Fera Science (United Kingdom)

Whole genome comparisons provide a quantitative, objective basis for taxonomic classification of bacterial pathogens important to food security.

Summary Weeds are major constraints on crop production, yet as part of the primary producers within farming systems, they may be important components of the agroecosystem. Using published literature, the role of weeds in arable systems for other above‐ground trophic levels are examined. In the UK, there is evidence that weed flora have changed over the past century, with some species declining in abundance, whereas others have increased. There is also some evidence for a decline in the size of arable weed seedbanks. Some of these changes reflect improved agricultural efficiency, changes to more winter‐sown crops in arable rotations and the use of more broad‐spectrum herbicide combinations. Interrogation of a database of records of phytophagous insects associated with plant species in the UK reveals that many arable weed species support a high diversity of insect species. Reductions in abundances of host plants may affect associated insects and other taxa. A number of insect groups and farmland birds have shown marked population declines over the past 30 years. Correlational studies indicate that many of these declines are associated with changes in agricultural practices. Certainly reductions in food availability in winter and for nestling birds in spring are implicated in the declines of several bird species, notably the grey partridge, Perdix perdix . Thus weeds have a role within agroecosystems in supporting biodiversity more generally. An understanding of weed competitivity and the importance of weeds for insects and birds may allow the identification of the most important weed species. This may form the first step in balancing the needs for weed control with the requirements for biodiversity and more sustainable production methods.

The aim of this review is to give a comprehensive overview of the current knowledge on plant metabolites of mycotoxins, also called masked mycotoxins. Mycotoxins are secondary fungal metabolites, toxic to human and animals. Toxigenic fungi often grow on edible plants, thus contaminating food and feed. Plants, as living organisms, can alter the chemical structure of mycotoxins as part of their defence against xenobiotics. The extractable conjugated or non-extractable bound mycotoxins formed remain present in the plant tissue but are currently neither routinely screened for in food nor regulated by legislation, thus they may be considered masked. Fusarium mycotoxins (deoxynivalenol, zearalenone, fumonisins, nivalenol, fusarenon-X, T-2 toxin, HT-2 toxin, fusaric acid) are prone to metabolisation or binding by plants, but transformation of other mycotoxins by plants (ochratoxin A, patulin, destruxins) has also been described. Toxicological data are scarce, but several studies highlight the potential threat to consumer safety from these substances. In particular, the possible hydrolysis of masked mycotoxins back to their toxic parents during mammalian digestion raises concerns. Dedicated chapters of this article address plant metabolism as well as the occurrence of masked mycotoxins in food, analytical aspects for their determination, toxicology and their impact on stakeholders.

Emerging diseases are among the greatest threats to honey bees. Unfortunately, where and when an emerging disease will appear are almost impossible to predict. The arrival of the parasitic Varroa mite into the Hawaiian honey bee population allowed us to investigate changes in the prevalence, load, and strain diversity of honey bee viruses. The mite increased the prevalence of a single viral species, deformed wing virus (DWV), from ~10 to 100% within honey bee populations, which was accompanied by a millionfold increase in viral titer and a massive reduction in DWV diversity, leading to the predominance of a single DWV strain. Therefore, the global spread of Varroa has selected DWV variants that have emerged to allow it to become one of the most widely distributed and contagious insect viruses on the planet.

SummaryGrowing evidence indicates that European managed honey bees are in decline, but information for Europe remains patchy and localized. Here we compile data from 18 European countries to assess trends in the number of honey bee colonies and beekeepers between 1965 and 2005. We found consistent declines in colony numbers in central European countries and some increases in Mediterranean countries. Beekeeper numbers have declined in all of the European countries examined. Our data support the view that honey bees are in decline at least in some regions, which is probably closely linked to the decreasing number of beekeepers. Our data on colony numbers and beekeepers must, however, be interpreted with caution due to different approaches and socioeconomic factors in the various countries, thereby limiting their comparability. We therefore make specific recommendations for standardized methodologies to be adopted at the national and global level to assist in the future monitoring of honey bees.

