Rothamsted Research
  • Harpenden, United Kingdom
Recent publications
The rapid increase of herbicide resistance in some of the most problematic annual weeds, and potential negative impacts of herbicides on human health and the environment have led growers to look for alternative non-chemical weed control. Harvest weed seed control (HWSC) is a non-chemical weed control tactic based on reduction of seed return of primarily annual weed species to the soil seed bank that has been successfully adopted by farmers in Australia. The strategy is to collect and/or destroy the weed seeds in the chaff material during harvest using chaff carts, bale direct system, integrated impact mills, windrow burning, chaff tramlining and chaff lining or other methods of targeting the chaff material containing the weed seeds. Two biological characteristics are exploited with successful HWSC: the level of weed seed retention at crop harvest above crop canopy height and coincidence of weed and crop maturity. Initial research efforts in Europe have found that there are several candidates for HWSC among weed species with a high importance in European cropping systems. The highest potential has been found for weeds such as Galium aparine, Lolium rigidum and Silene noctiflora. However, there are several challenges for the adoption of these systems under European conditions compared to e.g., Australia. The challenges include that crop and weed maturity are not concomitant which results in lower seed retention values at crop harvest. In addition, there has not been a concerted research effort to evaluate HWSC systems in European cropping systems. Until now, research on HWSC in Europe mainly focused on the rate of weed seed retention in specific weed species. For HWSC to contribute to the mitigation of herbicide resistance and add to the toolbox of integrated weed management measures, there is an urgent need to take HWSC research to the next level. Although HWSC is not functionally equivalent to herbicide application, it may help to reduce herbicide inputs in the long-term when used in combination with other tactics. Future research and development should focus on the evaluation of HWSC strategies for the practical adoption of these tactics in European cropping systems.
Trace elements may be either essential or toxic to organisms. The most common trace elements in soils are Cd, As, Cr, Hg, Pb, Ni, Zn, and Cu. Pollution of trace elements in soils may be natural or anthropogenic, with the latter including agricultural and industrial sources. Different trace elements pose variable potential risks to ecosystems, food safety and human health. Cadmium and As have low phytotoxicity, and a high risk of soil–food chain transfer posing a threat to food safety and human health, whereas Zn, Ni, Cu, and Cr are ecotoxic at elevated concentrations, thereby posing risks to productivity and functions of ecosystems including C and N cycles.
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosyn-thetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely char-acterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities , as well as protein domain selectivities. Together , these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
The application of the Mitscherlich-Baule equation to fertiliser response data from an extant experiment conducted in New Zealand is further investigated. An estimate of the relevant soil nutrient is obtained as a function of the fitted parameter values using a full model. Estimates of the Baule units are given. These also depend on the fitted parameters. Additionally, predicted estimates of asymptotes are compared with their fitted estimates. Thus, our primary purpose is to describe additional facets of using a Mitscherlich response function to fit crop yield data. We believe the extra results obtained enhance the value of crop growth experiments.
Increasing crop yields through plant breeding is time consuming and laborious, with the generation of novel combinations of alleles being limited by chromosomal linkage blocks and linkage‐drag. Meiotic recombination is essential to create novel genetic variation via the reshuffling of parental alleles. Exchange of genetic information between homologous chromosomes occurs at crossover (CO) sites but CO frequency is often low and unevenly distributed. This bias creates the problem of linkage‐drag in recombination ‘cold’ regions, where undesirable variation remains linked to useful traits. In plants, programmed meiosis‐specific DNA double‐strand breaks (DSBs), catalysed by the SPO11 complex, initiate the recombination pathway, although only ~5% result in the formation of COs. To study the role of SPO11‐1 in wheat meiosis, and as a prelude to manipulation, we used CRISPR/Cas9 to generate edits in all three SPO11‐1 homoeologues of hexaploid wheat. Characterisation of progeny lines shows plants deficient in all six SPO11‐1 copies fail to undergo chromosome synapsis, lack COs and are sterile. In contrast, lines carrying a single copy of any one of the three wild‐type homoeologues are phenotypically indistinguishable from unedited plants both in terms of vegetative growth and fertility. However, cytogenetic analysis of the edited plants suggests that homoeologues differ in their ability to generate COs and in the dynamics of synapsis. In addition, we show that transformation of wheat mutants carrying six edited copies of SPO11‐1 with the TaSPO11‐1B gene, restores synapsis, CO formation and fertility and hence opens a route to modifying recombination in this agronomically important crop.
