Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media

Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 μm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 μm × 35 μm × 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 μm) and strong chemoeffectors (γ-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.

Colloidal stability and aggregation kinetics of nanocrystal CdSe/ZnS quantum dots in aqueous systems: Effects of ionic strength, electrolyte type, and natural organic matter

Understanding the stability and aggregation of nanoparticles in aqueous milieu is critical for assessing their behavior in the natural and engineered environmental systems and establishing their threat to human and ecosystems health. In this study, the colloidal stability and aggregation kinetics of nanocrystal quantum dots (QDs) —CdSe/ZnS QDs—were thoroughly explored under a wide range of aqueous environmental conditions. The z-average hydrodynamic diameters (z-avg. HDs) and zeta potential (ξ potential) of CdSe/ZnS QDs were measured in monovalent electrolyte (NaCl) and divalent electrolyte (CaCl2) solutions in both the absence and presence of natural organic matter (NOM)—Suwannee River natural organic matter, SRNOM to assess the dynamic growth of these nanoaggregate-QD-complexes, and the evaluation of their colloidal stability. Results show that CaCl2 was more effective to destabilize the QDs compared to NaCl at similar concentrations. An increase in NaCl concentration from 0.01 to 3.5 M increased the z-avg. HD of QD aggregates from 61.4 nm to 107.2 nm. The aggregation rates of QDs increased from 0.007 to 0.042 nm·s−1 with an increase in ionic strength from 0.5 to 3.5 M NaCl solutions, respectively. In the presence of Na+ cations, the aggregation of QDs was limited as steric forces generated by the original surface coating of QDs prevailed. In the presence of CaCl2, the aggregation of QDs was observed at a low concentration of CaCl2 (0.0001 M) with a z-avg. HD of 74.2 nm that significantly increased when the CaCl2 was higher than 0.002 M. Larger sizes of QD aggregates were observed at each level of CaCl2 concentration in suspensions of 0.002–0.1 M, as the z-avg. HDs of QDs increased from 125.1 to 560.4 nm, respectively. In the case of CaCl2, an increase in aggregation rates occurred from 0.035 to 0.865 nm·s−1 with an increase in ionic strength from 0.0001 M to 0.004 M, respectively. With Ca2+ cations, the aggregation of QDs was enhanced due to the bridging effects from the formation of complexes between Ca2+ cations in solution and the carboxyl group located on the surface coating of QDs. In the presence of SRNOM, the aggregation of QDs was enhanced in both monovalent and divalent electrolyte solutions. The degree of aggregation formation between QDs through cation-NOM bridges was superior for Ca2+ cations compared to Na+ cations. The presence of SRNOM resulted in a small increase in the size of the QD aggregates for each of NaCl concentrations tested (i.e., 0.01 to 3.5 M, except 0.1 M), and induced a monodispersed and narrower size distribution of QDs suspended in the monovalent electrolyte NaCl concentrations. In the presence of SRNOM, the aggregation rates of QDs increased from 0.01 to 0.024 nm 1 with the increase of NaCl concentrations from 0.01 to 2 M, respectively. The presence of SRNOM in QDs suspended in divalent electrolyte CaCl2 solutions enhanced the aggregation of QDs, resulting in the increase of z-avg. HDs of QDs by approximately 19.3%, 42.1%, 13.8%, 1.5%, and 24.8%, at CaCl2 concentrations of 0.002, 0.003, 0.005, 0.01, and 0.1 M, respectively. In the case of CaCl2, an increase in aggregation rates occurred from 0.035 to 0.865 nm·s−1 with an increase in ionic strength from 0.0001 to 0.004 M, respectively. Our findings demonstrated the colloidal stability of QDs and cations-NOM-QD nanoparticle complexes under a broad spectrum of conditions encountered in the natural and engineered environment, indicating and the potential risks from these nanoparticles in terms of human and ecosystem health.

