Genomics technology for assessing soil pollution

Transcription and metabolite analysis is a powerful way to reveal physiological shifts in response to environmental pollution. Recent studies on earthworms, including one in BMC Biology, show that the type of pollution and its availability for uptake by organisms can differentially affect transcription and metabolism

Avoidance tests with the oribatid mite Oppia nitens (Acari: Oribatida) in cadmium-spiked natural soils

Avoidance behavior can be a useful parameter for assessing the ability of organisms to escape from pollutants in their environment. For soil evaluation, a variety of invertebrates is used including the oribatid mite Oppia nitens. Here, we tested the avoidance behavior of O. nitens using a two-chamber test and an escape test with exposures to different cadmium concentrations of up to 800 mg kg−1 dry LUFA 2.2 soil for 2, 4, and 6 days, and up to 7 weeks. With the two-chamber method, the oribatid mites had the choice between clean and polluted soils, whereas they were allowed to escape from a box with polluted soil to clean containers without soil with the escape method. Avoidance of cadmium was observed after 2 days in both tests and the net response of the mites in the two-chamber test increased with increasing cadmium exposure concentrations. Mite responses varied through time, especially with the escape method; with the avoidance behavior becoming more variable and overall non-significant with longer test durations. This is the first study investigating the escape test simultaneously with long-term avoidance of cadmium by O. nitens. This mite species is a promising species for avoidance testing in soil ecotoxicology, but more experiments are needed to evaluate the factors that influence its responses in laboratory tests and the consequences for its distribution in contaminated ecosystems

UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene

Background: Polycyclic aromatic hydrocarbons are common pollutants in soil, have negative effects on soil ecosystems, and are potentially carcinogenic. The Springtail (Collembola) Folsomia candida is often used as an indicator species for soil toxicity. Here we report a toxicogenomic study that translates the ecological effects of the polycyclic aromatic hydrocarbon phenanthrene in soil to the early transcriptomic responses in Folsomia candida. Results: Microarrays wereused to examine two different exposure concentrations of phenanthrene, namely the EC10 (24.95 mg kg-1 soil) and EC50 (45.80 mg kg-1 soil) on reproduction of this springtail, which evoked 405 and 251 differentially expressed transcripts, respectively. Fifty transcripts were differential in response to either concentration. Many transcripts encoding xenobiotic detoxification and biotransformation enzymes (phases I, II, and III) were upregulated in response to either concentration. Furthermore, indications of general and oxidative stress were found in response to phenanthrene. Chitin metabolism appeared to be disrupted particularly at the low concentration, and protein translation appeared suppressed at the high concentration of phenanthrene; most likely in order to reallocate energy budgets for the detoxification process. Finally, an immune response was evoked especially in response to the high effect concentration, which was also described in a previous transcriptomic study using the same effect concentration (EC50) of cadmium. Conclusion: Our study provides new insights in the molecular mode of action of the important polluting class of polycyclic aromatic hydrocarbons in soil animals. Furthermore, we present a fast, sensitive, and specific soil toxicity test which enhances traditional tests and may help to improve current environmental risk assessments and monitoring of potentially polluted sites. © 2009 Nota et al; licensee BioMed Central Ltd

Reliability and Interpretability of Sonographic Measurements of Palmar Dupuytren Nodules

Purpose: In the future, it is expected that treatment of Dupuytren disease (DD) may shift toward control of early disease. Ultrasound might be an accurate method to measure the outcome of such treatment. The aim of this study was to assess the reliability of sonographic measurement of palmar nodules. Methods: Fifty patients with nodules characteristic for early disease were assessed with ultrasound by 2 observers. Four different aspects of DD nodules were measured in the transversal and sagittal planes, width, depth, circumference, and area. The intra- and interobserver reliabilities were calculated using the intraclass correlation coefficient (ICC). The standard error of measurement (SEM) and the smallest detectable change (SDC) were also calculated for each aspect. Results: The intraobserver reliability was good (ICC, 0.724 [0.562–0.833] to 0.886 [0.808–0.934]), except for width in the sagittal direction (ICC, 0.671 [0.484–0.799]). The interobserver reliability was moderate (ICC, 0.385 [0.126–0.596] to 0.757 [0.538–0.869]). The intraobserver ICCs of area were highest (transverse, 0.847 [0.744–0.893]; sagittal, 0.886 [0.808–0.934]). The SEM and SDC of area were 6.1 and 16.9 mm2 in the transverse and 8.0 and 22.2 mm2 in the sagittal plane. Conclusions: The intraobserver reliability of sonographic assessment of DD nodules is good. The measurement of area is the most reliable and is, therefore, recommended for future studies. However, even single-observer measurements have a clear dispersion, and a change beyond 16.9 (61%) and 22.2 mm2 (79%) has to be observed in the transverse and sagittal planes, respectively, before it can be considered as regression or progression. Clinical relevance: Repeated ultrasonographic measurements in DD should ideally be done by a single observer, using area of the nodule in the sagittal plane. Change beyond 16.9 (transverse) and 22.2 (sagittal) mm2 can be considered as a real change in nodule size

Functional and compositional responses in soil microbial communities along two metal pollution gradients : does the level of historical pollution affect resistance against secondary stress?

