Susceptibility of Garden Plants to Phytophthora Root Rot.

Phytophthora root rot (PRR) is a serious disease of horticultural, forest, and ornamental plant species caused by species of the oomycete genus Phytophthora. Their wide host range makes the choice of resistant plants in the management of the disease difficult. We used the Royal Horticultural Society diagnostic dataset of PRR records from U.K. gardens to compare the susceptibility of different host genera to the disease. The dataset was compared with existing reports of plants recorded as notably resistant or notably susceptible to PRR. An index-based approach was used to separate 177 genera of woody plants into three categories: 85 were low index (<0.10: rarely affected), 34 were medium index (0.10 to 0.20: sometimes affected) and 58 were high index (>0.20: frequently affected). Similarly, genera of nonwoody plants were separated into: 45 low index (<0.22), 16 medium index (0.22 to 0.44), and 18 high index (>0.44). Taxus was the genus with the highest index, while most genera in the Malvales and Ericales were in the high-index group. Most genera in the Myrtales, Fabales, and Monocotyledons were low index. While 30 Phytophthora species were recorded in our study, the wide host range spp., P. plurivora, P. cryptogea, and P. cinnamomi, represented 63% of identifications. P. plurivora was the most common species on woody plants and P. cryptogea on nonwoody plants. These results provide confidence in the use of host resistance as part of the integrated management of PRR.

Susceptibility of Garden Trees and Shrubs to Armillaria Root Rot.

Armillaria root rot (ARR) is a serious disease of woody plants caused by several species of Armillaria. Armillaria isolates from diagnostic samples received in 2017 were identified by genus- and species-specific PCR and compared with isolates from an earlier survey (2004 to 2007). The results were comparable and, therefore, were combined for further analysis. Three species were identified: Armillaria mellea (83%), A. gallica (15%), and A. ostoyae (2%). Their wide host range makes choice of resistant plants in management of the disease difficult. We used the Royal Horticultural Society diagnostic dataset of ARR records from U.K. gardens to compare the susceptibility of different host genera to the disease. The dataset was compared with an earlier experiment at the University of California. An index-based approach was used to separate genera into three categories: 77 low-index (<0.99), 37 medium-index (0.99 to 1.76), and 56 high-index (>1.76) genera were recorded. All three species were associated with both angiosperms and gymnosperms; moreover, A. ostoyae did not show the host preference for gymnosperms that has been reported elsewhere. A. gallica was particularly common on herbaceous perennials and showed a trend to occur on resistant hosts that may be under other stress, supporting its description as an opportunistic pathogen. Four monocotyledons grown as trees or shrubs in U.K. gardens had a very low ARR index according to indices associated with A. mellea and A. ostoyae. Genera in the order Myrtales were almost always low index, while those in the Saxifragales and Fagales were mostly high index. These results provide confidence in the use of host resistance as part of the integrated management of ARR.

EFSA's scientific activities and achievements on the risk assessment of genetically modified organisms (GMOs) during its first decade of existence: looking back and ahead.

Genetically modified organisms (GMOs) and derived food and feed products are subject to a risk analysis and regulatory approval before they can enter the market in the European Union (EU). In this risk analysis process, the role of the European Food Safety Authority (EFSA), which was created in 2002 in response to multiple food crises, is to independently assess and provide scientific advice to risk managers on any possible risks that the use of GMOs may pose to human and animal health and the environment. EFSA's scientific advice is elaborated by its GMO Panel with the scientific support of several working groups and EFSA's GMO Unit. This review presents EFSA's scientific activities and highlights its achievements on the risk assessment of GMOs for the first 10 years of its existence. Since 2002, EFSA has issued 69 scientific opinions on genetically modified (GM) plant market registration applications, of which 62 for import and processing for food and feed uses, six for cultivation and one for the use of pollen (as or in food), and 19 scientific opinions on applications for marketing products made with GM microorganisms. Several guidelines for the risk assessment of GM plants, GM microorganisms and GM animals, as well as on specific issues such as post-market environmental monitoring (PMEM) were elaborated. EFSA also provided scientific advice upon request of the European Commission on safeguard clause and emergency measures invoked by EU Member States, annual PMEM reports, the potential risks of new biotechnology-based plant breeding techniques, evaluations of previously assessed GMOs in the light of new scientific publications, and the use of antibiotic resistance marker genes in GM plants. Future challenges relevant to the risk assessment of GMOs are discussed. EFSA's risk assessments of GMO applications ensure that data are analysed and presented in a way that facilitates scientifically sound decisions that protect human and animal health and the environment.

