Showing papers in "Frontiers in Environmental Science in 2016"

DeepTox: Toxicity Prediction using Deep Learning

Abstract: The Tox21 Data Challenge has been the largest effort of the scientific community to compare computational methods for toxicity prediction. This challenge comprised 12,000 environmental chemicals and drugs which were measured for 12 different toxic effects by specifically designed assays. We participated in this challenge to assess the performance of Deep Learning in computational toxicity prediction. Deep Learning has already revolutionized image processing, speech recognition, and language understanding but has not yet been applied to computational toxicity. Deep Learning is founded on novel algorithms and architectures for artificial neural networks together with the recent availability of very fast computers and massive datasets. It discovers multiple levels of distributed representations of the input, with higher levels representing more abstract concepts. We hypothesized that the construction of a hierarchy of chemical features gives Deep Learning the edge over other toxicity prediction methods. Furthermore, Deep Learning naturally enables multi-task learning, that is, learning of all toxic effects in one neural network and thereby learning of highly informative chemical features. In order to utilize Deep Learning for toxicity prediction, we have developed the DeepTox pipeline. First, DeepTox normalizes the chemical representations of the compounds. Then it computes a large number of chemical descriptors that are used as input to machine learning methods. In its next step, DeepTox trains models, evaluates them, and combines the best of them to ensembles. Finally, DeepTox predicts the toxicity of new compounds. In the Tox21 Data Challenge, DeepTox had the highest performance of all computational methods winning the grand challenge, the nuclear receptor panel, the stress response panel, and six single assays (teams ``Bioinf@JKU''). We found that Deep Learning excelled in toxicity prediction and outperformed many other computational approaches like naive Bayes, support vector machines, and random forests.

Nanotechnology in Agriculture: Which Innovation Potential Does It Have?

Abstract: Recent scientific data indicate that nanotechnology has the potential to positively impact the agrifood sector, minimizing adverse problems of agricultural practices on environment and human health, improving food security and productivity (as required by the predicted rise in global population), while promoting social and economic equity. In this context, we select and report on recent trends in nanomaterial-based systems and nanodevices that could provide benefits on the food supply chain specifically on sustainable intensification, and management of soil and waste. Among others, nanomaterials for controlled-release of nutrients, pesticides and fertilizers in crops are described as well as nanosensors for agricultural practices, food quality and safety.

Soil “Ecosystem” Services and Natural Capital: Critical Appraisal of Research on Uncertain Ground

Abstract: Over the last few years, considerable attention has been devoted in the scientific literature and in the media to the concept of "ecosystem" services of soils. The monetary valuation of these services, demanded by many governments and international agencies, is often depicted as a necessary condition for the preservation of the natural capital that soils represent. This focus on soil services is framed in the context of a general interest in ecosystem services that allegedly started in 1997, and took off in earnest after 2005. The careful analysis of the literature proposed in this article shows that, in fact, interest in the multifunctionality of soils emerged already in the mid-60s, at a time when hundreds of researchers worldwide were trying, and largely failing, to figure out how to put price tags meaningfully on "nature's services." Soil scientists, since, have tried to better understand various functions/services of soils, as well as their possible relation with key soil characteristics, like biodiversity. They have also tried to make progress on the challenging quantification of soil functions/services. However, researchers have shown very little interest in monetary valuation, undoubtedly in part because it is not clear what economic and financial markets might do with prices of soil functions/services, even if we could somehow come up with such numbers, and because there is no assurance at all, based on neoclassical economic theory, that markets would manage soil resources optimally. Instead of monetary valuation, focus in the literature has been put on decision-making methods, like Multi-Criteria Decision Analysis (MCDA) and Bayesian Belief Networks (BBN), which do not require the systematic monetization of soil functions/services and easily accommodate deliberative approaches involving a variety of stakeholders. A prerequisite to progress in such public deliberations is that participants be very cognizant of the extreme relevance of soils to many aspects of their daily life. We argue that, as long as this prerequisite is satisfied, the combination of deliberative decision-making methods and of a sound scientific approach to the quantification of soil functions/services is a very promising avenue to manage effectively and ethically the priceless heritage that soils constitute.

Environmental Impacts of the Deep-Water Oil and Gas Industry: A Review to Guide Management Strategies

Abstract: The industrialization of the deep sea is expanding worldwide. Expanding oil and gas exploration activities in the absence of sufficient baseline data in these ecosystems has made environmental management challenging. Here, we review the types of activities that are associated with global offshore oil and gas development in water depths over 200 m, the typical impacts of these activities, some of the more extreme impacts of accidental oil and gas releases, and the current state of management in the major regions of offshore industrial activity including 18 exclusive economic zones. Direct impacts of infrastructure installation, including sediment resuspension and burial by seafloor anchors and pipelines, are typically restricted to a radius of approximately 100 m on from the installation on the seafloor. Discharges of water-based and low-toxicity oil-based drilling muds and produced water can extend over 2 km, while the ecological impacts at the population and community levels on the seafloor are most commonly on the order of 200-300 m from their source. These impacts may persist in the deep sea for many years and likely longer for its more fragile ecosystems, such as cold-water corals. This synthesis of information provides the basis for a series of recommendations for the management of offshore oil and gas development. An effective management strategy, aimed at minimizing risk of significant environmental harm, will typically encompass regulations of the activity itself (e.g. discharge practices, materials used), combined with spatial (e.g. avoidance rules and marine protected areas) and temporal measures (e.g. restricted activities during peak reproductive periods). Spatial management measures that encompass representatives of all of the regional deep-sea community types is important in this context. Implementation of these management strategies should consider minimum buffer zones to displace industrial activity beyond the range of typical impacts: at least 2 km from any discharge points and surface infrastructure and 200 m from seafloor infrastructure with no expected discharges. Although managing natural resources is, arguably, more challenging in deep-water environments, inclusion of these proven conservation tools contributes to robust environmental management strategies for oil and gas extraction in the deep sea.

