SPLANG-a synthetic poisson-lognormal-based abundance and network generative model for microbial interaction inference algorithms.

Microbes are pervasive and their interaction with each other and the environment can impact fields as diverse as health and agriculture. While network inference and related algorithms that use abundance data from pyrosequencing can infer microbial interaction networks, the ambiguity surrounding the actual underlying networks hampers the validation of these algorithms. This study introduces a generative model to synthesize both the underlying interactive network and observable abundance data, serving as a test bed for the existing and future network inference algorithms.

The role of efflux transporters in cytotoxicity and intracellular concentration of chlorpyrifos and chlorpyrifos oxon in human cell lines.

In this study, we investigated the role of two efflux transporters, p-glycoprotein (P-gp) and breast cancer resistance protein (BCRP), in the cytotoxicity and intracellular accumulation of the organophosphate pesticide chlorpyrifos (CPF) and its active metabolite, CPF-oxon (CPFO), in a human-derived liver cell line (HepG2) and kidney epithelial cell line (HK-2). The cytotoxicity to CPF and CPFO differed between cell lines where HK-2 had lower IC50 values which could be attributed to lower basal expression and inducibility of metabolizing enzymes, transporters, and nuclear receptors in HK-2 cells. In HepG2 cells, co-exposure of CPF with a specific inhibitor of either P-gp or BCRP enhanced the cytotoxicity of CPF while co-exposure of CPFO with VRP enhanced the cytotoxicity of CPFO, suggesting the role of these transporters in the elimination CPF and CPFO.

Application of a new approach method to assess the hazard of complex legacy contaminated groundwater mixtures on fathead minnows in outdoor mesocosms.

Assessing the environmental risks of contaminated groundwater presents significant challenges due to its often-complex chemical composition and to dynamic processes affecting exposure of organisms in receiving surface waters. The objective of this study was to characterize the effects of groundwater collected from a legacy contaminated industrial site, in fish under environmentally relevant conditions. A 21-day fish short-term reproduction assay was conducted in outdoor wetland mesocosms by exposing adult fathead minnows (Pimephales promelas) to graded concentrations of groundwater (1 %, 3 %, and 6 %).

Do phosphorus amendments enhance biodegradation activity in stalled petroleum hydrocarbon-contaminated soil?

Phosphorus (P) fertilizers promote soil petroleum-hydrocarbon (PHC) bioremediation by correcting carbon-to-P ratio imbalances. While these inputs create conditions favorable to microbial growth, areas of a site or an entire site with low degradation rates (i.e.

Characterization of Adverse Outcomes from Legacy-Contaminated Groundwater Exposure to Early Life Stages of Fathead Minnow.

Complex mixtures of chemicals present in groundwater at legacy-contaminated industrial sites can pose significant risks to adjacent surface waters. The combination of short-term molecular and chronic apical effect assessments is a promising approach to characterize the potential hazard of such complex mixtures. The objectives of this study were to: (1) assess the apical effects (survival, growth, development, and liver histopathology) after chronic exposure of early life stages (ELSs) of fathead minnows (FHM; Pimephales promelas) to contaminated groundwater from a legacy-contaminated pesticide manufacturing and packaging plant, and (2) identify possible molecular mechanisms responsible for these effects by comparing results to mechanistic outcomes previously determined by a short-term reduced transcriptome assay (EcoToxChips).

Hazard assessment of complex legacy-contaminated groundwater mixtures using a novel approach method in adult fathead minnows.

Traditional risk assessment methods face challenges in the determination of drivers of toxicity for complex mixtures such as those present at legacy-contaminated sites. Bioassay-driven analysis across several levels of biological organization represents an approach to address these obstacles. This study aimed to apply a novel transcriptomics tool, the EcoToxChip, to characterize the effects of complex mixtures of contaminants in adult fathead minnows (FHMs) and to compare molecular response patterns to higher-level biological responses.