Feral genetically modified herbicide tolerant oilseed rape from seed import spills: are concerns scientifically justified?

One of the concerns surrounding the import (for food and feed uses or processing) of genetically modified herbicide tolerant (GMHT) oilseed rape is that, through seed spillage, the herbicide tolerance (HT) trait will escape into agricultural or semi-natural habitats, causing environmental or economic problems. Based on these concerns, three EU countries have invoked national safeguard clauses to ban the marketing of specific GMHT oilseed rape events on their territory. However, the scientific basis for the environmental and economic concerns posed by feral GMHT oilseed rape resulting from seed import spills is debatable. While oilseed rape has characteristics such as secondary dormancy and small seed size that enable it to persist and be redistributed in the landscape, the presence of ferals is not in itself an environmental or economic problem. Crucially, feral oilseed rape has not become invasive outside cultivated and ruderal habitats, and HT traits are not likely to result in increased invasiveness. Feral GMHT oilseed rape has the potential to introduce HT traits to volunteer weeds in agricultural fields, but would only be amplified if the herbicides to which HT volunteers are tolerant were used routinely in the field. However, this worst-case scenario is most unlikely, as seed import spills are mostly confined to port areas. Economic concerns revolve around the potential for feral GMHT oilseed rape to contribute to GM admixtures in non-GM crops. Since feral plants derived from cultivation (as distinct from import) occur at too low a frequency to affect the coexistence threshold of 0.9% in the EU, it can be concluded that feral GMHT plants resulting from seed import spills will have little relevance as a potential source of pollen or seed for GM admixture. This paper concludes that feral oilseed rape in Europe should not be routinely managed, and certainly not in semi-natural habitats, as the benefits of such action would not outweigh the negative effects of management.

A statistical assessment of differences and equivalences between genetically modified and reference plant varieties.

BACKGROUND: Safety assessment of genetically modified organisms is currently often performed by comparative evaluation. However, natural variation of plant characteristics between commercial varieties is usually not considered explicitly in the statistical computations underlying the assessment. RESULTS: Statistical methods are described for the assessment of the difference between a genetically modified (GM) plant variety and a conventional non-GM counterpart, and for the assessment of the equivalence between the GM variety and a group of reference plant varieties which have a history of safe use. It is proposed to present the results of both difference and equivalence testing for all relevant plant characteristics simultaneously in one or a few graphs, as an aid for further interpretation in safety assessment. A procedure is suggested to derive equivalence limits from the observed results for the reference plant varieties using a specific implementation of the linear mixed model. Three different equivalence tests are defined to classify any result in one of four equivalence classes. The performance of the proposed methods is investigated by a simulation study, and the methods are illustrated on compositional data from a field study on maize grain. CONCLUSIONS: A clear distinction of practical relevance is shown between difference and equivalence testing. The proposed tests are shown to have appropriate performance characteristics by simulation, and the proposed simultaneous graphical representation of results was found to be helpful for the interpretation of results from a practical field trial data set.

Biosafety of GM Crop Plants Expressing dsRNA: Data Requirements and EU Regulatory Considerations.