Background Inadequate dietary zinc (Zn) supplies and Zn deficiency (ZnD) are prevalent in Ethiopia, where cereals are major dietary sources, yet low in bioavailable Zn. Zinc agronomic biofortification (ZAB) of staple crops through application of Zn fertilizers may contribute to alleviating ZnD. However, large-scale promotion and adoption of ZAB requires evidence of the feasibility and public health benefits. This paper aimed to quantify the potential cost-effectiveness of ZAB of staple crops for alleviating ZnD in Ethiopia. Methods Current burden of ZnD among children in Ethiopia was quantified using a disability-adjusted life years (DALYs) framework. Evidence on baseline dietary Zn intake, cereal consumption, and fertilizer response ratio was compiled from existing literature and secondary data sources. Reduction in the burden of ZnD attributable to ZAB of three staple cereals (maize, teff, and wheat) via granular and foliar Zn fertilizer applications was calculated under optimistic and pessimistic scenarios. The associated costs for fertilizer, labor, and equipment were estimated in proportion to the cropping area and compared against DALYs saved and the national Gross Domestic Product capita –1 . Results An estimated 0.55 million DALYs are lost annually due to ZnD, mainly due to ZnD-related mortality (91%). The ZAB of staple cereals via granular Zn fertilizer could reduce the burden of ZnD by 29 and 38% under pessimistic and optimistic scenarios, respectively; the respective values for ZAB via foliar application were 32 and 40%. The ZAB of staple cereals via granular fertilizer costs US$502 and US$505 to avert each DALY lost under optimistic and pessimistic scenarios, respectively; the respective values for ZAB via foliar application were US$226 and US$ 496. Foliar Zn application in combination with existing pesticide use could reduce costs to US$260–353 for each DALY saved. Overall, ZAB of teff and wheat were found to be more cost-effective in addressing ZnD compared to maize, which is less responsive to Zn fertilizer. Conclusion ZAB of staple crops via granular or foliar applications could be a cost-effective strategy to address ZnD, which can be integrated with the existing fertilizer scheme and pesticide use to minimize the associated costs.
Predicting crop yields through simple methods would be helpful for crop breeding programs and could be deployed at farm level to achieve accurate crop management practices. This research proposes a new method for predicting wheat grain yieldsthroughout the crop growth cycle based on canopy cover (CC) and reflectance indices, named Yieldp Model. The model was evaluated by comparing grain yields with the outputs of the proposed model using phenotypic data collected for a wheat population grown under field conditions for the 2015 and 2016 seasons. Accumulated radiation (RAD), Normalized Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI), Water Index (WI), Harvest Index (HI) and CC indices were the components of the model. We found that the biomass accumulation predicted by the model was responsive throughout the crop cycle and the grain yield predicted was correlated to measured grain yield. The model was able to early predict grain yield based on biomass accumulated at anthesis. Evaluation of the model components enabled an improved understanding of the main factors limiting yield formation throughout the crop cycle. The proposed Yieldp Model explores a new concept of yield modelling and can be the starting point for the development of cheap and robust, on-farm, yield prediction during the crop cycle.
The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.
Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.