Silicon Nanoparticles More Efficiently Alleviate Arsenate Toxicity than Silicon in Maize Cultiver and Hybrid Differing in Arsenate Tolerance

Abstract: Though role of silicon (Si) in alleviation of various abiotic stresses is well known; however, role of silicon nanoparticles (SiNp) in mitigation of abiotic stresses is still not known. Therefore, hydroponic experiments were conducted to investigate if SiNPs are more effective than Si in mitigation of arsenate (AsV; 25 and 50 µM) toxicity in maize cultivar and hybrid differing in AsV tolerance. Under AsV stress, reduction in growth was accompanied by enhanced level of As and oxidative stress. AsV inhibited activities of antioxidant enzymes like ascorbate peroxidase, glutathione reductase and dehydroascorbate reductase (except superoxide dismutase). The redox status of ascorbate and glutathione was disturbed by AsV as indicated by a steep decline in their reduced/oxidized ratios. However, addition of Si and SiNp ameliorates AsV toxicity in maize. Si and SiNp both could reduce AsV toxicity in maize cultivar and hybrid, which could be related with decreased accumulation of As and oxidative stress, and enhanced components of the ascorbate-glutathione cycle (AsA-GSH cycle). But lowering in the accumulation of As and oxidative stress markers, and enhancement in components of the AsA-GSH cycle was prominent in SiNp fed seedlings under AsV stress. The results also showed that SiNp are more effective in reducing AsV toxicity than Si, which is due to their greater availability to seedlings. Comparing responses of cultivar and hybrid, maize cultivar shows more resistance against AsV than hybrid.

Influence of High and Low Levels of Plant-Beneficial Heavy Metal Ions on Plant Growth and Development

Abstract: Heavy metals (HMs) exists in the environment in both forms as essential and non-essential. These HM ions enter in soil biota from various sources like natural and anthropogenic. Essential HMs such as cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), molybdenum (Mo), nickel (Ni), and zinc (Zn) plays a beneficial role in plant growth and development. At optimum level these beneficial elements improves the plant’s nutritional level and also several mechanisms essential for the normal growth and better yield of plants. The range of their optimality for land plants is varied. Plant uptake heavy metals as a soluble component or solubilized them by root exudates. While their presence in excess become toxic for plants that switches the plant’s ability to uptake and accumulate other nonessential elements. The increased amount of HMs within the plant tissue displays direct and indirect toxic impacts. Such direct effects are the generation of oxidative stress which further aggravates inhibition of cytoplasmic enzymes and damage to cell structures. Although, indirect possession is the substitution of essential nutrients at plant’s cation exchange sites. These ions readily influence role of various enzymes and proteins, arrest metabolism, and reveal phytotoxicity. On account of recent advancements on beneficial HMs ions Co, Cu, Fe, Mn, Mo, Ni, and Zn in soil-plant system, the present paper: overview the sources of HMs in soils and their uptake and transportation mechanism, here we have discussed the role of metal transporters in transporting the essential metal ions from soil to plants. The role played by Co, Cu, Fe, Mn, Mo, Ni, and Zn at both low and high level on the plant growth and development and the mechanism to alleviate metal toxicity at high level have been also discussed. At the end, on concluding the article we have also discussed the future perspective in respect to beneficial HM ions interaction with plant at both levels.

Contamination of the Aquatic Environment with Neonicotinoids and its Implication for Ecosystems

Abstract: The widespread use of systemic neonicotinoid insecticides in agriculture results first in contamination of the soil of the treated crops, and secondly in the transfer of residues to the aquatic environment. The high toxicity of these insecticides to aquatic insects and other arthropods has been recognised, but there is little awareness of the impacts these chemicals have on aquatic environments and the ecosystem at large. Recent monitoring studies in several countries, however, have revealed a world-wide contamination of creeks, rivers and lakes with these insecticides, with residue levels in the low μg/L (ppb) range. The current extent of aquatic contamination by neonicotinoids is reviewed first, and the findings contrasted with the known acute and chronic toxicity of neonicotinoids to various aquatic organisms. Impacts on populations and aquatic communities, mostly using mesocosms, are reviewed next to identify the communities most at risk from those that undergo little or no impact. Finally, the ecological links between aquatic and terrestrial organisms are considered. The consequences for terrestrial vertebrate species that depend mainly on this food source are discussed together with impacts on ecosystem function. Gaps in knowledge stem from difficulties in obtaining long-term experimental data that relates the effects on individual organisms to impacts on populations and ecosystems. The paper concludes with a summary of findings and the implications they have for the larger ecosystem.