We examined how the exposure to secondary stressors affected the functional and compositional responses of microbial communities along two metal pollution gradients in Polish forests and whether responses were influenced by the level of metal pollution. Basal respiration rate and community composition, as determined by 16S rRNA gene-based denaturing gradient analysis, were studied in laboratory-incubated microcosms, containing soil samples taken from different locations in the field gradients, and subjected to secondary stress factors (arsenic, salt, benzo[a]pyrene or flooding). Soils adapted to higher metal contamination levels were more resistant to arsenic and salt stress compared to less polluted soils, indicating that functional and compositional responses to these stresses were related to the level of historical pollution in the long-term contaminated forest soils. However, community composition and functioning in soils along the two gradients were resistant to benzo[a]pyrene and flooding stress. Changes in respiration were significantly related to changes in community composition. Knowledge on the functional gene capabilities prior to adding the secondary stressor benefitted understanding the functional responses toward additional stressors. Our study highlights that microbial communities selected for metal resistance in the field might also become more resistant against some secondary stress factors; however, the type of stress and the level of historical pollution play a decisive role in community-level responses toward secondary stressors

No effect of selected engineered nanomaterials on reproduction and survival of the springtail Folsomia candida

Although the number of studies on engineered nanomaterial (NM) toxicity to soil invertebrates is increasing, only a few studies have reported toxicity of NMs to soil dwelling model species, such as the invertebrate Folsomia candida. The main objective of this study was to determine the toxicity of five different engineered NMs (WCCo, CuO, Fe2O3, organic pigment and MWCNTs) for the springtail F. candida. Copper(ii), cobalt and iron chlorides were taken as positive controls. A standardized OECD test was used to measure effects on reproduction and survival, and toxicity was related to metal concentrations in soil and pore water. None of the NMs exerted adverse effects on springtail reproduction and survival at concentrations up to 6400 mg per kg dry soil, whereas the Cu, Co and Fe chlorides resulted in 50% decline in springtail reproduction at 981, 469 and 569 mg metal ion per kg dry soil, respectively. The absence of toxicity of the NMs could partly be explained by the low porewater metal concentrations, suggesting low solubility or slow solubilisation. The fate of engineered NMs in soil is rather complex but needs better understanding to facilitate predicting exposure of soil organisms

Resilience of soil microbial communities to metals and additional stressors : DNA-based approaches for assessing "Stress-on-Stress" responses

International audienceMany microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the "costs" of adaptation to metals affect the responses of metal-tolerant communities to other stress factors ("stress-on-stress"). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors

Recombinational micro-evolution of functionally different metallothionein promoter alleles from Orchesella cincta

<p>Abstract</p> <p>Background</p> <p>Metallothionein (<it>mt</it>) transcription is elevated in heavy metal tolerant field populations of <it>Orchesella cincta </it>(Collembola). This suggests that natural selection acts on transcriptional regulation of <it>mt </it>in springtails at sites where cadmium (Cd) levels in soil reach toxic values This study investigates the nature and the evolutionary origin of polymorphisms in the metallothionein promoter (<it>pmt</it>) and their functional significance for <it>mt </it>expression.</p> <p>Results</p> <p>We sequenced approximately 1600 bp upstream the <it>mt </it>coding region by genome walking. Nine <it>pmt </it>alleles were discovered in NW-European populations. They differ in the number of some indels, consensus transcription factor binding sites and core promoter elements. Extensive recombination events between some of the alleles can be inferred from the alignment. A deviation from neutral expectations was detected in a cadmium tolerant population, pointing towards balancing selection on some promoter stretches. Luciferase constructs were made from the most abundant alleles, and responses to Cd, paraquat (oxidative stress inducer) and moulting hormone were studied in cell lines. By using paraquat we were able to dissect the effect of oxidative stress from the Cd specific effect, and extensive differences in <it>mt </it>induction levels between these two stressors were observed.</p> <p>Conclusion</p> <p>The <it>pmt </it>alleles evolved by a number of recombination events, and exhibited differential inducibilities by Cd, paraquat and molting hormone. In a tolerant population from a metal contaminated site, promoter allele frequencies differed significantly from a reference site and nucleotide polymorphisms in some promoter stretches deviated from neutral expectations, revealing a signature of balancing selection. Our results suggest that the structural differences in the <it>Orchesella cincta </it>metallothionein promoter alleles contribute to the metallothionein -over-expresser phenotype in cadmium tolerant populations.</p