The use of RNA interference (RNAi) enables the silencing of target genes in plants or plant-dwelling organisms, through the production of double stranded RNA (dsRNA) resulting in altered plant characteristics. Expression of properly synthesized dsRNAs in plants can lead to improved crop quality characteristics or exploit new mechanisms with activity against plant pests and pathogens. Genetically modified (GM) crops exhibiting resistance to viruses or insects via expression of dsRNA have received authorization for cultivation outside Europe. Some products derived from RNAi plants have received a favourable opinion from the European Food Safety Authority (EFSA) for import and processing in the European Union (EU). The authorization process in the EU requires applicants to produce a risk assessment considering food/feed and environmental safety aspects of living organisms or their derived food and feed products. The present paper discusses the main aspects of the safety assessment (comparative assessment, molecular characterization, toxicological assessment, nutritional assessment, gene transfer, interaction with target and non-target organisms) for GM plants expressing dsRNA, according to the guidelines of EFSA. Food/feed safety assessment of products from RNAi plants is expected to be simplified, in the light of the consideration that no novel proteins are produced. Therefore, some of the data requirements for risk assessment do not apply to these cases, and the comparative compositional analysis becomes the main source of evidence for food/feed safety of RNAi plants. During environmental risk assessment, the analysis of dsRNA expression levels of the GM trait, and the data concerning the observable effects on non-target organisms (NTO) will provide the necessary evidence for ensuring safety of species exposed to RNAi plants. Bioinformatics may provide support to risk assessment by selecting target gene sequences with low similarity to the genome of NTOs possibly exposed to dsRNA. The analysis of these topics in risk assessment indicates that the science-based regulatory process in Europe is considered to be applicable to GM RNAi plants, therefore the evaluation of their safety can be effectively conducted without further modifications. Outcomes from the present paper offer suggestions for consideration in future updates of the EFSA Guidance documents on risk assessment of GM organisms.

Monoclonal antibodies reveal changes in predator efficiency with prey spatial pattern.

Spatially explicit predator-prey interactions can alter the predatory potential of natural enemies augmented through conservation biological control. To test hypotheses regarding such interactions and predatory efficiency, we used a combination of molecular techniques and mark-release-recapture to study the foraging behaviour of a generalist carabid predator, Poecilus cupreus, in response to spatial patterns of its cereal aphid prey (Metapolophium dirhodum and Sitobion avenae). Beetle and aphid numbers were measured across two grids of sampling locations, within which aphid spatial pattern had been manipulated to generate patchy and more homogenous distributions. Aphid consumption was measured by enzyme-linked immunosorbent assays (ELISA) of beetle gut contents, using an aphid-specific monoclonal antibody. Movement and distribution patterns suggest that P. cupreus does not aggregate at, nor instigate prey-taxis within, aphid patches. However, more than two-thirds of the 2169 P. cupreus tested by ELISA had consumed aphids and the proportion of beetles containing aphid proteins was positively related to aphid density. Against expectation, the proportion of predators feeding on aphids was greatest where prey were homogenously distributed, and this was attributed to the loss of partial refuges for prey in aphid patches. The functional value of this type of uniform foraging strategy is ideally suited to early colonization of the crop habitat, when aphid numbers are low, before populations build up and form strong spatial patterns.

National-scale metacommunity dynamics of carabid beetles in UK farmland.

1. Understanding the wide-scale processes controlling communities across multiple sites is a foremost challenge of modern ecology. Here, data from a nation-wide network of field sites are used to describe the metacommunity dynamics of arable carabid beetles. This is done by modelling how communities are structured at a local level, by changes in the environment of the sampled fields and, at a regional level, by fitting spatial parameters describing latitudinal and longitudinal gradients. 2. Local and regional processes demonstrated independent and significant capacities for structuring communities. Within the local environment, crop type was found to be the primary determinant of carabid community composition. The regional component included a strong response to a longitudinal gradient, with significant increases in diversity in an east-to-west direction. 3. Carabid metacommunities seem to be structured by a combination of species sorting dynamics, operating at two different, but equally important, spatial scales. At a local scale, species are sorted along a resource gradient determined by crop type. At a wider spatial scale species appear to be sorted along a longitudinal gradient. 4. Nation-wide trends in communities coincided with known gradients of increased homogeneity of habitat mosaics and agricultural intensification. However, more work is required to understand fully how communities are controlled by the interaction of crops with changes in landscape structure at different spatial scales. 5. We conclude that crop type is a powerful determinant of carabid biodiversity, but that it cannot be considered in isolation from other components of the landscape for optimal conservation policy.

Assessing environmental impacts of genetically modified plants on non-target organisms: The relevance of in planta studies.