Achieving Sustainable Development Goals from a Water Perspective

Abstract: Efforts to meet human water needs only at local scales may cause negative environmental externality and stress on the water system at regional and global scales. Hence, assessing SDG targets requires a broad and in-depth knowledge of the global to local dynamics of water availability and use. Further, Interconnection and trade-offs between different SDG targets may lead to sub-optimal or even adverse outcome if the set of actions are not properly pre-designed considering such interlinkages. Thus scientific research and evidence have a role to play in facilitating the implementation of SDGs through assessments and policy engagement from global to local scales. The paper addresses some of these challenges related to implementation and monitoring the targets of the Sustainable Development Goals from a water perspective, based on the key findings of a conference organised in 2015 with the focus on three essential aspects of SDGs- indicators, interlinkages and implementation. The paper discusses that indicators should not be too simple but ultimately deliver sustainability measures. The paper finds that remote sensing and earth observation technologies can play a key role in supporting the monitoring of water targets. It also recognises that implementing SDGs is a societal process of development, and there is need to link how SDGs relate to public benefits and communicate this to the broader public.

Stream Biofilm Responses to Flow Intermittency: From Cells to Ecosystems

Abstract: Temporary streams are characterized by the alternation of dry and wet hydrological phases, creating both a harsh environment for the biota as well as a high diversity of opportunities for adaptation. These systems are eminently microbial-based during several of these hydrological phases, and those growing on all solid substrata (biofilms) accordingly change their physical structure and community composition. Biofilms experience large decreases on cell densities and biomass, both of bacteria and algae, during dryness. Algal and bacterial communities show remarkable decreases in their diversity, at least locally (at the habitat scale). Biofilms also respond with significant physiological plasticity to each of the hydrological changes. The decreasing humidity of the substrata through the drying process, and the changing quantity and quality of organic matter and nutrients available in the stream during that process, causes unequal responses on the biofilm bacteria and algae. Biofilm algae are affected faster than bacteria by the hydric stress, and as a result the ecosystem respiration resists longer than gross primary production to the increasing duration of flow intermittency. This response implies enhancing ecosystem heterotrophy, a pattern that can be exacerbated in temporary streams suffering of longer dry periods under global change.

Glyphosate: Too Much of a Good Thing?

Abstract: Although previously accepted as the less toxic alternative, with low impact on animals, farmers as well as consumers who are exposed to residues in food, glyphosate chemicals are now increasingly controversial as new evidence from research is emerging. We argue that specific aspects of the history, chemistry and safety of glyphosate and glyphosate-based herbicides should be thoroughly considered in present and future re-evaluations of these dominant agrochemicals: · Glyphosate is not a single chemical, it is a family of compounds with different chemical, physical and toxicological properties. · Glyphosate is increasingly recognized as having more profound toxicological effects than assumed from previous assessments. · Global use of glyphosate is continuously increasing and residues are detected in food, feed and drinking water. Thus, consumers are increasingly exposed to higher levels of glyphosate residues, and from an increasing number of sources. · Glyphosate regulation is predominantly still based on primary safety-assessment testing in various indicator organisms. However, archive studies indicate fraud and misbehavior committed by the commercial laboratories providing such research. We see emerging evidences from studies in test-animals, ecosystems indicators and studies in human health, which justify stricter regulatory measures. This implies revising glyphosate residue definitions and lowering Maximum Residue Limits (MRLs) permissible in biological material intended for food and feed, as well as strengthening environmental criteria such as accepted residue concentrations in surface waters. It seems that although recent research indicates that glyphosates are less harmless than previously assumed and have complex toxicological potential, still regulatory authorities accept industry demands for approving higher levels of these residues in food and feed.

Sensitivity of grapevine phenology to water availability, temperature and CO2 concentration

Abstract: In recent decades, mean global temperatures have increased in parallel with a sharp rise in atmospheric carbon dioxide (CO2) levels, with apparent implications for precipitation patterns. The aim of the present work is to assess the sensitivity of different phenological stages of grapevine to temperature and to study the influence of other factors related to climate change (water availability and CO2 concentration) on this relationship. Grapevine phenological records from 9 plantings between 42.75°N and 46.03°N consisting of dates for budburst, flowering and fruit maturity were used. In addition, we used phenological data collected from two years of experiments with grapevine fruit-bearing cuttings with two grapevine varieties under two levels of water availability, two temperature regimes and two levels of CO2. Dormancy breaking and flowering were strongly dependent on spring temperature, while neither variation in temperature during the chilling period nor precipitation significantly affected budburst date. The time needed to reach fruit maturity diminished with increasing temperature and decreasing precipitation. Experiments under semi-controlled conditions revealed great sensitivity of berry development to both temperature and CO2. Water availability had significant interactions with both temperature and CO2; however, in general, water deficit delayed maturity when combined with other factors. Sensitivities to temperature and CO2 varied widely, but higher sensitivities appeared in the coolest year, particularly for the late ripening variety, ‘White Tempranillo’. The knowledge gained in whole plant physiology and multi stress approaches is crucial to predict the effects of climate change and to design mitigation and adaptation strategies allowing viticulture to cope with climate change.