Microplastics (<5 mm) have been documented in environmental samples on a global scale. While these pollutants may enter aquatic environments via wastewater treatment facilities, the abundance of microplastics in these matrices has not been investigated. Although efficient methods for the analysis of microplastics in sediment samples and marine organisms have been published, no methods have been developed for detecting these pollutants within organic-rich wastewater samples. In addition, there is no standardized method for analyzing microplastics isolated from environmental samples. In many cases, part of the identification protocol relies on visual selection before analysis, which is open to bias. In order to address this, a new method for the analysis of microplastics in wastewater was developed. A pretreatment step using 30% hydrogen peroxide (H2O2) was employed to remove biogenic material, and focal plane array (FPA)-based reflectance micro-Fourier-transform (FT-IR) imaging was shown to successfully image and identify different microplastic types (polyethylene, polypropylene, nylon-6, polyvinyl chloride, polystyrene). Microplastic-spiked wastewater samples were used to validate the methodology, resulting in a robust protocol which was nonselective and reproducible (the overall success identification rate was 98.33%). The use of FPA-based micro-FT-IR spectroscopy also provides a considerable reduction in analysis time compared with previous methods, since samples that could take several days to be mapped using a single-element detector can now be imaged in less than 9 h (circular filter with a diameter of 47 mm). This method for identifying and quantifying microplastics in wastewater is likely to provide an essential tool for further research into the pathways by which microplastics enter the environment.

Published literature has been reviewed in order to (a) explore the (potential) applications of nanotechnology in pesticide formulation, (b) identify possible impacts on environmental fate, and (c) analyze the suitability of current exposure assessment procedures to account for the novel properties of nanopesticides within the EU regulatory context. The term nanopesticide covers a wide variety of products and cannot be considered to represent a single category. Many nanoformulations combine several surfactants, polymers, and metal nanoparticles in the nanometer size range. The aims of nanoformulations are generally common to other pesticide formulations, these being to increase the apparent solubility of poorly soluble active ingredients, to release the active ingredient in a slow/targeted manner and/or to protect against premature degradation. Nanoformulations are thus expected to (a) have significant impacts on the fate of active ingredients and/or (b) introduce new ingredients for which the environmental fate is still poorly understood (e.g., nanosilver). Therefore, it seems that adaptations of current exposure assessment approaches will be necessary, at least for some nanopesticides. The present analysis provides a useful framework to identify priorities for future research in order to achieve more robust risk assessments of nanopesticides.

Wild bee declines have been ascribed in part to neonicotinoid insecticides. While short-term laboratory studies on commercially bred species (principally honeybees and bumblebees) have identified sub-lethal effects, there is no strong evidence linking these insecticides to losses of the majority of wild bee species. We relate 18 years of UK national wild bee distribution data for 62 species to amounts of neonicotinoid use in oilseed rape. Using a multi-species dynamic Bayesian occupancy analysis, we find evidence of increased population extinction rates in response to neonicotinoid seed treatment use on oilseed rape. Species foraging on oilseed rape benefit from the cover of this crop, but were on average three times more negatively affected by exposure to neonicotinoids than non-crop foragers. Our results suggest that sub-lethal effects of neonicotinoids could scale up to cause losses of bee biodiversity. Restrictions on neonicotinoid use may reduce population declines.

Glucosinolates (GLS) are sulfur rich, anionic secondary metabolites found principally in the plant order Brassicales. This review focuses on identifying the range of GLS structures identified to date and summarises the current state of taxonomic reclassifications of GLS producing plants. Those Brassica species that are available to growers in the UK are highlighted and progress in the aspects of analytical chemistry relevant to conducting accurate determinations of GLS content of foods is reviewed. The degradation and derivatisation workflows that have been utilized for conducting “glucosinolate analysis” are summarized. A review is made of aspects of extraction, isolation, determination of purity, ultraviolet (UV) and mass spectrometry (MS) parameters, extinction coefficients, UV response factors, quantification procedures, and the availability of stable isotope labeled internal standards, and certified reference materials. An electronic database of structures, formulae and accurate masses of both the 200 known, and a further 180 predicted GLS, is provided for use in mass spectrometry.