Ecological risk of combined pollution on soil ecosystem functions: Insight from the functional sensitivity and stability

Assessing the ecological risk of combined pollution, especially from a holistic perspective with the consideration of the overarching functions of soil ecosystem, is crucial and beneficial to the improvement of ecological risk assessment (ERA) framework. In this study, four soils with similar physicochemical properties but contrasting heavy metals contamination levels were selected to explore changes in the integrated functional sensitivity (MSI), resistance (MRS) and resilience (MRL) of soil microbial communities subjected to herbicide siduron, based on which the ecological risk of the accumulation of siduron in the four studied soils were evaluated. The results suggested that the microbial biomass carbon, activity of denitrification enzyme and nitrogenase were indicative of MSI and MRS, and the same three parameters plus soil basal respiration were indicative of MRL. Significant dose-effect relationships between siduron residues in soils and MSI, MRS and MRL under combined pollution were observed. Heavy metal polluted soils showed higher sensitivity and lower resistance to the additional disturbance of herbicide siduron due to the lower microbial biomass, while the resilience of heavy metal polluted soils was much higher due to the pre-adaption to the chemical stresses. The quantifiable indicator microbial functional stability was incorporated in the framework of ERA and the results showed that the accumulation of siduron in the studied soils could exhibit potential harm to the integrated functional stability of soil microbial community. Thus, this work provides insights into the application of integrated function of soil microbial community into the framework of ERA.

Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil-atmosphere exchange of greenhouse gases

The goal of this comment is to show that the "aggregate reactor" framework recently proposed in an article published in this journal is severely limited by two kinds of indeterminacy. The first is related to the size of aggregates, which is not defined precisely. The second issue is with the impossibility to replicate boundary conditions that are identical to what chunks of soils would have experienced in their natural state. We suggest that the study of GHG release in undisturbed soil samples is a better way to proceed forward.

A modified method of separating Tl(I) and Tl(III) in aqueous samples using solid phase extraction

In spite of the development of new measurement techniques in recent years, the rapid and accurate speciation of thallium in environmental aqueous samples remains a challenge. In this context, a novel method of solid phase extraction (SPE), involving the anion exchange resin AG1-X8, is proposed to separate Tl(I) and Tl(III). In the presence of diethylene triamine pentacetate acid (DTPA), Tl(III) and Tl(I) can be separated by selective adsorption of Tl(III)-DTPA onto the resin, Tl(III) is then eluted by a solution of HCl with SO₂. The validity of this method was confirmed by assays of standard solutions of Tl(I) and Tl(III). The proposed method is shown to have an outstanding performance even in solutions with a high ratio of Tl(I)/Tl(III), and can be applied to aqueous samples with a high concentration of other electrolytes, which could interfere with the measurement. Portable equipment and reagents make it possible to use the proposed method routinely in the field.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.

Microcolumn-based speciation analysis of thallium in soil and green cabbage

Thallium (Tl) is a toxic trace metal, whose geochemical behavior and biological effects are closely controlled by its chemical speciation in the environment. However, little tends to be known about this speciation of Tl in soil and plant systems that directly affect the safety of food supplies. In this context, the objective of the present study was to elaborate an efficient method to separate and detect Tl(I) and Tl(III) species for soil and plant samples. This method involves the selective adsorption of Tl(I) on microcolumns filled with immobilized oxine, in the presence of DTPA (diethylenetriaminepentaacetic acid), followed by DTPA-enhanced ultrasonic and heating-induced extraction, coupled with ICP-MS detection. The method was characterized by a LOD of 0.037 μg/L for Tl(I) and 0.18 μg/L for Tl(III) in 10  mL samples. With this method, a second objective of the research was to assess the speciation of Tl in pot and field soils and in green cabbage crops. Experimental results suggest that DTPA extracted Tl was mainly present as Tl(I) in soils (>95%). Tl in hyperaccumulator plant green cabbage was also mainly present as Tl(I) (>90%). With respect to Tl uptake in plants, this study provides direct evidence that green cabbage mainly takes up Tl(I) from soil, and transports it into the aboveground organs. In soils, Tl(III) is reduced to Tl(I) even at the surface where the chemical environment promotes oxidation. This observation is conducive to understanding the mechanisms of Tl isotope fractionation in the soil-plant system. Based on geochemical fraction studies, the reducible fraction was the main source of Tl getting accumulated by plants. These results indicate that the improved analytical method presented in this study offers an economical, simple, fast, and sensitive approach for the separation of Tl species present in soils at trace levels.