Combination of Electrochemical Processes with Membrane Bioreactors for Wastewater Treatment and Fouling Control: A Review

Abstract: This paper provides a critical review about the integration of electrochemical processes into membrane bioreactors (MBR) in order to understand the influence of these processes on wastewater treatment performance and membrane fouling control. The integration can be realized either in an internal or an external configuration. Electrically enhanced membrane bioreactors or electro membrane bioreactors (eMBRs) combine biodegradation, electrochemical and membrane filtration processes into one system providing higher effluent quality as compared to conventional MBRs and activated sludge plants. Furthermore, electrochemical processes, such as electrocoagulation, electrophoresis and electroosmosis, help to mitigate deposition of foulants into the membrane and enhance sludge dewaterability by controlling the morphological properties and mobility of the colloidal particles and bulk liquid. Intermittent application of minute electric field has proven to reduce energy consumption and operational cost as well as minimize the negative effect of direct current field on microbial activity which are some of the main concerns in eMBR technology. The present review discusses important design considerations of eMBR, its advantages as well as its applications to different types of wastewater. It also presents several challenges that need to be addressed for future development of this hybrid technology which include treatment of high strength industrial wastewater and removal of emerging contaminants, optimization study, cost benefit analysis and the possible combination with microbial electrolysis cell for biohydrogen production.

Application of Biotests for the Determination of Soil Ecotoxicity after Exposure to Biodegradable Plastics

Abstract: Biodegradable plastics are mostly applied in packaging materials (eg shopping bags), waste collection bags, catering products, and agricultural applications In this last case, degradation takes place directly in soil where biodegradable plastic products are intentionally left after use (eg mulch films for weeds control) Due to the growing volumes of biodegradable polymers and plastics, interest in their environmental safety is increasing and more research is carried out Some attempt has been made to apply biotests, used in other sectors of environmental sciences, in the assessment of biodegradable plastics safety In this work, the quality of soils after biodegradation of the bioplastics Mater-Bi has been assessed with a large array of biotests based on model organisms representative of the different trophic levels in the food chains of the edaphic and aquatic ecosystems Mater-Bi was degraded under controlled conditions for 6 months at a 1% concentration The selected organisms included bacteria and protozoa (V fischeri and D discoideum, respectively), the green alga P subcapitata, plants (the monocotyledon S saccharatum and the dicotyledon L sativum), and invertebrates animals (D magna, a freshwater crustacean, and the Oligochaeta earthworm E andrei), using both acute and chronic endpoints The results of the applied ecotoxicological tests showed that the Mater-Bi materials tested at very high doses did not affect the soil quality Soil exposed to Mater-Bi has no noxious effects on edaphic organisms; in particular, mono and dicotyledon plants results, indicate that Mater-Bi plastic products are innocuous for agricultural uses The use of more sensitive chronic endpoints allows to exclude possible effects at population level This is the first time that such a comprehensive approach is applied to the assessment of possible ecotoxicity effects induced by biodegradable plastics in soil and represents a possible starting point for improved standardized testing schemes

QSAR Modeling of Tox21 Challenge Stress Response and Nuclear Receptor Signaling Toxicity Assays

Abstract: The ability to determine which environmental chemicals pose the greatest potential threats to human health remains one of the major concerns in regulatory toxicology. Computation methods that can accurately predict the chemicals’ toxic potential in silico are increasingly sought-after to replace in vitro high-throughput screening (HTS) as well as controversial and costly in vivo animal studies. To this end, we have built Quantitative Structure-Activity Relationship (QSAR) models of twelve (12) stress response and nuclear receptor signaling pathways toxicity assays as part of the 2014 Tox21 Challenge. Our models were built using the Random Forest, Deep Neural Networks and various combinations of descriptors and balancing protocols. All of our models were statistically significant for each of the 12 assays with the balanced accuracy in the range between 0.58 and 0.82. Our results also show that models built with Deep Neural Networks had high accuracy than those developed with simple machine learning algorithms and that dataset balancing led to a significant accuracy decrease.

Sustainable Management of Tropical Forests Can Reduce Carbon Emissions and Stabilize Timber Production

Abstract: The REDD+ scheme of the United Nations Framework Convention on Climate Change has provided opportunities to manage tropical forests for timber production and carbon emission reductions. To determine the appropriate logging techniques, we analyzed potential timber production and carbon emission reductions under two logging techniques over a 40-year period of selective logging. We found that use of reduced-impact logging (RIL) techniques alone in tropical production forests could reduce carbon emissions equivalent to 29-50% of net emissions from tropical deforestation and land use change, while also supplying 45% of global round-wood demand. Adopting RIL plus (RIL+) other improvements in forest management (adopting forest certification and DNA timber tracking to prevent illegal logging) and wood conversion practices (adopting technology to increase recovery of sawn wood), would result in increasing long-term carbon storage in sawn-wood and reduce logging-induced fire-prone wood wastes by 14-184%. For this to happen, about US$2 billion or $1.86 per Mg CO2 in financial incentives are needed annually for parties to adopt RIL+ and to prevent premature re-entry logging. Our findings suggest that future climate policies explicitly include RIL+ to satisfy the “sustainable management of forests” proviso in the REDD+ scheme, and also count carbon in wood products as eligible credits for trading.