Pest and pathogen losses jeopardise global food security and ever since the 19(th) century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen, Phytophthora infestans, undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed 13_A2, in the European P. infestans population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the 13_A2 lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a 13_A2 isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the 13_A2 isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly, 13_A2 isolates carry intact and in planta induced Avrblb1, Avrblb2 and Avrvnt1 effector genes that trigger resistance in potato lines carrying the corresponding R immune receptor genes Rpi-blb1, Rpi-blb2, and Rpi-vnt1.1. These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the 13_A2 lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

Nanopesticides or nano plant protection products represent an emerging technological development that, in relation to pesticide use, could offer a range of benefits including increased efficacy, durability, and a reduction in the amounts of active ingredients that need to be used. A number of formulation types have been suggested including emulsions (e.g., nanoemulsions), nanocapsules (e.g., with polymers), and products containing pristine engineered nanoparticles, such as metals, metal oxides, and nanoclays. The increasing interest in the use of nanopesticides raises questions as to how to assess the environmental risk of these materials for regulatory purposes. Here, the current approaches for environmental risk assessment of pesticides are reviewed and the question of whether these approaches are fit for purpose for use on nanopesticides is addressed. Potential adaptations to existing environmental risk assessment tests and procedures for use with nanopesticides are discussed, addressing aspects such as analysis and characterization, environmental fate and exposure assessment, uptake by biota, ecotoxicity, and risk assessment of nanopesticides in aquatic and terrestrial ecosystems. Throughout, the main focus is on assessing whether the presence of the nanoformulation introduces potential differences relative to the conventional active ingredients. The proposed changes in the test methodology, research priorities, and recommendations would facilitate the development of regulatory approaches and a regulatory framework for nanopesticides.

Dickeya species (formerly Erwinia chrysanthemi ) cause diseases on numerous crop and ornamental plants world‐wide. Dickeya spp. (probably D. dianthicola ) were first reported on potato in the Netherlands in the 1970s and have since been detected in many other European countries. However, since 2004–5 a new pathogen, with the proposed name ‘ D. solani ’, has been spreading across Europe via trade in seed tubers and is causing increasing economic losses. Although disease symptoms are often indistinguishable from those of the more established blackleg pathogen Pectobacterium spp., Dickeya spp. can initiate disease from lower inoculum levels, have a greater ability to spread through the plant’s vascular tissue, are considerably more aggressive, and have higher optimal temperatures for disease development (the latter potentially leading to increased disease problems as Europe’s climate warms). However, they also appear to be less hardy than Pectobacterium spp. in soil and other environments outside the plant. Scotland is currently the only country in Europe to enforce zero tolerance for Dickeya spp. in its potato crop in an attempt to keep its seed tuber industry free from disease. However, there are a number of other ways to control the disease, including seed tuber certification, on‐farm methods and the use of diagnostics. For diagnostics, new genomics‐based approaches are now being employed to develop D. dianthicola ‐ and ‘ D. solani ’‐specific PCR‐based tests for rapid detection and identification. It is hoped that these diagnostics, together with other aspects of ongoing research, will provide invaluable tools and information for controlling this serious threat to potato production.

Ever since the interest in organic environmental contaminants first emerged 50years ago, there has been a need to present discussion of such chemicals and their transformation products using simple abbreviations so as to avoid the repetitive use of long chemical names. As the number of chemicals of concern has increased, the number of abbreviations has also increased dramatically, sometimes resulting in the use of different abbreviations for the same chemical. In this article, we propose abbreviations for flame retardants (FRs) substituted with bromine or chlorine atoms or including a functional group containing phosphorus, i.e. BFRs, CFRs and PFRs, respectively. Due to the large number of halogenated and organophosphorus FRs, it has become increasingly important to develop a strategy for abbreviating the chemical names of FRs. In this paper, a two step procedure is proposed for deriving practical abbreviations (PRABs) for the chemicals discussed. In the first step, structural abbreviations (STABs) are developed using specific STAB criteria based on the FR structure. However, since several of the derived STABs are complicated and long, we propose instead the use of PRABs. These are, commonly, an extract of the most essential part of the STAB, while also considering abbreviations previously used in the literature. We indicate how these can be used to develop an abbreviation that can be generally accepted by scientists and other professionals involved in FR related work. Tables with PRABs and STABs for BFRs, CFRs and PFRs are presented, including CAS (Chemical Abstract Service) numbers, notes of abbreviations that have been used previously, CA (Chemical Abstract) name, common names and trade names, as well as some fundamental physico-chemical constants.

