Philippe C. Baveye

Aggregation and Toxicology of Titanium Dioxide Nanoparticles

In their study of inhalation exposure of titanium dioxide particles, Grassian et al. (2007) presented a transmission electron micrograph (TEM) (their Figure 2A) as an image of “dispersed” TiO2 nanoparticles. Yet, the TiO2 nanoparticles in this TEM do not appear to be dispersed. There is clear evidence of self-organization of the nanoparticles into distinct assemblages, separated by relatively large regions devoid of any particle. This spatial pattern, very unlikely to occur randomly, is even more apparent when Grassian et al.’s TEM is contrast-enhanced, sharpened, and thresholded (Figure 1A) to eliminate the initial grainy background. With this image, one can demonstrate quantitatively the extent of clustering by calculating the radial distribution function (Torquato 2002), defined as the probability of finding a nanoparticle, in any direction, at various distances away from the center of a given nanoparticle. We compared the values obtained for this function with those associated with an image in which the same nanoparticles have been artificially dispersed (with image processing software). In the dispersed case (Figure 1B), the probability of finding a black pixel drops precipitously when the distance exceeds the apparent radius of nanoparticles, and then stays close to zero thereafter. In the “original” case (Grassian et al.’s Figure 2A), there is also a drop, but the radial distribution function never gets to zero. It progressively increases again as the radial distance increases. This quantitative difference between the curves in Figure 1B leads to the conclusion that the nanoparticles in Figure 1A are clustered. Figure 1 (A) Contrast-enhanced, sharpened, and segmented version of a TEM of a TiO2 nanoparticle suspension (modified from Grassian et al. 2007). (B) Radial distribution function versus radial distance for a representative point in a nanoparticle in (A); the dashed ... However, this conclusion is intriguing in itself. Indeed, before obtaining their TEM, Grassian et al. (2007) suspended the TiO2 nanoparticles in methanol and sonicated the suspension for an unspecified, but presumably appreciable “period of time.” Given this strongly dispersive treatment, it is remarkable that aggregation still occurred to the extent it did. This observation suggests that the 2- to 5-nm size of the primary TiO2 “nano”-particles may be somewhat irrelevant to environmental and toxicologic concerns because in nature, under conditions far more conducive to aggregation than those imposed by Grassian et al. (2007), nanoparticles may never be found alone, but are part of significantly larger-sized aggregates. In a recent study, French et al. (French RA, Jacobson AR, Kim B, Isley SL, Penn RL, Baveye PC, unpublished data) observed that in aqueous suspensions under a range of environmentally relevant conditions of pH and ionic strength, TiO2 nanoparticles form aggregates of several hundred nanometers to several micrometers in diameter within minutes. This aggregation may have toxicologic implications. In any given system (e.g., aerosols), it is possible that even a slight change in pH or ionic strength may cause TiO2 nanoparticles to cluster differently, and therefore to have very dissimilar biological activity. In general, this might explain mixed results found in the literature on the toxicity of TiO2 nanoparticles to environmentally relevant species. Until now, these inconclusive results have been explained (Oberdorster et al. 2005) by arguing that the high biological activity of TiO2 nanoparticles, caused by their large specific surface area, creates a high potential for inflammatory, pro-oxidant, and antioxidant activity. Yet, conflicting observations may perhaps be imputable instead to compounding factors due to nanoparticle aggregation, which so far has not been given serious consideration.

Preferential transport of Cryptosporidium parvum oocysts in variably saturated subsurface environments

When oocysts of the protozoan Cryptosporidium parvum contaminate drinking water supplies, they can cause outbreaks of Cryptosporidiosis, a common waterborne disease. Of the different pathways by which oocysts can wind up in drinking water, one has received little attention to date; that is, because soils are often considered to be perfect filters, the transport of oocysts through the subsoil to groundwater is generally ignored. To evaluate the significance of this pathway, a series of laboratory experiments investigated subsurface transport of oocysts. Experiment 1 was carried out in a vertical 18-cm-long column filled either with glass beads or silica sand, under conditions known to foster fingered flow. Experiment 2 involved undisturbed, macroporous soil columns subjected to macropore flow. Experiment 3 aimed to study the lateral flow on an undisturbed soil block. The columns and soil samples were subjected to artificial rainfall and were allowed to reach steady state. At that point, feces of contaminated calves were applied at the surface along with a known amount of potassium chloride to serve as a tracer, and rainfall was continued at the same rate. The breakthrough of oocysts and chloride, monitored in the effluent, demonstrate the importance of preferential flow on the transport of oocysts. Compared with chloride, peak oocyst concentrations were not appreciably delayed and, in some cases, occurred even before the chloride peak. Recovery rates for oocysts were low, ranging from 0.1 to 10.4% of the oocysts originally applied on the columns. However, the numbers of oocysts present in the effluents were still orders of magnitude higher than 10 oocysts, the infectious dose considered by the U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, to be sufficient to cause Cryptosporidiosis in healthy adults. These results suggest that the transport of oocysts in the subsurface via preferential flow may create a significant risk of groundwater contamination in some situations.