Morphology of Modified Biochar and Its Potential for Phenol Removal from Aqueous Solutions

Abstract: In the present study, the efficiency of phenol removal from synthetic aqueous solutions by chemically modified biochar with the use of 1M KOH or 1M FeCl3 was investigated. Initially, biochar was produced after slow pyrolysis of three different agricultural wastes, namely pistachio (Pistacia vera L.) shells, pecan (Carya illinoinensis) shells and wood sawdust. The quality of biochar was assessed by evaluating its main properties, such as pH, surface area, porosity and C content. X-ray diffraction (XRD), Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) were used for the identification of biochar’s structure. The efficiency of phenol removal from synthetic solutions was assessed with the use of kinetic and equilibrium experiments. The experimental results show that the KOH-modified biochar exhibited the highest phenol removal efficiency. Hydrophobic sorption on its surface is the main phenol removal mechanism. The pseudo-second order model fits best the kinetic data, while the Freundlich model, as deduced from an equilibrium study describes very well sorption of phenols on all biochars examined.

Grand Challenge for the Future of Freshwater Ecosystems

Abstract: Our past approach to water management is unlikely to meet growing human water needs in the face of accelerated change to our freshwater ecosystems, let alone address the consequences of continuing environmental decline. The aim of this “grand challenge” article is to highlight what can be done to address these problems, from global scale governance initiatives to local-scale on-ground actions, aimed at tackling problems at their source. I also wish to explore what more we can do to improve engagement among the scientific and technical disciplines with interests in freshwater management, and more effectively communicate the cause and consequence of these problems, and possible solutions to them, to decision makers and the broader community.

Enhanced Anaerobic Digestion of Food Waste by Supplementing Trace Elements: Role of Selenium (VI) and Iron (II)

Abstract: This paper discusses the potential to enhance the anaerobic digestion of food waste FW by supplementing trace elements (Fe, Co, Ni, Zn, Mn, Cu, Se, and Mo) individually as well as in cocktails. A series of batch experiments on the biomethane potential of synthetic food waste were performed with low (FW-A) and high (FW-B) trace element background concentrations prepared in, respectively, Delft (The Netherlands) and Tampa (Florida, USA). The most effective trace elements for FW-A were Fe with an increase of 39.2 (± 0.6) % of biomethane production, followed by Se (34.1 ± 5.6 % increase), Ni (26.4 ± 0.2 % increase) and Co (23.8 ± 0.2 % increase). For FW-B supplementing these trace elements did not result in enhancement of the biomethane production, except for Se. FW-B had a Se concentration of 1.3 (± 0. 5) µg/gTS, while it was below the detection limit for FW-A. Regardless of the FW source, Se resulted in 30 – 35% increase of biomethane production at a concentration range of 25-50 µg/L (0.32 – 0.63 µM). Volatile fatty acids analysis revealed that TE supplementation enhances their consumption, thus yielding a higher biomethane production. Moreover, additional experiments on sulfide inhibition showed the enhancing effects of trace elements on the anaerobic digestion of food waste were not related with sulfide toxicity, but with the enzymatic reactions and/or microbial biomass aggregation.

Consensus Modeling for HTS Assays Using In silico Descriptors Calculates the Best Balanced Accuracy in Tox21 Challenge

Abstract: The need for filling information gaps while reducing toxicity testing in animals is becoming more predominant in risk assessment. Recent legislations are accepting in silico approaches for predicting toxicological outcomes. This article describes the results of Quantitative Structure Activity Relationship (QSAR) modeling efforts within Tox21 Data Challenge 2014, which calculated the best balanced accuracy across all molecular pathway endpoints as well as the highest scores for ATAD5 and mitochondrial membrane potential disruption. Automated QSPR workflow systems, OCHEM (http://ochem.eu), the analytics platform, KNIME and the statistics software, CRAN R, were used to conduct the analysis and develop consensus models using ten different descriptor sets. A detailed analysis of QSAR models for all 12 molecular pathways and the effect of underlying models’ accuracy on the quality of the consensus model are provided. The resulting consensus models yielded a balanced accuracy as high as 88.1%±0.6 for mitochondrial membrane disruptors. Such high balanced accuracy and use of the applicability domain show a promising potential for in silico modeling to complement design HTS screening experiments. The summary statistics of all models are publicly available online at https://github.com/amaziz/Tox21-Challenge-Publication while the developed consensus models can be accessed at http://ochem.eu/article/98009.

Arbuscular Mycorrhizal Fungi Alleviate the Negative Effects of Iron Oxide Nanoparticles on Bacterial Community in Rhizospheric Soils

Abstract: As a crucial reciprocal partner, arbuscular mycorrhizal fungi (AMF) can alleviate the negative effects of a variety of pollutants on their hosts and soil microbes. In our previous studies, such characteristics of AMF on plant growth were documented in response to metal engineered nanoparticle (ENP) treatments. However, the role of AMF in influencing ENP effects on soil microbes is still under debate. To address this, we investigated the responses of soil microorganisms to iron oxide nanoparticles (FeONPs) along a concentration gradient (0.1, 1.0 and 10.0 mg kg-1) in maize plants inoculated with or without AMF. The results showed that a high concentration of FeONPs significantly decreased the soil bacterial abundance and shifted the community composition, and these negative responses were associated with decreased DOC contents. However, in the presence of AMF, no significant changes in soil biota and DOC contents were observed under FeONPs treatment. These results indicate that AMF alter the effects of FeONPs on soil microorganisms, possibly by influencing plant growth and organic matter released from plant roots, as DOC contents were impacted by AMF. Our findings suggest that AMF can influence FeONP-plant-microbe interactions; therefore, more attention should be focused on plant-associated microbes when evaluating the biological effects of nanoparticles.