The fate of migrating insects that encounter rainfall in flight is a critical consideration when modelling insect movement, but few field observations of this common phenomenon have ever been collected due to the logistical challenges of witnessing these encounters. Operational cloud radars have been deployed around the world by meteorological agencies to study precipitation physics, and as a byproduct, provide a rich database of insect observations that is freely available to researchers. Although considered unwanted ‘clutter’ by the meteorologists who collect the data, the analysis method presented here enables ecologists to delineate co‐occurring signals from insects and raindrops. We present a method that uses image processing techniques on cloud radar velocity spectra to examine the fate of migrating insects when they encounter precipitation. By analysing velocity spectra, we can distinguish flying insects from falling rain and compare the relative density of insects in flight before, during and after the rainfall. We demonstrate the method on a case of insect migration in Oklahoma, USA. Using this method, we show the first reconstructed images of migrating insect layers in flight during rainfall. Our analysis shows that mild to moderate rainfall diminishes the number of insects aloft but does not cause full termination of migratory flight, as has previously been suggested. We hope this technique will spur further investigations of how changing weather conditions impact insect migration, and enable some of the first of such studies in regions of the world that are underrepresented in the literature.
Understanding the failure mechanisms of steel-bar reinforced ultra high performance fibre reinforced concrete (UHPFRC) beams is crucial to improving their design but challenging because of the contrast between beam size and fibre size. We develop a 2D mesoscale finite element model with the fibres explicitly resolved to bridge this gap by simulating the damaging and fracturing processes of the beams. To make fibre distribution in the model mechanically representative, we propose a method to project the fibres from 3D to 2D. The continuum damaged plasticity model is used as the constitutive law for the UHPC matrix, and the zero-thickness cohesive elements with softening constitutive law are used to model the nonlinear bond-slip behaviour of the fibre- and bar-matrix interfaces. The models are validated against experimental data obtained from 3 and 4-point loading tests by comparing the simulated and measured fracturing processes, crack patterns and the load-displacement curves. The validated models are then used to analyse the sensitivity of the shear strength of the beams to fibre content, shear span-to-depth ratio, as well as shear and longitudinal reinforcement ratios in the beam, from which a shear strength equation is proposed to improve the design of reinforced UHPFRC beams. The improvement of the new equation over the AFGC equation is demonstrated against experimental data measured from 32 beams with various material properties.
Zinc (Zn) deficiency remains a public health problem in Malawi, especially among poor and marginalized rural populations, linked with low dietary intake of Zn due to consumption of staple foods that are low in Zn content. The concentration of Zn in staple cereal grain can be increased through application of Zn‐enriched fertilizers, a process called agronomic biofortification or agro‐fortification. Field experiments were conducted at three Agricultural Research Station sites to assess the potential of agronomic biofortification to improve Zn concentration in maize grain in Malawi as described in registered report published previously. The hypotheses of the study were (i) that application of Zn‐enriched fertilizers would increase in the concentration of Zn in maize grain to benefit dietary requirements of Zn and (ii) that Zn concentration in maize grain and the effectiveness of agronomic biofortification would be different between soil types. At each site two different subsites were used, each corresponding to one of two agriculturally important soil types of Malawi, Lixisols and Vertisols. Within each subsite, three Zn fertilizer rates (1, 30, and 90 kg ha−1) were applied to experimental plots, using standard soil application methods, in a randomized complete block design. The experiment had 10 replicates at each of the three sites as informed by a power analysis from a pilot study, published in the registered report for this experiment, designed to detect a 10% increase in grain Zn concentration at 90 kg ha−1, relative to the concentration at 1 kg ha−1. At harvest, maize grain yield and Zn concentration in grain were measured, and Zn uptake by maize grain and Zn harvest index were calculated. At 30 kg ha−1, Zn fertilizer increased maize grain yields by 11% compared with nationally recommended application rate of 1 kg ha−1. Grain Zn concentration increased by 15% and uptake by 23% at the application rate of 30 kg ha−1 relative to the national recommendation rate. The effects of Zn fertilizer application rate on the response variables were not dependent on soil type. The current study demonstrates the importance of increasing the national recommendation rate of Zn fertilizer to improve maize yield and increase the Zn nutritional value of the staple crop.