Fenton's reagent was used to isolate microplastics from organic-rich wastewater. The catalytic reaction did not affect microplastic chemistry or size, enabling its use as a pre-treatment method for focal plane array-based micro-FT-IR imaging. Compared with previously described microplastic treatment methods, Fenton's reagent offers a considerable reduction in sample preparation times.

A novel, unbiased approach to plant viral disease diagnosis has been developed which requires no a priori knowledge of the host or pathogen. Next-generation sequencing coupled with metagenomic analysis was used to produce large quantities of cDNA sequence in a model system of tomato infected with Pepino mosaic virus. The method was then applied to a sample of Gomphrena globosa infected with an unknown pathogen originally isolated from the flowering plant Liatris spicata. This plant was found to contain a new cucumovirus, for which we suggest the name 'Gayfeather mild mottle virus'. In both cases, the full viral genome was sequenced. This method expedites the entire process of novel virus discovery, identification, viral genome sequencing and, subsequently, the development of more routine assays for new viral pathogens.

Abstract Recent estimates for global warming predict increases in global mean surface air temperatures (relative to 1990) of between 1 and 3.5 °C, by 2100. The impact of such changes on agricultural systems in mid‐ to high‐latitude regions are predicted to be less severe than in low‐latitude regions, and possibly even beneficial, although the influence of pests and diseases is rarely taken into account. Most studies have concluded that insect pests will generally become more abundant as temperatures increase, through a number of inter‐related processes, including range extensions and phenological changes, as well as increased rates of population development, growth, migration and over‐wintering. A gradual, continuing rise in atmospheric CO 2 will affect pest species directly (i.e. the CO 2 fertilization effect) and indirectly (via interactions with other environmental variables). However, individual species responses to elevated CO 2 vary: consumption rates of insect herbivores generally increase, but this does not necessarily compensate fully for reduced leaf nitrogen. The consequent effects on performance are strongly mediated via the host species. Some recent experiments under elevated CO 2 have suggested that aphids may become more serious pests, although other studies have discerned no significant effects on sap‐feeding homopterans. However, few, if any of these experiments have fully considered the effects on pest population dynamics. Climate change is also considered from the perspective of changes in the distribution and abundance of species and communities. Marked changes in the distribution of well‐documented species – including Odonata, Orthoptera and Lepidoptera – in north‐western Europe, in response to unusually hot summers, provide useful indications of the potential effects of climate change. Migrant pests are expected to respond more quickly to climate change than plants, and may be able to colonize newly available crops/habitats. Range expansions, and the removal of edge effects, could result in the increased abundance of species presently near the northern limits of their ranges in the UK. However, barriers to range expansions, or shifts, may include biotic (competition, predation, parasitism and disease), as well as abiotic, factors. Climatic phenomena, ecosystem processes and human activities are interactive and interdependent, making long‐term predictions extremely tenuous. Nevertheless, it appears prudent to prepare for the possibility of increases in the diversity and abundance of pest species in the UK, in the context of climate change.

Multiple-herbicide resistance (MHR) in black-grass (Alopecurus myosuroides) and annual rye-grass (Lolium rigidum) is a global problem leading to a loss of chemical weed control in cereal crops. Although poorly understood, in common with multiple-drug resistance (MDR) in tumors, MHR is associated with an enhanced ability to detoxify xenobiotics. In humans, MDR is linked to the overexpression of a pi class glutathione transferase (GSTP1), which has both detoxification and signaling functions in promoting drug resistance. In both annual rye-grass and black-grass, MHR was also associated with the increased expression of an evolutionarily distinct plant phi (F) GSTF1 that had a restricted ability to detoxify herbicides. When the black-grass A. myosuroides (Am) AmGSTF1 was expressed in Arabidopsis thaliana, the transgenic plants acquired resistance to multiple herbicides and showed similar changes in their secondary, xenobiotic, and antioxidant metabolism to those determined in MHR weeds. Transcriptome array experiments showed that these changes in biochemistry were not due to changes in gene expression. Rather, AmGSTF1 exerted a direct regulatory control on metabolism that led to an accumulation of protective flavonoids. Further evidence for a key role for this protein in MHR was obtained by showing that the GSTP1- and MDR-inhibiting pharmacophore 4-chloro-7-nitro-benzoxadiazole was also active toward AmGSTF1 and helped restore herbicide control in MHR black-grass. These studies demonstrate a central role for specific GSTFs in MHR in weeds that has parallels with similar roles for unrelated GSTs in MDR in humans and shows their potential as targets for chemical intervention in resistant weed management.