Soybean Seed Treatment with Nickel Improves Biological Nitrogen Fixation and Urease Activity

Abstract: Nickel (Ni) is an essential micronutrient required for plants’ metabolism due to its role as a structural component of urease and hydrogenase, which in turn perform nitrogen (N) metabolism in many legume species. Seed treatment with cobalt, molybdenum and Bradyrhizobium strains has been widely practiced to improve crops. Additionally, seed treatment together with Ni fertilization of soybean might improve the efficiency of biological nitrogen fixation (BNF), boosting grain dry matter yield and N content. The objective of this study was to evaluate the effect of soybean seed treatment with Ni rates (0, 45, 90,135, 180, 360 and 540 mg kg-1) on biological nitrogen fixation (BNF), directly by the 15N natural abundance method (δ15N‰) and by measurement of urease [E.C. 3.5.1.5] activity, as well as indirectly by nitrogenase (N-ase) activity [E.C. 1.18.6.1]. Soybean plants (cultivar BMX Potencia RR) were grown in a sandy soil up to the R7 developmental stage (grain maturity), at which point the nutrient content in the leaves, chlorophyll content, urease and N-ase activities, Ni and N content in the grains, nodulation (at R1 - flowering stage), as well as the contribution of biological nitrogen fixation (δ15N ‰), were evaluated. The proportion of N derived from N2 fixation varied from 77 to 99% using the natural 15N abundance method and non-nodulating Panicum miliaceum and Phalaris canariensis as references. A Ni rate of 45 mg kg-1 increased BNF by 12% compared to the control. The increased N uptake in the grains was closely correlated with chlorophyll content in the leaves, urease and N-ase activities, as well as with nodulation. Grain dry matter yield and aerial part dry matter yield increased, respectively, by 84% and 51% in relation to the control plants at 45 mg kg-1 Ni via seed treatment. Despite, Ni concentration was increased with Ni-seed treatment, Ni rates higher than 135 mg kg-1 promoted negative effects on plant growth and yield. In these experimental conditions, seed treatment with low Ni rates caused higher dry matter yield of plants and grains.

Sustainable Intensification of Tropical Agro-Ecosystems: Need and Potentials

Abstract: Rapid population growth, increasingly complex economies and novel industrial uses of agricultural products call for further intensification of agriculture, particularly in the tropics. How to achieve sustainable intensification of food production systems in tropical regions that are challenged by ongoing climate change, loss of natural resources and biodiversity is a matter of debate. Here we highlight the major knowledge gaps in agricultural research and policy that must be addressed to develop adequate governance and regulatory frameworks for sustainable agricultural intensification. They include quantification of the i) value of (public/private) goods generated by ecosystem services, ii) costs to conserve the natural resources and biodiversity that maintain ecosystem services, and iii) true costs of different types of agriculture (in environmental, social and health dimensions) as well as iv) required adaptations that will make alternative farming strategies feasible at a global scale. We discuss the synergies and potential of agro-ecology and organic agriculture to transform our food systems and highlight the importance of controlling demand for food through societal (behavioral) and political (structural) changes in agricultural value chains. Finally, we review the sustainability standards and participatory guarantee systems in developed and developing countries, respectively, and argue that exemplars from developed countries could be role models in adapting governance and regulatory frameworks for developing countries.

Biomass and Diversity of Soil Mite Functional Groups Respond to Extensification of Land Management, Potentially Affecting Soil Ecosystem Services

Abstract: Soil mites (Acari) are ubiquitous in soil ecosystems and show a vast taxonomic diversity with a wide range of life history characteristics and feeding strategies. Various taxa contribute directly or indirectly to soil processes, including nutrient cycling, soil formation and pest control. Mites thus support important ecosystem services of soils. Yet, their community composition, and therewith service provisioning, may differ between for instance intensively managed agricultural soils and extensively managed grassland soils. We therefore hypothesized that successional changes in the abundance and diversity of soil mite functional groups (feeding types) will occur following a conversion of arable land to grassland, affecting their contribution to ecosystem services. To test this, we studied the succession of mite communities on two Long Term Observatories (LTOs) in Lusignan (France) and Veluwe (the Netherlands). At Lusignan, sampling involved four combinations of recent and historic land use types. At the Veluwe, samples were taken in a secondary succession chronosequence in grasslands, representing a time frame up to 29 years after the conversion from arable land to grassland. Biodiversity and biomass were higher in grassland than in arable land, especially for the total mite community, the predators and the main taxa aiding in decomposition. After conversion of grassland to arable land, or vice versa, both taxon richness and biomass rapidly developed towards the prevailing conditions. Our results indicated that the taxon richness and biomass of the total mite community in grassland still continued to increase up to 29 years after the conversion from arable land to grassland. Total taxon richness increased with time since conversion, which was mainly due to the immigration of decomposers and predators. The biomass of different feeding guilds increased at variable speeds. The observed changes imply an increase in nutrient cycling and in the suppression of some potential pests. We discuss the relevance of these ecosystem services in extensively managed grasslands and agricultural systems. Furthermore, our results suggest that in agricultural rotational schemes that include one or more years of grassland, mite communities and associated ecosystem services may be partially, but not completely, restored to the conditions of long term grassland.