Tropical peatlands are a globally important carbon store. They host significant biodiversity and provide a range of other important ecosystem services, including food and medicines for local communities. Tropical peatlands are increasingly modified by humans in the rapid and transformative way typical of the “Anthropocene,” with the most significant human—driven changes to date occurring in Southeast Asia. This review synthesizes the dominant changes observed in human interactions with tropical peatlands in the last 200 years, focusing on the tropical lowland peatlands of Southeast Asia. We identify the beginning of transformative anthropogenic processes in these carbon-rich ecosystems, chart the intensification of these processes in the 20th and early 21st centuries, and assess their impacts on key ecosystem services in the present. Where data exist, we compare the tropical peatlands of Central Africa and Amazonia, which have experienced very different scales of disturbance in the recent past. We explore their global importance and how environmental pressures may affect them in the future. Finally, looking to the future, we identify ongoing efforts in peatland conservation, management, restoration, and socio-economic development, as well as areas of fruitful research toward sustainability of tropical peatlands.
Background: Sugar beet is threatened by virus yellows, a disease complex vectored by aphids that reduces sugar content. We present an analysis of Myzus persicae population dynamics with and without neonicotinoid seed treatment. We use six years' yellow water trap and field-collected aphid data and two decades of 12.2 m suction-trap aphid migration data. We investigate both spatial synchrony and forecasting error to understand the structure and spatial scale of field counts and why forecasting aphid migrants lacks accuracy. Our aim is to derive statistical parameters to inform regionwide pest management strategies. Results: Spatial synchrony, indicating the coincident change in counts across the region over time, is rarely present and is best described as stochastic. Uniquely, early season field populations in 2019 did show spatial synchrony to 90 km compared to the overall average weekly correlation length of 23 km. However, 70% of the time series were spatially heterogenous, indicating patchy between-field dynamics. Field counts lacked the same seasonal trend and did not peak in the same week. Forecasts tended to under-predict mid-season log10 counts. A strongly negative correlation between forecasting error and the proportion of zeros was shown. Conclusion: Field populations are unpredictable and stochastic, regardless of neonicotinoid seed treatment. This outcome presents a problem for decision-support that cannot usefully provide a single regionwide solution. Weighted permutation entropy inferred that M. persicae 12.2 m suction-trap time series had moderate to low intrinsic predictability. Early warning using a migration model tended to predict counts at lower levels than observed. This article is protected by copyright. All rights reserved.
Background: Understanding of mechanisms that underpin high-yielding cropping systems is essential for optimizing management practices. Currently, the contribution of plant traits such as leaf area, chlorophyll content and intercepted photosynthetically active radiation (PARi ) to yield and nitrogen use efficiency (NUE) are not fully understood. In addition, the understanding of how canopy traits are affected by nitrogen management practices are unclear. The aim of this study was to determine the effect of amendment with controlled release urea (CR), common urea or no urea on NUE and plant eco-physiological characteristics in a two-year field study in a double rice cropping system. Results: Regulation of N release through amendment with CR significantly increased grain yield, NUE and leaf morpho-physiological attributes. CR coupled with common urea (at comparable total N rates) increased leaf area index (LAI), relative chlorophyll content index (CCI) and PARi , leading to higher grain yield and NUE (increased 24.4% and 25.3% in early and late rice, respectively) compared with local farming practice. Structural equation model (SEM) analysis showed that differences in N application, between CR and common urea, directly accounted for differences observed in soil nutrient, PARi and NUE rather than yield components. Additionally, compared to traditional yield determinants, LAI and PARi (between booting and filling stage) are capable of predicting and explaining grain yield by 0.69 and 0.92 of R2 in early and late rice, respectively. Conclusion: Leaf morpho-physiological traits are important for developing N management practices to increase NUE and improve food security for paddy agriculture in southern China. This article is protected by copyright. All rights reserved.
Conservation agriculture is increasingly preferred to conventional methods due to its benefits in promoting more sustainable soil management. Our study aims to compare physical and morphological properties, at the microscale, of soils under long-term no tillage (NT) and minimum-tillage (MT) to adjacent ‘natural’ soils under long-term secondary forest (SF). Soil aggregates of c. 2 cm length were imaged by X-ray Computed Tomography (XCT). The three-dimensional (3D) images were segmented and analyzed in order to assess properties such as porosity, number of pores, degree of anisotropy, pore shape, volume classifications, Euler number for pore connectivity, and pore tortuosity. The pore architecture of soils under NT and MT, for c. 40 years, was similar to that from the SF in terms of imaged porosity, pore size, and shape distributions, as hypothesized in our study. However, we observed some important differences; for instance, SF had larger, more connected, and more complex pores, likely due to the greater biological activity. In addition, SF had more isotropic pores than NT and MT, i.e., without preferential flow paths for water redistribution. Therefore, we concluded that long-term conservation agriculture was efficient at reversing structural damage typically associated with conventional, intensive agriculture, but some large differences remain, particularly concerning the pore network complexity and connectivity.