In legal frameworks worldwide, genetically modified plants (GMPs) are subjected to pre-market environmental risk assessment (ERA) with the aim of identifying potential effects on the environment. In the European Union, the EFSA Guidance Document introduces the rationale that GMPs, as well as their newly produced metabolites, represent the potential stressor to be evaluated during ERA. As a consequence, during several phases of ERA for cultivation purposes, it is considered necessary to use whole plants or plant parts in experimental protocols. The importance of in planta studies as a strategy to address impacts of GMPs on non-target organisms is demonstrated, to evaluate both effects due to the intended modification in plant phenotype (e.g. expression of Cry proteins) and effects due to unintended modifications in plant phenotype resulting from the transformation process (e.g. due to somaclonal variations or pleiotropic effects). In planta tests are also necessary for GMPs in which newly expressed metabolites cannot easily be studied in vitro. This paper reviews the scientific literature supporting the choice of in planta studies as a fundamental tool in ERA of GMPs in cultivation dossiers; the evidence indicates they can realistically mimic the ecological relationships occurring in their receiving environments and provide important insights into the biology and sustainable management of GMPs.

Response to Kruse-Plass et al. (2017) regarding the risk to non-target lepidopteran larvae exposed to pollen from one or more of three Bt maize events (MON810, Bt11 and 1507).

We respond to the paper of Kruse-Plass et al. (Environ Sci Eur 29:12, 2017), published in this journal, regarding the risk to non-target lepidopteran larvae exposed to pollen from one or more of three Bt maize events (MON810, Bt11 and 1507). We emphasise that what is important for environmental risk assessment is not the number of pollen grains per se, but the degree of exposure of a NT lepidopteran larva to Bt protein contained in maize pollen. The main text of this response deals with general issues which Kruse-Plass et al. have failed to understand; more detailed refutations of each of their claims are given in Additional file 1. Valid environmental risk assessment requires direct measurement of pollen on leaves at varying distances outside a source field(s); such measurements reflect the potential exposure experienced by an individual larva on a host plant. There are no new data in the Kruse-Plass et al. paper, or indeed any data directly quantifying pollen on actual host-plant leaves outside a maize field; only data gathered within or at the edge of maize crops were reported. Values quoted by Kruse-Plass et al. for deposition on host plants outside the field were estimates only. We reiterate the severe methodological criticisms made by EFSA [Relevance of a new scientific publication (Hofmann et al. 2016) for previous environmental risk assessment conclusions and risk management recommendations on the cultivation of Bt-maize events MON810, Bt11 and 1507. EFSA Supp Publ; EN-1070, 2016], which render this estimation procedure unreliable. Furthermore, criticisms of EFSA (EFSA J 2015(13):4127, 2015) and of EFSA [Relevance of a new scientific publication (Hofmann et al. 2016) for previous environmental risk assessment conclusions and risk management recommendations on the cultivation of Bt-maize events MON810, Bt11 and 1507. EFSA Supp Publ; EN-1070, 2016] made by Kruse-Plass et al. are shown in Additional file 1 to be without foundation. We therefore consider that there is no valid evidence presented by Kruse-Plass et al. to justify their conclusions.

Farm Scale Evaluations of spring-sown genetically modified herbicide-tolerant crops: a statistical assessment.

Primary results from the Farm Scale Evaluations (FSEs) of spring-sown genetically modified herbicide-tolerant crops were published in 2003. We provide a statistical assessment of the results for count data, addressing issues of sample size (n), efficiency, power, statistical significance, variability and model selection. Treatment effects were consistent between rare and abundant species. Coefficients of variation averaged 73% but varied widely. High variability in vegetation indicators was usually offset by large n and treatment effects, whilst invertebrate indicators often had smaller n and lower variability; overall, achieved power was broadly consistent across indicators. Inferences about treatment effects were robust to model misspecification, justifying the statistical model adopted. As expected, increases in n would improve detectability of effects whilst, for example, halving n would have resulted in a loss of significant results of about the same order. 40% of the 531 published analyses had greater than 80% power to detect a 1.5-fold effect; reducing n by one-third would most likely halve the number of analyses meeting this criterion. Overall, the data collected vindicated the initial statistical power analysis and the planned replication. The FSEs provide a valuable database of variability and estimates of power under various sample size scenarios to aid planning of more efficient future studies.