Biophysical and Biochemical Markers of Metal/Metalloid-Impacts in Salt Marsh Halophytes and Their Implications

Abstract: As a major sink, estuarine/salt marsh ecosystem can receive discharges laden with myriads of contaminants including metals/metalloids from man-made activities. Two among the major consequences of metal/metalloid-exposure in estuarine/salt marsh ecosystem flora such as halophytic plants are: (a) the excessive accumulation of light energy that in turn leads to severe impairments in the photosystem II (PS II), and (b) metal/metalloids-accrued elevation in reactive oxygen species (ROS) in cells that causes imbalance in cellular redox homeostasis. On one hand, plants adopt several strategies to dissipate excessive energy hence eventually to avoid damage in the PS II and maintain optimum photosynthesis. On the other hand, components of cellular redox system quickly respond to metal/metalloid exposure, where plants try to maintain a fine-tuning therein and tightly control the level of ROS and its potential consequences. Based on recent reports this paper: (a) overviews in separate sections major insights into and the significance of major biophysical and biochemical markers in metal/metalloid-exposed halophytes; and (b) concludes the paper and highlights major points so far unexplored in the current context. Discussion reflects the need of integrating studies on major biophysical and biochemical markers in order finally to unveil tolerance/resistance mechanisms in halophytes under metal/metalloid exposed conditions.

Safe and Sustainable Traditional Production: The Water Buffalo in Asia

Abstract: The water buffalo (Bubalus bubalis) is considered an efficient converter of poor quality forages into high quality milk and meat. This species is ubiquitous, with prevalence though in Asian and Mediterranean countries. From a genetic standpoint, the species is characterized by two main subspecies: river and swamp type. The former to be found predominantly in Mediterranean countries, whereas the latter is found only in the Asia continent. At present, the majority of the total world buffalo population is distributed in Asia, holding around 95% of the available stock. There, animals are mostly fed on low quality roughages and crop residues with poor nutritive value, resulting inevitably in reduced productive and reproductive performances. A distinctive differential production system is in effect between river and swamp type buffaloes, due to a significant production capacity of the two sub-species. An overview of production systems and their sustainability in the two sub-species with an emphasis on country of origin and feed availability is presented.

Drug-Induced Behavioral Changes : Using Laboratory Observations to Predict Field Observations

Abstract: Behavioral assays constitute important research tools when assessing how fish respond to environmental change. However, it is unclear how behavioral modifications recorded in laboratory assays are expressed in natural ecosystems, a limitation that makes it difficult to evaluate the predictive power of laboratory-based measurements. In this study, we hypothesized that exposure to a benzodiazepine (i.e., oxazepam) increases boldness and activity in laboratory assays as well as in field assays – that is, laboratory results can be used to predict field results. Moreover, we expected the modified behavior to affect other important ecological measures such as habitat selection and home range. To test our hypothesis, we exposed European perch (Perca fluviatilis) to oxazepam and measured subsequent changes in behavioral trials both in laboratory assays and in a lake ecosystem populated with a predatory fish species, pike (Esox lucius). In the lake, the positions of both perch and pike were tracked every three minutes for a month using acoustic telemetry. In the laboratory assay, the oxazepam-exposed perch were bolder and more active than the non-exposed perch. In the lake assay, the oxazepam-exposed perch were also more bold and active, had a larger home range, and used pelagic habitats more than the non-exposed perch. We conclude that ecotoxicological behavioral assays are useful for predicting the effects of exposure in natural systems. However, although individual responses to exposure were similar in both the laboratory and field trials, effects were more obvious in the field study, mainly due to reduced variability in the behavior measures from the lake. Hence, short-term behavioral assays may fail to detect all the effects expressed in natural environments. Nevertheless, our study clearly demonstrates that behavior modifications observed in laboratory settings can be used to predict how fish perform in aquatic ecosystems.

