A new mechanistic model of weather-dependent Septoria tritici blotch disease risk

This is the final version. Available on open access from the Royal Society via the DOI in this record.Data accessibility: All data and code associated with this work are available as supplementary material or on Github (https://github.com/thomaschaloner/A_new_mechanistic_model_of_weather-dependent_Septoria_tritici_blotch_disease_risk), respectively.We present a new mechanistic model for predicting Septoria tritici blotch (STB) disease, parameterized with experimentally derived data for temperature- and wetness-dependent germination, growth and death of the causal agent, Zymoseptoria tritici. The output of this model (A) was compared with observed disease data for UK wheat over the period 2002-2016. In addition, we compared the output of a second model (B), in which experimentally derived parameters were replaced by a modified version of a published Z. tritici thermal performance equation, with the same observed disease data. Neither model predicted observed annual disease, but model A was able to differentiate UK regions with differing average disease risks over the entire period. The greatest limitations of both models are: broad spatial resolution of the climate data, and lack of host parameters. Model B is further limited by its lack of explicitly defined pathogen death, leading to a cumulative overestimation of disease over the course of the growing season. Comparison of models A and B demonstrates the importance of accounting for the temperature-dependency of pathogen processes important in the initiation and progression of disease. However, effective modelling of STB will probably require similar experimentally derived parameters for host and environmental factors, completing the disease triangle. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'

Geometry and evolution of the ecological niche in plant-associated microbes

This is the final version. Available from Nature Research via the DOI in this record. The ecological niche can be thought of as a volume in multidimensional space, where each dimension describes an abiotic condition or biotic resource required by a species. The shape, size, and evolution of this volume strongly determine interactions among species and influence their current and potential geographical distributions, but the geometry of niches is poorly understood. Here, we analyse temperature response functions and host plant ranges for hundreds of potentially destructive plant-associated fungi and oomycetes. We demonstrate that niche specialization is uncorrelated on abiotic (i.e. temperature response) and biotic (i.e. host range) axes, that host interactions restrict fundamental niche breadth to form the realized niche, and that both abiotic and biotic niches show limited phylogenetic constraint. The ecological terms ‘generalist’ and ‘specialist’ therefore do not apply to these microbes, as specialization evolves independently on different niche axes. This adaptability makes plant pathogens a formidable threat to agriculture and forestry.BBSRCCIFA

Plant pathogen infection risk tracks global crop yields under climate change

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordThe fungal and oomycete cardinal temperature data are available in Dryad42 (https://doi.org/10.5061/dryad.tqjq2bvw6) and from ref. 16. The data on annual crop yield projections used in this study are from the Inter-Sectoral Model Intercomparison Project (https://www.isimip.org). The fungal and oomycete host plant data and geographical distributions (the Plantwise database) were used under license for the current study and are available with permission from CABI. The FAOSTAT commodity list is available from http://www.fao.org. The global gridded climate data and climate projections are available from WorldClim (https://www.worldclim.org). The global gridded crop distribution data used in this study are available from EarthStat (https://www.earthstat.org) and MIRCA2000 (https://www.uni-frankfurt.de/45218031/data_download). The fungal and oomycete names and name disambiguation data were obtained from Species Fungorum (http://www.speciesfungorum.org/) and MycoBank (http://www.mycobank.org/). The annual per capita GDP (PPP) data were obtained from the World Bank (https://data.worldbank.org/). Coupled Model Intercomparison Project 5 single-level monthly near-surface RH data were obtained from the Climate Data Store (https://cds.climate.copernicus.eu). Administrative boundaries for the maps were obtained from GADM (https://www.gadm.org). The coastal outlines were obtained from package rworldmap version 1.3–6 for R version 4.0.1.All analyses were conducted using existing functions for R version 4.0.1. No substantial custom code was used. R code used for data manipulation is available from the corresponding author on reasonable request.Global food security is strongly determined by crop production. Climate change-induced losses to production can occur directly or indirectly, including via the distributions and impacts of plant pathogens. However, the likely changes in pathogen pressure in relation to global crop production are poorly understood. Here we show that temperature-dependent infection risk, r(T), for 80 fungal and oomycete crop pathogens will track projected yield changes in 12 crops over the twenty-first century. For most crops, both yields and r(T) are likely to increase at high latitudes. In contrast, the tropics will see little or no productivity gains, and r(T) is likely to decline. In addition, the United States, Europe and China may experience major changes in pathogen assemblages. The benefits of yield gains may therefore be tempered by the greater burden of crop protection due to increased disease and unfamiliar pathogens.Biotechnology and Biological Sciences Research CouncilBill and Melinda Gates FoundationCIFA

Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men

The metabolic health benefits of fermented milks have already been investigated using clinical biomarkers but the development of transcriptomic analytics in blood offers an alternative approach that may help to sensitively characterise such effects. We aimed to assess the effects of probiotic yoghurt intake, compared to non-fermented, acidified milk intake, on clinical biomarkers and gene expression in peripheral blood. To this end, a randomised, crossover study was conducted in fourteen healthy, young men to test the two dairy products. For a subset of seven subjects, RNA sequencing was used to measure gene expression in blood collected during postprandial tests and after two weeks daily intake. We found that the postprandial response in insulin was different for probiotic yoghurt as compared to that of acidified milk. Moreover changes in several clinical biomarkers were associated with changes in the expression of genes representing six metabolic genesets. Assessment of the postprandial effects of each dairy product on gene expression by geneset enrichment analysis revealed significant, similar modulation of inflammatory and glycolytic genes after both probiotic yoghurt and acidified milk intake, although distinct kinetic characteristics of the modulation differentiated the dairy products. The aryl hydrocarbon receptor was a major contributor to the down-regulation of the inflammatory genesets and was also positively associated with changes in circulating insulin at 2h after yoghurt intake (p = 0.05). Daily intake of the dairy products showed little effect on the fasting blood transcriptome. Probiotic yoghurt and acidified milk appear to affect similar gene pathways during the postprandial phase but differences in the timing and the extent of this modulation may lead to different physiological consequences. The functional relevance of these differences in gene expression is supported by their associations with circulating biomarkers

A heterozygous moth genome provides insights into herbivory and detoxification

How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants1, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood2. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.Minsheng You … Simon W Baxter … et al

An ecological future for weed science to sustain crop production and the environment. A review

Sustainable strategies for managing weeds are critical to meeting agriculture's potential to feed the world's population while conserving the ecosystems and biodiversity on which we depend. The dominant paradigm of weed management in developed countries is currently founded on the two principal tools of herbicides and tillage to remove weeds. However, evidence of negative environmental impacts from both tools is growing, and herbicide resistance is increasingly prevalent. These challenges emerge from a lack of attention to how weeds interact with and are regulated by the agroecosystem as a whole. Novel technological tools proposed for weed control, such as new herbicides, gene editing, and seed destructors, do not address these systemic challenges and thus are unlikely to provide truly sustainable solutions. Combining multiple tools and techniques in an Integrated Weed Management strategy is a step forward, but many integrated strategies still remain overly reliant on too few tools. In contrast, advances in weed ecology are revealing a wealth of options to manage weedsat the agroecosystem levelthat, rather than aiming to eradicate weeds, act to regulate populations to limit their negative impacts while conserving diversity. Here, we review the current state of knowledge in weed ecology and identify how this can be translated into practical weed management. The major points are the following: (1) the diversity and type of crops, management actions and limiting resources can be manipulated to limit weed competitiveness while promoting weed diversity; (2) in contrast to technological tools, ecological approaches to weed management tend to be synergistic with other agroecosystem functions; and (3) there are many existing practices compatible with this approach that could be integrated into current systems, alongside new options to explore. Overall, this review demonstrates that integrating systems-level ecological thinking into agronomic decision-making offers the best route to achieving sustainable weed management

Women and economic statecraft: The negative impact international economic sanctions visit on women

Though it is widely accepted that advancing women\u27s rights is crucial to promoting more economic prosperity, good governance, and social equality, very few studies have analyzed the gender-specific effects of foreign policy tools. In this study, we focus on the impact that a frequently used coercive tool - international economic sanctions - has on women\u27s well-being. Sanctions can have a devastating impact on both the target country\u27s economic and political stability, and women often suffer significantly from the effects of such external shocks due to their vulnerable socioeconomic and political status. We thus argue that foreign economic pressures will reduce the level of respect for women\u27s rights in the targeted countries. We use four different measures of women\u27s economic, political, and social status to analyze the gender-specific consequences of economic coercion. Results from the analysis for the period 1971-2005 indicate that sanctions are likely to exacerbate women\u27s rights. The data analysis also shows that the suggested negative impact of economic coercion on women\u27s well-being is conditioned by the wealth of a targeted country; women in poor countries are hit the hardest by economic sanctions. © The Author(s) 2012