Weed seed resources for birds in fields with contrasting conventional and genetically modified herbicide-tolerant crops.

The UK Farm Scale Evaluations (FSEs) have shown that the use of broad spectrum herbicides on genetically modified herbicide-tolerant (GMHT) crops can have dramatic effects on weed seed production compared to management of conventional varieties. Here, we use FSE data and information on bird diets to determine how GMHT cropping might change the food resources available to farmland birds. More than 60 fields of each of four crops, spring- and winter-sown oilseed rape, beet and maize, were split, one half being sown with a conventional variety, the other with a GMHT variety. Seed rain from weeds known to be important in the diets of 17 granivorous farmland bird species was measured under the two treatments. In beet and spring oilseed rape, rain of weed seeds important in the diets of 16 bird species was significantly reduced in GMHT compared to conventional halves; for no species did it increase. In winter oilseed rape, rain of weed seeds important in the diets of 10 species was significantly reduced in GMHT halves; for only one species did it increase significantly. By contrast, in maize, rain of weed seeds important in the diets of seven species was significantly greater in GMHT halves; for no species was it reduced. Treatment effects for the total weed seed energy available to each bird species were very similar to those for seed rain alone. Measuring the effects on individual bird species was outside the scope of this study. Despite this, these results suggest that should beet, spring and winter rape crops in the UK be largely replaced by GMHT varieties and managed as in the FSEs, this would markedly reduce important food resources for farmland birds, many of which declined during the last quarter of the twentieth century. By contrast, GMHT maize would be beneficial to farmland birds.

Invertebrate biodiversity in maize following withdrawal of triazine herbicides.

Responses of key invertebrates within Farm Scale Evaluations (FSEs) of maize reflected advantageous effects for weeds under genetically modified herbicide-tolerant (GMHT) management. Triazine herbicides constitute the main weed control in current conventional systems, but will be withdrawn under future EU guidelines. Here, we reappraise FSE data to predict effects of this withdrawal on invertebrate biodiversity under alternative management scenarios. Invertebrate indicators showed remarkably consistent and sensitive responses to weed abundance. Their numbers were consistently reduced by atrazine used prior to seedling emergence, but at reduced levels compared to similar observations for weeds. Large treatment effects were, therefore, maintained for invertebrates when comparing other conventional herbicide treatments with GMHT, despite reduced differences in weed abundance. In particular, benefits of GMHT remained under comparisons with best estimates of future conventional management without triazines. Pitfall trapped Collembola, seed-feeding carabids and a linyphiid spider followed closely trends for weeds and may, therefore, prove useful for modelling wider biodiversity effects of herbicides. Weaker responses to triazines applied later in the season, at times closer to the activity and capture of invertebrates, suggest an absence of substantial direct effects. Contrary responses for some suction-sampled Collembola and the carabid Loricera pilicornis were probably caused by a direct deleterious effect of triazines.

Effects on weed and invertebrate abundance and diversity of herbicide management in genetically modified herbicide-tolerant winter-sown oilseed rape.

We evaluated the effects of the herbicide management associated with genetically modified herbicide-tolerant (GMHT) winter oilseed rape (WOSR) on weed and invertebrate abundance and diversity by testing the null hypotheses that there is no difference between the effects of herbicide management of GMHT WOSR and that of comparable conventional varieties. For total weeds, there were few treatment differences between GMHT and conventional cropping, but large and opposite treatment effects were observed for dicots and monocots. In the GMHT treatment, there were fewer dicots and monocots than in conventional crops. At harvest, dicot biomass and seed rain in the GMHT treatment were one-third of that in the conventional, while monocot biomass was threefold greater and monocot seed rain almost fivefold greater in the GMHT treatment than in the conventional. These differential effects persisted into the following two years of the rotation. Bees and Butterflies that forage and select for dicot weeds were less abundant in GMHT WORS management in July. Year totals for Collembola were greater under GMHT management. There were few other treatment effects on invertebrates, despite the marked effects of herbicide management on the weeds.

Sensitive dependencies and separation distances for genetically modified herbicide-tolerant crops.