Analysis of metal(loid)s contamination and their continuous input in soils around a zinc smelter: Development of methodology and a case study in South Korea

Soil contamination due to atmospheric deposition of metals originating from smelters is a global environmental problem. A common problem associated with this contamination is the discrimination between anthropic and natural contributions to soil metal concentrations: In this context, we investigated the characteristics of soil contamination in the surrounding area of a world class smelter. We attempted to combine several approaches in order to identify sources of metals in soils and to examine contamination characteristics, such as pollution level, range, and spatial distribution. Soil samples were collected at 100 sites during a field survey and total concentrations of As, Cd, Cr, Cu, Fe, Hg, Ni, Pb, and Zn were analyzed. We conducted a multivariate statistical analysis, and also examined the spatial distribution by 1) identifying the horizontal variation of metals according to particular wind directions and distance from the smelter and 2) drawing a distribution map by means of a GIS tool. As, Cd, Cu, Hg, Pb, and Zn in the soil were found to originate from smelter emissions, and As also originated from other sources such as abandoned mines and waste landfill. Among anthropogenic metals, the horizontal distribution of Cd, Hg, Pb, and Zn according to the downwind direction and distance from the smelter showed a typical feature of atmospheric deposition (regression model: y = y₀ + αe^-βx). Lithogenic Fe was used as an indicator, and it revealed the continuous input and accumulation of these four elements in the surrounding soils. Our approach was effective in clearly identifying the sources of metals and analyzing their contamination characteristics. We believe this study will provide useful information to future studies on soil pollution by metals around smelters.

Visible and near-infrared reflectance spectroscopy is of limited practical use to monitor soil contamination by heavy metals

In recent years, several authors have suggested repeatedly that visible and near-infrared reflectance spectroscopy (VNIRS) could be an advantageous alternative to traditional wet-laboratory methods for the measurement of heavy metal concentrations in soils. In this comment, we argue that, on the contrary, VNIRS is of limited practical use in such a context and should not serve as an excuse to get rid of direly needed laboratory facilities. The key reasons are that VNIRS spectra are irremediably insensitive to the presence of heavy metals, that the effect of soil moisture and surface rugosity on VNIR sensing still has to be satisfactorily accounted for, and finally that VNIRS probes an extremely thin layer of soil at the surface, which is generally irrelevant in terms of plant growth. Given these intrinsic limitations, it seems indicated to put the persistent VNIRS myth to rest, and to explore other measurement techniques that may have more potential.

Potential health risk in areas with high naturally-occurring cadmium background in southwestern China

In various parts of the world, high cadmium (Cd) concentrations in environment are not related to anthropogenic contamination but have natural origins. Less is known about health risks that arise under these conditions. This study aimed to discuss the pollution of Cd with natural sources, and to investigate the concentration of Cd in food crops and the urine of inhabitants in an area of southwestern China. The results showed that the arable soils are moderately contaminated by Cd (I(geo)=1.51) relative to the local background, with a high ecological risk (Er=218). The chemical fractions of Cd in soils with natural sources are probably controlled by parent materials and mostly in residual phase. The average Cd concentrations were 0.68 mg kg(-1) (fresh weight) in local vegetables, 0.04 mg kg(-1) in rice, and 0.14 μg L(-1) in water. Leafy vegetable tends to accumulate more Cd than the other crops. The calculated Target Hazard Quotient (THQ) had a much higher value (4.33) for Cd, suggesting that Cd represents a significant potential risk to the local population. The urinary Cd concentrations (mean at 3.92 μg L(-1) for male and 4.85 μg L(-1) for female) of inhabitants in the study area were significantly higher (p<0.05) than those from the control area (mean at 0.8 μg L(-1) for male and 0.42 μg L(-1) for female). Male and female test subjects had similar urinary Cd levels (p>0.05), but age seemed to lead to an increase in Cd in the urine. These findings show that naturally-occurring Cd in local soils is taken up appreciably by local food crops, and that dietary exposure of Cd through vegetable ingestion is a major exposure pathway for local populations, and a potential risk to public health in the study area.

