microbial bioremediation

The industrial revolution, the first agricultural 'green revolution', and the development of antibiotics and therapeutic chemicals have brought significant and undeniable benefits to the human race. However, these advances demand high levels of energy, exploit natural resources and create large amounts of waste that creates an environmental burden for our planet. The pollution rate and character of many of the pollutants results in a rapid deterioration of the environment. Bioremediation functions to isolate and select microorganisms that operate under aerobic and anoxic conditions to remove these harmful pollutants. Current 'omics' technologies allow the exploitation of the catabolic potential of microbes without the need to cultivate them. Synthetic microbiology builds new catabolic pathways to remove recalcitrant pollutants from the environment.