The amount of land available for the coexistent growing of both organic and genetically modified herbicide-tolerant (GMHT) crops depends on the separation distance between the two types of crop. The form of the decline in the proportion of land available for growing one of these crop types due to increasing separation distance is linear on a suitable scale, but with a slope and intercept that are sensitively dependent on the proportion of the other crop already present. Spatially explicit simulations from realistic scenarios indicate that a major increase in separation distances, currently under review by the UK government, may have serious implications for the future coexistence of organic and GMHT crops in the UK.

Cereal aphid colony turnover and persistence in winter wheat.

An understanding of spatial and temporal processes in agricultural ecosystems provides a basis for rational decision-making with regards to the management and husbandry of crops, supporting the implementation of integrated farming strategies. In this study we investigated the spatial and temporal distribution of aphid pests (Sitobion avenae and Metopolophium dirhodum) within winter wheat fields. Using an intensive sampling programme we investigated distributions at both the small (single shoot) and large (field) scales. Within two fields, a grid with 82 locations was established (area 120 m by 168 m). At each location, 25 shoots were individually marked and aphid counts by observation conducted on 21 and 22 occasions as the crop matured, resulting in 43,050 and 45,100 counts being conducted in the two fields respectively. We quantified field scale spatial distributions, demonstrating that spatial pattern generally emerged, with temporal stability being both species- and field- dependent. We then measured turnover of colonies at the small (individual shoot) and large (field) scales by comparing consecutive pairs of sampling occasions. Four turnover categories were defined: Empty (no aphids recorded on either occasion); Colonised (aphids recorded on the second occasion but not the first); Extinction (aphids recorded on the first occasion but not the second); Stable (aphids recorded on both occasions). At the field scale, population stability soon established, but, at the small scale there was a consistently high proportion of unoccupied shoots with considerable colonisation and extinction and low stability. The redistribution of aphids within the crop at the local scale is a vulnerability which could be used to disrupt population development--by mediating exposure to ground-active natural enemies and by incurring a metabolic cost caused by the physiological demands to re-establish on a nearby host plant.

Estimating the effects of Cry1F Bt-maize pollen on non-target Lepidoptera using a mathematical model of exposure.

In farmland biodiversity, a potential risk to the larvae of non-target Lepidoptera from genetically modified (GM) Bt-maize expressing insecticidal Cry1 proteins is the ingestion of harmful amounts of pollen deposited on their host plants. A previous mathematical model of exposure quantified this risk for Cry1Ab protein. We extend this model to quantify the risk for sensitive species exposed to pollen containing Cry1F protein from maize event 1507 and to provide recommendations for management to mitigate this risk.A 14-parameter mathematical model integrating small- and large-scale exposure was used to estimate the larval mortality of hypothetical species with a range of sensitivities, and under a range of simulated mitigation measures consisting of non-Bt maize strips of different widths placed around the field edge.The greatest source of variability in estimated mortality was species sensitivity. Before allowance for effects of large-scale exposure, with moderate within-crop host-plant density and with no mitigation, estimated mortality locally was <10% for species of average sensitivity. For the worst-case extreme sensitivity considered, estimated mortality locally was 99·6% with no mitigation, although this estimate was reduced to below 40% with mitigation of 24-m-wide strips of non-Bt maize. For highly sensitive species, a 12-m-wide strip reduced estimated local mortality under 1·5%, when within-crop host-plant density was zero. Allowance for large-scale exposure effects would reduce these estimates of local mortality by a highly variable amount, but typically of the order of 50-fold.Mitigation efficacy depended critically on assumed within-crop host-plant density; if this could be assumed negligible, then the estimated effect of mitigation would reduce local mortality below 1% even for very highly sensitive species.Synthesis and applications. Mitigation measures of risks of Bt-maize to sensitive larvae of non-target lepidopteran species can be effective, but depend on host-plant densities which are in turn affected by weed-management regimes. We discuss the relevance for management of maize events where cry1F is combined (stacked) with a herbicide-tolerance trait. This exemplifies how interactions between biota may occur when different traits are stacked irrespective of interactions between the proteins themselves and highlights the importance of accounting for crop management in the assessment of the ecological impact of GM plants.