Direct simulation of magnetic resonance relaxation rates and line shapes from molecular trajectories

We simulate spin relaxation processes, which may be measured by either continuous wave or pulsed magnetic resonance techniques, using trajectory-based simulation methodologies. The spin-lattice relaxation rates are extracted numerically from the relaxation simulations. The rates obtained from the numerical fitting of the relaxation curves are compared to those obtained by direct simulation from the relaxation Bloch-Wangsness-Abragam-Redfield theory (BWART). We have restricted our study to anisotropic rigid-body rotational processes, and to the chemical shift anisotropy (CSA) and a single spin-spin dipolar (END) coupling mechanisms. Examples using electron paramagnetic resonance (EPR) nitroxide and nuclear magnetic resonance (NMR) deuterium quadrupolar systems are provided. The objective is to compare those rates obtained by numerical simulations with the rates obtained by BWART. There is excellent agreement between the simulated and BWART rates for a Hamiltonian describing a single spin (an electron) interacting with the bath through the chemical shift anisotropy (CSA) mechanism undergoing anisotropic rotational diffusion. In contrast, when the Hamiltonian contains both the chemical shift anisotropy (CSA) and the spin-spin dipolar (END) mechanisms, the decay rate of a single exponential fit of the simulated spin-lattice relaxation rate is up to a factor of 0.2 smaller than that predicted by BWART. When the relaxation curves are fit to a double exponential, the slow and fast rates extracted from the decay curves bound the BWART prediction. An extended BWART theory, in the literature, includes the need for multiple relaxation rates and indicates that the multiexponential decay is due to the combined effects of direct and cross-relaxation mechanisms.

Influence of ionic strength, pH, and cation valence on aggregation kinetics of titanium dioxide nanoparticles

The extensive use of titanium dioxide nanoparticles (nano-TiO2) in many consumer products has raised concerns about possible risks to the environment The magnitude of the threat may depend on whether nano-TiO2 remains dispersed in the environment, or forms much larger-sized aggregates or clusters. Currently, limited information is available on the issue. In this context, the purpose of the present article is to report initial measurements of the morphology and rate of formation of nano-TiO2 aggregates in aqueous suspensions as a function of ionic strength and of the nature of the electrolyte in a moderately acid to circumneutral pH range typical of soil and surface water conditions. Dynamic light scattering results show that 4-5 nm titanium dioxide particles readily form stable aggregates with an average diameter of 50-60 nm at pH approximately 4.5 in a NaCl suspension adjusted to an ionic strength of 0.0045 M. Holding the pH constant but increasing the ionic strength to 0.0165 M, leads to the formation of micron-sized aggregates within 15 min. At all other pH values tested (5.8-8.2), micron-sized aggregates form in less than 5 min (minimum detection time), even at low ionic strength (0.0084-0.0099 M with NaCl). In contrast, micron-sized aggregates form within 5 min in an aqueous suspension of CaCl2 at an ionic strength of 0.0128 M and pH of 4.8, which is significantly faster than observed for NaCI suspensions with similar ionic strength and pH. This result indicates that divalent cations may enhance aggregation of nano-TiO2 in soils and surface waters. Optical micrographs show branching aggregates of sizes ranging from the 1 microm optical limit of the microscope to tens of micrometers in diameter.