Emergent behavior of soil fungal dynamics: influence of soil architecture and water distribution

Abstract Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a “looped” configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass.

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.

Individual-based modeling of carbon and nitrogen dynamics in soils:: parameterization and sensitivity analysis of abiotic components

The need to predict with reasonable accuracy the fate of soil C and N compounds in soils in response to climate change is stimulating interest in a new generation of microscale models of soil ecosystem processes. Essential to the development of such models is the ability to describe the growth and metabolism of small numbers of individual microorganisms. In this context, the key objective of the research described in this article was to further develop an individual-based soil organic matter (SOM) model, INDISIM-SOM, first proposed a few years ago, and to assess its performance with a broader data set than previously considered. The INDISIM-SOM models the dynamics and evolution of C and N associated with organic matter in soils. The model involves a number of state variables and parameters related to SOM and microbial activity, including growth and decay of microbial biomass, temporal evolution of mineralized intermediate C and N, mineral N in ammonium and nitrate, carbon dioxide, and O2. Simulation results demonstrate good fit of the model to experimental data from laboratory incubation experiments performed on three different types of Mediterranean soils. A second objective was to determine the sensitivity of the model toward its various parameters. Sensitivity was small for several of the parameters, suggesting possible simplifications of the model for specific uses, but was significant particularly for the parameter associated with the fraction of the soil C present in the biomass. These results suggest that research should be focused on improving the measurement of this latter parameter.

Microscale Heterogeneity Explains Experimental Variability and Non-Linearity in Soil Organic Matter Mineralisation

Soil respiration represents the second largest CO2 flux from terrestrial ecosystems to the atmosphere, and a small rise could significantly contribute to further increase in atmospheric CO2. Unfortunately, the extent of this effect cannot be quantified reliably, and the outcomes of experiments designed to study soil respiration remain notoriously unpredictable. In this context, the mathematical simulations described in this article suggest that assumptions of linearity and presumed irrelevance of micro-scale heterogeneity, commonly made in quantitative models of microbial growth in subsurface environments and used in carbon stock models, do not appear warranted. Results indicate that microbial growth is non-linear and, at given average nutrient concentrations, strongly dependent on the microscale distribution of both nutrients and microbes. These observations have far-reaching consequences, in terms of both experiments and theory. They indicate that traditional, macroscopic soil measurements are inadequate to predict microbial responses, in particular to rising temperature conditions, and that an explicit account is required of microscale heterogeneity. Furthermore, models should evolve beyond traditional, but overly simplistic, assumptions of linearity of microbial responses to bulk nutrient concentrations. The development of a new generation of models along these lines, and in particular incorporating upscaled information about microscale processes, will undoubtedly be challenging, but appears to be key to understanding the extent to which soil carbon mineralization could further accelerate climate change.

Sampling Method For The Observation Of Microorganisms In Unconsolidated Porous Media Via Scanning Electron Microscopy

A sampling and mounting procedure is proposed that minimizes macroscopic rearrangements of solid particles when preparing unconsolidated samples for scanning electron microscopy.

Alleviating Moisture Content Effects on the Visible Near-Infrared Diffuse-Reflectance Sensing of Soils

With rising ambient temperature and atmospheric carbon dioxide levels, there is an urgent need to monitor soil carbon stocks over large regions of the earth. Near-infrared diffuse reflectance sensing (NIRS) of soils, using satellite- or airplane-based instruments, is increasingly regarded as a potential method of choice for this purpose. Considerable research has been devoted to NIRS in the last few years, but this research has been generally restricted to sieved air-dried soils analyzed under laboratory conditions. For NIRS to be useful for the estimation of soil carbon stocks in the field, a technique must be developed to account, among other things, for the presence of moisture in the surface layer of soils. In this context, a first objective of the research described in this article was to determine whether, for three soils with contrasting characteristics, a simple constant proportionality factor relates NIR spectra obtained at different moisture contents, and whether there is relative constancy of this proportionality factor among soils, suggesting the possibility of a practical strategy to correct NIR spectra for soil moisture. A second objective of the research was to use ratio and derivative analysis to identify portions of NIR spectra that appear least affected by moisture content and on which a determination of other parameters such as organic matter content could be based. Because constant proportionality of the spectra at different moisture contents seems elusive, at best, the most significant result obtained is the identification of specific wavelength ranges in the NIR spectra, at 800 to 1400 nm, 1600 to 1700 nm, 2100 to 2200 nm, and 2300 to 2500 nm, where the first derivative of the spectra seems independent of the moisture content of the soil samples. This observation suggests that an operational method could be developed, focused on these wavelength intervals, to obtain moisture-independent estimates of a range of soil parameters under field conditions.