Predictive Modeling of Estrogen Receptor Binding Agents Using Advanced Cheminformatics Tools and Massive Public Data

Abstract: Estrogen receptors (ERα) are a critical target for drug design as well as a potential source of toxicity when activated unintentionally. Thus, evaluating potential ERα binding agents is critical in both drug discovery and chemical toxicity areas. Using computational tools, e.g. Quantitative Structure-Activity Relationship (QSAR) models, can predict potential ERα binding agents before chemical synthesis. The purpose of this project was to develop enhanced predictive models of ERα binding agents by utilizing advanced cheminformatics tools that can integrate publicly available bioassay data. The initial ERα binding agent data set, consisting of 446 binders and 8,307 non-binders, was obtained from the Tox21 Challenge project organized by the NIH Chemical Genomics Center (NCGC). After removing the duplicates and inorganic compounds, this data set was used to create a training set (259 binders and 259 non-binders). This training set was used to develop QSAR models using chemical descriptors. The resulting models were then used to predict the binding activity of 264 external compounds, which were available to us after the models were developed. The cross-validation results of training set [Correct Classification Rate (CCR)) = 0.72] were much higher than the external predictivity of the unknown compounds (CCR= 0.59). To improve the conventional QSAR models, all compounds in the training set were used to search PubChem and generate a profile of their biological responses across thousands of bioassays. The most important bioassays were prioritized to generate a similarity index that was used to calculate the biosimilarity score between each two compounds. The nearest neighbors for each compound within the set were then identified and its ERα binding potential was predicted by its nearest neighbors in the training set. The hybrid model performance (CCR=0.94 for cross validation; CCR=0.68 for external prediction) showed significant improvement over the original QSAR models, particularly for the activity cliffs that induce prediction errors. The results of this study indicate that the response profile of chemicals from public data provides useful information for modeling and evaluation purposes. The public big data resources should be considered along with chemical structure information when predicting new compounds, such as unknown ERα binding agents.

Recent Development of VUV-Based Processes for Air Pollutant Degradation

Abstract: As air pollution become more and more serious nowadays, it is essential to find out a way to efficiently degrade the air pollutants. Vacuum ultraviolet (VUV)-based processes are an emerging and promising technologies for environmental remediation such as air cleaning, wastewater treatment and air/water disinfection. With VUV irradiation, photolysis, photocatalyst is and ozone-assisted oxidation are involved at the same time, resulting in the fast degradation of air pollutants because of their strong oxidizing capacity. The mechanisms of how the oxidants are produced and reacted are discussed in this review. This paper mainly focuses on the three VUV-based oxidation processes including VUV photolysis, VUV combined with ozone-assisted oxidation and VUV-PCO with emphasis on their mechanisms and applications. Also, the outlooks of these processes are outlined in this paper.

Current Pesticide Risk Assessment Protocols Do Not Adequately Address Differences between Honey Bees (Apis mellifera) and Bumble Bees (Bombus spp.)

Abstract: Recent research has demonstrated colony-level sublethal effects of imidacloprid on bumble bees, affecting foraging and food consumption, and thus colony growth and reproduction, at lower pesticide concentrations than for honey bee colonies. However, these studies may not reflect the full effects of neonicotinoids on bumble bees because bumble bee life cycles are different from those of honey bees. Unlike honey bees, bumble bees live in colonies for only a few months each year. Assessing the sublethal effects of systemic insecticides only on the colony level is appropriate for honey bees, but for bumble bees, this approach addresses just part of their annual life cycle. Queens are solitary from the time they leave their home colonies in fall until they produce their first workers the following year. Queens forage for pollen and nectar, and are thus exposed to more risk of direct pesticide exposure than honey bee queens. Almost no research has been done on pesticide exposure to and effects on bumble bee queens. Additional research should focus on critical periods in a bumble bee queen’s life which have the greatest nutritional demands, foraging requirements, and potential for exposure to pesticides, particularly the period during and after nest establishment in the spring when the queen must forage for the nutritional needs of her brood and for her own needs while she maintains an elevated body temperature in order to incubate the brood.

Temperature-Dependence of Glyphosate-Based Herbicide's Effects on Egg and Tadpole Growth of Common Toads

Abstract: Glyphosate-based herbicide formulations are broadly used in agriculture, silviculture, horticulture as well as in private gardens all over the world, thus posing the risk of potential contamination of nearby aquatic bodies inhabited by amphibians. Concurrently, climate change can be expected to alter the temperature of amphibian breeding sites. However, while either glyphosate-based herbicides or temperature have been shown to separately affect the development of amphibians, very little is known on possible interactive effects. We studied the impact of herbicide concentrations and temperature on growth and development of eggs and tadpoles of the Common toad (Bufo bufo L.). We hypothesized that (i) eggs would be better protected against herbicides than tadpoles because of their jelly coating, (ii) that higher temperatures would reduce potential herbicide effects because of an accelerated growth and a lower sensitivity of larger specimens. We conducted one experiment starting with eggs (Gosner stage, GS 9) and another experiment starting with tadpoles (GS 21-24) using a full factorial design with 5 concentrations of the herbicide formulation Roundup® LB Plus (0 mg acid equivalent L-1, 0.5 mg a.e. L-1, 1.0 mg a.e. L-1 or 1.5 mg a.e. L-1 and a pulse treatment with 3-4 times addition of 0.5 a.e. mg L-1 over the course of several weeks) and two temperature levels (15°C and 20°C). Contrary to our expectation, our results showed that toad eggs are more sensitive to herbicides than tadpoles leading to an averaged 31% increase in total length, tail length and body length compared to the herbicide-free control. Tadpole morphology, development or mortality was not influenced by herbicides. Higher temperature accelerated growth of both eggs and tadpoles. This is among the first study showing interactive effects between herbicides and temperature especially for egg development resulting in more pronounced herbicide effects at lower temperatures than at higher temperatures.