Modern agriculture is heavily dependent on fossil resources. Both direct energy use for crop management and indirect energy use for fertilizers, pesticides and machinery production have contributed to the major increases in food production seen since the 1960s. However, the relationship between energy inputs and yields is not linear. Low-energy inputs can lead to lower yields and perversely to higher energy demands per tonne of harvested product. At the other extreme, increasing energy inputs can lead to ever-smaller yield gains. Although fossil fuels remain the dominant source of energy for agriculture, the mix of fuels used differs owing to the different fertilization and cultivation requirements of individual crops. Nitrogen fertilizer production uses large amounts of natural gas and some coal, and can account for more than 50 per cent of total energy use in commercial agriculture. Oil accounts for between 30 and 75 per cent of energy inputs of UK agriculture, depending on the cropping system. While agriculture remains dependent on fossil sources of energy, food prices will couple to fossil energy prices and food production will remain a significant contributor to anthropogenic greenhouse gas emissions. Technological developments, changes in crop management, and renewable energy will all play important roles in increasing the energy efficiency of agriculture and reducing its reliance of fossil resources.

Abstract Many alien taxa are known to cause socio‐economic impacts by affecting the different constituents of human well‐being (security; material and non‐material assets; health; social, spiritual and cultural relations; freedom of choice and action). Attempts to quantify socio‐economic impacts in monetary terms are unlikely to provide a useful basis for evaluating and comparing impacts of alien taxa because they are notoriously difficult to measure and important aspects of human well‐being are ignored. Here, we propose a novel standardised method for classifying alien taxa in terms of the magnitude of their impacts on human well‐being, based on the capability approach from welfare economics. The core characteristic of this approach is that it uses changes in peoples' activities as a common metric for evaluating impacts on well‐being. Impacts are assigned to one of five levels, from Minimal Concern to Massive, according to semi‐quantitative scenarios that describe the severity of the impacts. Taxa are then classified according to the highest level of deleterious impact that they have been recorded to cause on any constituent of human well‐being. The scheme also includes categories for taxa that are not evaluated, have no alien population, or are data deficient, and a method for assigning uncertainty to all the classifications. To demonstrate the utility of the system, we classified impacts of amphibians globally. These showed a variety of impacts on human well‐being, with the cane toad ( Rhinella marina ) scoring Major impacts. For most species, however, no studies reporting impacts on human well‐being were found, i.e. these species were data deficient. The classification provides a consistent procedure for translating the broad range of measures and types of impact into ranked levels of socio‐economic impact, assigns alien taxa on the basis of the best available evidence of their documented deleterious impacts, and is applicable across taxa and at a range of spatial scales. The system was designed to align closely with the Environmental Impact Classification for Alien Taxa ( EICAT ) and the Red List, both of which have been adopted by the International Union of Nature Conservation ( IUCN ), and could therefore be readily integrated into international practices and policies.

It is inevitable that, during their use, engineered nanoparticles will be released into soils and waters. There is therefore increasing concern over the potential impacts of engineered nanoparticles in the environment on aquatic and terrestrial organisms and on human health. Once released into the environment, engineered nanoparticles will aggregate to some degree; they might also associate with suspended solids, sediment, be accumulated by organisms and enter drinking water sources and food materials. These fate processes are dependent on the characteristics of the particle and the characteristics of the environmental system. A range of ecotoxicological effects have also been reported, including effects on microbes, plants, invertebrates and fish. Although available data indicate that current risks of engineered nanoparticles in the environment to environmental and human health are probably low, our knowledge of the potential impacts of engineered nanoparticles in the environment on human health is still limited. There is therefore a need for continued work to develop an understanding of the exposure levels for engineered nanoparticles in environmental systems and to begin to explore the implications of these levels in terms of the ecosystem and human health. This will require research in a range of areas, including detection and characterization, environmental fate and transport, ecotoxicology and toxicology.