Sticker Shock and Looming Tsunami: The High Cost of Academic Serials in Perspective

Recession is currently causing a resurgence of the academic serials crisis. Profit-mongering by commercial publishers is once again denounced as the key driver of the crisis. However, a critical analysis of institutional and bibliometric data does not reveal excessive corporate greed in recent years; instead, it suggests that the present hurdles stem largely from years of inadequate budget allocations to academic libraries and from a publishing frenzy fuelled by simplistic methods of evaluating faculty productivity. To prevent what is likely to be the publishing equivalent of a tsunami in the next few years, universities and research institutions urgently need to re-emphasize quality over quantity in the publishing process, and they must find ways to include peer-reviewing efficiency among their criteria for productivity and impact. Achieving these goals will require concerted efforts by researchers, librarians, and publishers.

To sequence or not to sequence the whole-soil metagenome?

The recent editorial by Timothy Vogel et al. (TerraGenome: a consortium for the sequencing of a whole-soil metagenome. Nature Rev. Microbiol. 7, 252 (2009))1 appears to represent a departure from the previous literature on sequencing soil metagenomes. In this editorial, the usual arguments are presented about the welldocumented lack of understanding of many soil processes that contribute, for example, to environmental and climate change. As other authors have done repeatedly in recent years2,3, Vogel et al. emphasize the fact that “Although microorganisms are responsible for key functions in soils, only a small percentage (less than 0.5%) have been grown in the laboratory and genome sequences are only available for a select few.” However, unlike other articles that start with these same preambles and move on to describe the advantages of metagenomics, Vogel et al. are careful not to present metagenomics explicitly as a way to resolve the problem of unculturable microorganisms. On the contrary, they acknowledge that they “...will need to develop and apply new approaches to cultivate the previously uncultivated and rare members of the soil community to assign functions to the vast number of unknown or hypothetical genes that will undoubtedly be found.” This candid admission suggests a form of circularity in the traditional reasoning behind whole-soil metagenome sequencing projects. Many readers of this editorial are likely to be left with the impression that, when all is said and done and after large financial resources have been spent on developing the appropriate extraction methods and on sequencing the estimated terabases of the metagenome in the Park Grass soil (Rothamsted, United Kingdom), one will be back to square one, faced with the task of having to deal with the 99.5% of microorganisms that are still unculturable, or at least uncultured, to make sense of the metagenomic data. At that point, as well as a sizeable effort to finally culture these uncultured organisms, additional large pots of money will be needed to carry out indispensable research efforts in other ‘meta-omics’ approaches (for example, metatranscriptomics, metaproteomics and metametabolomics)4–6 to obtain information that complements the metagenomic data. In the absence of clear indications from metagenomics researchers that the scenario described above is not going to unfold, the scientific community should perhaps reflect on whether the proposed sequencing of the whole-soil metagenome is a wise step to take at this stage or a good way to spend scarce research money, even though it is technically feasible and regardless of the opportunity that it affords to keep financially struggling sequencing facilities in business. Alternative approaches such as traditional ecological research, complemented by molecular biology techniques7,8, may ultimately yield better results, especially if they were to be carried out in the context of current work on the spatial microheterogeneity of soils and emergent behaviours at the macroscopic scale. Recent research9–12 indicates that, under various circumstances in soils, bulk (spatially averaged) measurements provide insufficient or even misleading information, a feature that may be shared by the outcomes of metagenome sequencing. From this perspective, spatially targeted metagenomics might be a better step forward than whole-soil metagenomics, provided that one could design methods to sample microorganisms at a fine resolution in soils and then analyse their genetic make-up. Another appealing alternative to wholesoil metagenomics is functionally targeted metagenomics, carried out by substratespecific labelling of microbial DNA using stable isotope probing13. At this juncture, it seems that the field of environmental microbiology would benefit from an in-depth debate in which the various interested parties, including molecular biologists, microbial ecologists and non-microbiologists, present and discuss, in detail, the ultimate, true benefits of whole-soil metagenomics, before proceeding head-first with this time-consuming and potentially onerous operation.