A shift from individual species to ecosystem services effect: Introducing the Eco-indicator Sensitivity Distribution (EcoSD) as an ecosystem services approach to redefining the species sensitivity distribution (SSD) for soil ecological risk assessment.

Incorporating the ecosystem services (ES) approach into soil ecological risk assessment (ERA) has been advocated over the years, but implementing the approach in ERA faces some challenges. However, several researchers have made significant improvements to the soil ERA, such as applying the species sensitivity distribution (SSD) to discern chemical effects on the soil ecosystem. Despite the considerable contributions of SSD to ERA, SSD fails to relate chemical impact on individual species to ES and account for functional redundancy as well as soil ecosystem complexity.

Characterization of molecular and apical effects of legacy-contaminated groundwater on early life stages of fathead minnows.

Mechanistic toxicology approaches represent a promising alternative to traditional live animal testing; however, the often-noted uncertainties concerning the linkages between effects observed at molecular and apical levels curtails the adoption of such approaches. The objective of this study was to apply a novel transcriptomics tool, EcoToxChips, to characterize the effects of complex mixtures of contaminants in fish and to compare molecular response patterns to higher-level biological responses including swimming behavior, deformities, and mortality. Fathead minnow (FHM) embryos were exposed for seven days to increasing concentrations of groundwater collected from moderate (MIAZ) and high (HIAZ) industrial activity zones of a legacy contaminated site.

Integument colour change: Tracking delayed growth of Oppia nitens as a sub-lethal indicator of soil toxicity.

Growth is an important toxicity end-point in ecotoxicology but is rarely used in soil ecotoxicological studies. Here, we assessed the growth change of Oppia nitens when exposed to reference and heavy metal toxicants. To assess mite growth, we developed an image analysis methodology to measure colour spectrum changes of the mite integument at the final developmental stage, as a proxy for growth change.

Linking niche size and phylogenetic signals to predict future soil microbial relative abundances.

Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict.

Rocks, lichens, and woody litter influenced the soil invertebrate density in upland tundra heath.

Soil invertebrates are an integral part of Arctic ecosystems through their roles in the breakdown of litter, soil formation, and nutrient cycling. However, studies examining soil invertebrates in the Arctic are limited and our understanding of the abiotic and biotic drivers of these invertebrate communities remains understudied. We examined differences in soil invertebrate taxa (mites, collembolans, enchytraeids) among several undisturbed upland tundra heath sites in Nunavut Canada and identified the drivers (vegetation and substrate cover, soil nutrients and pH) of the soil invertebrate community across these sites.

Correlation between in vitro toxicity of pesticides and in vivo risk guidelines in support of complex operating site risk management: A meta-analysis.

In vitro cell systems can support hazard characterization and identify mechanisms involved in toxicity; however, using in vitro data for risk assessment still is challenging. As part of an effort to develop approaches for a complex operating site used for biocide packaging and distribution, we evaluated in vitro assays that could be used in a site management format. Across 66 studies, 108 pesticides were assessed on ten human-derived cell types at four endpoints.

More than just a substrate for mites: Moss-dominated biological soil crust protected population of the oribatid mite, Oppia nitens against cadmium toxicity in soil.

Metal-impacted sites often need aggressive ecorestoration strategies to restore a functional plant-soil system. The use of biological soil crusts for soil stabilization, moisture retention and C and N input in disturbed and contaminated soils is becoming a more common ecorestoration practice. Biological soil crusts comprise cyanobacteria, fungi, lichens, and bryophytes (mostly moss).

Response addition is more protective of biogeochemical cycles of carbon and phosphorus compared to concentration addition.

In soils, enzymes are crucial to catalyzing reactions and cycling elements such as carbon (C), nitrogen (N), and phosphorus (P). Although these soil enzymes are sensitive to metals, they are often disregarded in risk assessments, and regulatory laws governing their existence are unclear. Nevertheless, there is a need to develop regulatory standards for metal mixtures that protect biogeochemical cycles because soil serve as a sink for metals and exposures occur as mixtures.

Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.

Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils.

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH oxidation. CH oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur.

A sustainable colloidal material with sorption and nutrient-supply capabilities for in situ groundwater bioremediation.

Microbial degradation of subsurface organic contaminants is often hindered by the low availability of both contaminants and nutrients, especially phosphorus (P). The use of activated carbon and traditional P fertilizers to overcome these challenges has proved ineffective; therefore, we sought to find an innovative and effective solution. By heating bone meal-derived organic residues in water in a closed reactor, we synthesized nonporous colloids composed of aromatic and aliphatic structures linked to P groups.

Are structural and functional endpoints of soil communities similarly affected by metal mixtures? - A terrestrial model ecosystem approach.

Soils are habitat to a variety of flora and fauna in a linked ecosystem which provides essential ecosystem services. In soil, metals can accumulate at high concentrations, because of anthropogenic activities, leading to toxic effects, threatening the ecosystem and the services it provides. In most real-world contamination scenarios, metals occur as complex mixtures which can interact and produce different toxicity than predicted from individual metal data.

Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation.

Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils.

The role of monodentate tetrahedral borate complexes in boric acid binding to a soil organic matter analogue.

Boron is an essential plant micronutrient responsible for several important functions. Boron availability in soils may be influenced by binding with soil organic matter (SOM), particularly with aromatic diol and polyphenol groups on SOM. The mechanism by which aromatic diols bind boron, however, remains unclear.

Community effect concentrations as a new concept to easily incorporate community data in environmental effect assessment of complex metal mixtures.

The goal of this study was to incorporate community data into the effect assessment of environmental and regulatory relevant metal mixtures. In this experiment three fixed mixture ratios (Canadian soil quality guideline ratio - CSQG; Agricultural, residential and Loamy ratio - ARL; and Sudbury ratio - SUD) were tested in a natural community microcosm with 11 doses for each mixture ratio. The effect of metal mixtures on the community was measured using the community effect concentration (EC) concept which assumes that as contamination increases, the community similarity between test and control treatments decreases producing a dose response curve allowing the calculation of community effect concentrations.

Does habitat quality matter to soil invertebrates in metal-contaminated soils?

This study investigated the influence of habitat quality (HQ) on the reproduction and bioenergetics (energy reserve and metabolic enzyme activities) of the oribatid mite, Oppia nitens, in response to cadmium (Cd). In the baseline toxicity test, Cd elevated the carbohydrate reserve of adult mites at intermediate Cd concentrations (88 and 175 mg Cd kg) but without a change in lipid and protein reserve across 0-700 mg Cd kg. The activities of glucose metabolism enzymes, glucose-6-phosphate dehydrogenase (G6PDH) and pyruvate kinase (PK) were inhibited in the mites at 700 mg Cd kg.

Is assuming additivity of single-metal toxicity thresholds a conservative approach to assessing risk of ecotoxicity from elevated soil concentrations of cobalt, copper, and nickel at contaminated sites?

Multiple metal-impacted soils are often realistic scenarios for risk assessments, but tools to address these are currently lacking. The objective of this work was to evaluate whether assuming concentration addition (CA) of metal mixture effects was conservative for prospective risk assessment of soils that were elevated mainly in Ni and Cu and somewhat with Co, Pb, or As. Observed whole mixture toxicity for field soils with aged metal mixtures was compared to the expected whole mixture toxicity, assuming additivity of prospective single-metal thresholds ("toxic units") for the mixture components.

From the Outside in: An Overview of Positron Imaging of Plant and Soil Processes.

Positron-emitting nuclides have long been used as imaging agents in medical science to spatially trace processes non-invasively, allowing for real-time molecular imaging using low tracer concentrations. This ability to non-destructively visualize processes in real time also makes positron imaging uniquely suitable for probing various processes in plants and porous environmental media, such as soils and sediments. Here, we provide an overview of historical and current applications of positron imaging in environmental research.