Substantial ammonia (NH3) losses from rice production result in poor nitrogen (N) use efficiency and environmental damage. A data synthesis using the published literature (127 studies with 700 paired observations), combined with an incubation experiment using 50 paddy soils from across China, were conducted to improve the current understanding of the NH3 loss from paddy rice and its drivers. The efficacy of the urease inhibitor Limus® for reducing NH3 losses was also evaluated. The mean loss of N, through NH3 volatilization, was 16.2% of the urea-N applied to paddy rice. The largest losses were from double rice cropping systems, and losses increased with the N application rate, surface application of N, unstable N types (ammonium bicarbonate and urea), and high floodwater pH. Under simulated flooded conditions, urea amended with Limus® reduced NH3 loss by 36.6%, compared to urea alone, but floodwater pH had a significant effect on inhibitor efficacy. Key driving factors were air temperature, N application rate, and floodwater pH. The effectiveness and limitations of the inhibitor in NH3 emission mitigation was examined, as well as its basis as one means of N pollution control in paddy rice cropping systems.
Natural products possess structural complexity, diversity and chirality with attractive functions and biological activities that have significantly impacted drug discovery initiatives. Chiral natural products are abundant in nature but rarely occur as racemates. The occurrence of natural products as racemates is very intriguing from a biosynthetic point of view; as enzymes are chiral molecules, enzymatic reactions generating natural products should be stereospecific and lead to single-enantiomer products. Despite several reports in the literature describing racemic mixtures of stereoisomers isolated from natural sources, there has not been a comprehensive review of these intriguing racemic natural products. The discovery of many more natural racemates and their potential enzymatic sources in recent years allows us to describe the distribution and chemical diversity of this ‘class of natural products’ to enrich discussions on biosynthesis. In this Review, we describe the chemical classes, occurrence and distribution of pairs of enantiomers in nature and provide insights about recent advances in analytical methods used for their characterization. Special emphasis is on the biosynthesis, including plausible enzymatic and non-enzymatic formation of natural racemates, and their pharmacological significance.
Buffer strips continue to feature in the management of agricultural runoff and water pollution in many countries. Existing research has explored their efficacy for reducing environmental problems in different geoclimatic settings but, the evidence on the efficacy of different vegetation treatments is less abundant than that for other buffer strip characteristics, including width, and is more contradictory in nature. With policy targets for various environmental outcomes including water or air quality and net zero pointing to the need for conversion of agricultural land, the need for robust experimental evidence on the relative benefits of different vegetation types in buffer strips is now renewed. Our experiment used a replicated plot scale facility to compare the efficacy of 12 m wide buffer strips for controlling runoff and suspended sediment loss during 15 sampled storms spanning 2017‐2020. The buffer strips comprised three vegetation treatments: a deep rooting grass (Festulolium cv. Prior), a short rotation coppice willow and native broadleaved woodland trees. Over the duration of the monitoring period, reductions in total runoff, compared with the experimental control, were in the order: willow buffer strips (49%); deciduous woodland buffer strips (46%); grass buffer strips (33%). The corresponding reductions in suspended sediment loss, relative to the experimental control, were ordered: willow buffer strips (44%) > deciduous woodland buffer strips (30%) > grass buffer strips (29%). Given the three‐year duration of our new dataset, our results should be seen as providing evidence on the impacts during the establishment phase of the of the treatments. This article is protected by copyright. All rights reserved.
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380 members
Jon West
  • Department of Biointeractions and Crop Protection
Matthew Paul
  • Plant Sciences
Abrar Hussain
  • Plant Sciences
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Harpenden, United Kingdom