Influence of ionic strength, pH, and cation valence on aggregation kinetics of titanium dioxide nanoparticles

The extensive use of titanium dioxide nanoparticles (nano-TiO2) in many consumer products has raised concerns about possible risks to the environment The magnitude of the threat may depend on whether nano-TiO2 remains dispersed in the environment, or forms much larger-sized aggregates or clusters. Currently, limited information is available on the issue. In this context, the purpose of the present article is to report initial measurements of the morphology and rate of formation of nano-TiO2 aggregates in aqueous suspensions as a function of ionic strength and of the nature of the electrolyte in a moderately acid to circumneutral pH range typical of soil and surface water conditions. Dynamic light scattering results show that 4-5 nm titanium dioxide particles readily form stable aggregates with an average diameter of 50-60 nm at pH approximately 4.5 in a NaCl suspension adjusted to an ionic strength of 0.0045 M. Holding the pH constant but increasing the ionic strength to 0.0165 M, leads to the formation of micron-sized aggregates within 15 min. At all other pH values tested (5.8-8.2), micron-sized aggregates form in less than 5 min (minimum detection time), even at low ionic strength (0.0084-0.0099 M with NaCl). In contrast, micron-sized aggregates form within 5 min in an aqueous suspension of CaCl2 at an ionic strength of 0.0128 M and pH of 4.8, which is significantly faster than observed for NaCI suspensions with similar ionic strength and pH. This result indicates that divalent cations may enhance aggregation of nano-TiO2 in soils and surface waters. Optical micrographs show branching aggregates of sizes ranging from the 1 microm optical limit of the microscope to tens of micrometers in diameter.

Facilitated transport of diuron and glyphosate in high copper vineyard soils

The fate of organic herbicides applied to agricultural fields may be affected by other soil amendments, such as copper applied as a fungicide. The effect of copper on the leaching of diuron and glyphosate through a granitic and a calcareous soil was studied in the laboratory using sieved-soil columns. Each soil was enriched with copper sulfate to obtain soil copper concentrations of 125, 250, 500, and 1000 mg kg(-1). Glyphosate leaching was influenced by soil pH and copper concentration, whereas diuron leaching was not. In the calcareous soil, glyphosate leaching decreased as copper levels increased from 17 mg kg(-1) (background) to 500 mg kg(-1). In the granitic soil, glyphosate leaching increased as copper levels increased from 34 mg kg(-1) (background) to 500 mg kg(-1). The shapes of the copper elution curves in presence of glyphosate were similar to shapes of the glyphosate curves, suggesting the formation of Cu-glyphosate complexes that leach through the soil. Soil copper concentration does not influence diuron leaching. In contrast, increasing copper concentrations reduces glyphosate leaching through calcareous soils, and conversely, increases glyphosate leaching through granitic soils. Our findings suggest that the risk of groundwater contamination by glyphosate increases in granitic soils with elevated copper concentrations.

Electron microprobe and synchrotron x-ray fluorescence mapping of the heterogeneous distribution of copper in high-copper vineyard soils

The response of microorganisms to metal contamination of soils varies significantly from one investigation to another. One explanation is that metals are heterogeneously distributed at spatial scales relevant to microbes and that microoorganisms are able to avoid zones of intense contamination. This article aims to assess the microscale distribution of Cu in a vineyard soil. The spatial distribution of Cu was measured at two resolutions (0.3 mm and 20 microm) in thin sections of the surface 4 cm of undisturbed soil by electron microprobe and synchrotron X-ray microfluo-rescence spectroscopy. Bulk physicochemical analyses of Cu, pH, organic matter, texture, and mineralogy were performed. The results indicate that the Cu distribution is strongly heterogeneous at both scales of observation. Entire regions of the thin sections are virtually devoid of Cu, whereas highly localized "hotspots" have Cu signal intensities thousands of times higher than background. The distribution of Rb, or Al and Si, indicators of clay minerals, or Fe (iron (hydr)oxides), show that Cu is not preferentially associated with these mineral phases. Instead, Cu hotspots are associated with particulate organic matter. These observations suggest modification of current sampling protocols, and design of ecotoxicological experiments involving microorganisms, for contaminated soils.